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Sequence Analysis, DNA

  • 1.
    Chen K, Cofer E, Zhou J, Troyanskaya O. Selene: a PyTorch-based deep learning library for sequence data. Nat Methods. 2019;16(4):315–318. PMCID: PMC7148117
    Reference Link
  • 1.
    Li X, Patena W, Fauser F, Jinkerson R, Saroussi S, Meyer M, Ivanova N, Robertson J, Yue R, Zhang R, Vilarrasa-Blasi J, Wittkopp T, Ramundo S, Blum S, Goh A, Laudon M, Srikumar T, Lefebvre P, Grossman A, Jonikas M. A genome-wide algal mutant library and functional screen identifies genes required for eukaryotic photosynthesis. Nat Genet. 2019;51(4):627–635. PMCID: PMC6636631
    Reference Link
  • 1.
    Tianero M, Balaich J, Donia M. Localized production of defence chemicals by intracellular symbionts of Haliclona sponges. Nat Microbiol. 2019;4(7):1149–1159. PMCID: PMC8647704
    Reference Link
  • 1.
    Madej G, Dang S, Yan N, Kaback R. Evolutionary mix-and-match with MFS transporters. Proc Natl Acad Sci U S A. 2013;110(15):5870–4. PMCID: PMC3625355
    Reference Link
  • 1.
    Madej G, Sun L, Yan N, Kaback R. Functional architecture of MFS D-glucose transporters. Proc Natl Acad Sci U S A. 2014;111(7):E719–27. PMCID: PMC3932877
    Reference Link
  • 1.
    Hannon C, Blythe S, Wieschaus E. Concentration dependent chromatin states induced by the bicoid morphogen gradient. Elife. 2017;6. PMCID: PMC5624782
    Reference Link
  • 1.
    McCulloch K, Yuan F, Zhen Y, Aardema M, Smith G, Llorente-Bousquets J, Andolfatto P, Briscoe A. Sexual Dimorphism and Retinal Mosaic Diversification following the Evolution of a Violet Receptor in Butterflies. Mol Biol Evol. 2017;34(9):2271–2284. PMID: 28505307
    Reference Link
  • 1.
    Koch I, Clark M, Thompson M, Deere-Machemer K, Wang J, Duarte L, Gnanadesikan G, McCoy E, Rubbi L, Stahler D, Pellegrini M, Ostrander E, Wayne R, Sinsheimer J, vonHoldt B. The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves. Mol Ecol. 2016;25(8):1838–55. PMCID: PMC4849173
    Reference Link
  • 1.
    vonHoldt B, Kays R, Pollinger J, Wayne R. Admixture mapping identifies introgressed genomic regions in North American canids. Mol Ecol. 2016;25(11):2443–53. PMID: 27106273
    Reference Link
  • 1.
    Shirvani-Dastgerdi E, Winer B, Celià-Terrassa T, Kang Y, Tabernero D, Yagmur E, Rodríguez-Frías F, Gregori J, Luedde T, Trautwein C, Ploss A, Tacke F. Selection of the highly replicative and partially multidrug resistant rtS78T HBV polymerase mutation during TDF-ETV combination therapy. J Hepatol. 2017;67(2):246–254. PMCID: PMC6016549
    Reference Link
  • 1.
    Snir S, vonHoldt B, Pellegrini M. A Statistical Framework to Identify Deviation from Time Linearity in Epigenetic Aging. PLoS Comput Biol. 2016;12(11):e1005183. PMCID: PMC5106012
    Reference Link
  • 1.
    Smith H, White B, Kundert P, Cheng C, Romero-Severson J, Andolfatto P, Besansky N. Genome-wide QTL mapping of saltwater tolerance in sibling species of Anopheles (malaria vector) mosquitoes. Heredity (Edinb). 2015;115(5):471–9. PMCID: PMC4611235
    Reference Link
  • 1.
    Diner B, Li T, Greco T, Crow M, Fuesler J, Wang J, Cristea I. The functional interactome of PYHIN immune regulators reveals IFIX is a sensor of viral DNA. Mol Syst Biol. 2015;11(1):787. PMCID: PMC4358659
    Reference Link
  • 1.
    Li X, Zhang R, Patena W, Gang S, Blum S, Ivanova N, Yue R, Robertson J, Lefebvre P, Fitz-Gibbon S, Grossman A, Jonikas M. An Indexed, Mapped Mutant Library Enables Reverse Genetics Studies of Biological Processes in Chlamydomonas reinhardtii. Plant Cell. 2016;28(2):367–87. PMCID: PMC4790863
    Reference Link
  • 1.
    Schweizer R, vonHoldt B, Harrigan R, Knowles J, Musiani M, Coltman D, Novembre J, Wayne R. Genetic subdivision and candidate genes under selection in North American grey wolves. Mol Ecol. 2016;25(1):380–402. PMID: 26333947
    Reference Link
  • 1.
    Beh L, Müller M, Muir T, Kaplan N, Landweber L. DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome. Genome Res. 2015;25(11):1727–38. PMCID: PMC4617968
    Reference Link
  • 1.
    Schumer M, Cui R, Powell D, Rosenthal G, Andolfatto P. Ancient hybridization and genomic stabilization in a swordtail fish. Mol Ecol. 2016;25(11):2661–79. PMID: 26937625
    Reference Link
  • 1.
    Bassler B, Wright M, Silverman M. Sequence and function of LuxO, a negative regulator of luminescence in Vibrio harveyi. Mol Microbiol. 1994;12(3):403–12. PMID: 8065259
    Reference Link
  • 1.
    Henke J, Bassler B. Quorum sensing regulates type III secretion in Vibrio harveyi and Vibrio parahaemolyticus. J Bacteriol. 2004;186(12):3794–805. PMCID: PMC419960
    Reference Link
  • 1.
    Pompeani A, Irgon J, Berger M, Bulyk M, Wingreen N, Bassler B. The Vibrio harveyi master quorum-sensing regulator, LuxR, a TetR-type protein is both an activator and a repressor: DNA recognition and binding specificity at target promoters. Mol Microbiol. 2008;70(1):76–88. PMCID: PMC2628434
    Reference Link
  • 1.
    van Kessel J, Ulrich L, Zhulin I, Bassler B. Analysis of activator and repressor functions reveals the requirements for transcriptional control by LuxR, the master regulator of quorum sensing in Vibrio harveyi. mBio. 2013;4(4). PMCID: PMC3705450
    Reference Link

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