2015 2014 2013 2012 2011 2010 2009 2008 2007

2015

  • Staller MV, Vincent BJ, Bragdon MD, Lydiard-Martin T, Wunderlich Z, Estrada J, DePace AH. (2015).  Shadow enhancers enable Hunchback bifunctionality in the Drosophila embryo. Proc Natl Acad Sci U S A. 112(3):785-90. PMCID: PMC4311800.

  • Staller MV, Fowlkes CC, Bragdon MD, Wunderlich Z, Estrada J, DePace AH. (2015). A gene expression atlas of a bicoid-depleted Drosophila embryo reveals early canalization of cell fate. Development. ;142(3):587-96. PMCID: PMC4302997.

  • Vincent BJ, Scholes C, Staller MV, Wunderlich Z, Estrada J, Park J, Bragdon MD, Lopez Rivera F, Biette KM, DePace AH. (2015). Yearly Planning Meetings: Individualized Development Plans Aren't Just More Paperwork. Mol Cell. 58(5):718-21. PMID: 26046646.

  • Kelsic ED, Zhao J, Vetsigian K, Kishony R. (2015). Counteraction of antibiotic production and degradation stabilizes microbial communities. Nature. 521(7553):516-9. PMID: 25992546.

  • Broadbent KM, Broadbent JC, Ribacke U, Wirth D, Rinn JL, Sabeti PC. (2015).  Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNA. BMC Genomics. 16:454. PMCID: PMC4465157.

  • Wang J, Atolia E, Hua B, Savir Y, Escalante-Chong R, Springer M. (2015).  Natural variation in preparation for nutrient depletion reveals a cost-benefit tradeoff.  PLoS Biol. 13(1):e1002041.  PMCID: PMC4308108.

  • Escalante-Chong R, Savir Y, Carroll SM, Ingraham JB, Wang J, Marx CJ, Springer M. (2015). Galactose metabolic genes in yeast respond to a ratio of galactose and glucose. Proc Natl Acad Sci U S A. 112(5):1636-41. PMCID: PMC4321281.

  • Price AC, Pilkiewicz KR, Graham TG, Song D, Eaves JD, Loparo JJ. (2015). DNA motion capture reveals the mechanical properties of DNA at the mesoscale. Biophys J. 108(10):2532-40.  PMCID: PMC4457004.

  • Budzowska M, Graham TG, Sobeck A, Waga S, Walter JC. (2015). Regulation of the Rev1-pol ζ complex during bypass of a DNA interstrand cross-link. EMBO J. 34(14):1971-85. PMID: 26071591.

  • Beliveau BJ, Boettiger AN, Avendaño MS, Jungmann R, McCole RB, Joyce EF, Kim-Kiselak C, Bantignies F, Fonseka CY, Erceg J, Hannan MA, Hoang HG, Colognori D, Lee JT, Shih WM, Yin P, Zhuang X, Wu CT. (2015). Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH  probes. Nat Commun. PMCID: PMC4430122.

  • Baym M, Kryazhimskiy S, Lieberman TD, Chung H, Desai MM, Kishony R. (2015). Inexpensive multiplexed library preparation for megabase-sized genomes. PLoS One. 10(5).  PMCID: PMC4441430.

  • Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Ferrante TC, Terry R, Turczyk BM, Yang JL, Lee HS, Aach J, Zhang K, Church GM. (2015). Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues. Nat Protoc. 10(3):442-58. PMCID: PMC4327781.

  • Hays SG, Ducat DC. (2015). Engineering cyanobacteria as photosynthetic feedstock factories. Photosynth Res. 2015 Mar;123(3):285-95. PMID: 24526260.

  • Hiscock TW, Megason SG.(2015).  Mathematically guided approaches to distinguish models of periodic patterning. Development. 142(3):409-19.PMCID: PMC4302999.

  • Myhrvold C, Silver PA. (2015). Using synthetic RNAs as scaffolds and regulators. Nat Struct Mol Biol. 22(1):8-10.PMID: 25565027.

  • Goff LA, Groff AF, Sauvageau M, Trayes-Gibson Z, Sanchez-Gomez DB, Morse M, Martin RD, Elcavage LE, Liapis SC, Gonzalez-Celeiro M, Plana O, Li E, Gerhardinger C, Tomassy GS, Arlotta P, Rinn JL. (2015). Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain. Proc Natl Acad Sci U S A.  PMCID: PMC4460505.

  • Chapman AR, He Z, Lu S, Yong J, Tan L, Tang F, Xie XS. (2015). Single cell transcriptome amplification with MALBAC. PLoS One. 10(3):e0120889. PMCID: PMC4378937.

  • Torella JP, Gagliardi CJ, Chen JS, Bediako DK, Colón B, Way JC, Silver PA, Nocera DG. (2015). Efficient solar-to-fuels production from a hybrid microbial-water-splitting catalyst system. Proc Natl Acad Sci U S A. ;112(8):2337-42.  PMCID: PMC4345567.

  • Dexter JP, Xu P, Gunawardena J, McClean MN. (2015). Robust network structure of the Sln1-Ypd1-Ssk1 three-component phospho-relay prevents unintended activation of the HOG MAPK pathway in Saccharomyces cerevisiae. BMC Syst Biol. 9:17. PMCID: PMC4377207.

  • Ran FA, Cong L, Yan WX, Scott DA, Gootenberg JS, Kriz AJ, Zetsche B, Shalem O, Wu X, Makarova KS, Koonin EV, Sharp PA, Zhang F. (2015).  In vivo genome editing using Staphylococcus aureus Cas9. Nature.520(7546):186-91. PMCID: PMC4393360.

  • Konermann S, Brigham MD, Trevino AE, Joung J, Abudayyeh OO, Barcena C, Hsu PD, Habib N, Gootenberg JS, Nishimasu H, Nureki O, Zhang F. (2015).Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature. 517(7536):583-8.  PMCID: PMC4420636.

  • Hopf TA, Schärfe CP, Rodrigues JP, Green AG, Kohlbacher O, Sander C, Bonvin AM, Marks DS. (2014). Sequence co-evolution gives 3D contacts and structures of protein complexes. Elife.PMCID: PMC4360534.

  • Schwartz S, Bernstein DA, Mumbach MR, Jovanovic M, Herbst RH, León-Ricardo BX, Engreitz JM, Guttman M, Satija R, Lander ES, Fink G, Regev A. (2014). Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA.
    Cell. 159(1):148-62.  PMCID: PMC4180118.

  • Hernandez-Nunez L, Belina J, Klein M, Si G, Claus L, Carlson JR, Samuel AD. (2015). Reverse-correlation analysis of navigation dynamics in Drosophila larva using optogenetics. Elife. PMCID: PMC4466337.

  • Klein M, Afonso B, Vonner AJ, Hernandez-Nunez L, Berck M, Tabone CJ, Kane EA, Pieribone VA, Nitabach MN, Cardona A, Zlatic M, Sprecher SG, Gershow M, Garrity PA, Samuel AD. (2015). Sensory determinants of behavioral dynamics in Drosophila thermotaxis. Proc Natl Acad Sci U S A. 2015 112(2):E220-9. PMCID: PMC4299240.

  • Klein AM, Mazutis L, Akartuna I, Tallapragada N, Veres A, Li V, Peshkin L, Weitz DA, Kirschner MW. (2015). Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell. 61(5):1187-201.  PMCID: PMC4441768.

  • Kugelman JR, Sanchez-Lockhart M, Andersen KG, Gire S, Park DJ, Sealfon R, Lin AE, Wohl S, Sabeti PC, Kuhn JH, Palacios GF. (2015). Evaluation of the potential impact of Ebola virus genomic drift on the efficacy of sequence-based candidate therapeutics. MBio. 6(1).PMCID: PMC4313914.

  • Park DJ, Dudas G, Wohl S, Goba A, Whitmer SL, Andersen KG, Sealfon RS, Ladner JT, Kugelman JR, Matranga CB, Winnicki SM, Qu J, Gire SK, Gladden-Young A, Jalloh S, Nosamiefan D, Yozwiak NL, Moses LM, Jiang PP, Lin AE, Schaffner SF, Bird B, Towner J, Mamoh M, Gbakie M, Kanneh L, Kargbo D, Massally JL, Kamara FK, Konuwa E, Sellu J, Jalloh AA, Mustapha I, Foday M, Yillah M, Erickson BR, Sealy T, Blau D, Paddock C, Brault A, Amman B, Basile J, Bearden S, Belser J, Bergeron E, Campbell S, Chakrabarti A, Dodd K, Flint M, Gibbons A, Goodman C, Klena J, McMullan L, Morgan L, Russell B, Salzer J, Sanchez A, Wang D, Jungreis I, Tomkins-Tinch C, Kislyuk A, Lin MF, Chapman S, MacInnis B, Matthews A, Bochicchio J, Hensley LE, Kuhn JH, Nusbaum C, Schieffelin JS, Birren BW, Forget M, Nichol ST, Palacios GF, Ndiaye D, Happi C, Gevao SM, Vandi MA, Kargbo B, Holmes EC, Bedford T, Gnirke A, Ströher U, Rambaut A, Garry RF, Sabeti PC. (2015). Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone. Cell. ;161(7):1516-26.  PMID:26091036.

2014

  • Ishihara K, Nguyen PA, Wühr M, Groen AC, Field CM, Mitchison TJ. (2014). Organization of early frog embryos by chemical waves emanating from centrosomes. Philos Trans R Soc Lond B Biol Sci.;369(1650). PMCID:
    PMC4113098.

  • Nguyen PA, Groen AC, Loose M, Ishihara K, Wühr M, Field CM, Mitchison TJ. (2014). Spatial organization of cytokinesis signaling reconstituted in a cell-free system. Science. 2346(6206):244-7. PMCID: PMC4281018

  • Ishihara K, Nguyen PA, Groen AC, Field CM, Mitchison TJ. (2014). Microtubule nucleation remote from centrosomes may explain how asters span large cells. Proc Natl Acad Sci U S A. 111(50):17715-22. PMCID: PMC4273342.

  • Gire SK, Goba A, Andersen KG, Sealfon RS, Park DJ, Kanneh L, Jalloh S, Momoh M, Fullah M, Dudas G, Wohl S, Moses LM, Yozwiak NL, Winnicki S, Matranga CB, Malboeuf CM, Qu J, Gladden AD, Schaffner SF, Yang X, Jiang PP, Nekoui M, Colubri A, Coomber MR, Fonnie M, Moigboi A, Gbakie M, Kamara FK, Tucker V, Konuwa E, Saffa S, Sellu J, Jalloh AA, Kovoma A, Koninga J, Mustapha I, Kargbo K, Foday M, Yillah M, Kanneh F, Robert W, Massally JL, Chapman SB, Bochicchio J, Murphy C, Nusbaum C, Young S, Birren BW, Grant DS, Scheiffelin JS, Lander ES, Happi C, Gevao SM, Gnirke A, Rambaut A, Garry RF, Khan SH, Sabeti PC. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science. 2014 PMCID: PMC4431643.

  • Gaglia G, Lahav G. Constant rate of p53 tetramerization in response to DNA damage controls the p53 response. Mol Syst Biol. 2014 Oct 24;10(10):753.  PMID: 25344068.

  • Romero-Aristizabal C, Marks DS, Fontana W, Apfeld J. Regulated spatial organization and sensitivity of cytosolic protein oxidation in Caenorhabditis elegans. Nat Commun. 2014 Sep 29;5:5020. l PMCID: PMC4181376.

  • Busskamp V, Lewis NE, Guye P, Ng AH, Shipman SL, Byrne SM, Sanjana NE, Murn J, Li Y, Li S, Stadler M, Weiss R, Church GM. Rapid neurogenesis through
    transcriptional activation in human stem cells. Mol Syst Biol. 2014 Nov 17;10(11):760. PMID: 25403753.

  • Graham TG, Wang X, Song D, Etson CM, van Oijen AM, Rudner DZ, Loparo JJ. ParB spreading requires DNA bridging. Genes Dev. 2014 Jun 1;28(11):1228-38. PMCID: PMC4052768.

  • Xiong F, Ma W, Hiscock TW, Mosaliganti KR, Tentner AR, Brakke KA, Rannou N, Gelas A, Souhait L, Swinburne IA, Obholzer ND, Megason SG. Interplay of cell shape and division orientation promotes robust morphogenesis of developing epithelia. Cell. 2014 Oct 9;159(2):415-27. PMID: 25303534.

  • Lieber DS, Hershman SG, Slate NG, Calvo SE, Sims KB, Schmahmann JD, Mootha VK. (2014). Next generation sequencing with copy number variant detection expands the phenotypic spectrum of HSD17B4-deficiency. BMC Med Genet. 15:30.

  • Lieber DS, Hershman SG, Slate NG, Calvo SE, Sims KB, Schmahmann JD, Mootha VK. (2014). Next generation sequencing with copy number variant detection expands the phenotypic spectrum of HSD17B4-deficiency. BMC Med Genet. 15:30.

  • Jinich A, Rappoport D, Dunn I, Sanchez-Lengeling B, Olivares-Amaya R, Noor E, Even AB, Aspuru-Guzik A. Quantum chemical approach to estimating the
    thermodynamics of metabolic reactions. Sci Rep. 2014 Nov 12;4:7022. PMID: 25387603.

  • N M Mangan and M P Brenner Systems level description of the carbon concentrating mechanism in cyanobacteria. eLife  2014 10.7554/eLife.02043

  • Torella JP, Lienert F, Boehm CR, Chen JH, Way JC, Silver PA (2014) Unique nucleotide sequence (UNS)-guided assembly of repetitive DNA parts for synthetic biology applications. Nat Protoc.

  • Torella JP, Boehm CR, Lienert F, Chen JH, Way JC, Silver PA. (2014). Rapid construction of insulated genetic circuits via synthetic sequence-guidedisothermal assembly. Nucleic Acids Res. PMCID:    PMC3874176

  • M.S. Avendano*, R. Jungmann*, J.B. Woehrstein*, M. Dai, W.M. Shih, P. Yin. (2014). Multiplexed 3D Cellular Super-Resolution Imaging with DNA-PAINT and Exchange-PAINT. Nature Methods, 11, 313-318 .

  • Field CM, Nguyen PA, Ishihara K, Groen AC, Mitchison TJ. Xenopus egg cytoplasm with intact actin. Methods Enzymol. 2014;540:399-415.

  • Groen AC, Ngyuen PA, Field CM, Ishihara K, Mitchison TJ. (2014). Glycogen-supplemented mitotic cytosol for analyzing Xenopus egg microtubule organization. Methods Enzymol. 540:417-33.

  • Harcombe WR, Riehl WJ, Dukovski I, Granger BR, Betts A, Lang AH, Bonilla G, Kar A, Leiby N, Mehta P, Marx CJ, Segrè D. Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics. Cell Rep. 2014 Apr 30. pii: S2211-1247(14)00280-0. doi: 10.1016/j.celrep.2014.03.070. [Epub ahead of print] PubMed PMID: 24794435."

  • J Plucain, T Hindré , M Le Gac, O Tenaillon, S Cruveiller, C Médigue, N Leiby, Harcombe WR, Marx CJ, Lenski RE, Schneider D. (2014) Epistasis and Allele Specificity in the Emergence of a Stable Polymorphism in Escherichia coli. Science 343:1366–1369.

  • Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Yang JL, Ferrante TC, Terry R, Jeanty SS, Li C, Amamoto R, Peters DT, Turczyk BM, Marblestone AH, Inverso SA, Bernard A, Mali P, Rios X, Aach J, Church GM. Highly multiplexed subcellular RNA sequencing in situ. Science. 2014 Mar 21;343(6177):1360-3.

  • Wolf A.R, Mootha VK. (2014). Functional genomics of mitochondrial RNA processing. Cell Reports. In press.

  • Marquardt S., Escalante-Chong R., Pho, N., Wang, J., Churchman S, Springer M, Buratowski, S. (2014). Chromatin-based mechanism for limiting divergent non-coding transcription. Cell. In press.

  • Fernandes de Abreu DA, Caballero A, Fardel P, Stroustrup N, Chen Z, Lee K, Keyes WD, Nash ZM, López-Moyado IF, Vaggi F, Cornils A, Regenass M, Neagu A, Ostojic I, Liu C, Cho Y, Sifoglu D, Shen Y, Fontana W, Lu H, Csikasz-Nagy A, Murphy CT, Antebi A, Blanc E, Apfeld J, Zhang Y, Alcedo J, Ch'ng Q. (2014). An insulin-to-insulin regulatory network orchestrates phenotypic specificity in development and physiology. PLoS Genet. 10(3):e1004225. PMCID: PMC3967928.

2013

  • N Leiby, CJ Marx. (2013). Metabolic erosion primarily through mutation accumulation, and not tradeoffs, drives limited evolution of substrate specificity in Escherichia coli. PLoS Biology. PMCID:PMC3928024.

  • Staller MV, Yan D, Randklev S, Bragdon MD, Wunderlich ZB, Tao R, Perkins LA, Depace AH, Perrimon N. (2013) Depleting gene activities in early Drosophila embryos with the "maternal-Gal4-shRNA" system. Genetics. PMCID: PMC3527254.

  • Sarosiek KA, Chi X, Bachman JA, Sims JJ, Montero J, Patel L, Flanagan A, Andrews DW, Sorger P, Letai A. BID preferentially activates BAK while BIM preferentially activates BAX, affecting chemotherapy response. Mol Cell. 2013 Sep 26;51(6):751-65. PMID: 24074954.

  • Lopez CF, Muhlich JL, Bachman JA, Sorger PK. (2013) Programming biological models in Python using PySB. Mol Syst Biol. 2013;9:646. PMCID: PMC3588907.

  • Maamar H, Cabili MN, Rinn J, Raj A.(2013). linc-HOXA1 is a noncoding RNA that represses Hoxa1 transcription in cis. Genes Dev. (11):1260-71.PMCID: PMC3690399.

  • Giedt RJ, Koch PD, Weissleder R. (2013). Single cell analysis of drug distribution by intravital imaging. PLoS One. 8(4):e60988. PMCID: PMC3622689.

  • Harcombe WR, Delaney NF, Leiby N, Klitgord N, Marx CJ. (2013)The ability of flux balance analysis to predict evolution of central metabolism scales with the initial distance to the optimum. PLoS Comput Biol. PMCID: PMC3688462.

  • Avendaño, M. S., Leidy, C., & Pedraza, J. M. (2013). Tuning the range and stability of multiple phenotypic states with coupled positive–negative feedback loops. Nature Communications, 4, 1–8.

  • Wintermute EH, Lieberman TD, Silver PA. (2013). An objective function exploiting suboptimal solutions in metabolic networks. BMC Syst Biol. 7(1):98.

  • Torella JP, Ford TJ, Kim SN, Chen AM, Way JC, Silver PA. (2013) Tailored fatty acid synthesis via dynamic control of fatty acid elongation. Proc Natl Acad Sci U S A.110(28):11290-5.  PMCID: PMC3710846.

  • Lienert F, Torella JP, Chen JH, Norsworthy M, Richardson RR, Silver PA. (2013). Two-and three-input TALE-based AND logic computation in embryonic stem cells. Nucleic Acids Res.

  • Torella JP, Boehm CR, Lienert F, Chen JH, Way JC, Silver PA. (2013). Rapid construction of insulated genetic circuits via synthetic sequence-guidedisothermal assembly. Nucleic Acids Res.

  • Chen AH, Robinson-Mosher A, Savage DF, Silver PA, Polka JK. (2013). The bacterial carbon-fixing organelle is formed by shell envelopment of preassembled cargo. PLoS One. 8(9):e76127. PMCID: PMC3762834.

  • Myhrvold C, Dai M, Silver PA, and Yin P. (2013). Isothermal self-assembly of complex DNA structures under diverse and biocompatible conditions. Nano Letters. 13(9) 4242-8.

  • Petry S, Groen AC, Ishihara K, Mitchison TJ, Vale RD. (2013). Branching microtubule nucleation in Xenopus egg extracts mediated by augmin and TPX2. Cell. 152(4):768-77. PMCID: PMC3680348.

  • Palmer AC, Kishony R. (2013) Understanding, predicting and manipulating the genotypic evolution of antibiotic resistance. Nat Rev Genet. PMID: 23419278.

  • Stroustrup N, Ulmschneider BE, Nash ZM, López-Moyado IF, Apfeld J, Fontana W. (2013). The Caenorhabditis elegans Lifespan Machine. Nat Methods. PMID: 23666410.

  • Karanam K, Loewer A, Lahav G. (2013). Dynamics of the DNA damage response: insights from live-cell imaging. Brief Funct Genomics. PMCID: PMC3609438.

  • Vijayan V, O'Shea EK. (2013). Sequence determinants of circadian gene expression phase in cyanobacteria. J Bacteriol. PMCID: PMC3562104.

  • Wang Q, Moore MJ, Adelmant G, Marto JA, Silver PA.(2013).  PQBP1, a factor linked to intellectual disability, affects alternative splicing associated with neurite outgrowth. Genes Dev.  PMC3613609.

  • Lopez CF, Muhlich JL, Bachman JA, Sorger PK. (2013) Programming biological models in Python using PySB. Mol Syst Biol.  PMC3588907.

  • Lieber DS, Calvo SE, Shanahan K, Slate NG, Liu S, Hershman SG, Gold NB, Chapman BA, Thorburn DR, Berry GT, Schmahmann JD, Borowsky ML, Mueller DM, Sims KB, Mootha VK. (2013)Targeted exome sequencing of suspected mitochondrial disorders. Neurology. PMID: 23596069.

  • Lieber DS, Vafai SB, Horton LC, Slate NG, Liu S, Borowsky ML, Calvo SE, Schmahmann JD, Mootha VK. (2012). Atypical case of Wolfram syndrome revealed through targeted exome sequencing in a patient with suspected mitochondrial disease. BMC Med Genet. PMCID: PMC3281774.

2012

  • Staller MV, Yan D, Randklev S, Bragdon MD, Wunderlich ZB, Tao R, Perkins LA , DePace AH, Perrimon N. (2012). Characterization of the Gal4-UAS system to drive shRNA-mediated RNAi in early Drosophila embryos. Genetics. In Press.

  • Karanam, K, Kafri, R, Loewer, A, and Lahav, G. (2012). Quantitative Live Cell Imaging Reveals a Gradual Shift between DNA Repair Mechanisms and a Maximal Use of HR in Mid S Phase. Mol Cell 47, 320-329.

  • Wunderlich Z, Bragdon MD, Eckenrode KB, Lydiard-Martin T, Pearl-Waserman S, Depace AH. (2012). Dissecting sources of quantitative gene expression pattern divergence between Drosophila species. Mol Syst Biol. PMCID: PMC3435502.

  • Deeds EJ, Bachman JA, Fontana W. (2012). Optimizing ring assembly reveals the strength of weak interactions. Proc Natl Acad Sci U S A. PMCID: PMC3289332.

  • Leiby N, Harcombe WR, Marx CJ. (2012). Multiple long-term, experimentally-evolved populations of Escherichia coli acquire dependence upon citrate as an iron chelator for optimal growth on glucose. BMC Evol Biol. 12(1):151. PMID:22909317.

  • Bonacci, W., Teng, P.K., Afonso, B., Niederholtmeyer, H., Grob, P., Silver, P.A., & Savage, D.F. (2012). Modularity of a carbon-fixing organelle.. Proc Natl Acad Sci USA, 109(2), 478-83.  PMCID: PMC3258634.

  • Landgraf, D., Okumus, B., Chien, P., Baker, T.A., & Paulsson, J. (2012). Segregation of molecules at cell division reveals native protein localization. Nature Methods, 9(5), 480-2. PMID: 22484850.

  • Jain IH, Vijayan V, O'Shea EK.(2012). Spatial ordering of chromosomes enhances the fidelity of chromosome partitioning in cyanobacteria. Proc Natl Acad Sci U S A. 109(34):13638-43. PMID: 22869746.

  • Hacisuleyman E, Cabili MN, Rinn JL. (2012) A Keystone for ncRNA.Genome Biol.13(5):315. PMID: 22632630

  • Slavoff SA, Mitchell AJ*, Schwaid AG*, Cabili MN, Ma J, Levin JZ,  Karger AD, Budnik BA, Rinn JL, Saghatelian A. (2012). Peptidomic discovery of short open reading frame-encoded peptides in human cells. Nature Chemical Biology. In Press. 

  • Kirby A, Gnirke A, Jaffe DB, Barešová V, Pochet N, Blumenstiel B, Ye C, Aird D, Stevens C, Robinson JT, Cabili MN, Gat-Viks I, Kelliher, E, Daza R, DeFelice M, Hůlková H, Sovová J, Antignac C, Guttman M,  Handsaker ME, Lindblad-Toh K, Gabriel S, Hart PS, Regev A,  Nusbaum C,  Kmoch S, Bleyer AJ, Lander ES, Daly MJ.(2012). Combination of modern and traditional techniques identify MCKD1 causal frameshift variants within the MUC1 VNTR. Nature Genetics. In press.

  • Calvo SE, Compton AG, Hershman SG, Lim SC, Lieber DS, Tucker EJ, Laskowski A, Garone C, Liu S, Jaffe DB, Christodoulou J, Fletcher JM, Bruno DL, Goldblatt J, Dimauro S, Thorburn DR, Mootha VK. (2012). Molecular diagnosis of infantile mitochondrial disease with targeted next-generation sequencing. Sci Transl Med. 4(118):118ra10. PMID: 22277967.

  • Skurnik, D., Davis, M.R. Jr., Benedetti, D., Moravec, K.L., Cywes-Bentley, C., Roux, D., Traficante, D.C., Walsh, R.L., Maira-Litràn, T., Cassidy, S.K., Hermos, C.R., Martin, T.R., Thakkallapalli, E.L., Vargas, S.O., McAdam, A.J., Lieberman, T.D., Kishony, R., Lipuma, J.J., Pier, G.B., Goldberg, J.B., & Priebe, G.P. (2012). Targeting pan-resistant bacteria with antibodies to a broadly conserved surface polysaccharide expressed during infection. J Infect Dis, 205(11), 1709-18. PMID: 22448004

  • Mitchison TJ, Wuhr M, Nguyen P, Ishihara K, Groen A, & Field CM (2012). Growth, interaction and positioning of microtubule asters in extremely large vertebrate embryo cells. Cytoskeleton. PMID: 22786885.

  • Nguyen PA, Ishihara K, Wühr M, Mitchison TJ. (2012). Pronuclear migration: no attachment? No union, but a futile cycle! Curr Biol. 22(10):R409-11. PMID:22625860.

  • Purvis, JE, Karhohs, KW, Mock, C, Batchelor, E, Loewer, A, & Lahav, G (2012). p53 dynamics control cell fate. Science, 336(6087), 1440-4. PMID: 22700930.

  • Chen A & Silver PA (2012). Designing biological compartmentalization. Trends in Cell Biol. PMID:22841504

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2011

  • Broadbent KM, Park D, Wolf AR, Van Tyne D, Sims JS, Ribacke U, Volkman S, Duraisingh M, Wirth D, Sabeti PC, Rinn JL. A global transcriptional analysis of Plasmodium falciparum malaria reveals a novel family of telomere-associated lncRNAs. Genome Biol. 2011 Jun 20;12(6):R56.

  • Millard BL, Niepel M, Menden MP, Muhlich JL, Sorger PK. Adaptive informatics for multifactorial and high-content biological data. Nat Methods. 2011 Jun;8(6):487-93. PMCID:PMC3105758.

  • Kwiatkowski N, Deng X, Wang J, Tan L, Villa F, Santaguida S, Huang HC,Mitchison T, Musacchio A, Gray N. Selective Aurora Kinase Inhibitors Identified.  Using a Taxol-Induced Checkpoint Sensitivity Screen. ACS Chem Biol. 2011 Oct 21.

  • Shi J, Zhou Y, Huang HC, Mitchison TJ. Navitoclax (ABT-263) accelerates apoptosis during drug-induced mitotic arrest by antagonizing Bcl-xL. Cancer Res. 2011 Jul 1;71(13):4518-26. PMCID: PMC3129452.

  • Field CM, Wühr M, Anderson GA, Kueh HY, Strickland D, Mitchison TJ. Actin behavior in bulk cytoplasm is cell cycle regulated in early vertebrate embryos. J Cell Sci. 2011 Jun 15;124(Pt 12):2086-95. PMCID: PMC3104037.

  • Wühr M, Obholzer ND, Megason SG, Detrich HW 3rd, Mitchison TJ. Live imaging of the cytoskeleton in early cleavage-stage zebrafish embryos. Methods Cell Biol. 2011;101:1-18.

  • Toprak, E., Veres, A., Michel, J.B., Chait, R., Hartl, D.L., & Kishony, R. (2011). Evolutionary paths to antibiotic resistance under dynamically sustained drug selection. Nat Genet, 44(1), 101-5.

  • Tsou P, Zheng B, Hsu CH, Sasaki AT, Cantley LC. A fluorescent reporter of AMPK activity and cellular energy stress. Cell Metab. 2011 Apr 6;13(4):476-86. PMCID: PMC3070961.

  • Waks Z, Klein AM, Silver PA. Cell-to-cell variability of alternative RNA splicing. Mol Syst Biol. 2011 Jul 5;7:506. PMCID: PMC3159976.

  • Shih JD, Waks Z, Kedersha N, Silver PA. Visualization of single mRNAs reveals temporal association of proteins with microRNA-regulated mRNA. Nucleic Acids Res. 2011 Sep 1;39(17):7740-9. PMCID: PMC3177202.

  • Barstow B, Agapakis CM, Boyle PM, Grandl G, Silver PA, Wintermute EH. A synthetic system links FeFe-hydrogenases to essential E. coli sulfur metabolism. J Biol Eng. 2011 May 26;5:7. PMCID: PMC3130634.

  • Lieberman, T.,*, Michel, J.B.,*Aingaran, M., Potter-Bynoe, G.,  Roux, D., Davis, M.R.,  Skurnik, D., Leiby, N., LiPuma J.J., Goldberg, J.B., McAdam, A.J., Priebe G.P., Kishony, R. (2011) Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes. Nature Genetics. In press.

  • Michel JB, Shen YK, Aiden AP, Veres A, Gray MK; Google Books Team, Pickett JP, Hoiberg D, Clancy D, Norvig P, Orwant J, Pinker S, Nowak MA, Aiden EL. Quantitative analysis of culture using millions of digitized books. Science. 2011 Jan 14;331(6014):176-82.

  • Chai Y, Norman T, Kolter R, Losick R. Evidence that metabolism and chromosome copy number control mutually exclusive cell fates in Bacillus subtilis. EMBO J. 2011 Apr 6;30(7):1402-13. PMCID: PMC3094124.

  • Vijayan V, Jain IH, O'Shea EK. A high resolution map of a cyanobacterial transcriptome. Genome Biol. 2011;12(5):R47.

  • Bachman JA, Sorger P. New approaches to modeling complex biochemistry. Nat Methods. 2011 Feb;8(2):130-1. PMCID: PMC3100653.

  • Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011 Sep 15;25(18):1915-27. PMCID: PMC3185964.

  • Tucker EJ, Hershman SG, Köhrer C, Belcher-Timme CA, Patel J, Goldberger OA,Christodoulou J, Silberstein JM, McKenzie M, Ryan MT, Compton AG, Jaffe JD, Carr SA, Calvo SE, RajBhandary UL, Thorburn DR, Mootha VK. Mutations in MTFMT underlie a human disorder of formylation causing impaired mitochondrial translation. Cell Metab. 2011 Sep 7;14(3):428-34.

  • Broadbent KM, Park D, Wolf AR, Van Tyne D, Sims JS, Ribacke U, Volkman S, Duraisingh M, Wirth D, Sabeti PC, Rinn JL. A global transcriptional analysis of Plasmodium falciparum malaria reveals a novel family of telomere-associated lncRNAs. Genome Biol. 2011 Jun 20;12(6):R56.

  • Agapakis CM, Niederholtmeyer H, Noche RR, Lieberman TD, Megason SG, Way JC, Silver PA. (2011). Towards a Synthetic Chloroplast. PLoS ONE, 6(4): e18877.

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2010

  • Huang HC, Mitchison TJ, Shi J. Stochastic competition between mechanistically independent slippage and death pathways determines cell fate during mitotic arrest. PLoS One. 2010 Dec 21;5(12):e15724. PMCID: PMC3006339.

  • Huang H.C., Shi J., Orth J.D., & Mitchison T.J. (2010). Cell death when the SAC is out of commission. Cell Cycle, 9(11).

  • Merbl Y. & Kirschner M.W. (2010).  Protein microarrays for genome-wide posttranslational modification analysis. Wiley Interdiscip Rev Syst Biol Med,Sep 23.

  • Wu T., Merbl Y., Huo Y., Gallop J.L., Tzur A., & Kirschner M.W. (2010). UBE2S drives elongation of K11-linked ubiquitin chains by the anaphase-promoting complex. Proc Natl Acad Sci U S A, 107(4), 1355-60. PMCID: PMC2802591.

  • Chait, R., Shrestha, S., Shah, A., Michel, J-B., Kishony, R. (2010). A Differential Drug Screen for Compounds that Select Against Antibiotic Resistance. PLoS ONE, 5(12). PMCID: PMC2999542

  • Torella J.P., Chait R., &Kishony R. (2010). Optimal drug synergy in antimicrobial treatments. PLoS Comput Biol, 6(6), e1000796. PMCID: PMC2880566.

  • Waks Z, Silver PA. Nuclear origins of cell-to-cell variability. Cold Spring Harb Symp Quant Biol. 2010;75:87-94. Epub 2011 Mar 29.

  • Wintermute E.H. & Silver P.A. (2010). Dynamics in the mixed microbial concourse. Genes Dev. In Press

  • Wintermute E.H., & Silver P.A. (2010). Emergent cooperation in microbial metabolism. Mol Syst Biol, 6:407. PMCID: PMC2964121

  • Agapakis C.M., Ducat D.C., Boyle P.M., Wintermute E.H., Way J.C., & Silver P.A. (2010). Insulation of a synthetic hydrogen metabolism circuit in bacteria. J Biol Eng, 4, 3. PMCID: PMC2847965.

  • Afonso B., Savage D.F., Chen A.H., & Silver P.A. (2010). Spatially ordered dynamics of the bacterial carbon fixation machinery. Science, 327(5970), 1258-61.

  • Afonso B., Silver P.A., & Ajo-Franklin C.M. (2010). A synthetic circuit for selectively arresting daughter cells to create aging populations. Nucleic Acids Res, 38(8), 2727-35. PMCID:PMC2860115.

  • Grossman S.R., Shylakhter I., Karlsson E.K., Byrne E.H., Morales S., Frieden G., Hostetter E., Angelino E., Garber M., Zuk O., Lander E.S., Schaffner S.F., & Sabeti P.C., (2010). A Composite of Multiple Signals Distinguishes Causal Variants in Regions of Positive Selection. Science, 327(5967), 883-6.

  • Palmer A.C., Angelino E., & Kishony R. (2010). Chemical decay of an antibiotic inverts selection for resistance. Nat Chem Biol, 6(2), 105-7. PMCID: PMC2811317.

  • Hill AL, Rand DG, Nowak MA, Christakis NA. Emotions as infectious diseases in a large social network: the SISa model. Proc Biol Sci. 2010 Dec 22;277(1701):3827-35. PMCID: PMC2992714.

  • Hill AL, Rand DG, Nowak MA, Christakis NA. Infectious disease modeling of social contagion in networks. PLoS Comput Biol. 2010 Nov 4;6(11):e1000968. PMCID: PMC2973808.

  • Loewer A., Batchelor E., Gaglia G., Lahav G. (2010). Basal Dynamics of p53 Reveal Transcriptionally Attenuated Pulses in Cycling Cells. Cell, 142(1):89-100.

  • Chastanet A., Vitkup D., Yuan G.C., Norman T.M., Liu J.S., & Losick R.M. (2010). Broadly heterogeneous activation of the master regulator for sporulation in Bacillus subtilis. Proc Natl Acad Sci U S A, 107(18), 8486-91. PMCID: PMC2889527.

  • Chai Y., Norman T., Kolter R., & Losick R. (2010). An epigenetic switch governing daughter cell separation in Bacillus subtilis. Genes Dev, 24(8), 754-65. PMCID: PMC2854391.

  • Wang Q, Silver PA. Genome-wide RNAi screen discovers functional coupling of alternative splicing and cell cycle control to apoptosis regulation. Cell Cycle. 2010 Nov 15;9(22):4419-21. PMCID: PMC3142361.

  • Moore M.J., Wang Q., Kennedy C.J., & Silver P.A. (2010). An alternative splicing network links cell-cycle control to apoptosis. Cell, 142(4), 625-36. PMCID: PMC2924962.

  • Loewer S., Cabili M.N., Guttman M., Loh Y.H., Thomas K., Park I.H., Garber M., Curran M.,Onder T., Agarwal S., Manos P.D., Datta S., Lander E.S., Schlaeger T.M., Daley G.Q., & Rinn J.L. (2010). Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. Nat Genet. 25(18):1915-27.PMCID: PMC3185964

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2009

  • Huang H.C., Shi J., Orth J.D., & Mitchison T.J. (2009). Evidence that mitotic exit is a better cancer therapeutic target than spindle assembly. Cancer Cell, 16(4), 347-58.  PMCID: PMC2758291

  • Wühr M., Tan E.S., Parker S.K., Detrich H.W., & Mitchison T.J. (2010). A Model for Cleavage Plane Determination in Early Amphibian and Fish Embryos. Curr Biol.

  • Wühr M., Mitchison T.J., & Field C.M. (2009). Size and speed go hand in hand in cytokinesis. Cell, 137(5), 798-800.

  • Wühr M., Dumont S., Groen A.C., Needleman D.J., & Mitchison T.J. (2009). How does a millimeter-sized cell find its center? Cell Cycle, 8(8), 1115-21. PMCID: PMC2880816.

  • Merbl Y., & Kirschner M.W. (2009). Large-scale detection of ubiquitination substrates using cell extracts and protein microarrays. Proc Natl Acad Sci U S A, 106(8), 2543-8. PMCID: PMC2633216

  • Bollenbach T., Quan S., Chait R., & Kishony R. (2009). Nonoptimal microbial response to antibiotics underlies suppressive drug interactions. Cell, 139(4), 707-18. PMCID: PMC2838386.

  • Kennedy C.J., Boyle P.M., Waks Z., & Silver P.A. (2009). Systems-level engineering of nonfermentative metabolism in yeast. Genetics, 183(1), 385-97. PMCID: PMC2746161

  • Waks Z., & Silver P.A. (2009). Engineering a synthetic dual-organism system for hydrogen production. Appl Environ Microbiol, 75(7), 1867-75. PMCID: PMC2663214

  • Rand D.G., Dreber A., Ellingsen T., Fudenberg D., & Nowak M.A.  (2009). Positive interactions promote public cooperation. Science, 325(5945), 1272-5. PMCID: PMC2875121

  • Rand D.G., Pfeiffer T., Dreber A., Sheketoff R.W., Wernerfelt N.C., & Benkler Y. (2009).  Dynamic remodeling of in-group bias during the 2008 presidential election. Proc Natl Acad Sci U S A, 106(15), 6187-91. PMCID: PMC2664153

  • Pfeiffer T., Rand D.G., & Dreber A. (2009). Decision-making in research tasks with sequential testing. PLoS One, 4(2),e4607. PMCID: PMC2643008

  • Vijayan V., Zuzow R., & O'Shea E.K. (2009). Oscillations in supercoiling drive circadian gene expression in cyanobacteria, PNAS, 106(52), 22564-8. PMCID: PMC2799730.

  • Amit I., Garber M., Chevrier N., Leite A.P., Donner Y., Eisenhaure T., Guttman M.,Grenier J.K., Li W., Zuk O., Schubert L.A., Birditt B., Shay T., Goren A., Zhang X., Smith Z., Deering R., McDonald R.C., Cabili M., Bernstein B.E., Rinn J.L., Meissner A., Root D.E., Hacohen N., & Regev A. (2009). Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science, 326(5950), 257-63. PMCID: PMC2879337.

  • Guttman M., Amit I., Garber M., French C., Lin M.F., Feldser D., Huarte M., Zuk O.,Carey B.W., Cassady J.P., Cabili M.N., Jaenisch R., Mikkelsen T.S., Jacks T., Hacohen N., Bernstein B.E., Kellis M., Regev A., Rinn J.L., & Lander E.S. (2009). Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature, 458(7235), 223-7. PMCID: PMC2754849.

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2008

  • Wühr M., Mitchison T.J., & Field C.M. (2008). Mitosis: new roles for myosin-X and actin at the spindle. Curr Biol., 18(19), R912-4.

  • Wühr M., Chen Y., Dumont S., Groen A.C., Needleman D.J., Salic A., & Mitchison T.J. (2008). Evidence for an upper limit to mitotic spindle length. Curr Biol., 18(16), 1256-61. PMCID: PMC2561182

  • Saez-Rodriguez J., Goldsipe A., Muhlich J., Alexopoulos L.G., Millard B., Lauffenburger D.A., & Sorger P.K.(2008). Flexible informatics for linking experimental data to mathematical models via DataRail. Bioinformatics, 24(6), 840-7.PMCID: PMC2617752

  • Michel J.B., Yeh P.J., Chait R., Moellering R.C., &  Kishony R. (2008). Drug Interactions Modulate the Potential for Evolution of Resistance. PNAS, 105(39),14918-23.  PMCID: PMC2567468

  • Michel JB, Yeh PJ, Chait R, Moellering RC, & Kishony R, (2008). Drug Interactions Modulate the Potential for Evolution of Resistance.  PNAS, 105(39), 14918-23.  PMCID: PMC2567468

  • Daniels R., Volkman S.K., Milner D.A., Mahesh N., Neafsey D.E., Park D.J., Rosen D., Angelino E., Sabeti P.C., Wirth D.F., & Wiegand R.C. (2008). A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking. Malar J., 7:223. PMCID: PMC2584654

  • Dreber A., Rand D.G., Fudenberg D., & Nowak M.A. (2008). Winners don’t punish.  Nature, 452:348-351. PMCID: PMC2292414

  • Rand D.G., Ohtsuki H., & Nowak M.A. (2008). Direct reciprocity with costly punishment: Generous tit-for-tat prevails. J Theor Biol, 256(1):45-57.  PMCID: PMC2614626

  • Rand D.G., Zhou Q., Buzzard G.T., & Fox J.J. (2008). Computationally efficient strategy for modeling the effect of ion current modifiers. IEEE Trans Biomed Eng., 55(1):3-13.

  • Swinburne I.A., Miguez D.G., Landgraf D., & Silver P.A. (2008). Intron length increases oscillatory periods of gene expression in animal cells. Genes Dev., 22(17), 2342-6.  PMCID: PMC2532923

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2007

  • Chait, R., Craney, A. & Kishony R. (2007). Antibiotic interactions that select against resistance. Nature, 446(7136), 668-71.

  • Lieberman E, Michel JB, Jackson J, Tang T, Nowak MA. Quantifying the evolutionary dynamics of language. Nature. 2007 Oct 11;449(7163):713-6. PMCID: PMC2460562.

  • Lieberman E., Michel J.B., Jackson, J., Tang, T., & Nowak, M. A. (2007). Quantifying the Evolutionary Dynamics of Language. Nature, 449, 713-716. PMCID: PMC2460562

  • Angelino, E. & Brenner, M.P. (2007). Excitability Constraints of Voltage-Gated Sodium Channel.  PLoS Comput. Biol., 3: 1751-1760. PMCID: PMC1988852

  • Ajo-Franklin C.M., Drubin D.A., Eskin J.A., Gee E.P., Landgraf D., Phillips I.,&  Silver P.A. (2007). Rational design of memory in eukaryotic cells. Genes Dev., 21(18), 271-6. PMCID: PMC1973140

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