Basic Sciences Publications 2012-2017

Basic Sciences Division

Publications 2012-2017

2017

Crook ZR,Sevilla GP,Friend D,Brusniak M-Y,Bandaranayake AD,Clarke M,Gewe M,Mhyre AJ,Baker D,Strong RK,Bradley P,Olson JM. (2017). Mammalian display screening of diverse cystine-dense peptides for difficult to drug targets. Nat Commun, 8(1), 2244. PMCID: PMC5740061.
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Weile J,Sun S,Cote AG,Knapp J,Verby M,Mellor JC,Wu Y,Pons C,Wong C,van Lieshout N,Yang F,Tasan M,Tan G,Yang S,Fowler DM,Nussbaum R,Bloom JD,Vidal M,Hill DE,Aloy P,Roth FP. (2017). A framework for exhaustively mapping functional missense variants. Mol Syst Biol, 13(12), 957.
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Molaro A, Malik HS. (2017). Sex Chromosome Evolution: Culture shock eLife eLife 2017; Elife, 6. PMCID: PMC5734872.
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Barsh GR,Isabella AJ,Moens CB. (2017). Vagus Motor Neuron Topographic Map Determined by Parallel Mechanisms of hox5 Expression and Time of Axon Initiation. Curr Biol.
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Ramachandran S,Ahmad K,Henikoff S. (2017). Transcription and Remodeling Produce Asymmetrically Unwrapped Nucleosomal Intermediates. Mol Cell.
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Henikoff S,Thakur J,Kasinathan S,Talbert PB. (2017). Remarkable Evolutionary Plasticity of Centromeric Chromatin. Cold Spring Harb Symp Quant Biol.
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Pinto-Santini DM,Stenbak CR,Linial ML. (2017). Foamy virus zoonotic infections. Retrovirology, 14(1), 55. PMCID: PMC5712078.
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Roh-Johnson M,Shah AN,Stonick JA,Poudel KR,Kargl J,Yang GH,di Martino J,Hernandez RE,Gast CE,Zarour LR,Antoku S,Houghton AM,Bravo-Cordero JJ,Wong MH,Condeelis J,Moens CB. (2017). Macrophage-Dependent Cytoplasmic Transfer during Melanoma Invasion In Vivo. Dev Cell, 43(5), 549-562.e546.
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Rabinowitch I,Treinin M,Bai J. (2016). Artificial Optogenetic TRN Stimulation of C. elegans. Bio Protoc, 6(20). PMCID: PMC5697792.
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Tomko EJ,Fishburn J,Hahn S,Galburt EA. (2017). TFIIH generates a six-base-pair open complex during RNAP II transcription initiation and start-site scanning. Nat Struct Mol Biol.
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Henikoff S. (2017). Structural Biology: Probing the Origins of Chromatin. Curr Biol, 27(20), R1118-r1120.
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Donczew R,Hahn S. (2017). Mechanistic differences in transcription initiation at TATA-less and TATA-containing promoters. Mol Cell Biol.
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Spain MM,Swygert SG,Tsukiyama T. (2018). Preparation and Analysis of Saccharomyces cerevisiae Quiescent Cells. Methods Mol Biol, 1686, 125-135.
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Stainier DYR,Raz E,Lawson ND,Ekker SC,Burdine RD,Eisen JS,Ingham PW,Schulte-Merker S,Yelon D,Weinstein BM,Mullins MC,Wilson SW,Ramakrishnan L,Amacher SL,Neuhauss SCF,Meng A,Mochizuki N,Panula P,Moens CB. (2017). Guidelines for morpholino use in zebrafish. PLoS Genet, 13(10), e1007000.
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Rajan A,Housden BE,Wirtz-Peitz F,Holderbaum L,Perrimon N. (2017). A Mechanism Coupling Systemic Energy Sensing to Adipokine Secretion. Dev Cell, 43(1), 83-98.e86.
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Dou J,Doyle L,Greisen P, Jr.,Schena A,Park H,Johnsson K,Stoddard BL,Baker D. (2017). Sampling and Energy Evaluation Challenges in Ligand Binding Protein Design. Protein Sci.
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Baptista T,Grunberg S,Minoungou N,Koster MJE,Timmers HTM,Hahn S,Devys D,Tora L. (2017). SAGA Is a General Cofactor for RNA Polymerase II Transcription. Mol Cell.
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Black GE,Sokol KK,Moe DM,Simmons JD,Muscat D,Pastukh V,Capley G,Gorodnya O,Ruchko M,Roth MB,Gillespie M,Martin MJ. (2017). Impact of a novel phosphoinositol-3 kinase inhibitor in preventing mitochondrial DNA damage and damage-associated molecular pattern accumulation: Results from the Biochronicity Project. J Trauma Acute Care Surg, 83(4), 683-689.
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Nakamura M,Verboon JM,Parkhurst SM. (2017). Prepatterning by RhoGEFs governs Rho GTPase spatiotemporal dynamics during wound repair. J Cell Biol.
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Warfield L,Ramachandran S,Baptista T,Devys D,Tora L,Hahn S. (2017). Transcription of Nearly All Yeast RNA Polymerase II-Transcribed Genes Is Dependent on Transcription Factor TFIID. Mol Cell.
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Ailion M,Malik HS. (2017). Genetics: Master Regulator or Master of Disguise?. Curr Biol, 27(17), R844-r847.
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Peters LA,Perrigoue J,Mortha A,Iuga A,Song W-M,Neiman EM,Llewellyn SR,Di Narzo A,Kidd BA,Telesco SE,Zhao Y,Stojmirovic A,Sendecki J,Shameer K,Miotto R,Losic B,Shah H,Lee E,Wang M,Faith JJ,Kasarskis A,Brodmerkel C,Curran M,Das A,Friedman JR,Fukui Y,Humphrey MB,Iritani BM,Sibinga N,Tarrant TK,Argmann C,Hao K,Roussos P,Zhu J,Zhang B,Dobrin R,Mayer LF,Schadt EE. (2017). A functional genomics predictive network model identifies regulators of inflammatory bowel disease. Nat Genet.
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Pilling C,Cooper JA. (2017). SOCS2 Binds to and Regulates EphA2 through Multiple Mechanisms. Sci Rep, 7(1), 10838. PMCID: PMC5589800.
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Kasinathan B,Ahmad K,Malik HS. (2017). Waddington Redux: De Novo Mutations Underlie the Genetic Assimilation of Stress-Induced Phenocopies in Drosophila melanogaster. Genetics, 207(1), 49-51.
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Moffett HF,Coon ME,Radtke S,Stephan SB,McKnight L,Lambert A,Stoddard BL,Kiem HP,Stephan MT. (2017). Hit-and-run programming of therapeutic cytoreagents using mRNA nanocarriers. Nat Commun, 8(1), 389.
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Deblonde GJP,Sturzbecher-Hoehne M,Rupert PB,An DD,Illy M-C,Ralston CY,Brabec J,de Jong WA,Strong RK,Abergel RJ. (2017). Chelation and stabilization of berkelium in oxidation state +IV. Nat Chem, 9(9), 843-849.
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Hilton SK,Doud MB,Bloom JD. (2017). phydms: software for phylogenetic analyses informed by deep mutational scanning. PeerJ, 5, e3657. PMCID: PMC5541924.
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Bull JJ,Malik HS. (2017). The gene drive bubble: New realities. PLoS Genet, 13(7), e1006850.
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Jagannathan S,Bradley RK. (2017). Congenital myotonic dystrophy-an RNA-mediated disease across a developmental continuum. Genes Dev, 31(11), 1067-1068.
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Feng Q,Jagannathan S,Bradley RK. (2017). The RNA Surveillance Factor UPF1 Represses Myogenesis via Its E3 Ubiquitin Ligase Activity. Mol Cell.
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Werther R,Hallinan JP,Lambert AR,Havens K,Pogson M,Jarjour J,Galizi R,Windbichler N,Crisanti A,Nolan T,Stoddard BL. (2017). Crystallographic analyses illustrate significant plasticity and efficient recoding of meganuclease target specificity. Nucleic Acids Res.
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Xue KS,Stevens-Ayers T,Campbell AP,Englund JA,Pergam SA,Boeckh M,Bloom JD. (2017). Parallel evolution of influenza across multiple spatiotemporal scales. Elife, 6.
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Nuckolls NL,Bravo Nunez MA,Eickbush MT,Young JM,Lange JJ,Yu JS,Smith GR,Jaspersen SL,Malik HS,Zanders SE. (2017). wtf genes are prolific dual poison-antidote meiotic drivers. Elife, 6.
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Strauch E-M,Bernard SM,La D,Bohn AJ,Lee PS,Anderson CE,Nieusma T,Holstein CA,Garcia NK,Hooper KA,Ravichandran R,Nelson JW,Sheffler W,Bloom JD,Lee KK,Ward AB,Yager P,Fuller DH,Wilson IA,Baker D. (2017). Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site. Nat Biotechnol.
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Tubman ES,Biggins S,Odde DJ. (2017). Stochastic Modeling Yields a Mechanistic Framework for Spindle Attachment Error Correction in Budding Yeast Mitosis. Cell Syst.
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Dingens AS,Haddox HK,Overbaugh J,Bloom JD. (2017). Comprehensive Mapping of HIV-1 Escape from a Broadly Neutralizing Antibody. Cell Host Microbe.
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Kasinathan S,Zentner GE,Xin B,Rohs R,Henikoff S. (2017). Correspondence: Reply to 'DNA shape is insufficient to explain binding'. Nat Commun, 8, 15644.
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Jossin Y,Lee M,Klezovitch O,Kon E,Cossard A,Lien W-H,Fernandez TE,Cooper JA,Vasioukhin V. (2017). Llgl1 Connects Cell Polarity with Cell-Cell Adhesion in Embryonic Neural Stem Cells. Dev Cell.
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Black GE,Sokol KK,Moe DM,Simmons J,Muscat D,Pastukh V,Capley G,Gorodnya O,Ruchko M,Roth MB,Gillespie M,Martin MJ. (2017). Impact of a Novel PI3-KINASE Inhibitor in Preventing Mitochondrial DNA Damage and Damage Associated Molecular Pattern Accumulation: Results from the Biochronicity Project. J Trauma Acute Care Surg.
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Levin TC,Malik HS. (2017). Rapidly evolving Toll-3/4 genes encode male-specific Toll-like receptors in Drosophila. Mol Biol Evol.
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Miller AC,Whitebirch AC,Shah AN,Marsden KC,Granato M,O'Brien J,Moens CB. (2017). A genetic basis for molecular asymmetry at vertebrate electrical synapses. Elife, 6.
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Cai X,Caballero-Benitez A,Gewe MM,Jenkins IC,Drescher CW,Strong RK,Spies T,Groh V. (2017). Control of Tumor Initiation by NKG2D Naturally Expressed on Ovarian Cancer Cells. Neoplasia, 19(6), 471-482. PMCID: PMC5429243.
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Ferrin MA,Subramaniam AR. (2017). Kinetic modeling predicts a stimulatory role for ribosome collisions at elongation stall sites in bacteria. Elife, 6.
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Ma L,Fowler KR,Martin-Castellanos C,Smith GR. (2017). Functional organization of protein determinants of meiotic DNA break hotspots. Sci Rep, 7(1), 1393.
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Rinaldi FC,Doyle LA,Stoddard BL,Bogdanove AJ. (2017). The effect of increasing numbers of repeats on TAL effector DNA binding specificity. Nucleic Acids Res.
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Uo T,Dvinge H,Sprenger CC,Bradley RK,Nelson PS,Plymate SR. (2017). Systematic and functional characterization of novel androgen receptor variants arising from alternative splicing in the ligand-binding domain. Oncogene, 36(10), 1440-1450. PMCID: PMC5344735.
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Adolph MB,Ara A,Feng Y,Wittkopp CJ,Emerman M,Fraser JS,Chelico L. (2017). Cytidine deaminase efficiency of the lentiviral viral restriction factor APOBEC3C correlates with dimerization. Nucleic Acids Res, 45(6), 3378-3394.
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Mendenhall A,Crane MM,Leiser S,Sutphin G,Tedesco PM,Kaeberlein M,Johnson TE,Brent R. (2017). Environmental Canalization of Life Span and Gene Expression in Caenorhabditis elegans. J Gerontol A Biol Sci Med Sci.
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Ashenberg O,Padmakumar J,Doud MB,Bloom JD. (2017). Deep mutational scanning identifies sites in influenza nucleoprotein that affect viral inhibition by MxA. PLoS Pathog, 13(3), e1006288.
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Bennett CF,Kwon JJ,Chen C,Russell J,Acosta K,Burnaevskiy N,Crane MM,Bitto A,Vander Wende H,Simko M,Pineda V,Rossner R,Wasko BM,Choi H,Chen S,Park S,Jafari G,Sands B,Perez Olsen C,Mendenhall AR,Morgan PG,Kaeberlein M. (2017). Transaldolase inhibition impairs mitochondrial respiration and induces a starvation-like longevity response in Caenorhabditis elegans. PLoS Genet, 13(3), e1006695.
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Han B,Dong Y,Zhang L,Liu Y,Rabinowitch I,Bai J. (2017). Dopamine signaling tunes spatial pattern selectivity in C. elegans. Elife, 6.
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Hyppa RW,Fowler KR,Smith GR. (2017). Quantitative Genome-Wide Measurements of Meiotic DNA Double-Strand Breaks and Protein Binding in S. pombe. Methods Mol Biol, 1471, 25-49.
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Momeni B,Xie L,Shou W. (2017). Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions. Elife, 6.
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Kursel LE,Malik HS. (2017). Recurrent gene duplication leads to diverse repertoires of centromeric histones in Drosophila species. Mol Biol Evol.
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Doud MB,Hensley SE,Bloom JD. (2017). Complete mapping of viral escape from neutralizing antibodies. PLoS Pathog, 13(3), e1006271.
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Wang L,Cooper JA. (2017). Optogenetic control of the Dab1 signaling pathway. Sci Rep, 7, 43760.
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Baldauf HM,Stegmann L,Schwarz SM,Ambiel I,Trotard M,Martin M,Burggraf M,Lenzi GM,Lejk H,Pan X,Fregoso OI,Lim ES,Abraham L,Nguyen LA,Rutsch F,Konig R,Kim B,Emerman M,Fackler OT,Keppler OT. (2017). Vpx overcomes a SAMHD1-independent block to HIV reverse transcription that is specific to resting CD4 T cells. Proc Natl Acad Sci U S A.
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Mendenhall A,Crane MM,Tedesco PM,Johnson TE,Brent R. (2017). Caenorhabditis elegans Genes Affecting Interindividual Variation in Life-span Biomarker Gene Expression. J Gerontol A Biol Sci Med Sci.
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Hatch EM. (2017). Y chromothripsis?. Nature Cell Biology, 19(1), 12-14.
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Kanatsu-Shinohara M,Tanaka T,Ogonuki N,Ogura A,Morimoto H,Cheng PF,Eisenman RN,Trumpp A,Shinohara T. (2016). Myc/Mycn-mediated glycolysis enhances mouse spermatogonial stem cell self-renewal. Genes & Development, 30(23), 2637-2648.
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Ramachandran S,Ahmad K,Henikoff S. (2017). Capitalizing on disaster Establishing chromatin specificity behind the replication fork. Bioessays.
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Bloom JD. (2017). Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models. Biol Direct, 12(1), 1.
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Cheng CY,Young JM,Lin CG,Chao JL,Malik HS,Yao MC. (2016). The piggyBac transposon-derived genes TPB1 and TPB6 mediate essential transposon-like excision during the developmental rearrangement of key genes in Tetrahymena thermophila. Genes Dev, 30(24), 2724-2736.
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Davey CF,Moens CB. (2017). Planar cell polarity in moving cells think globally, act locally. Development, 144(2), 187-200.
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Sugioka K,Hamill DR,Lowry JB,McNeely ME,Enrick M,Richter AC,Kiebler LE,Priess JR,Bowerman B. (2017). Centriolar SAS-7 acts upstream of SPD-2 to regulate centriole assembly and pericentriolar material formation. Elife, 6.
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McLaughlin RN, Jr.,Malik HS. (2017). Genetic conflicts the usual suspects and beyond. J Exp Biol, 220(Pt 1), 6-17.
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Sandmann M,Talbert P,Demidov D,Kuhlmann M,Rutten T,Conrad U,Lermontova I. (2017). Targeting of A. thaliana KNL2 to centromeres depends on the conserved CENPC-k motif in its C-terminus. Plant Cell.
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Skene PJ,Henikoff S. (2017). An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. Elife, 6.
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Peichel CL,Marques DA. (2017). The genetic and molecular architecture of phenotypic diversity in sticklebacks. Philos Trans R Soc Lond B Biol Sci, 372(1713).
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Peichel CL. (2017). Chromosome Evolution Molecular Mechanisms and Evolutionary Consequences. J Hered, 108(1), 1-2.
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2016

Black GE,Sokol KK,Shawhan RR,Eckert MJ,Salgar S,Marko ST,Hoffer ZS,Keyes CC,Roth MB,Martin MJ. (2016). Inducing metabolic suppression in severe hemorrhagic shock Pilot study results from the Biochronicity Project. Journal of Trauma and Acute Care Surgery, 81(6), 1003-1011.
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Jiang Y,Peichel CL,Ling F,Bolnick DI. (2016). Sensory trait variation contributes to biased dispersal of threespine stickleback in flowing water. J Evol Biol.
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Haddox HK,Dingens AS,Bloom JD. (2016). Experimental Estimation of the Effects of All Amino-Acid Mutations to HIV's Envelope Protein on Viral Replication in Cell Culture. PLoS Pathog, 12(12), e1006114.
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Shen BW,Heiter DF,Lunnen KD,Wilson GG,Stoddard BL. (2016). DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair AT-rich target. Nucleic Acids Res.
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Talbert PB,Henikoff S. (2016). Histone variants on the move substrates for chromatin dynamics. Nat Rev Mol Cell Biol.
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Andrews SS,Peria WJ,Yu RC,Colman-Lerner A,Brent R. (2016). Push-Pull and Feedback Mechanisms Can Align Signaling System Outputs with Inputs. Cell Syst, 3(5), 444-455.e2.
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Drechsler R,Chen SW,Dancy BC,Mehrabkhani L,Olsen CP. (2016). HPLC-Based Mass Spectrometry Characterizes the Phospholipid Alterations in Ether-Linked Lipid Deficiency Models Following Oxidative Stress. PLoS One, 11(11), e0167229.
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Rodriguez J,Lee L,Lynch B,Tsukiyama T. (2016). Nucleosome occupancy as a novel chromatin parameter for replication origin functions. Genome Res.
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Bedford T,Malik HS. (2016). Did a Single Amino Acid Change Make Ebola Virus More Virulent?. Cell, 167(4), 892-894.
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Barasch J,Hollmen M,Deng R,Hod EA,Rupert PB,Abergel RJ,Allred BE,Xu K,Darrah SF,Tekabe Y,Perlstein A,Wax R,Bruck E,Stauber J,Corbin KA,Buchen C,Slavkovich V,Graziano J,Spitalnik SL,Bao G,Strong RK,Qiu A. (2016). Disposal of iron by a mutant form of lipocalin 2. Nat Commun, 7, 12973.
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Berger S,Procko E,Margineantu D,Lee EF,Shen BW,Zelter A,Silva DA,Chawla K,Herold MJ,Garnier JM,Johnson R,MacCoss MJ,Lessene G,Davis TN,Stayton PS,Stoddard BL,Fairlie WD,Hockenbery DM,Baker D. (2016). Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer. Elife, 5.
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Captain I,Deblonde GJ,Rupert PB,An DD,Illy MC,Rostan E,Ralston CY,Strong RK,Abergel RJ. (2016). Engineered Recognition of Tetravalent Zirconium and Thorium by Chelator-Protein Systems Toward Flexible Radiotherapy and Imaging Platforms. Inorg Chem.
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Deyter GM,Hildebrand EM,Barber AD,Biggins S. (2016). Histone H4 Facilitates the Proteolysis of the Budding Yeast CENP-ACse4 Centromeric Histone Variant. Genetics.
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Grunberg S,Henikoff S,Hahn S,Zentner GE. (2016). Mediator binding to UASs is broadly uncoupled from transcription and cooperative with TFIID recruitment to promoters. Embo j.
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Fei DL,Motowski H,Chatrikhi R,Prasad S,Yu J,Gao S,Kielkopf CL,Bradley RK,Varmus H. (2016). Wild-Type U2AF1 Antagonizes the Splicing Program Characteristic of U2AF1-Mutant Tumors and Is Required for Cell Survival. PLoS Genet, 12(10), e1006384.
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Romano Ibarra GS,Paul B,Sather BD,Younan PM,Sommer K,Kowalski JP,Hale M,Stoddard B,Jarjour J,Astrakhan A,Kiem HP,Rawlings DJ. (2016). Efficient Modification of the CCR5 Locus in Primary Human T Cells With megaTAL Nuclease Establishes HIV-1 Resistance. Mol Ther Nucleic Acids, 5(8), e352.
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Wittkopp CJ,Adolph MB,Wu LI,Chelico L,Emerman M. (2016). A Single Nucleotide Polymorphism in Human APOBEC3C Enhances Restriction of Lentiviruses. PLoS Pathog, 12(10), e1005865.
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Hatch EM,Hetzer MW. (2016). Nuclear envelope rupture is induced by actin-based nucleus confinement. J Cell Biol.
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Uo T,Dvinge H,Sprenger CC,Bradley RK,Nelson PS,Plymate SR. (2016). Systematic and functional characterization of novel androgen receptor variants arising from alternative splicing in the ligand-binding domain. Oncogene.
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Burian A,Wang KL,Finton KA,Lee N,Ishitani A,Strong RK,Geraghty DE. (2016). HLA-F and MHC-I Open Conformers Bind Natural Killer Cell Ig-Like Receptor KIR3DS1. PLoS One, 11(9), e0163297.
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Jagannathan S,Bradley RK. (2016). Translational plasticity facilitates the accumulation of nonsense genetic variants in the human population. Genome Res.
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Teckchandani A,Cooper JA. (2016). The ubiquitin-proteasome system regulates focal adhesions at the leading edge of migrating cells. Elife, 5.
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Cao RF,Jenkins P,Peria W,Sands B,Naivar M,Brent R,Houston JP. (2016). Phasor plotting with frequency-domain flow cytometry. Optics Express, 24(13), 14596-14607.
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Fregoso OI,Emerman M. (2016). Activation of the DNA Damage Response Is a Conserved Function of HIV-1 and HIV-2 Vpr That Is Independent of SLX4 Recruitment. MBio, 7(5). PMCID: PMC5021806.
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Anderson S,Poudel KR,Roh-Johnson M,Brabletz T,Yu M,Borenstein-Auerbach N,Grady WN,Bai J,Moens CB,Eisenman RN,Conacci-Sorrell M. (2016). MYC-nick promotes cell migration by inducing fascin expression and Cdc42 activation. Proc Natl Acad Sci U S A.
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Cech JN,Peichel CL. (2016). Centromere inactivation on a neo-Y fusion chromosome in threespine stickleback fish. Chromosome Res.
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Miles S,Breeden L. (2016). A common strategy for initiating the transition from proliferation to quiescence. Curr Genet.
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Rossi A,Gauvrit S,Marass M,Pan L,Moens CB,Stainier DY. (2016). Regulation of Vegf signaling by natural and synthetic ligands. Blood.
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Jagannathan S,Shadle S,Resnick R,Snider L,Tawil RN,van der Maarel SM,Bradley RK,Tapscott SJ. (2016). Model systems of DUX4 expression recapitulate the transcriptional profile of FSHD cells. Hum Mol Genet.
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Henikoff S. (2016). Mechanisms of Nucleosome Dynamics In Vivo. Cold Spring Harb Perspect Med.
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Patel MR,Miriyala GK,Littleton AJ,Yang H,Trinh K,Young JM,Kennedy SR,Yamashita YM,Pallanck LJ,Malik HS. (2016). A mitochondrial DNA hypomorph of cytochrome oxidase specifically impairs male fertility in Drosophila melanogaster. Elife, 5. PMCID: PMC4970871.
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Henikoff S,Greally JM. (2016). Epigenetics, cellular memory and gene regulation. Curr Biol, 26(14), R644-8.
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Shah AN,Moens CB,Miller AC. (2016). Targeted candidate gene screens using CRISPR/Cas9 technology. Methods Cell Biol, 135, 89-106.
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Amundsen SK,Sharp JW,Smith GR. (2016). RecBCD Enzyme "Chi Recognition" Mutants Recognize Chi Recombination Hotpots in the Right DNA Context. Genetics.
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Thakur J,Henikoff S. (2016). CENPT bridges adjacent CENPA nucleosomes on young human alpha-satellite dimers. Genome Res.
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Warfield L,Luo J,Ranish J,Hahn S. (2016). Function of conserved topological regions within the S. cerevisiae basal transcription factor TFIIH. Mol Cell Biol.
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Kursel LE,Malik HS. (2016). Centromeres. Curr Biol, 26(12), R487-90.
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Stoddard BL,Fox K. (2016). Editorial CRISPR in Nucleic Acids Research. Nucleic Acids Res, 44(11), 4989-90. PMCID: PMC4914129.
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Taylor AF,Amundsen SK,Smith GR. (2016). Unexpected DNA context-dependence identifies a new determinant of Chi recombination hotspots. Nucleic Acids Res.
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Dvinge H,Kim E,Abdel-Wahab O,Bradley RK. (2016). RNA splicing factors as oncoproteins and tumour suppressors. Nat Rev Cancer.
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Kim DW,Wu N,Kim YC,Cheng PF,Basom R,Kim D,Dunn CT,Lee AY,Kim K,Lee CS,Singh A,Gazdar AF,Harris CR,Eisenman RN,Park KS,MacPherson D. (2016). Genetic requirement for Mycl and efficacy of RNA Pol I inhibition in mouse models of small cell lung cancer. Genes Dev, 30(11), 1289-99.
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Polakova S,Molnarova L,Hyppa RW,Benko Z,Misova I,Schleiffer A,Smith GR,Gregan J. (2016). Dbl2 Regulates Rad51 and DNA Joint Molecule Metabolism to Ensure Proper Meiotic Chromosome Segregation. PLoS Genet, 12(6), e1006102.
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Doud MB,Bloom JD. (2016). Accurate Measurement of the Effects of All Amino-Acid Mutations on Influenza Hemagglutinin. Viruses, 8(6).
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Miles S,Croxford MW,Abeysinghe AP,Breeden LL. (2016). Msa1 and Msa2 Modulate G1-Specific Transcription to Promote G1 Arrest and the Transition to Quiescence in Budding Yeast. PLoS Genet, 12(6), e1006088
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Daugherty MD,Schaller AM,Geballe AP,Malik HS. (2016). Evolution-guided functional analyses reveal diverse antiviral specificities encoded by IFIT1 genes in mammals. Elife, 5. PMCID: PMC4887208.
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Amrit FR,Steenkiste EM,Ratnappan R,Chen SW,McClendon TB,Kostka D,Yanowitz J,Olsen CP,Ghazi A. (2016). DAF-16 and TCER-1 Facilitate Adaptation to Germline Loss by Restoring Lipid Homeostasis and Repressing Reproductive Physiology in C. elegans. PLoS Genet, 12(2), e1005788.
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Franks TM,Benner C,Narvaiza I,Marchetto MC,Young JM,Malik HS,Gage FH,Hetzer MW. (2016). Evolution of a transcriptional regulator from a transmembrane nucleoporin. Genes Dev
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Hahn S,Buratowski S. (2016). Structural biology: Snapshots of transcription initiation. Nature, 533(7603), 331-2.
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McLaughlin RN, Jr.,Gable JT,Wittkopp CJ,Emerman M,Malik HS. (2016). Conservation and Innovation of APOBEC3A Restriction Functions during Primate Evolution. Mol Biol Evol 
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Rabinowitch I,Bai J. (2016). The foundations of cross-modal plasticity. Commun Integr Biol, 9(2), e1158378. PMCID: PMC4857785.
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Saraiva LR,Kondoh K,Ye X,Yoon KH,Hernandez M,Buck LB. (2016). Combinatorial effects of odorants on mouse behavior. Proc Natl Acad Sci U S A
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Stawicki TM,Hernandez L,Esterberg R,Linbo T,Owens KN,Shah AN,Thapa N,Roberts B,Moens CB,Rubel EW,Raible DW. (2016). Cilia-Associated Genes Play Differing Roles in Aminoglycoside-Induced Hair Cell Death in Zebrafish. G3 (Bethesda)
abstract >

Miller MP,Asbury CL,Biggins S. (2016). A TOG Protein Confers Tension Sensitivity to Kinetochore-Microtubule Attachments. Cell.
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Poudel KR,Dong Y,Yu H,Su A,Ho T,Liu Y,Schulten K,Bai J. (2016). A time-course of orchestrated endophilin action in sensing, bending, and stabilizing curved membranes. Mol Biol Cell.
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Inoue D,Bradley RK,Abdel-Wahab O. (2016). Spliceosomal gene mutations in myelodysplasia: molecular links to clonal abnormalities of hematopoiesis. Genes Dev, 30(9), 989-1001.
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ambert AR,Hallinan JP,Shen BW,Chik JK,Bolduc JM,Kulshina N,Robins LI,Kaiser BK,Jarjour J,Havens K,Scharenberg AM,Stoddard BL. (2016). Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity. Structure 
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Lee SC,Dvinge H,Kim E,Cho H,Micol JB,Chung YR,Durham BH,Yoshimi A,Kim YJ,Thomas M,Lobry C,Chen CW,Pastore A,Taylor J,Wang X,Krivtsov A,Armstrong SA,Palacino J,Buonamici S,Smith PG,Bradley RK,Abdel-Wahab O. (2016). Modulation of splicing catalysis for therapeutic targeting of leukemia with mutations in genes encoding spliceosomal proteins. Nat Med 
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Sands B,Brent R. (2016). Overview of post Cohen-Boyer methods for single segment cloning and for multisegment DNA assembly. Curr Protoc Mol Biol, 113, 3.26.1-3.26.20. PMCID: PMC4853029.
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Adamson SE,Griffiths R,Moravec R,Senthivinayagam S,Montgomery G,Chen WS,Han J,Sharma PR,Mullins GR,Gorski SA,Cooper JA,Kadl A,Enfield K,Braciale TJ,Harris TE,Leitinger N. (2016). Disabled homolog 2 controls macrophage phenotypic polarization and adipose tissue inflammation. Journal of Clinical Investigation, 126(4), 1311-1322.
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Fishburn J,Galburt E,Hahn S. (2016). Transcription Start Site Scanning and the Requirement for ATP During Transcription Initiation by RNA Polymerase II. J Biol Chem
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Hughes AL,Hughes CE,Henderson KA,Yazvenko N,Gottschling DE. (2016). Selective sorting and destruction of mitochondrial membrane proteins in aged yeast. Elife, 5.
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Ramachandran S,Henikoff S. (2016). Transcriptional Regulators Compete with Nucleosomes Post-replication. Cell
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Greenwood AK,Mills MG,Wark AR,Archambeault SL,Peichel CL. (2016). Evolution of Schooling Behavior in Threespine Sticklebacks Is Shaped by the Eda Gene. Genetics.
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Alcid EA,Tsukiyama T. (2016). Expansion of antisense lncRNA transcriptomes in budding yeast species since the loss of RNAi. Nat Struct Mol Biol.
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Asan A,Raiders SA,Priess JR. (2016). Morphogenesis of the C. elegans Intestine Involves Axon Guidance Genes. PLoS Genet, 12(4), e1005950.
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Widder S,Allen RJ,Pfeiffer T,Curtis TP,Wiuf C,Sloan WT,Cordero OX,Brown SP,Momeni B,Shou W,Kettle H,Flint HJ,Haas AF,Laroche B,Kreft JU,Rainey PB,Freilich S,Schuster S,Milferstedt K,van der Meer JR,Groszkopf T,Huisman J,Free A,Picioreanu C,Quince C,Klapper I,Labarthe S,Smets BF,Wang H,Soyer OS. (2016). Challenges in microbial ecology: building predictive understanding of community function and dynamics. Isme j
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Berg RD,Levitte S,O'Sullivan MP,O'Leary SM,Cambier CJ,Cameron J,Takaki KK,Moens CB,Tobin DM,Keane J,Ramakrishnan L. (2016). Lysosomal Disorders Drive Susceptibility to Tuberculosis by Compromising Macrophage Migration. Cell, 165(1), 139-52.
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Kondoh K,Lu Z,Ye X,Olson DP,Lowell BB,Buck LB. (2016). A specific area of olfactory cortex involved in stress hormone responses to predator odours. Nature.
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Li P,Silvis MR,Honaker Y,Lien WH,Arron ST,Vasioukhin V. (2016). alphaE-catenin inhibits a Src-YAP1 oncogenic module that couples tyrosine kinases and the effector of Hippo signaling pathway. Genes Dev.
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Shah AN,Moens CB. (2016). Approaching Perfection: New Developments in Zebrafish Genome Engineering. Dev Cell, 36(6), 595-6.
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Davey CF,Mathewson AW,Moens CB. (2016). PCP Signaling between Migrating Neurons and their Planar-Polarized Neuroepithelial Environment Controls Filopodial Dynamics and Directional Migration. PLoS Genet, 12(3), e1005934.
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Draizen EJ,Shaytan AK,Marino-Ramirez L,Talbert PB,Landsman D,Panchenko AR. (2016). HistoneDB 2.0: a histone database with variants-an integrated resource to explore histones and their variants. Database (Oxford), 2016.
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Hildebrand EM,Biggins S. (2016). Regulation of Budding Yeast CENP-A levels Prevents Misincorporation at Promoter Nucleosomes and Transcriptional Defects. PLoS Genet, 12(3), e1005930.
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Levine MT,Vander Wende HM,Hsieh E,Baker EP,Malik HS. (2016). Recurrent gene duplication diversifies genome defense repertoire in Drosophila. Mol Biol Evol.
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McKnight JN,Tsukiyama T,Bowman GD. (2016). Sequence-targeted nucleosome sliding in vivo by a hybrid Chd1 chromatin remodeler. Genome Res.
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Xue KS,Hooper KA,Ollodart AR,Dingens AS,Bloom JD. (2016). Cooperation between distinct viral variants promotes growth of H3N2 influenza in cell culture. Elife, 5.
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Lindemann SR,Bernstein HC,Song HS,Fredrickson JK,Fields MW,Shou W,Johnson DR,Beliaev AS. (2016). Engineering microbial consortia for controllable outputs. Isme j.
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Ramachandran S,Henikoff S. (2016). Nucleosome dynamics during chromatin remodeling in vivo. Nucleus, 7-Jan.
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Casasola A,Scalzo D,Nandakumar V,Halow J,Recillas-Targa F,Groudine M,Rincon-Arano H. (2016). Prelamin A Processing, Accumulation and Distribution in Normal Cells and Laminopathy Disorders. Nucleus, 0.
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Conerly ML,Yao Z,Zhong JW,Groudine M,Tapscott SJ. (2016). Distinct Activities of Myf5 and MyoD Indicate Separate Roles in Skeletal Muscle Lineage Specification and Differentiation. Dev Cell, 36(4), 375-85.
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McGuire AT,Gray MD,Dosenovic P,Gitlin AD,Freund NT,Petersen J,Correnti C,Johnsen W,Kegel R,Stuart AB,Glenn J,Seaman MS,Schief WR,Strong RK,Nussenzweig MC,Stamatatos L. (2016). Specifically modified Env immunogens activate B-cell precursors of broadly neutralizing HIV-1 antibodies in transgenic mice. Nat Commun, 7, 10618.
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Strong RK,Finton KA. (2016). The Broadly Neutralizing, Anti-HIV Antibody 4E10: an Open and Shut Case?. J Virol, 90(6), 3274-5.
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Drinnenberg IA,Henikoff S,Malik HS. (2016). Evolutionary Turnover of Kinetochore Proteins: A Ship of Theseus?. Trends Cell Biol.
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Scognamiglio R,Cabezas-Wallscheid N,Thier MC,Altamura S,Reyes A,Prendergast AM,Baumgartner D,Carnevalli LS,Atzberger A,Haas S,von Paleske L,Boroviak T,Worsdorfer P,Essers MA,Kloz U,Eisenman RN,Edenhofer F,Bertone P,Huber W,van der Hoeven F,Smith A,Trumpp A. (2016). Myc Depletion Induces a Pluripotent Dormant State Mimicking Diapause. Cell, 164(4), 668-80.
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Nambiar M,Smith GR. (2016). Repression of harmful meiotic recombination in centromeric regions. Semin Cell Dev Biol.
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Alcid EA,Tsukiyama T. (2016). Systematic approaches to identify functional lncRNAs. Curr Opin Genet Dev, 37, 46-50
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Molaro A,Malik HS. (2016). Hide and seek: how chromatin-based pathways silence retroelements in the mammalian germline. Curr Opin Genet Dev, 37, 51-58
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Vigdorovich V,Strong RK,Miller AD. (2016). Correction for Vigdorovich et al., Expression and Characterization of a Soluble, Active Form of the Jaagsiekte Sheep Retrovirus Receptor, Hyal2. J Virol, 90(4), 2159
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Mathsyaraja H, Eisenman RN. (2016). Parsing Myc Paralogs in Oncogenesis. Cancer Cell, 29(1), 1-2.
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Rabinowitch I, Laurent P, Zhao B, Walker D, Beets I, Schoofs L, Bai J, Schafer WR, Treinin M. (2016). Neuropeptide-Driven Cross-Modal Plasticity following Sensory Loss in Caenorhabditis elegans. PLoS Biol, 14(1), e1002348.
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2015

 

Shou W. (2015). Acknowledging selection at sub-organismal levels resolves controversy on pro-cooperation mechanisms. Elife, 4.
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Yong L, Peichel CL, McKinnon JS. (2015). Genetic Architecture of Conspicuous Red Ornaments in Female Threespine Stickleback. G3.
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McKnight JN, Tsukiyama T. (2015). The conserved HDAC Rpd3 drives transcriptional quiescence in S. cerevisiae. Genom Data, 6, 245-8. PMCID: PMCPMC4664762.
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Politz JCR, Scalzo D, Groudine M. (2015). The redundancy of the mammalian heterochromatic compartment. Curr Opin Genet Dev, 37, 1-8.
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Shen BW, Lambert A, Walker BC, Stoddard BL, Kaiser BK. (2015). The structural basis of asymmetry in DNA binding and cleavage as exhibited by the I-SmaMI LAGLIDADG meganuclease. J Mol Biol.
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Waite AJ, Cannistra C, Shou W. (2015). Defectors Can Create Conditions That Rescue Cooperation. PLoS Comput Biol, 11(12), e1004645.
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Doyle L, Hallinan J, Bolduc J, Parmeggiani F, Baker D, Stoddard BL, Bradley P. (2015). Rational design of alpha-helical tandem repeat proteins with closed architectures. Nature.
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Mitchell PS, Young JM, Emerman M, Malik HS. (2015). Evolutionary Analyses Suggest a Function of MxB Immunity Proteins Beyond Lentivirus Restriction. PLoS Pathog, 11(12), e1005304.
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Phadnis N, Baker EP, Cooper JC, Frizzell KA, Hsieh E, de la Cruz AFA, Shendure J, Kitzman JO, Malik HS. (2015). An essential cell cycle regulation gene causes hybrid inviability in Drosophila. Science, 350(6267), 1552-5.
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King IC, Gleixner J, Doyle L, Kuzin A, Hunt JF, Xiao R, Montelione GT, Stoddard BL, DiMaio F, Baker D. (2015). Precise assembly of complex beta sheet topologies from de novo designed building blocks. Elife, 4.
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Mendenhall AR, Driscoll M, Brent R. (2015). Using measures of single-cell physiology and physiological state to understand organismic aging. Aging Cell.
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Hunt LC, Xu B, Finkelstein D, Fan Y, Carroll PA, Cheng P-F, Eisenman RN, Demontis F. (2015). The glucose-sensing transcription factor MLX promotes myogenesis via myokine signaling. Genes Dev.
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Hickey TE, Irvine CM, Dvinge H, Tarulli GA, Hanson AR, Ryan NK, Pickering MA, Birrell SN, Hu DG, Mackenzie PI, Russell R, Caldas C, Raj GV, Dehm SM, Plymate SR, Bradley RK, Tilley WD, Selth LA. (2015). Expression of androgen receptor splice variants in clinical breast cancers. Oncotarget.
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Dancy BCR, Chen S-W, Drechsler R, Gafken PR, Olsen CP. (2015). 13C- and 15N-Labeling Strategies Combined with Mass Spectrometry Comprehensively Quantify Phospholipid Dynamics in C. elegans. PLoS One, 10(11), e0141850.
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Hanchate NK, Kondoh K, Lu Z, Kuang D, Ye X, Qiu X, Pachter L, Trapnell C, Buck LB. (2015). Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis. Science.
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McKnight JN, Breeden LL, Tsukiyama T. (2015). A Molecular Off Switch for Transcriptional Quiescence. Cell cycle.
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Thakur J, Talbert PB, Henikoff S. (2015). Inner Kinetochore Protein Interactions with Regional Centromeres of Fission Yeast. Genetics, 201(2), 543-61. PMCID: PMC4596668.
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Bachmann-Gagescu R, Dona M, Hetterschijt L, Tonnaer E, Peters T, de Vrieze E, Mans DA, van Beersum SEC, Phelps IG, Arts HH, Keunen JE, Ueffing M, Roepman R, Boldt K, Doherty D, Moens CB, Neuhauss SCF, Kremer H, van Wijk E. (2015). The Ciliopathy Protein CC2D2A Associates with NINL and Functions in RAB8-MICAL3-Regulated Vesicle Trafficking. PLoS Genet, 11(10), e1005575.
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Zentner GE, Kasinathan S, Xin B, Rohs R, Henikoff S. (2015). ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo. Nat Commun, 6, 8733. PMCID: PMCPMC4618392.
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Oke KB, Bukhari M, Kaeuffer R, Rolshausen G, Rasanen K, Bolnick DI, Peichel CL, Hendry AP. (2015). Does plasticity enhance or dampen phenotypic parallelism? A test with three lake-stream stickleback pairs. J Evol Biol.
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Kim E, Ilagan JO, Lee S, Ramakrishnan A, Chung YR, Micol JB, Murphy ME, Kim MK, Zebari AS, Buonamici S, Smith P, Deeg HJ, Lobry C, Aifantis I, Bradley RK, Abdel-Wahab O. (2015). SRSF2 mutations impair hematopoietic differentiation by altering exonic splicing enhancer preference., Clinical Cancer Research;21(Suppl. 17).
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Cech JN, Peichel CL. (2015). Identification of the centromeric repeat in the threespine stickleback fish (Gasterosteus aculeatus). Chromosome Res.
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Etienne L, Bibollet-Ruche F, Sudmant PH, Wu LI, Hahn BH, Emerman M. (2015). The Role of the Antiviral APOBEC3 Gene Family in Protecting Chimpanzees against Lentiviruses from Monkeys. PLoS Pathog, 11(9), e1005149.
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Henikoff S. (2015). Epigenomic Landscapes Reflect Neuronal Diversity. Neuron, 86(6), 1319-21.
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Conte GL, Arnegard ME, Best J, Chan YF, Jones FC, Kingsley DM, Schluter D, Peichel CL. (2015). Extent of QTL Reuse During Repeated Phenotypic Divergence of Sympatric Threespine Stickleback. Genetics.
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Greenwood AK, Peichel CL. (2015). Social Regulation of Gene Expression in Threespine Sticklebacks. PLoS One, 10(9), e0137726. PMCID: PMC4569571.
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Klezovitch O, Vasioukhin V. (2015). Cadherin signaling: keeping cells in touch. F1000Res, 4(F1000 Faculty Rev), 550. PMCID: PMCPMC4544379.
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Luo J, Cimermancic P, Viswanath S, Ebmeier CC, Kim B, Dehecq M, Raman V, Greenberg CH, Pellarin R, Sali A, Taatjes DJ, Hahn S, Ranish J. (2015). Architecture of the Human and Yeast General Transcription and DNA Repair Factor TFIIH. Mol Cell, 59(5), 794-806. PMCID: PMCPMC4560838.
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Machkovech HM, Bedford T, Suchard MA, Bloom JD. (2015). Positive selection in CD8+ T-cell epitopes of influenza nucleoprotein revealed by a comparative analysis of human and swine viral lineages. J Virol.
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McKnight JN, Boerma JW, Breeden LL, Tsukiyama T. (2015). Global Promoter Targeting of a Conserved Lysine Deacetylase for Transcriptional Shutoff during Quiescence Entry. Mol Cell.
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Verboon JM, Sugumar B, Parkhurst SM. (2015). Wiskott-Aldrich Syndrome proteins in the nucleus: aWASH with possibilities. Nucleus.
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Allred BE, Rupert PB, Gauny SS, An DD, Ralston CY, Sturzbecher-Hoehne M, Strong RK, Abergel RJ. (2015). Siderocalin-mediated recognition, sensitization, and cellular uptake of actinides. Proc Natl Acad Sci U S A.
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Zanders SE, Malik HS. (2015). Chromosome Segregation: Human Female Meiosis Breaks All the Rules. Curr Biol, 25(15), R654-6.
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Akbari BOS, Bellen HJ, Bier E, Bullock SL, Burt A, Church GM, Cook KR, Duchek P, Edwards OR, Esvelt KM, Gantz VM, Golic KG, Gratz SJ, Harrison MM, Hayes KR, James AA, Kaufman TC, Knoblich J, Malik HS, Matthews KA, O'Connor-Giles KM, Parks AL, Perrimon N, Port F, Russell S, Ueda R, Wildonger J. (2015). Safeguarding gene drive experiments in the laboratory. Science.
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Doud MB, Ashenberg O, Bloom JD. (2015). Site-specific amino-acid preferences are mostly conserved in two closely related protein homologs. Mol Biol Evol.
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Henikoff S. (2015). The Genetic Map Enters Its Second Century. Genetics, 200(3), 671-4. PMCID: PMC4512531.
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Jiang Y, Torrance L, Peichel CL, Bolnick DI. (2015). Differences in rheotactic responses contribute to divergent habitat use between parapatric lake and stream threespine stickleback. Evolution.
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McCoy CO, Bedford T, Minin VN, Bradley P, Robins H, Matsen FAt. (2015). Quantifying evolutionary constraints on B-cell affinity maturation. Philos Trans R Soc Lond B Biol Sci, 370(1676).
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Biggins S. (2015). Under Tension: Kinetochores and Basic Research. Genetics, 200(3), 681-2.
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McLaughlin RNJ, Malik HS. (2015). LINE-1 Retroelements Get ZAPped! PLoS Genet, 11(7), e1005364. PMCID: PMC4504689.
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Shou W, Bergstrom CT, Chakraborty AK, Skinner FK. (2015). Theory, models and biology. Elife, 4. PMCID: PMC4501050.
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Levine MT, Vander Wende HM, Malik HS. (2015). Mitotic fidelity requires transgenerational action of a testis-restricted HP1. Elife, 4. PMCID: PMC4491702.
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Li-Villarreal N, Forbes MM, Loza AJ, Chen J, Ma T, Helde K, Moens CB, Shin J, Sawada A, Hindes AE, Dubrulle J, Schier AF, Longmore GD, Marlow FL, Solnica-Krezel L. (2015). Dachsous1b cadherin regulates actin and microtubule cytoskeleton during early zebrafish embryogenesis. Development.
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Shah AN, Davey CF, Whitebirch AC, Miller AC, Moens CB. (2015). Rapid Reverse Genetic Screening Using CRISPR in Zebrafish. Zebrafish.
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Steiner FA, Henikoff S. (2015). Diversity in the organization of centromeric chromatin. Curr Opin Genet Dev, 31, 28-35.
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Hiler D, Chen X, Hazen J, Kupriyanov S, Carroll PA, Qu C, Xu B, Johnson D, Griffiths L, Frase S, Rodriguez AR, Martin G, Zhang J, Jeon J, Fan Y, Finkelstein D, Eisenman RN, Baldwin K, Dyer MA. (2015). Quantification of Retinogenesis in 3D Cultures Reveals Epigenetic Memory and Higher Efficiency in iPSCs Derived from Rod Photoreceptors. Cell Stem Cell, 17(1), 101-15.
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Ma L, Milman N, Nambiar M, Smith GR. (2015). Two separable functions of Ctp1 in the early steps of meiotic DNA double-strand break repair. Nucleic Acids Res.
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Dvinge H, Bradley RK. (2015). Widespread intron retention diversifies most cancer transcriptomes. Genome Med, 7(1), 45. PMCID: PMC4480902.
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LaMacchia JC, Frazier HNr, Roth MB. (2015). Glycogen Fuels Survival During Hyposmotic-Anoxic Stress in Caenorhabditis elegans. Genetics.
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Shu Kuan Y, Roberson S, Akitake CM, Fortuno L, Gamse J, Moens CB, Halpern ME. (2015). Distinct requirements for Wntless in habenular development. Dev Biol.
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Skene PJ, Henikoff S. (2015). A simple method for generating high-resolution maps of genome wide protein binding. Elife, 4.
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Li L, Miles S, Breeden LL. (2015). A Genetic Screen for Saccharomyces cerevisiae Mutants that Fail to Enter Quiescence. G3.
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Phadnis N, Cipak L, Polakova S, Hyppa RW, Cipakova I, Anrather D, Karvaiova L, Mechtler K, Smith GR, Gregan J. (2015). Casein Kinase 1 and Phosphorylation of Cohesin Subunit Rec11 (SA3) Promote Meiotic Recombination through Linear Element Formation. PLoS Genet, 11(5), e1005225. PMCID: PMC4439085.
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Zentner GE, Henikoff S. (2015). Epigenome editing made easy. Nat Biotechnol, 33(6), 606-7.
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Bloom JD. (2015). Software for the analysis and visualization of deep mutational scanning data. BMC Bioinformatics, 16, 168.
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LaMacchia JC, Roth MB. (2015). Aquaporins 2 and 4 Regulate Glycogen Metabolism and Survival during Hyposmotic-Anoxic Stress in Caenorhabditis Elegans. Am J Physiol Cell Physiol, ajpcell 00131 2015.
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Pennell MW, Kirkpatrick M, Otto SP, Vamosi JC, Peichel CL, Valenzuela N, Kitano J. (2015). Y fuse? Sex chromosome fusions in fishes and reptiles. PLoS Genet, 11(5), e1005237.
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Rosinski SL, Storb R, Strong RK, Sale GE, Stone DM, Gewe MM, Friend DJ, Abrams VK, Randolph-Habecker J, Graves SS. (2015). Anti-CD28 Antibody-Initiated Cytokine Storm in Canines. Transplant Direct, 1(2). PMCID: PMC4433175.
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Kim E, Ilagan JO, Liang Y, Daubner GM, Lee SC-W, Ramakrishnan A, Li Y, Chung YR, Micol J-B, Murphy ME, Cho H, Kim M-K, Zebari AS, Aumann S, Park CY, Buonamici S, Smith PG, Deeg HJ, Lobry C, Aifantis I, Modis Y, Allain FH-T, Halene S, Bradley RK, Abdel-Wahab O. (2015). SRSF2 Mutations Contribute to Myelodysplasia by Mutant-Specific Effects on Exon Recognition. Cancer Cell, 27(5), 617-30. PMCID: PMC4429920.
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Kisiela DI, Avagyan H, Friend D, Jalan A, Gupta S, Interlandi G, Liu Y, Tchesnokova V, Rodriguez VB, Sumida JP, Strong RK, Wu X-R, Thomas WE, Sokurenko EV. (2015). Inhibition and Reversal of Microbial Attachment by an Antibody with Parasteric Activity against the FimH Adhesin of Uropathogenic E. coli. PLoS Pathog, 11(5), e1004857.
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Mendenhall AR, Tedesco PM, Sands B, Johnson TE, Brent R. (2015). Single Cell Quantification of Reporter Gene Expression in Live Adult Caenorhabditis elegans Reveals Reproducible Cell-Specific Expression Patterns and Underlying Biological Variation. PLoS One, 10(5), e0124289.
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Craig KL, Hasan MK, Jackson DL, Engel GA, Soliven K, Feeroz MM, Wang X, Jones-Engel L, Linial ML. (2015). A semi-nomadic population in Bangladesh with extensive exposure to macaques does not exhibit high levels of zoonotic simian foamy virus infection. J Virol.
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Dong Y, Gou Y, Li Y, Liu Y, Bai J. (2015). Synaptojanin cooperates with endophilin through an unexpected mechanism. Elife, 4.
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Yoon K-H, Ragoczy T, Lu Z, Kondoh K, Kuang D, Groudine M, Buck LB. (2015). Olfactory receptor genes expressed in distinct lineages are sequestered in different nuclear compartments. Proc Natl Acad Sci U S A.
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Pan L, Shah AN, Phelps IG, Doherty D, Johnson EA, Moens CB. (2015). Rapid identification and recovery of ENU-induced mutations with next-generation sequencing and Paired-End Low-Error analysis. BMC Genomics, 16(1), 83.
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Shah AN, Davey CF, Whitebirch AC, Miller AC, Moens CB. (2015). Rapid reverse genetic screening using CRISPR in zebrafish. Nat Methods
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Chang C-W, Hui E, Bai J, Bruns D, Chapman ER, Jackson MB. (2015). A structural role for the synaptobrevin 2 transmembrane domain in dense-core vesicle fusion pores. J Neurosci, 35(14), 5772-80.
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Henikoff JG, Thakur J, Kasinathan S, Henikoff S. (2015). A unique chromatin complex occupies young α-satellite arrays of human centromeres. Science Advances, 1(1), e1400234.
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Iwata A, Morrison ML, Blackwood JE, Roth MB. (2015). Selenide Targets to Reperfusing Tissue and Protects It From Injury. Crit Care Med.
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Verboon JM, Parkhurst SM. (2015). Rho family GTPase functions in Drosophila epithelial wound repair. Small GTPases, 6(1), 33-40.
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Verboon JM, Parkhurst SM. (2015). Rho family GTPases bring a familiar ring to cell wound repair. Small GTPases, 6(1), 1-7.
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Orsi GA, Kasinathan S, Zentner GE, Henikoff S, Ahmad K. (2015). Mapping regulatory factors by immunoprecipitation from native chromatin. Current protocols in molecular biology / edited by Frederick M Ausubel  [et al], 110, 21 31 1-21 31 25.
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White MA, Kitano J, Peichel CL. (2015). Purifying selection maintains dosage-sensitive genes during degeneration of the threespine stickleback Y chromosome. Mol Biol Evol.
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Williams BP, Pignatta D, Henikoff S, Gehring M. (2015). Methylation-sensitive expression of a DNA demethylase gene serves as an epigenetic rheostat. PLoS Genet, 11(3), e1005142.
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Wragg RT, Gouzer G, Bai J, Arianna G, Ryan TA, Dittman JS. (2015). Synaptic activity regulates the abundance and binding of complexin. Biophys J, 108(6), 1318-29.
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Cooper JA, Kaneko T, Li SSC. (2015). Cell regulation by phosphotyrosine-targeted ubiquitin ligases. Mol Cell Biol.
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Fishburn J, Tomko E, Galburt E, Hahn S. (2015). Double-stranded DNA translocase activity of transcription factor TFIIH and the mechanism of RNA polymerase II open complex formation. Proc Natl Acad Sci U S A.
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Pan L, Shah AN, Phelps IG, Doherty D, Johnson EA, Moens CB. (2015). Rapid identification and recovery of ENU-induced mutations with next-generation sequencing and Paired-End Low-Error analysis. BMC Genomics, 16(1), 1263.
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Siegel JB, Smith AL, Poust S, Wargacki AJ, Bar-Even A, Louw C, Shen BW, Eiben CB, Tran HM, Noor E, Gallaher JL, Bale J, Yoshikuni Y, Gelb MH, Keasling JD, Stoddard BL, Lidstrom ME, Baker D. (2015). Computational protein design enables a novel one-carbon assimilation pathway. Proc Natl Acad Sci U S A, 112(12), 3704-9.
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Verboon JM, Rincon-Arano H, Werwie TR, Delrow JJ, Scalzo D, Nandakumar V, Groudine M, Parkhurst SM. (2015). Wash interacts with lamin and affects global nuclear organization. Curr Biol, 25(6), 804-10.
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Verboon JM, Rahe TK, Rodriguez-Mesa E, Parkhurst SM. (2015). Wash functions downstream of Rho1 GTPase in a subset of Drosophila immune cell developmental migrations. Mol Biol Cell.
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Greenwood AK, Ardekani R, McCann SR, Dubin ME, Sullivan A, Bensussen S, Tavare S, Peichel CL. (2015). Genetic Mapping of Natural Variation in Schooling Tendency in the Threespine Stickleback. G3.
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Gu H, Du J, Carnevale Neto F, Carroll PA, Turner SJ, Chiorean EG, Eisenman RN, Raftery D. (2015). Metabolomics method to comprehensively analyze amino acids in different domains. The Analyst.
abstract >

Lee LJ, Rodriguez J, Tsukiyama T. (2015). Chromatin Remodeling Factors Isw2 and Ino80 Regulate Checkpoint Activity and Chromatin Structure in S Phase. Genetics.
abstract >

Yang F, Kemp CJ, Henikoff S. (2015). Anthracyclines induce double-strand DNA breaks at active gene promoters. Mutation research Fundamental and molecular mechanisms of mutagenesis, 773, 9-15. PMCID: PMC4332850.
abstarct >

Singh PK, Bourque G, Craig NL, Dubnau JT, Feschotte C, Flasch DA, Gunderson KL, Malik HS, Moran JV, Peters JE, Slotkin RK, Levin HL. (2014). Mobile genetic elements and genome evolution 2014. Mobile DNA, 5(Artn 26).
abstract >

Zanders SE, Malik HS. (2015). R2d2 and Hyperdrive Mechanisms (in Mouse Meiosis). PLoS Genet, 11(2), e1004950.
abstract >

Carroll PA, Diolaiti D, McFerrin L, Gu H, Djukovic D, Du J, Cheng PF, Anderson S, Ulrich M, Hurley JB, Raftery D, Ayer DE, Eisenman RN. (2015). Deregulated Myc Requires MondoA/Mlx for Metabolic Reprogramming and Tumorigenesis. Cancer Cell.
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Tong Q, Mazur SJ, Rincon-Arano H, Rothbart SB, Kuznetsov DM, Cui G, Liu WH, Gete Y, Klein BJ, Jenkins L, Mer G, Kutateladze AG, Strahl BD, Groudine M, Appella E, Kutateladze TG. (2015). An Acetyl-Methyl Switch Drives a Conformational Change in p53. Structure, 23(2), 322-31. PMCID: PMC4317571.
abstarct >

Carroll PA, Eisenman RN. (2015). Growing old with myc. Cell, 160(3), 365-6.
abstract >

Hooper KA, Crowe JEJ, Bloom JD. (2015). Influenza viruses with receptor-binding N1 neuraminidases occur sporadically in several lineages and show no attenuation in cell culture or mice. J Virol.
abstract >

Mandell DJ, Lajoie MJ, Mee MT, Takeuchi R, Kuznetsov G, Norville JE, Gregg CJ, Stoddard BL, Church GM. (2015). Biocontainment of genetically modified organisms by synthetic protein design. Nature.
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Ratnappan R, Amrit FRG, Chen S-W, Gill H, Holden K, Ward J, Yamamoto KR, Olsen CP, Ghazi A. (2014). Germline signals deploy NHR-49 to modulate fatty-acid beta-oxidation and desaturation in somatic tissues of C. elegans. PLoS Genet, 10(12), e1004829. PMCID: PMC4256272.
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Henikoff S, Smith MM. (2015). Histone Variants and Epigenetics. Cold Spring Harbor perspectives in biology, 7(1).
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Park K, Shen BW, Parmeggiani F, Huang P-S, Stoddard BL, Baker D. (2015). Control of repeat-protein curvature by computational protein design. Nat Struct Mol Biol.
abstarct >

Zhao H, Faltermeier CM, Mendelsohn L, Porter PL, Clurman BE, Roberts JM. (2014). Mislocalization of p27 to the cytoplasm of breast cancer cells confers resistance to anti-HER2 targeted therapy. Oncotarget, 5(24), 12704-14.
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Feng Q, Snider L, Jagannathan S, Tawil R, van der Maarel SM, Tapscott SJ, Bradley RK. (2015). A feedback loop between nonsense-mediated decay and the retrogene in facioscapulohumeral muscular dystrophy. Elife, 4.
abstract >

2014

Reyes NL, Banks GB, Tsang M, Margineantu D, Gu H, Djukovic D, Chan J, Torres M, Liggitt HD, Hirenallur-S DK, Hockenbery DM, Raftery D, Iritani BM. (2014). Fnip1 regulates skeletal muscle fiber type specification, fatigue resistance, and susceptibility to muscular dystrophy. Proc Natl Acad Sci U S A
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Ragoczy T, Telling A, Scalzo D, Kooperberg C, Groudine M. (2014). Functional redundancy in the nuclear compartmentalization of the late-replicating genome. Nucleus, 0.
abstract >

Bogenschutz NL, Rodriguez J, Tsukiyama T. (2014). Initiation of DNA replication from non-canonical sites on an origin-depleted chromosome. PLoS One, 9(12), e114545.
abstract >

Miller AC, Voelker LH, Shah AN, Moens CB. (2014). Neurobeachin Is Required Postsynaptically for Electrical and Chemical Synapse Formation. Curr Biol.
abstract >

Ramachandran S, Zentner GE, Henikoff S. (2014). Asymmetric nucleosomes flank promoters in the budding yeast genome. Genome Res.
abstract >

Chou S, Daugherty MD, Peterson SB, Biboy J, Yang Y, Jutras BL, Fritz-Laylin LK, Ferrin MA, Harding BN, Jacobs-Wagner C, Yang XF, Vollmer W, Malik HS, Mougous JD. (2014). Transferred interbacterial antagonism genes augment eukaryotic innate immune function. Nature.
abstract >

Miller AD. (2014). Retroviral Vectors: From Cancer Viruses to Therapeutic Tools. Hum Gene Ther.
abstract >

Phadnis N, Malik HS. (2014). Speciation via Autoimmunity: A Dangerous Mix. Cell, 159(6), 1247-9.
abstract >

Teves SS, Weber CM, Henikoff S. (2014). Transcribing through the nucleosome. Trends Biochem Sci, 39(12), 577-86.
abstract >

Cooper JA. (2014) Molecules and mechanisms that regulate multipolar migration in the intermediate zone. Front Cell Neurosci. 14;8:386. eCollection.
abstract
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Bennett G. (2014). Nature natured and nature denatured. Hastings Cent Rep, 44 Suppl 5, S38-9.
abstract >

Lynch M, Field MC, Goodson HV, Malik HS, Pereira-Leal JB, Roos DS, Turkewitz AP, Sazer S. (2014). Evolutionary cell biology: Two origins, one objective. Proc Natl Acad Sci U S A.
abstarct >

Stergachis AB, Neph S, Sandstrom R, Haugen E, Reynolds AP, Zhang M, Byron R, Canfield T, Stelhing-Sun S, Lee K, Thurman RE, Vong S, Bates D, Neri F, Diegel M, Giste E, Dunn D, Vierstra J, Hansen RS, Johnson AK, Sabo PJ, Wilken MS, Reh TA, Treuting PM, Kaul R, Groudine M, Bender MA, Borenstein E, Stamatoyannopoulos JA. (2014). Conservation of trans-acting circuitry during mammalian regulatory evolution. Nature, 515(7527), 365-70.
abstract >

Takeuchi R, Choi M, Stoddard BL. (2015). Engineering of Customized Meganucleases via In Vitro Compartmentalization and In Cellulo Optimization. Methods in molecular biology, 1239, 105-32.
abstract >

Vierstra J, Rynes E, Sandstrom R, Zhang M, Canfield T, Hansen RS, Stehling-Sun S, Sabo PJ, Byron R, Humbert R, Thurman RE, Johnson AK, Vong S, Lee K, Bates D, Neri F, Diegel M, Giste E, Haugen E, Dunn D, Wilken MS, Josefowicz S, Samstein R, Chang K-H, Eichler EE, De Bruijn M, Reh TA, Skoultchi A, Rudensky A, Orkin SH, Papayannopoulou T, Treuting PM, Selleri L, Kaul R, Groudine M, Bender MA, Stamatoyannopoulos JA. (2014). Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution. Science, 346(6212), 1007-12.
abstract
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Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See L-H, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine M, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu Y-C, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang K-H, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou X-Q, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B, Consortium ME. (2014). A comparative encyclopedia of DNA elements in the mouse genome. Nature, 515(7527), 355-64.
abstract >

Radoff DT, Dong Y, Snead D, Bai J, Eliezer D, Dittman JS. (2014). The accessory helix of complexin functions by stabilizing central helix secondary structure. Elife, 3.
abstract >

Steigedal M, Marstad A, Haug M, Damas JK, Strong RK, Roberts PL, Himpsl SD, Stapleton A, Hooton TM, Mobley HLT, Hawn TR, Flo TH. (2014). Lipocalin 2 Imparts Selective Pressure on Bacterial Growth in the Bladder and Is Elevated in Women with Urinary Tract Infection. Journal of immunology.
abstract >

Dvinge H, Ries RE, Ilagan JO, Stirewalt DL, Meshinchi S, Bradley RK. (2014). Sample processing obscures cancer-specific alterations in leukemic transcriptomes. Proc Natl Acad Sci U S A.
abstract >

Iwata A, Morrison ML, Roth MB. (2014). Iodide protects heart tissue from reperfusion injury. PLoS One, 9(11), e112458.
abstract >

Alcid EA1, Tsukiyama T. (2014) ATP-dependent chromatin remodeling shapes the long noncoding RNA landscape. Genes Dev. 28(21):2348-60. doi: 10.1101/gad.250902.114.
abstract >

Linderman SL, Chambers BS, Zost SJ, Parkhouse K, Li Y, Herrmann C, Ellebedy AH, Carter DM, Andrews SF, Zheng N-Y, Huang M, Huang Y, Strauss D, Shaz BH, Hodinka RL, Reyes-Teran G, Ross TM, Wilson PC, Ahmed R, Bloom JD, Hensley SE. (2014). Potential antigenic explanation for atypical H1N1 infections among middle-aged adults during the 2013-2014 influenza season. Proc Natl Acad Sci U S A.
abstract
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Hahn S. (2014). Ellis englesberg and the discovery of positive control in gene regulation. Genetics, 198(2), 455-60. PMCID: PMC4196604.
abstract >

Kasinathan S, Henikoff S. (2014). 5-Aza-CdR Delivers a Gene Body Blow. Cancer Cell, 26(4), 449-51.
Full-text Article:  http://scholars.fhcrc.org/5518/
abstract >

Russell CA, Kasson PM, Donis RO, Riley S, Dunbar J, Rambaut A, Asher J, Burke S, Davis CT, Garten RJ, Gnanakaran S, Hay SI, Herfst S, Lewis NS, Lloyd-Smith JO, Macken CA, Maurer-Stroh S, Neuhaus E, Parrish CR, Pepin KM, Shepard SS, Smith DL, Suarez DL, Trock SC, Widdowson M-A, George DB, Lipsitch M, Bloom JD. (2014). Improving pandemic influenza risk assessment. Elife, 3. PMCID: PMC4199076.
abstract >

Steiner FA, Henikoff S. (2015). Cell type-specific affinity purification of nuclei for chromatin profiling in whole animals. Methods in molecular biology, 1228, 3-14.
abstract >

Agarwal A, Mackenzie RJ, Besson A, Jeng S, Carey A, LaTocha DH, Fleischman AG, Duquesnes N, Eide CA, Vasudevan KB, Loriaux MM, Firpo E, Cortes JE, McWeeney S, O'Hare T, Roberts JM, Druker BJ, Deininger MW. (2014). BCR-ABL1 promotes leukemia by converting p27 into a cytoplasmic oncoprotein. Blood
Abstract >

London N, Biggins S. (2014). Signalling dynamics in the spindle checkpoint response. Nature reviews Molecular cell biology.
Abstract >

Ross BD, Malik HS. (2014). Genetic Conflicts: Stronger Centromeres Win Tug-of-War in Female Meiosis. Curr Biol, 24(19), R966-8.
Abstract >

Sands B, Jenkins P, Peria WJ, Naivar M, Houston JP, Brent R. (2014). Measuring and sorting cell populations expressing isospectral fluorescent proteins with different fluorescence lifetimes. PLoS One, 9(10), e109940.
Abstract
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Zentner GE, Henikoff S. (2014). High-resolution digital profiling of the epigenome. Nature reviews Genetics.
Abstract >

Rodriguez J, McKnight JN, Tsukiyama T. (2014). Genome-Wide Analysis of Nucleosome Positions, Occupancy, and Accessibility in Yeast: Nucleosome Mapping, High-Resolution Histone ChIP, and NCAM. Current protocols in molecular biology / edited by Frederick M Ausubel  [et al], 108, 21 8 1- 8 16. PMCID: PMC4183977.
Abstract >

Umbreit NT, Miller MP, Tien JF, Cattin Ortola J, Gui L, Lee KK, Biggins S, Asbury CL, Davis TN. (2014). Kinetochores require oligomerization of Dam1 complex to maintain microtubule attachments against tension and promote biorientation. Nat Commun, 5, 4951.
Abstract >

Finton KAK, Friend D, Jaffe J, Gewe M, Holmes MA, Larman HB, Stuart A, Larimore K, Greenberg PD, Elledge SJ, Stamatatos L, Strong RK. (2014). Ontogeny of Recognition Specificity and Functionality for the Broadly Neutralizing Anti-HIV Antibody 4E10. PLoS Pathog, 10(9), e1004403.
Abstract >

Thayer NH, Leverich CK, Fitzgibbon MP, Nelson ZW, Henderson KA, Gafken PR, Hsu JJ, Gottschling DE. (2014). Identification of long-lived proteins retained in cells undergoing repeated asymmetric divisions. Proc Natl Acad Sci U S A.
Abstract >

Han, Y., Luo, J., Ranish, J., Hahn, S. (2014). Architecture of the Saccharomyces cerevisiae SAGA transcription coactivator complex. EMBO J.
Abstract >

Horowitz, L.F., Saraiva, L.R., Kuang, D., Yoon, K.-H., Buck, L.B. (2014). Olfactory receptor patterning in a higher primate. J Neurosci, 34(37), 12241-52.
Abstract >

McLaughlin, R.N.J., Young, J.M., Yang, L., Neme, R., Wichman, H.A., Malik, H.S. (2014). Positive Selection and Multiple Losses of the LINE-1-Derived L1TD1 Gene in Mammals Suggest a Dual Role in Genome Defense and Pluripotency. PLoS Genet, 10(9), e1004531.
Abstract >

Sarangapani, K.K., Duro, E., Deng, Y., Alves, F.d.L., Ye, Q., Opoku, K.N., Ceto, S., Rappsilber, J., Corbett, K.D., Biggins, S., Marston, A.L., Asbury, C.L. (2014). Sister kinetochores are mechanically fused during meiosis I in yeast. Science.
Abstract >

Tsai, H.-J., Huang, C.-L., Chang, Y.-W., Huang, D.-Y., Lin, C.-C., Cooper, J.A., Cheng, J.-C., Tseng, C.-P. (2014). Disabled-2 Is Required for Efficient Hemostasis and Platelet Activation by Thrombin in Mice. Arterioscler Thromb Vasc Biol.
Abstract >

Henderson, K.A., Hughes, A.L., Gottschling, D.E. (2014). Mother-daughter asymmetry of pH underlies aging and rejuvenation in yeast. Elife, e03504.
Abstract >

Strongin, D.E., Groudine, M., Politz, J.C.R. (2014). Nucleolar tethering mediates pairing between the IgH and Myc loci. Nucleus, 5(5).
Abstract >

Talbert, P.B., Henikoff, S. (2014). Environmental responses mediated by histone variants. Trends Cell Biol.
Abstract >

Teves, S.S., Henikoff, S. (2014). DNA torsion as a feedback mediator of transcription and chromatin dynamics. Nucleus, 5(3), 211-8. PMCID: PMC4133216.
Abstract >

Ventura, A.C., Bush, A., Vasen, G., Goldin, M.A., Burkinshaw, B., Bhattacharjee, N., Folch, A., Brent, R., Chernomoretz, A., Colman-Lerner, A. (2014). Utilization of extracellular information before ligand-receptor binding reaches equilibrium expands and shifts the input dynamic range. Proc Natl Acad Sci U S A.
Abstract >

Blasky, A.J., Pan, L., Moens, C.B., Appel, B. (2014). Pard3 regulates contact between neural crest cells and the timing of Schwann cell differentiation but is not essential for neural crest migration or myelination. Dev Dyn.
Abstract >

Deyter, G.M.R., Biggins, S. (2014). The FACT complex interacts with the E3 ubiquitin ligase Psh1 to prevent ectopic localization of CENP-A. Genes Dev, 28(16), 1815-26.
Abstract >

Knutson, B.A., Luo, J., Ranish, J., Hahn, S. (2014). Architecture of the Saccharomyces cerevisiae RNA polymerase I Core Factor complex. Nat Struct Mol Biol.
Abstract >

Mills, J., Khare, S.D., Bolduc, J.M., Forouhar, F., Mulligan, V.K., Lew, S., Seetharaman, J., Tong, L., Stoddard, B.L., Baker, D. (2014). Computational Design of an Unnatural Amino Acid Dependent Metalloprotein with Atomic Level Accuracy.Protein Sci, 23, 170-1.

Warfield, L., Tuttle, L.M., Pacheco, D., Klevit, R.E., Hahn, S. (2014). A sequence-specific transcription activator motif and powerful synthetic variants that bind Mediator using a fuzzy protein interface. Proc Natl Acad Sci U S A.
Abstract >

Daugherty, M.D., Malik, H.S. (2014). How a Virus Blocks a Cellular Emergency Access Lane to the Nucleus, STAT! Cell Host Microbe, 16(2), 150-2.
Abstract >

Engel, G.A., Small, C.T., Soliven, K., Feeroz, M.M., Wang, X., Hasan, M.K., Oh, G., Alam, S.M.R., Craig, K.L., Jackson, D.L., Matsen, F.A., Linial, M.L., Jones-Engel, L. (2013). Zoonotic simian foamy virus in Bangladesh reflects diverse patterns of transmission and co-infection. Emerg Microbes Infec, 2.

Skene, P.J., Henikoff, S. (2014). Histones push the envelope. Nat Struct Mol Biol, 21(8), 651-2.
Abstract >

Taylor, A.F., Amundsen, S.K., Guttman, M., Lee, K.K., Luo, J., Ranish, J., Smith, G.R. (2014). Control of RecBCD Enzyme Activity by DNA Binding- and Chi Hotspot-dependent Conformational Changes. J Mol Biol.
Abstract >

Bloom, J.D. (2014). An experimentally informed evolutionary model improves phylogenetic fit to divergent lactamase homologs. Mol Biol Evol.
Abstract >

Fowler, K.R., Sasaki, M., Milman, N., Keeney, S., Smith, G.R. (2014). Evolutionarily diverse determinants of meiotic DNA break and recombination landscapes across the genome. Genome Res.
Abstract >

Bachtrog, D., Mank, J.E., Peichel, C.L., Kirkpatrick, M., Otto, S.P., Ashman, T.-L., Hahn, M.W., Kitano, J., Mayrose, I., Ming, R., Perrin, N., Ross, L., Valenzuela, N., Vamosi, J.C., Tree of Sex, C. (2014). Sex determination: why so many ways of doing it? PLoS Biol, 12(7), e1001899. PMCID: PMC4077654.
Abstract >

Thyagarajan B., Bloom, JD. The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin. eLife 2014;10.7554/eLife.03300
Abstract >

Zanders, S.E., Eickbush, M.T., Yu, J.S., Kang, J.-W., Fowler, K.R., Smith, G.R., Malik, H.S. (2014). Genome rearrangements and pervasive meiotic drive cause hybrid infertility in fission yeast. Elife, 3, e02630. PMCID: PMC4066438.
Abstract >

Machkovech, H., Bloom, J.D. (2014). Generation Of a Human T-Cell Receptor Cell Line to Evaluate Influenza Peptide Presentation. J Invest Med, 62(1), 279-.

Procko, E., Berguig, G.Y., Shen, B.W., Song, Y., Frayo, S., Convertine, A.J., Margineantu, D., Booth, G., Correia, B.E., Cheng, Y., Schief, W.R., Hockenbery, D.M., Press, O.W., Stoddard, B.L., Stayton, P.S., Baker, D. (2014). A computationally designed inhibitor of an epstein-barr viral bcl-2 protein induces apoptosis in infected cells. Cell, 157(7), 1644-56.
Abstract >

Belfort, M., Marraffini, L., Macfarlan, T., Boeke, J., Slotkin, K., Malik, H., Maquat, L. (2014). Mobile DNA: an evolving field. Mobile DNA, 5, 16. PMCID: PMC4046146.
Abstract >

Galizi, R., Doyle, L.A., Menichelli, M., Bernardini, F., Deredec, A., Burt, A., Stoddard, B.L., Windbichler, N., Crisanti, A. (2014). A synthetic sex ratio distortion system for the control of the human malaria mosquito. Nat Commun, 5, 3977. PMCID: PMC4057611.
Abstract >

Daugherty, M.D., Young, J.M., Kerns, J.A., Malik, H.S. (2014). Rapid Evolution of PARP Genes Suggests a Broad Role for ADP-Ribosylation in Host-Virus Conflicts. PLoS Genet, 10(5), e1004403.
Abstract >

Diolaiti, D., McFerrin, L., Carroll, P., Eisenman, R.N. (2014). Functional interactions among members of the MAX and MLX transcriptional network during oncogenesis. Biochim Biophys Acta.
Abstract >

Kamenova, I., Warfield, L., Hahn, S. (2014). Mutations on the DNA binding surface of TBP discriminate between yeast TATA and TATA-less gene transcription. Mol Cell Biol.
Abstract >

Green, R., Shou, W. (2014). Modeling community population dynamics with the open-source language R. Methods in molecular biology, 1151, 209-31.
Abstract >

Waite, A.J., Shou, W. (2014). Constructing synthetic microbial communities to explore the ecology and evolution of symbiosis. Methods in molecular biology, 1151, 27-38.
Abstract >

Sinnar, S.A., Antoku, S., Saffin, J.-M., Cooper, J.A., Halpain, S. (2014). Capping Protein Is Essential for Cell Migration in Vivo and for Filopodial Morphology and Dynamics. Mol Biol Cell.
Abstract >

Villamaria, C.Y., Fries, C.A., Spencer, J.R., Roth, M.B., Davis, M.R. (2014). Hydrogen sulfide mitigates reperfusion injury in a porcine model of vascularized composite autotransplantation. Annals of plastic surgery, 72(5), 594-8.
Abstract >

Bloom, J. An experimentally determined evolutionary model dramatically improves phylogenetic fit. Mol Biol Evol first published online May 24, 2014 doi:10.1093/molbev/msu173
Abstract >

Gong LI, Bloom JD (2014) Epistatically Interacting Substitutions Are Enriched during Adaptive Protein Evolution. PLoS Genet 10(5): e1004328. doi:10.1371/journal.pgen.1004328.
Abstract >

Conacci-Sorrell, M., Ngouenet, C., Anderson, S., Brabletz, T., Eisenman, R.N. (2014). Stress-induced cleavage of Myc promotes cancer cell survival. Genes Dev, 28(7), 689-707.
Abstract >

Henikoff, S., Ramachandran, S., Krassovsky, K., Bryson, T.D., Codomo, C.A., Brogaard, K., Widom, J., Wang, J.-P., Henikoff, J.G. (2014). The budding yeast Centromere DNA Element II wraps a stable Cse4 hemisome in either orientation in vivo. Elife, 3, e01861.
Abstract >

Skene, P.J., Hernandez, A.E., Groudine, M., Henikoff, S. (2014). The nucleosomal barrier to promoter escape by RNA polymerase II is overcome by the chromatin remodeler Chd1. Elife, 3, e02042.
Abstract >

Ye, X., Linton, J.M., Schork, N.J., Buck, L.B., Petrascheck, M. (2014). A pharmacological network for lifespan extension in Caenorhabditis elegans. Aging Cell, 13(2), 206-15. PMCID: PMC3955372.
Abstract >

Steiner, F.A., Henikoff, S. (2014). Holocentromeres are dispersed point centromeres localized at transcription factor hotspots. Elife, 3, e02025.
Abstract >

Orsi, G.A., Kasinathan, S., Hughes, K.T., Saminadin-Peter, S., Henikoff, S., Ahmad, K. (2014). High-resolution mapping defines the cooperative architecture of Polycomb response elements. Genome Res.
Abstract >

Tenthorey, J.L., Kofoed, E.M., Daugherty, M.D., Malik, H.S., Vance, R.E. (2014). Molecular Basis for Specific Recognition of Bacterial Ligands by NAIP/NLRC4 Inflammasomes. Mol Cell.
Abstract >

Butler, J., Hooper, K.A., Petrie, S., Lee, R., Maurer-Stroh, S., Reh, L., Guarnaccia, T., Baas, C., Xue, L., Vitesnik, S., Leang, S.-K., McVernon, J., Kelso, A., Barr, I.G., McCaw, J.M., Bloom, J.D., Hurt, A.C. (2014). Estimating the Fitness Advantage Conferred by Permissive Neuraminidase Mutations in Recent Oseltamivir-Resistant A(H1N1)pdm09 Influenza Viruses. PLoS Pathog, 10(4), e1004065.
Abstract >

Biggins S, Welch MD. (2014). Editorial overview: Cell architecture: Cellular organization and function. Current opinion in cell biology, 26, v-vii.
Abstract >

Driver JW, Powers AF, Sarangapani KK, Biggins S, Asbury CL. (2014). Measuring kinetochore-microtubule interaction in vitro. Methods Enzymol, 540, 321-37.
Abstract >

Miller CT, Glazer AM, Summers BR, Blackman BK, Norman AR, Shapiro MD, Cole BL, Peichel CL, Schluter D, Kingsley DM. (2014). Modular Skeletal Evolution in Sticklebacks Is Controlled by Additive and Clustered Quantitative Trait Loci. Genetics.
Abstract >

Quillien, A., Moore, J.C., Shin, M., Siekmann, A.F., Smith, T., Pan, L., Moens, C.B., Parsons, M.J., Lawson, N.D. (2014). Distinct Notch signaling outputs pattern the developing arterial system. Development.
Abstract >

Stoddard, B.L. (2014). Homing endonucleases from mobile group I introns: discovery to genome engineering. Mobile DNA, 5(1), 7. PMCID: PMC3943268.
Abstract >

Takeuchi, R., Choi, M., Stoddard, B.L. (2014). Redesign of extensive protein-DNA interfaces of meganucleases using iterative cycles of in vitro compartmentalization. Proc Natl Acad Sci U S A.
Abstract >

Weber, C.M., Ramachandran, S., Henikoff, S. (2014). Nucleosomes Are Context-Specific, H2A.Z-Modulated Barriers to RNA Polymerase. Mol Cell, 53(5), 819-30.
Abstract >

Yoshida, K., Makino, T., Yamaguchi, K., Shigenobu, S., Hasebe, M., Kawata, M., Kume, M., Mori, S., Peichel, C.L., Toyoda, A., Fujiyama, A., Kitano, J. (2014). Sex Chromosome Turnover Contributes to Genomic Divergence between Incipient Stickleback Species. PLoS Genet, 10(3), e1004223.
Abstract >

Dillin, A., Gottschling, D.E., Nystrom, T. (2014). The good and the bad of being connected: the integrons of aging. Current opinion in cell biology, 26C, 107-12. PMCID: PMC3927154.
Abstract >

Poudel, K.R., Bai, J. (2014). Synaptic vesicle morphology: a case of protein sorting? Current opinion in cell biology, 26C, 28-33.
Abstract >

Momeni, B., Waite, A.J., Shou, W. (2013). Spatial self-organization favors heterotypic cooperation over cheating. Elife, 2, e00960. PMCID: PMC3823188.
Abstract >

Mills, M.G., Greenwood, A.K., Peichel, C.L. (2014). Pleiotropic effects of a single gene on skeletal development and sensory system patterning in sticklebacks. EvoDevo, 5(1), 5.
Abstract >

Krassovsky, K., Henikoff, S. (2014). Distinct chromatin features characterize different classes of repeat sequences in Drosophila melanogaster. BMC Genomics, 15(1), 105.
Abstract >

Correia, B.E., Bates, J.T., Loomis, R.J., Baneyx, G., Carrico, C., Jardine, J.G., Rupert, P., Correnti, C., Kalyuzhniy, O., Vittal, V., Connell, M.J., Stevens, E., Schroeter, A., Chen, M., Macpherson, S., Serra, A.M., Adachi, Y., Holmes, M.A., Li, Y., Klevit, R.E., Graham, B.S., Wyatt, R.T., Baker, D., Strong, R.K., Crowe, J.E., Johnson, P.R., Schief, W.R. (2014). Proof of principle for epitope-focused vaccine design. Nature.
Abstract >

Qin L-X, Breeden L, Self SG. (2014). Finding gene clusters for a replicated time course study. BMC research notes, 7(1), 60.
Abstract >

Lopez-Yglesias, A.H., Zhao, X., Quarles, E.K., Lai, M.A., Vandenbos, T., Strong, R.K., Smith, K.D. (2014). Flagellin Induces Antibody Responses through a TLR5- and Inflammasome-Independent Pathway. Journal of immunology.|
Abstract >

Zigman, M., Laumann-Lipp, N., Titus, T., Postlethwait, J., Moens, C.B. (2014). Hoxb1b controls oriented cell division, cell shape and microtubule dynamics in neural tube morphogenesis. Development, 141(3), 639-49.
Abstract >

Klein, B.J., Piao, L., Xi, Y., Rincon-Arano, H., Rothbart, S.B., Peng, D., Wen, H., Larson, C., Zhang, X., Zheng, X., Cortazar, M.A., Pena, P.V., Mangan, A., Bentley, D.L., Strahl, B.D., Groudine, M., Li, W., Shi, X., Kutateladze, T.G. (2014). The Histone-H3K4-Specific Demethylase KDM5B Binds to Its Substrate and Product through Distinct PHD Fingers. Cell Rep.
Abstract >

Abreu-Blanco, M.T., Verboon, J.M., Parkhurst, S.M. (2013). Coordination of Rho Family GTPase Activities to Orchestrate Cytoskeleton Responses during Cell Wound Repair. Curr Biol.
Abstract >

Codomo, C.A., Furuyama, T., Henikoff, S. (2014). CENP-A octamers do not confer a reduction in nucleosome height by AFM. Nat Struct Mol Biol, 21(1), 4-5.
Abstract >

London, N., Biggins, S. (2014). Mad1 kinetochore recruitment by Mps1-mediated phosphorylation of Bub1 signals the spindle checkpoint. Genes Dev.
Abstract >

Cipak, L., Polakova, S., Hyppa, R.W., Smith, G.R., Gregan, J. (2014). Synchronized fission yeast meiosis using an ATP analog-sensitive Pat1 protein kinase. Nature protocols, 9(1), 223-31.
Abstract >

Conacci-Sorrell, M., McFerrin, L., Eisenman, R.N. (2014). An Overview of MYC and Its Interactome. Cold Spring Harb Perspect Med, 4(1).
Abstract >

Dynan, W., Fox, K., Stoddard, B. (2014). Editorial: NAR Surveys the Past, Present and Future of Restriction Endonucleases. Nucleic Acids Res, 42(1), 1-2. PMCID: PMC3874147.
Abstract >

2013

Ruiz M, Ganfornina MD, Correnti C, Strong RK, Sanchez D. (2013). Ligand binding-dependent functions of the lipocalin NLaz: an in vivo study in Drosophila. FASEB journal : official publication of the Federation of American Societies for Experimental Biology.
Abstract >

Yang F, Teves SS, Kemp CJ, Henikoff S. (2013). Doxorubicin, DNA torsion, and chromatin dynamics. Biochim Biophys Acta.
Abstract >

Ardekani, R., Greenwood, A.K., Peichel, C.L., Tavare, S. (2013). Automated quantification of the schooling behaviour of sticklebacks. Eurasip J Image Vide.

Blackledge, N.P., Thomson, J.P., Skene, P.J. (2013). CpG island chromatin is shaped by recruitment of ZF-CxxC proteins. Cold Spring Harbor perspectives in biology, 5(11), a018648.
Abstract >

Kasinathan, S., Orsi, G.A., Zentner, G.E., Ahmad, K., Henikoff, S. (2013). High-resolution mapping of transcription factor binding sites on native chromatin. Nat Methods.
Abstract >

Ashenberg, O., Gong, L.I., Bloom, J.D. (2013). Mutational effects on stability are largely conserved during protein evolution. Proc Natl Acad Sci U S A.
Abstract >

Hickman, J.W., Kotovic, K.M., Miller, C., Warrener, P., Kaiser, B., Jurista, T., Budde, M., Cross, F., Roberts, J.M., Carleton, M. (2013). Glycogen synthesis is a required component of the nitrogen stress response in Synechococcus elongatus PCC 7942. Algal Res, 2(2), 98-106.

Spragg, C.J., Emerman, M. (2013). Antagonism of SAMHD1 is actively maintained in natural infections of simian immunodeficiency virus. Proc Natl Acad Sci U S A.
Abstract >

Teves, S.S., Henikoff, S. (2013). Transcription-generated torsional stress destabilizes nucleosomes. Nat Struct Mol Biol.
Abstract >

Finton K, Jaffe J, Larman B, Larimore K, Friend D, Correnti C, Stuart A, Vanden Bos T, Elledge S, Greenberg P, Stamatatos L, Strong RK. Characterizing the functional autoreactivity and polyspecificity of the MPER-specific bNAb 4E10 and an ensemble of its germline-encoded precursors. AIDS Res Hum Retroviruses. 2013 NOV 1; 29(11): A48-A48.

Wang Y, Pan L, Moens CB, Appel B. Notch3 establishes brain vascular integrity by regulating pericyte number. Development. 2013 Dec 4.
Abstract >

Boissel S, Jarjour J, Astrakhan A, Adey A, Gouble A, Duchateau P, Shendure J, Stoddard BL, Certo MT, Baker D, Scharenberg AM. megaTALs: A rare-cleaving nuclease architecture for therapeutic genome engineering. Nucleic Acids Res. 2013 Nov 26.
Abstract >

Delaurier A, Huycke TR, Nichols JT, Swartz ME, Larsen A, Walker C, Dowd J, Pan L, Moens CB, Kimmel CB. Role of mef2ca in developmental buffering of the zebrafish larval hyoid dermal skeleton. Dev Biol. 2013 Nov 21.
Abstract >

Teckchandani A, Laszlo GS, Simo S, Shah K, Pilling C, Strait AA, Cooper JA. Cullin5 destabilizes cas to inhibit src-dependent cell transformation. J Cell Sci. 2013 Nov 27.
Abstract >

Ashenberg O, Gong I, Bloom J. Mutational effects on stability are largely conserved during protein evolution. PNAS Early edition, Dec 2013.
Full paper >

Nair RN, Bannister TD, Hodder P, Eberhart C, Vega VF, Spicer T, Mercer B, Amundsen SK, Karabulut A, Smith G. Inhibitors of AddAB and RecBCD bacterial DNA repair enzymes: A novel class of antibiotics identified through molecular probe development efforts. Abstr Pap Am Chem Soc. 2013 APR 7; 245.

Paudyal P, Shrestha S, Madanayake T, Shuster CB, Rohrschneider LR, Rowland A, Lyons BA. Grb7 and filamin-a associate and are colocalized to cell membrane ruffles upon EGF stimulation. J Mol Recognit. 2013 Nov; 26(11): 532-541.
Abstract >

Miles S, Li L, Davison J, Breeden LL. Xbp1 directs global repression of budding yeast transcription during the transition to quiescence and is important for the longevity and reversibility of the quiescent state. PLoS Genet. 2013 Oct; 9(10): e1003854.
Abstract >

Stenbak CR, Craig KL, Ivanov SB, Wang X, Soliven KC, Jackson DL, Gutierrez GA, Engel G, Jones-Wengel L, Linial ML. New world simian foamy virus infections in vivo and in vitro. J Virol. 2013 Nov 6.
Abstract >

Su CY, Kemp HA, Moens CB. Cerebellar development in the absence of gbx function in zebrafish. Dev Biol. 2013 Oct 30.
Abstract >

Simó S, Cooper JA. Rbx2 Regulates Neuronal Migration through Different Cullin 5-RING Ligase Adaptors. Dev Cell. 2013 Nov 6. pii: S1534-5807(13)00570-4. doi: 10.1016/j.devcel.2013.09.022. [Epub ahead of print]
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Li L, Anderson S, Secombe J, Eisenman RN. The drosophila ubiquitin-specific protease puffyeye regulates dMyc-mediated growth. Development. 2013 Oct 30.
Abstract >

Malfavon-Borja R, Sawyer SL, Wu LI, Emerman M, Malik HS. An evolutionary screen highlights canonical and non-canonical candidate antiviral genes within the primate TRIM gene family. Genome Biol Evol. 2013 Oct 24.
Abstract >

Zentner GE, Henikoff S. Mot1 redistributes TBP from TATA-containing to TATA-less promoters. Mol Cell Biol. 2013 Oct 21.
Abstract >

Grunberg S, Hahn S. Structural insights into transcription initiation by RNA polymerase II. Trends Biochem Sci. 2013 Oct 11.
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Soliven K, Wang X, Small CT, Feeroz MM, Lee EG, Craig KL, Hasan K, Engel GA, Jones-Engel L, Matsen FA,4th, Linial ML. Simian foamy virus infection of rhesus macaques in bangladesh: Relationship of latent proviruses and transcriptionally active viruses. J Virol.2013 Oct 9.
Abstract >

Bandura JL, Jiang H, Nickerson DW, Edgar BA. The molecular chaperone Hsp90 is required for cell cycle exit in. PLoS Genet. 2013 Sep; 9(9): e1003835.
Abstract >

Hyppa RW, Fowler KR, Cipak L, Gregan J, Smith GR. DNA intermediates of meiotic recombination in synchronous S. pombe at optimal temperature. Nucleic Acids Res. 2013 Oct 1.
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Klezovitch O, Vasioukhin V. Your gut is right to turn left. Dev Cell. 2013 Sep 30; 26(6): 553-554.
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Kuo Y, Ren S, Lao U, Edgar BA, Wang T. Suppression of polyglutamine protein toxicity by co-expression of a heat-shock protein 40 and a heat-shock protein 110. Cell Death Dis. 2013 Oct 3; 4: e833.
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Li L, Miles S, Melville Z, Prasad A, Bradley G, Breeden LL. Key events during the transition from rapid growth to quiescence in budding yeast require posttranscriptional regulators. Mol Biol Cell. 2013 Oct 2.
Abstract >

Talbert PB, Henikoff S. Phylogeny as the basis for naming histones. Trends Genet. 2013 Sep; 29(9): 499-500.
Abstract >

Rasmussen JP, Feldman JL, Reddy SS, Priess JR. Cell interactions and patterned intercalations shape and link epithelial tubes in C. elegans. PLoS Genet. 2013 Sep; 9(9): e1003772.
Abstract >

Ng TM, Lenstra TL, Duggan N, Jiang S, Ceto S, Holstege FC, Dai J, Boeke JD, Biggins S. Kinetochore function and chromosome segregation rely on critical residues in histones H3 and H4 in budding yeast. Genetics. 2013 Sep 20.
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Greenwood AK, Wark AR, Yoshida K, Peichel CL. Genetic and neural modularity underlie the evolution of schooling behavior in threespine sticklebacks. Curr Biol. 2013 Sep 10.
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Cheng C, Ansari MM, Cooper JA, Gong X. EphA2 and src regulate equatorial cell morphogenesis during lens development. Development. 2013 Sep 11.
Abstract >

Cooper JA. Cell biology in neuroscience: Mechanisms of cell migration in the nervous system. J Cell Biol. 2013 Sep 2; 202(5): 725-734.
Abstract >

Etienne L, Emerman M. The mongoose, the pheasant, the pox, and the retrovirus. PLoS Biol. 2013 Aug; 11(8): e1001641.
Abstract >

Tinberg CE, Khare SD, Dou J, Doyle L, Nelson JW, Schena A, Jankowski W, Kalodimos CG, Johnsson K, Stoddard BL, Baker D. Computational design of ligand-binding proteins with high affinity and selectivity. Nature. 2013 Sep 12; 501(7466): 212-216.
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Hooper KA, Bloom JD. A mutant influenza virus that uses an N1 neuraminidase as the receptor-binding protein. Published ahead of print 11 September 2013, doi: 10.1128/JVI.01889-13 JVI.01889-13.
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Hendry AP, Peichel CL, Matthews B, Boughman JW, Nosil P. Stickleback research: The now and the next. Evol Ecol Res. 2013 Feb; 15(2): 111-141.

Compton AA, Malik HS, Emerman M. Host gene evolution traces the evolutionary history of ancient primate lentiviruses. Philos Trans R Soc Lond B Biol Sci. 2013 Aug 12; 368(1626): 20120496.
Abstract >

Knutson BA. Emergence and expansion of TFIIB-like factors in the plant kingdom. Gene. 2013 Aug 15; 526(1): 30-38.
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Lenkowski JR, Qin Z, Sifuentes CJ, Thummel R, Soto CM, Moens CB, Raymond PA. Retinal regeneration in adult zebrafish requires regulation of TGFbeta signaling. Glia. 2013 Aug 5.
Abstract >

Mills JH, Khare SD, Bolduc JM, Forouhar F, Mulligan VK, Lew S, Seetharaman J, Tong L, Stoddard BL, Baker D. Computational design of an unnatural amino acid dependent metalloprotein with atomic level accuracy. J Am Chem Soc. 2013 Aug 7.
Abstract >

Biggins S. The composition, functions, and regulation of the budding yeast kinetochore. Genetics. 2013 Aug; 194(4): 817-846.
Abstract >

Rincon-Arano H, Parkhurst SM, Groudine M. UpSET-ing the balance: Modulating open chromatin features in metazoan genomes. Fly (Austin). 2013 May 6; 7(3).
Abstract >

Alunni A, Krecsmarik M, Bosco A, Galant S, Pan L, Moens CB, Bally-Cuif L. Notch3 signaling gates cell cycle entry and limits neural stem cell amplification in the adult pallium. Development. 2013 Jul 17.
Abstract >

O'Keefe DD, Thomas SR, Bolin K, Griggs E, Edgar BA, Buttitta LA. Combinatorial control of temporal gene expression in the drosophila wing by enhancers and core promoters. BMC Genomics. 2012 Sep 20; 13: 498-2164-13-498.
Abstract >

Yadon AN, Tsukiyama T. DNA looping-dependent targeting of a chromatin remodeling factor. Cell Cycle. 2013 Jun 15; 12(12): 1809-1810.
Abstract >

Carter JJ, Daugherty MD, Qi X, Bheda-Malge A, Wipf GC, Robinson K, Roman A, Malik HS, Galloway DA. Identification of an overprinting gene in merkel cell polyomavirus provides evolutionary insight into the birth of viral genes. Proc Natl Acad Sci U S A. 2013 Jul 11.
Abstract >

Gatchalian J, Futterer A, Rothbart SB, Tong Q, Rincon-Arano H, Sanchez de Diego A, Groudine M, Strahl BD, Martinez-A C, van Wely KH, Kutateladze TG. Dido3 PHD modulates cell differentiation and division. Cell Rep. 2013 Jul 11; 4(1): 148-158.
Abstract >

Patel MR, Malik HS. Convergent evolution of escape from hepaciviral antagonism in primates. Am J Phys Anthropol. 2013; 150: 217-217.

Ritland Politz JC, Scalzo D, Groudine M. Something silent this way forms: The functional organization of the nuclear repressive compartment. Annu Rev Cell Dev Biol. 2013 Jul 5.
Abstract >

Weber ND, Takeuchi R, Jarjour J, Stone D, Stoddard BL, Jerome KR. Enzyme engineering of homing endonucleases to target HBV cccDNA. Mol Ther. 2013 JUN; 21: S75-S76.

Wang Z, Halbert CL, Lee D, Butts T, Storb R, Tapscott SH, Miller D. Elimination of contaminating capsid-expressing genes in AAV vectors reduces immune responses to vector administration in a canine gene therapy model. Mol Ther. 2013 JUN; 21: S171-S171.

Wang Y, Jarjour J, Boissel S, Thyme S, Khan I, Pangallo J, Baker D, Stoddard B, Scharenberg AM, Rawlings DJ. Engineering an XID-site specific I-AniI homing endonuclease through combination of rational design and directed evolution. Mol Ther. 2013 JUN; 21: S122-S123.

Mintzer E, Jarjour J, Scharenberg A, Stoddard B, Baker D, Weber N, Stone D, Jerome KR. Development of designer homing endonucleases for inactivation of the HIV provirus. Mol Ther. 2013 JUN; 21: S73-S74.

Ali M, Rincon-Arano H, Zhao W, Rothbart SB, Tong Q, Parkhurst SM, Strahl BD, Deng LW, Groudine M, Kutateladze TG. Molecular basis for chromatin binding and regulation of MLL5. Proc Natl Acad Sci U S A. 2013 Jun 24.
Abstract >

Allred BE, Correnti C, Clifton MC, Strong RK, Raymond KN. Siderocalin outwits the coordination chemistry of vibriobactin, a siderophore of vibrio cholerae. ACS Chem Biol. 2013 Jun 18.
Abstract >

Duggal NK, Fu W, Akey JM, Emerman M. Identification and antiviral activity of common polymorphisms in the APOBEC3 locus in human populations. Virology. 2013 Jun 8.
Abstract >

Ross BD, Rosin L, Thomae AW, Hiatt MA, Vermaak D, de la Cruz AF, Imhof A, Mellone BG, Malik HS. Stepwise evolution of essential centromere function in a drosophila neogene. Science. 2013 Jun 7; 340(6137): 1211-1214.
Abstract >

Balazs AB, Bloom JD, Hong CM, Rao DS, Baltimore D. Broad protection against influenza infection by vectored immunoprophylaxis in mice. Nat Biotechnol. 2013 Jun 2.
Abstract >

Mitchell PS, Emerman M, Malik HS. An evolutionary perspective on the broad antiviral specificity of MxA. Curr Opin Microbiol. 2013 May 28.
Abstract >

Ross BD, Rosin L, Thomae AW, Hiatt MA, Vermaak D, de la Cruz AF, Imhof A, Mellone BG, Malik HS. Stepwise evolution of essential centromere function in a drosophila neogene. Science. 2013 Jun 7; 340(6137): 1211-1214.
Abstract >

Politz JC, Ragoczy T, Groudine M. When untethered, something silent inside comes. Nucleus. 2013 May 15; 4(3).
Abstract >

Skene PJ, Henikoff S. Histone variants in pluripotency and disease. Development. 2013 Jun; 140(12): 2513-2524.
Abstract >

Levine MT, Malik HS. A rapidly evolving genomic toolkit for drosophila heterochromatin. Fly (Austin). 2013 Mar 21; 7(3).
Abstract >

Metzger MJ, Stoddard BL, Monnat RJ,Jr. PARP-mediated repair, homologous recombination, and back-up non-homologous end joining-like repair of single-strand nicks. DNA Repair (Amst). 2013 May 16.
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Hubert CG, Bradley RK, Ding Y, Toledo CM, Herman J, Skutt-Kakaria K, Girard EJ, Davison J, Berndt J, Corrin P, Hardcastle J, Basom R, Delrow JJ, Webb T, Pollard SM, Lee J, Olson JM, Paddison PJ. Genome-wide RNAi screens in human brain tumor isolates reveal a novel viability requirement for PHF5A. Genes Dev. 2013 May 1; 27(9): 1032-1045.
Abstract >

Akiyoshi B, Nelson CR, Biggins S. The aurora B kinase promotes inner and outer kinetochore interactions in budding yeast. Genetics. 2013 May 1.
Abstract >

Lizhi Ian Gong, Marc A Suchard, Jesse D Bloom. Stability-mediated epistasis constrains the evolution of an influenza protein. eLife 2013;2:e00631. May 14, 2013.
Abstract >

Furuyama T, Codomo CA, Henikoff S. Reconstitution of hemisomes on budding yeast centromeric DNA. Nucleic Acids Res. 2013 Apr 24.
Abstract >

Martin-Castellanos C, Fowler KR, Smith GR. Making chromosomes hot for breakage. Cell Cycle. 2013 Apr 11; 12(9).
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Sarangapani KK, Akiyoshi B, Duggan NM, Biggins S, Asbury CL. Phosphoregulation promotes release of kinetochores from dynamic microtubules via multiple mechanisms. Proc Natl Acad Sci U S A. 2013 Apr 15.
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Lee EG, Stenbak CR, Linial ML. Foamy virus assembly with emphasis on pol encapsidationViruses. 2013 Mar 20; 5(3): 886-900.
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Yadon AN, Singh BN, Hampsey M, Tsukiyama T. DNA looping facilitates targeting of a chromatin remodeling enzymeMol Cell. 2013 Mar 5
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Nechiporuk T, Klezovitch O, Nguyen L, Vasioukhin V. Dlg5 maintains apical aPKC and regulates progenitor differentiation during lung morphogenesis. Dev Biol. 2013 Mar 2
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Zentner GE, Henikoff S. Regulation of nucleosome dynamics by histone modifications. Nat Struct Mol Biol. 2013 Mar 5; 20(3): 259-266.
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Teves SS, Henikoff S. The heat shock response: A case study of chromatin dynamics in gene regulationBiochem Cell Biol. 2013 Feb; 91(1): 42-48.
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Hewamadduma CA, Grierson AJ, Ma TP, Pan L, Moens CB, Ingham PW, Ramesh T, Shaw PJ. Tardbpl splicing rescues motor neuron and axonal development in a mutant tardbp zebrafish. Hum Mol Genet. 2013 Feb 19.
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Zentner GE, Tsukiyama T, Henikoff S (2013) ISWI and CHD Chromatin Remodelers Bind Promoters but Act in Gene Bodies. PLoS Genet 9(2): e1003317.
Abstract >

Akiyoshi B, Nelson CR, Duggan N, Ceto S, Ranish JA, Biggins S. The Mub1/Ubr2 ubiquitin ligase complex regulates the conserved Dsn1 kinetochore protein. PLoS Genet. 2013 Feb; 9(2): e1003216.
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Fowler KR, Gutierrez-Velasco S, Martin-Castellanos C, Smith GR. Protein determinants of meiotic DNA break hot spots. Mol Cell. 2013 Feb 7.
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Momeni B, Brileya KA, Fields MW, Shou W. Strong inter-population cooperation leads to partner intermixing in microbial communities. elife. 2013; 2: e00230.
Abstract >

Nakayama M, Nakayama A, van Lessen M, Yamamoto H, Hoffmann S, Drexler HC, Itoh N, Hirose T, Breier G, Vestweber D, Cooper JA, Ohno S, Kaibuchi K, Adams RH. Spatial regulation of VEGF receptor endocytosis in angiogenesis. Nat Cell Biol. 2013 Jan 27
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Wragg RT, Snead D, Dong Y, Ramlall TF, Menon I, Bai J, Eliezer D, Dittman JS. Synaptic vesicles position complexin to block spontaneous fusion. Neuron. 2013 Jan 23; 77(2): 323-334.
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Malfavon-Borja R, Wu LI, Emerman M, Malik HS. Birth, decay, and reconstruction of an ancient TRIMCyp gene fusion in primate genomesProc Natl Acad Sci U S A. 2013 Jan 14.
Abstract >

Sanchez-Arevalo Lobo VJ, Doni M, Verrecchia A, Sanulli S, Faga G, Piontini A, Bianchi M, Conacci-Sorrell M, Mazzarol G, Peg V, Losa JH, Ronchi P, Ponzoni M, Eisenman RN, Doglioni C, Amati B. Dual regulation of myc by ablOncogene. 2013 Jan 14.
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Hoot S, McGuire AT, Cohen KW, Strong RK, Hangartner L, Klein F, Diskin R, Scheid JF, Sather DN, Burton DR, Stamatatos L. Recombinant HIV envelope proteins fail to engage germline versions of anti-CD4bs bNAbsPLoS Pathog. 2013 Jan; 9(1): e1003106.
Abstract >

Miller AC, Obholzer ND, Shah AN, Megason SG, Moens CB. RNA-seq based mapping and candidate identification of mutations from forward genetic screensGenome Res. 2013 Jan 8.
Abstract >

2012

Wark AR, Mills MG, Dang LH, Chan YF, Jones FC, Brady SD, Absher DM, Grimwood J, Schmutz J, Myers RM, Kingsley DM, Peichel CL. Genetic architecture of variation in the lateral line sensory system of threespine sticklebacksG3 (Bethesda). 2012 Sep; 2(9): 1047-1056.
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Momeni B, Shou W. Cryosectioning yeast communities for examining fluorescence patterns. J Vis Exp. 2012 Dec 26; (70). pii: 50101. doi(70): 10.3791/50101.
Abstract >

Rodriguez J, Tsukiyama T. ATR-like kinase Mec1 facilitates both chromatin accessibility at DNA replication forks and replication fork progression during replication stress. Genes Dev. 2013 27: 74-86.
Abstract >

Talbert PB, Henikoff S. Chromatin: Packaging without nucleosomes. Curr Biol. 2012 Dec 18; 22(24): R1040-3.
Abstract >

Rincon-Arano H, Halow J, Delrow JJ, Parkhurst SM, Groudine M. UpSET recruits HDAC complexes and restricts chromatin accessibility and acetylation at promoter regions. Cell. 2012 Nov 20.
Abstract >

Fior R, Maxwell AA, Ma TP, Vezzaro A, Moens CB, Amacher SL, Lewis J, Saude L. The differentiation and movement of presomitic mesoderm progenitor cells are controlled by mesogenin 1Development. 2012 Dec; 139(24): 4656-4665.
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Hughes AL, Gottschling DE. An early age increase in vacuolar pH limits mitochondrial function and lifespan in yeast. Nature. 2012 Nov 21.
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News Article >

Rodriguez-Mesa E, Abreu-Blanco MT, Rosales-Nieves AE, Parkhurst SM. Developmental expression of drosophila wiskott-aldrich syndrome family proteins. Dev Dyn. 2012 Dec; 241(12): C1.

Momeni B, Brileya KA, Fields MW, Shou W. Strong inter-population cooperation leads to partner intermixing in microbial communities. In press.

Waite AJ, Shou W. Feature Article: Adaptation to a new environment allows cooperators to purge cheaters stochastically. Proc Natl Acad Sci U S A. 2012 Nov 20;109(47):19079-86. doi: 10.1073/pnas.1210190109. Epub 2012 Oct 22.
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Abreu-Blanco MT, Verboon JM, Liu R, Watts JJ, Parkhurst SM. 2012. Drosophila embryos close epithelial wounds using a combination of cellular protrusions and an actomyosin purse string. J Cell Sci. Epub ahead of print, doi: 10.1242/​jcs.109066.
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Abstract >