Publications

1198 Publications

#

1.

A

1.
Aardema ML, Zhen Y, Andolfatto P. The evolution of cardenolide-resistant forms of Na⁺,K⁺ -ATPase in Danainae butterflies. Mol Ecol. 2012;21(2):340–9.
1.
Abbondanzieri EA, Greenleaf WJ, Shaevitz JW, Landick R, Block SM. Direct observation of base-pair stepping by RNA polymerase. Nature. 2005;438(7067):460–5.
1.
Abbondanzieri EA, Shaevitz JW, Block SM. Picocalorimetry of transcription by RNA polymerase. Biophys J. 2005;89(6):L61–3.
1.
Abitua PB, Gainous B, Kaczmarczyk AN, Winchell CJ, Hudson C, Kamata K, Nakagawa M, Tsuda M, Kusakabe TG, Levine M. The pre-vertebrate origins of neurogenic placodes. Nature. 2015;524(7566):462–5.
1.
Abitua PB, Wagner E, Navarrete IA, Levine M. Identification of a rudimentary neural crest in a non-vertebrate chordate. Nature. 2012;492(7427):104–7.
1.
Abouchar L, Petkova MD, Steinhardt CR, Gregor T. Fly wing vein patterns have spatial reproducibility of a single cell. J R Soc Interface. 2014;11(97):20140443.
1.
Adamson B, Norman T, Jost M, Cho M, Nuñez J, Chen Y, Villalta J, Gilbert L, Horlbeck M, Hein M, Pak R, Gray A, Gross C, Dixit A, Parnas O, Regev A, Weissman J. A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response. Cell. 2016;167(7):1867–1882.e21. PMCID: PMC5315571
1.
Adamson B, Smogorzewska A, Sigoillot F, King R, Elledge S. A genome-wide homologous recombination screen identifies the RNA-binding protein RBMX as a component of the DNA-damage response. Nature cell biology. 2012;14(3):318–28. PMCID: PMC3290715
1.
Adelman TL, Bialek W, Olberg RM. The information content of receptive fields. Neuron. 2003;40(4):823–33.
1.
Agüera y Arcas B, Fairhall AL, Bialek W. Computation in a single neuron: Hodgkin and Huxley revisited. Neural Comput. 2003;15(8):1715–49.
1.
Ahmed Y, Nouri A, Wieschaus E. Drosophila Apc1 and Apc2 regulate Wingless transduction throughout development. Development. 2002;129(7):1751–62.
1.
Ahmed Y, Hayashi S, Levine A, Wieschaus E. Regulation of armadillo by a Drosophila APC inhibits neuronal apoptosis during retinal development. Cell. 1998;93(7):1171–82.
1.
Airoldi EM, Huttenhower C, Gresham D, Lu C, Caudy AA, Dunham M, Broach JR, Botstein D, Troyanskaya OG. Predicting cellular growth from gene expression signatures. PLoS Comput Biol. 2009;5(1):e1000257.
1.
Aluru C, Singh M. Improved inference of tandem domain duplications. Bioinformatics (Oxford, England). 2021;37(Suppl_1):i133-i141. PMCID: PMC8275333
1.
Amador-Noguez D, Feng X-J, Fan J, Roquet N, Rabitz H, Rabinowitz JD. Systems-level metabolic flux profiling elucidates a complete, bifurcated tricarboxylic acid cycle in Clostridium acetobutylicum. J Bacteriol. 2010;192(17):4452–61.
1.
Amador-Noguez D, Brasg IA, Feng X-J, Roquet N, Rabinowitz JD. Metabolome remodeling during the acidogenic-solventogenic transition in Clostridium acetobutylicum. Appl Environ Microbiol. 2011;77(22):7984–97.
1.
1.
Andolfatto P. Adaptive evolution of non-coding DNA in Drosophila. Nature. 2005;437(7062):1149–52.
1.
Andolfatto P, Davison D, Erezyilmaz D, Hu TT, Mast J, Sunayama-Morita T, Stern DL. Multiplexed shotgun genotyping for rapid and efficient genetic mapping. Genome Res. 2011;21(4):610–7.
1.
Anikeeva P, Boyden E, Brangwynne C, Troyanskaya O, al. et. Voices in methods development. Nat Methods. 2019;16(10):945–951.
1.
Arey R, Murphy CT. Conserved regulators of cognitive aging: From worms to humans. Behav Brain Res. 2017;322(Pt B):299–310. PMCID: PMC5164975
1.
Aristilde L, Lewis IA, Park JO, Rabinowitz JD. Hierarchy in Pentose Sugar Metabolism in Clostridium Acetobutylicum. Appl Environ Microbiol. 2014;.
1.
Armand P, Knapp AC, Hirsch AJ, Wieschaus EF, Cole MD. A novel basic helix-loop-helix protein is expressed in muscle attachment sites of the Drosophila epidermis. Mol Cell Biol. 1994;14(6):4145–54.
1.
Arrow KJ, Axelrod J, Benacerraf B, Berg P, Bishop JM, Bloembergen N, Brown HC, Cibelli J, Cohen S, Cooper LN, Corey EJ, Cronin JW, Curl R, Dulbecco R, Fischer EH, Fitch L V, Fogel R, Friedman JI, Furchgott RF, Gell-Mann M, Gilbert W, Gilman A, Glaser D, Glashow SL, Green RM, Greengard P, Guillemin R, Hayflick L, Hauptman HA, Heckman JJ, Heeger A, Herschbach D, Hubel DH, Hulse R, Kandel E, Karle J, Klein LR, Kohn W, Kornberg A, Krebs EG, Lanza RP, Laughlin R, Lederman L, Lee DM, Lewis E, Lipscomb W, Marcus RA, McFadden D, Merrifield RB, Merton R, Modigliani F, Molina MJ, Murad F, Nirenberg MW, North DC, Olah GA, Osheroff D, Palade GE, Perl M, Ramsey NF, Richter B, Roberts RJ, Samuelson PA, Schwartz M, Sharp PA, Smalley RE, Smith HO, Solow RM, Stormer H, Taube H, Taylor R, Thomas ED, Tobin J, Tonegawa S, Townes C, Watson JD, Weinberg S, Weller TH, West MD, Wieschaus EF, Wiesel TN, Wilson RW. Nobel laureates’ letter to President Bush. Washington Post. 2001;:A02.
1.
Aure MR, Leivonen S-K, Fleischer T, Zhu Q, Overgaard J, Alsner J, Tramm T, Louhimo R, Alnæs GIG, Perälä M, Busato F, Touleimat N, Tost J, Børresen-Dale A-L, Hautaniemi S, Troyanskaya OG, Lingjærde OC, Sahlberg KK, Kristensen VN. Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors. Genome Biol. 2013;14(11):R126.
1.
Ayroles J, Gibson G. Analysis of variance of microarray data. Methods Enzymol. 2006;411:214–33.
1.
Ayroles J, Hughes KA, Rowe KC, Reedy MM, Rodriguez-Zas SL, Drnevich JM, Cáceres CE, Paige KN. A genomewide assessment of inbreeding depression: gene number, function, and mode of action. Conserv Biol. 2009;23(4):920–30.
1.
Ayroles J, Buchanan SM, O’Leary C, Skutt-Kakaria K, Grenier JK, Clark A, Hartl DL, de Bivort BL. Behavioral idiosyncrasy reveals genetic control of phenotypic variability. Proc Natl Acad Sci U S A. 2015;112(21):6706–11.
1.
Ayroles J, Laflamme BA, Stone EA, Wolfner MF, Mackay TFC. Functional genome annotation of Drosophila seminal fluid proteins using transcriptional genetic networks. Genet Res (Camb). 2011;93(6):387–95.
1.
Ayroles J, Carbone MA, Stone EA, Jordan KW, Lyman RF, Magwire MM, Rollmann SM, Duncan L, Lawrence F, Anholt R, Mackay TFC. Systems genetics of complex traits in Drosophila melanogaster. Nat Genet. 2009;41(3):299–307.

B

1.
Bachtrog D, Andolfatto P. Selection, recombination and demographic history in Drosophila miranda. Genetics. 2006;174(4):2045–59.
1.
Bachtrog D, Thornton K, Clark A, Andolfatto P. Extensive introgression of mitochondrial DNA relative to nuclear genes in the Drosophila yakuba species group. Evolution. 2006;60(2):292–302.
1.
Bae E, Calhoun VC, Levine M, Lewis EB, Drewell RA. Characterization of the intergenic RNA profile at abdominal-A and Abdominal-B in the Drosophila bithorax complex. Proc Natl Acad Sci U S A. 2002;99(26):16847–52.
1.
Bailis W, Shyer JA, Zhao J, Canaveras JCG, Khazal FJA, Qu R, Steach HR, Bielecki P, Khan O, Jackson R, Kluger Y, Maher LJ, Rabinowitz J, Craft J, Flavell RA. Distinct modes of mitochondrial metabolism uncouple T cell differentiation and function. Nature. 2019;571(7765):403–407. PMCID: PMC6939459
1.
Bajad SU, Lu W, Kimball EH, Yuan J, Peterson C, Rabinowitz JD. Separation and quantitation of water soluble cellular metabolites by hydrophilic interaction chromatography-tandem mass spectrometry. J Chromatogr A. 2006;1125(1):76–88.
1.
Balagam R, Litwin DB, Czerwinski F, Sun M, Kaplan HB, Shaevitz JW, Igoshin OA. Myxococcus xanthus gliding motors are elastically coupled to the substrate as predicted by the focal adhesion model of gliding motility. PLoS Comput Biol. 2014;10(5):e1003619.
1.
Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry M. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD). Nucleic Acids Res. 2005;33(Database issue):D374–7.
1.
Banigan EJ, Gelbart MA, Gitai Z, Wingreen NS, Liu AJ. Filament depolymerization can explain chromosome pulling during bacterial mitosis. PLoS Comput Biol. 2011;7(9):e1002145.
1.
Banks E, Nabieva E, Chazelle B, Singh M. Organization of physical interactomes as uncovered by network schemas. PLoS Comput Biol. 2008;4(10):e1000203.
1.
Banks E, Nabieva E, Peterson R, Singh M. NetGrep: fast network schema searches in interactomes. Genome Biol. 2008;9(9):R138.
1.
Bao Q, Lu W, Rabinowitz JD, Shi Y. Calcium blocks formation of apoptosome by preventing nucleotide exchange in Apaf-1. Mol Cell. 2007;25(2):181–92.
1.
Barry RM, Bitbol A-F, Lorestani A, Charles EJ, Habrian CH, Hansen JM, Li H-J, Baldwin EP, Wingreen NS, Kollman JM, Gitai Z. Large-scale filament formation inhibits the activity of CTP synthetase. Elife. 2014;3:e03638.
1.
Bartlett TM, Bratton BP, Duvshani A, Miguel A, Sheng Y, Martin NR, Nguyen JP, Persat A, Desmarais SM, VanNieuwenhze MS, Huang KC, Zhu J, Shaevitz JW, Gitai Z. A Periplasmic Polymer Curves Vibrio cholerae and Promotes Pathogenesis. Cell. 2017;168(1-2):172–185.e15. PMCID: PMC5287421
1.
Bartolomei MS, Zemel S, Tilghman SM. Parental imprinting of the mouse H19 gene. Nature. 1991;351(6322):153–5.