Publications

Basic Sciences Division

Publications

2018

Ahmad K,Henikoff S. (2018). No strand left behind. Science, 361(6409), 1311-1312.
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Hino K,Simo S,Cooper JA. (2018). Comparative analysis of cul5 and rbx2 expression in the developing and adult murine brain and their essentiality during mouse embryogenesis. Dev Dyn.
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Kurshan PT,Merrill SA,Dong Y,Ding C,Hammarlund M,Bai J,Jorgensen EM,Shen K. (2018). gamma-Neurexin and Frizzled Mediate Parallel Synapse Assembly Pathways Antagonized by Receptor Endocytosis. Neuron.
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Nakamura M,Dominguez ANM,Decker JR,Hull AJ,Verboon JM,Parkhurst SM. (2018). Into the breach: how cells cope with wounds. Open Biol, 8(10).
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Fowler KR,Hyppa RW,Cromie GA,Smith GR. (2018). Physical basis for long-distance communication along meiotic chromosomes. Proc Natl Acad Sci U S A.
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Phillips AM,Ponomarenko AI,Chen K,Ashenberg O,Miao J,McHugh SM,Butty VL,Whittaker CA,Moore CL,Bloom JD,Lin Y-S,Shoulders MD. (2018). Destabilized adaptive influenza variants critical for innate immune system escape are potentiated by host chaperones. PLoS Biol, 16(9), e3000008.
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Farrukee R,Zarebski AE,McCaw JM,Bloom JD,Reading PC,Hurt AC. (2018). CHARACTERIZATION OF INFLUENZA B VIRUS VARIANTS WITH REDUCED NEURAMINIDASE INHIBITOR SUSCEPTIBILITY. Antimicrob Agents Chemother.
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Dou J,Vorobieva AA,Sheffler W,Doyle LA,Park H,Bick MJ,Mao B,Foight GW,Lee MY,Gagnon LA,Carter L,Sankaran B,Ovchinnikov S,Marcos E,Huang P-S,Vaughan JC,Stoddard BL,Baker D. (2018). De novo design of a fluorescence-activating beta-barrel. Nature.
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Bloom JD. (2018). Estimating the frequency of multiplets in single-cell RNA sequencing from cell-mixing experiments. PeerJ, 6, e5578. PMCID: PMC6126471.
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Suzuki A,Gupta A,Long SK,Evans R,Badger BL,Salmon ED,Biggins S,Bloom K. (2018). A Kinesin-5, Cin8, Recruits Protein Phosphatase 1 to Kinetochores and Regulates Chromosome Segregation. Curr Biol.
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Phillips AM,Doud MB,Gonzalez LO,Butty VL,Lin Y-S,Bloom JD,Shoulders MD. (2018). Enhanced ER proteostasis and temperature differentially impact the mutational tolerance of influenza hemagglutinin. Elife, 7.
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Chew YL,Tanizawa Y,Cho Y,Zhao B,Yu AJ,Ardiel EL,Rabinowitch I,Bai J,Rankin CH,Lu H,Beets I,Schafer WR. (2018). An Afferent Neuropeptide System Transmits Mechanosensory Signals Triggering Sensitization and Arousal in C. elegans. Neuron.
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Lang J,Barber A,Biggins S. (2018). An assay for de novo kinetochore assembly reveals a key role for the CENP-T pathway in budding yeast. Elife, 17;7.
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Lee JM,Huddleston J,Doud MB,Hooper KA,Wu NC,Bedford T,Bloom JD. (2018). Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants. Proc Natl Acad Sci U S A.
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Lee SC-W,North K,Kim E,Jang E,Obeng E,Lu SX,Liu B,Inoue D,Yoshimi A,Ki M,Yeo M,Zhang XJ,Kim MK,Cho H,Chung YR,Taylor J,Durham BH,Kim YJ,Pastore A,Monette S,Palacino J,Seiler M,Buonamici S,Smith PG,Ebert BL,Bradley RK,Abdel-Wahab O. (2018). Synthetic Lethal and Convergent Biological Effects of Cancer-Associated Spliceosomal Gene Mutations. Cancer Cell, 34(2), 225-241.e228.
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Ramachandran S,Henikoff S. (2018). MINCE-Seq: Mapping In Vivo Nascent Chromatin with EdU and Sequencing. Methods Mol Biol, 1832, 159-168.
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Nambiar M,Smith GR. (2018). Pericentromere-Specific Cohesin Complex Prevents Meiotic Pericentric DNA Double-Strand Breaks and Lethal Crossovers. Mol Cell.
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Molaro A,Drinnenberg IA. (2018). Studying the Evolution of Histone Variants Using Phylogeny. Methods Mol Biol, 1832, 273-291.
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Morrison ML,Iwata A,Keyes CC,Langston W,Insko MA,Langdale LA,Roth MB. (2018). Iodide Improves Outcome After Acute Myocardial Infarction in Rats and Pigs. Crit Care Med.
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Carroll PA,Freie BW,Mathsyaraja H,Eisenman RN. (2018). The MYC transcription factor network: balancing metabolism, proliferation and oncogenesis. Front Med.
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Darnell AM,Subramaniam AR,O'Shea EK. (2018). Translational Control through Differential Ribosome Pausing during Amino Acid Limitation in Mammalian Cells. Mol Cell, 71(2), 229-243.e211.
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Davis AKF,McCormick K,Gumina ME,Petrie JG,Martin ET,Xue KS,Bloom JD,Monto AS,Bushman FD,Hensley SE. (2018). Sera from individuals with narrowly focused influenza virus antibodies rapidly select viral escape mutations in ovo. J Virol.
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Henikoff S,Ramachandran S. (2018). Pioneers Invade the Nucleosomal Landscape. Mol Cell, 71(2), 193-194.
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Raiders SA,Eastwood MD,Bacher M,Priess JR. (2018). Binucleate germ cells in Caenorhabditis elegans are removed by physiological apoptosis. PLoS Genet, 14(7), e1007417.
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Dingens AS,Acharya P,Haddox HK,Rawi R,Xu K,Chuang G-Y,Wei H,Zhang B,Mascola JR,Carragher B,Potter CS,Overbaugh J,Kwong PD,Bloom JD. (2018). Complete functional mapping of infection- and vaccine-elicited antibodies against the fusion peptide of HIV. PLoS Pathog, 14(7), e1007159.
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Poudel KR,Roh-Johnson M,Su A,Ho T,Mathsyaraja H,Anderson S,Grady WM,Moens CB,Conacci-Sorrell M,Eisenman RN,Bai J. (2018). Competition between TIAM1 and Membranes Balances Endophilin A3 Activity in Cancer Metastasis. Dev Cell, 45(6):738-752.e6.
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Geyer EA,Miller MP,Brautigam CA,Biggins S,Rice LM. (2018). Design principles of a microtubule polymerase. Elife, 7.
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Petersdorf EW,Stevenson P,Malkki M,Strong RK,Spellman SR,Haagenson MD,Horowitz MM,Gooley T,Wang T. (2018). Patient HLA Germline Variation and Transplant Survivorship. J Clin Oncol, Jco2017776534.
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Talbert PB,Henikoff S. (2018). Transcribing Centromeres: Noncoding RNAs and Kinetochore Assembly. Trends Genet.Talbert PB,Henikoff S. (2018). Transcribing Centromeres: Noncoding RNAs and Kinetochore Assembly. Trends Genet.
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Cox LL,Cox TC,Moreno Uribe LM,Zhu Y,Richter CT,Nidey N,Standley JM,Deng M,Blue E,Chong JX,Yang Y,Carstens RP,Anand D,Lachke SA,Smith JD,Dorschner MO,Bedell B,Kirk E,Hing AV,Venselaar H,Valencia-Ramirez LC,Bamshad MJ,Glass IA,Cooper JA,Haan E,Nickerson DA,van Bokhoven H,Zhou H,Krahn KN,Buckley MF,Murray JC,Lidral AC,Roscioli T. (2018). Mutations in the Epithelial Cadherin-p120-Catenin Complex Cause Mendelian Non-Syndromic Cleft Lip with or without Cleft Palate. Am J Hum Genet.
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Gupta A,Evans RK,Koch LB,Littleton AJ,Biggins S. (2018). Purification of kinetochores from the budding yeast Saccharomyces cerevisiae. Methods Cell Biol, 144, 349-370.
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Schroeder CM,Malik HS. (2018). Kindr Motors Drive in Meiosis. Cell, 173(4), 813-815.
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Bogdanove AJ,Bohm A,Miller JC,Morgan RD,Stoddard BL. (2018). Engineering altered protein-DNA recognition specificity. Nucleic Acids Res.
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Henikoff S,Church GM. (2018). Simultaneous Discovery of Cell-Free DNA and the Nucleosome Ladder. Genetics, 209(1), 27-29.
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Chang C-J,Kotini AG,Olszewska M,Georgomanoli M,Teruya-Feldstein J,Sperber H,Sanchez R,DeVita R,Martins TJ,Abdel-Wahab O,Bradley RK,Papapetrou EP. (2018). Dissecting the Contributions of Cooperating Gene Mutations to Cancer Phenotypes and Drug Responses with Patient-Derived iPSCs. Stem Cell Reports.
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Forsberg KJ,Malik HS. (2018). Microbial Genomics: The Expanding Universe of Bacterial Defense Systems. Curr Biol, 28(8), R361-r364.

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Pineda JMB,Bradley RK. (2018). Most human introns are recognized via multiple and tissue-specific branchpoints. Genes Dev.Pineda JMB,Bradley RK. (2018). Most human introns are recognized via multiple and tissue-specific branchpoints. Genes Dev.
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Skene PJ,Henikoff JG,Henikoff S. (2018). Targeted in situ genome-wide profiling with high efficiency for low cell numbers. Nat Protoc, 13(5), 1006-1019.
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Doud MB,Lee JM,Bloom JD. (2018). How single mutations affect viral escape from broad and narrow antibodies to H1 influenza hemagglutinin. Nat Commun, 9(1), 1386.
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Pesce CG,Zdraljevic S,Peria WJ,Bush A,Repetto MV,Rockwell D,Yu RC,Colman-Lerner A,Brent R. (2018). Single-cell profiling screen identifies microtubule-dependent reduction of variability in signaling. Mol Syst Biol, 14(4), e7390.
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Haddox HK,Dingens AS,Hilton SK,Overbaugh J,Bloom JD. (2018). Mapping mutational effects along the evolutionary landscape of HIV envelope. Elife, 7.
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Schaub FX,Dhankani V,Berger AC,Trivedi M,Richardson AB,Shaw R,Zhao W,Zhang X,Ventura A,Liu Y,Ayer DE,Hurlin PJ,Cherniack AD,Eisenman RN,Bernard B,Grandori C. (2018). Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas. Cell Syst, 6(3), 282-300.e282.
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Kidwell CU,Su C-Y,Hibi M,Moens CB. (2018). Multiple zebrafish atoh1 genes specify a diversity of neuronal types in the zebrafish cerebellum. Dev Biol.
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Molaro A,Young JM,Malik HS. (2018). Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals. Genome Res.
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Tuttle LM,Pacheco D,Warfield L,Luo J,Ranish J,Hahn S,Klevit RE. (2018). Gcn4-Mediator Specificity Is Mediated by a Large and Dynamic Fuzzy Protein-Protein Complex. Cell Rep, 22(12), 3251-3264.
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Verboon JM,Decker JR,Nakamura M,Parkhurst SM. (2018). Wash exhibits context dependent phenotypes and, along with the WASH Regulatory Complex, regulates Drosophila oogenesis. J Cell Sci.
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Thapliyal S,Vasudevan A,Dong Y,Bai J,Koushika SP,Babu K. (2018). The C-terminal of CASY-1/Calsyntenin regulates GABAergic synaptic transmission at the Caenorhabditis elegans neuromuscular junction. PLoS Genet, 14(3), e1007263.
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Xue KS,Moncla LH,Bedford T,Bloom JD. (2018). Within-Host Evolution of Human Influenza Virus. Trends Microbiol.
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Pacheco D,Warfield L,Brajcich M,Robbins H,Luo J,Ranish J,Hahn S. (2018). Transcription activation domains of the yeast factors Met4 and Ino2: tandem activation domains with properties similar to the yeast Gcn4 activator. Mol Cell Biol.
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Stoddard BL,Khvorova A,Corey DR,Dynan WS,Fox KR. (2018). Editorial: Nucleic Acids Research and Nucleic Acid Therapeutics. Nucleic Acids Res, 46(4), 1563-1564. PMCID: PMC5829634.
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Xue KS,Bloom JD. (2017). Looking Deep inside Influenza Infections. Cell Syst, 5(1), 4-4.
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Correnti CE,Gewe MM,Mehlin C,Bandaranayake AD,Johnsen WA,Rupert PB,Brusniak M-Y,Clarke M,Burke SE,De Van Der Schueren W,Pilat K,Turnbaugh SM,May D,Watson A,Chan MK,Bahl CD,Olson JM,Strong RK. (2018). Screening, large-scale production and structure-based classification of cystine-dense peptides. Nat Struct Mol Biol, 25(3), 270-278.
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Hatch EM. (2018). Nuclear envelope rupture: little holes, big openings. Curr Opin Cell Biol, 52, 66-72.
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Kursel LE,Malik HS. (2018). The cellular mechanisms and consequences of centromere drive. Curr Opin Cell Biol, 52, 58-65.
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Chang C-J,Kotini AG,Olszewska M,Georgomanoli M,Teruya-Feldstein J,Sperber H,Sanchez R,DeVita R,Martins TJ,Abdel-Wahab O,Bradley RK,Papapetrou EP. (2018). Dissecting the Contributions of Cooperating Gene Mutations to Cancer Phenotypes and Drug Responses with Patient-Derived iPSCs. Stem Cell Reports.
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Russell AB,Trapnell C,Bloom JD. (2018). Extreme heterogeneity of influenza virus infection in single cells. Elife, 7.
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Chereji RV,Ramachandran S,Bryson TD,Henikoff S. (2018). Precise genome-wide mapping of single nucleosomes and linkers in vivo. Genome Biol, 19(1), 19.
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Khan AS,Bodem J,Buseyne F,Gessain A,Johnson W,Kuhn JH,Kuzmak J,Lindemann D,Linial ML,Lochelt M,Materniak-Kornas M,Soares MA,Switzer WM. (2018). Spumaretroviruses: Updated taxonomy and nomenclature. Virology, 516, 158-164.
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Li Q,Ingram L,Kim S,Beharry Z,Cooper JA,Cai H. (2018). Paracrine Fibroblast Growth Factor Initiates Oncogenic Synergy with Epithelial FGFR/Src Transformation in Prostate Tumor Progression. Neoplasia, 20(3), 233-243.
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Thakur J,Henikoff S. (2018). Unexpected conformational variations of the human centromeric chromatin complex. Genes Dev.
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Kasinathan S,Henikoff S. (2018). Non-B-form DNA is enriched at centromeres. Mol Biol Evol.
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Talbert P,Kasinathan S,Henikoff S. (2018). Simple and Complex Centromeric Satellites in Drosophila Sibling Species. Genetics.
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Xue KS,Greninger AL,Perez-Osorio A,Bloom JD. (2018). Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. mSphere, 3(1). PMCID: PMC5750391.
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