Publications

Basic Sciences Division

Publications

2017

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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