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Sequence Analysis, DNA

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  • Pompeani, Audra J, Joseph J Irgon, Michael F Berger, Martha L Bulyk, Ned S Wingreen, and Bonnie L Bassler. (2008) 2008. “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 70 (1): 76-88.
    Reference Link
  • Garrigan, Daniel, Sarah B Kingan, Anthony J Geneva, Peter Andolfatto, Andrew Clark, Kevin R Thornton, and Daven C Presgraves. (2012) 2012. “Genome Sequencing Reveals Complex Speciation in the Drosophila Simulans Clade.”. Genome Res 22 (8): 1499-511.
    Reference Link
  • Ober, Ulrike, Julien Ayroles, Eric A Stone, Stephen Richards, Dianhui Zhu, Richard A Gibbs, Christian Stricker, et al. 2012. “Using Whole-Genome Sequence Data to Predict Quantitative Trait Phenotypes in Drosophila Melanogaster.”. PLoS Genet 8 (5): e1002685.
    Reference Link
  • Slotte, Tanja, Khaled M Hazzouri, David Stern, Peter Andolfatto, and Stephen I Wright. (2012) 2012. “Genetic Architecture and Adaptive Significance of the Selfing Syndrome in Capsella.”. Evolution 66 (5): 1360-74.
    Reference Link
  • Shi, Weiyang, Michael Levine, and Brad Davidson. (2005) 2005. “Unraveling Genomic Regulatory Networks in the Simple Chordate, Ciona Intestinalis.”. Genome Res 15 (12): 1668-74.
    Reference Link
  • Park, Christopher Y, Aaron K Wong, Casey S Greene, Jessica Rowland, Yuanfang Guan, Lars A Bongo, Rebecca Burdine, and Olga G Troyanskaya. 2013. “Functional Knowledge Transfer for High-Accuracy Prediction of under-Studied Biological Processes.”. PLoS Comput Biol 9 (3): e1002957.
    Reference Link
  • Gresham, David, Viktor M Boer, Amy A Caudy, Naomi Ziv, Nathan J Brandt, John D Storey, and David Botstein. (2011) 2011. “System-Level Analysis of Genes and Functions Affecting Survival During Nutrient Starvation in Saccharomyces Cerevisiae.”. Genetics 187 (1): 299-317.
    Reference Link
  • Aardema, Matthew L, Ying Zhen, and Peter Andolfatto. (2012) 2012. “The Evolution of Cardenolide-Resistant Forms of Na⁺,K⁺ -ATPase in Danainae Butterflies.”. Mol Ecol 21 (2): 340-9.
    Reference Link
  • Bejsovec, A, and E Wieschaus. (1995) 1995. “Signaling Activities of the Drosophila Wingless Gene Are Separately Mutable and Appear to Be Transduced at the Cell Surface.”. Genetics 139 (1): 309-20.
    Reference Link
  • Schumer, Molly, Rongfeng Cui, Bastien Boussau, Ronald Walter, Gil Rosenthal, and Peter Andolfatto. (2013) 2013. “An Evaluation of the Hybrid Speciation Hypothesis for Xiphophorus Clemenciae Based on Whole Genome Sequences.”. Evolution 67 (4): 1155-68.
    Reference Link
  • Troyanskaya, Olga G, Ora Arbell, Yair Koren, Gad M Landau, and Alexander Bolshoy. (2002) 2002. “Sequence Complexity Profiles of Prokaryotic Genomic Sequences: A Fast Algorithm for Calculating Linguistic Complexity.”. Bioinformatics 18 (5): 679-88.
    Reference Link
  • Chikina, Maria D, and Olga G Troyanskaya. (2012) 2012. “An Effective Statistical Evaluation of ChIPseq Dataset Similarity.”. Bioinformatics 28 (5): 607-13.
    Reference Link
  • Khan, Zia, Joshua S Bloom, Leonid Kruglyak, and Mona Singh. (2009) 2009. “A Practical Algorithm for Finding Maximal Exact Matches in Large Sequence Datasets Using Sparse Suffix Arrays.”. Bioinformatics 25 (13): 1609-16.
    Reference Link
  • Hayashi, S, B Rubinfeld, B Souza, P Polakis, E Wieschaus, and A J Levine. (1997) 1997. “A Drosophila Homolog of the Tumor Suppressor Gene Adenomatous Polyposis Coli down-Regulates Beta-Catenin But Its Zygotic Expression Is Not Essential for the Regulation of Armadillo.”. Proc Natl Acad Sci U S A 94 (1): 242-7.
    Reference Link
  • Gresham, David, Bo Curry, Alexandra Ward, Benjamin Gordon, Leonardo Brizuela, Leonid Kruglyak, and David Botstein. (2010) 2010. “Optimized Detection of Sequence Variation in Heterozygous Genomes Using DNA Microarrays With Isothermal-Melting Probes.”. Proc Natl Acad Sci U S A 107 (4): 1482-7.
    Reference Link
  • Putnam, Andrea S, Mark Scriber, and Peter Andolfatto. (2007) 2007. “Discordant Divergence Times Among Z-Chromosome Regions Between Two Ecologically Distinct Swallowtail Butterfly Species.”. Evolution 61 (4): 912-27.
    Reference Link
  • Troyanskaya, Olga G, Mitchell E Garber, Patrick O Brown, David Botstein, and Russ B Altman. (2002) 2002. “Nonparametric Methods for Identifying Differentially Expressed Genes in Microarray Data.”. Bioinformatics 18 (11): 1454-61.
    Reference Link
  • Pane, Attilio, Peng Jiang, Dorothy Yanling Zhao, Mona Singh, and Trudi Schüpbach. (2011) 2011. “The Cutoff Protein Regulates PiRNA Cluster Expression and PiRNA Production in the Drosophila Germline.”. EMBO J 30 (22): 4601-15.
    Reference Link
  • Rowe, Kevin C, Sonal Singhal, Matthew D Macmanes, Julien Ayroles, Toni Lyn Morelli, Emily M Rubidge, Ke Bi, and Craig C Moritz. (2011) 2011. “Museum Genomics: Low-Cost and High-Accuracy Genetic Data from Historical Specimens.”. Mol Ecol Resour 11 (6): 1082-92.
    Reference Link
  • Erives, Albert, and Michael Levine. (2004) 2004. “Coordinate Enhancers Share Common Organizational Features in the Drosophila Genome.”. Proc Natl Acad Sci U S A 101 (11): 3851-6.
    Reference Link
  • Andolfatto, Peter, Dan Davison, Deniz Erezyilmaz, Tina T Hu, Joshua Mast, Tomoko Sunayama-Morita, and David L Stern. (2011) 2011. “Multiplexed Shotgun Genotyping for Rapid and Efficient Genetic Mapping.”. Genome Res 21 (4): 610-7.
    Reference Link
  • Osada, Robert, Elena Zaslavsky, and Mona Singh. (2004) 2004. “Comparative Analysis of Methods for Representing and Searching for Transcription Factor Binding Sites.”. Bioinformatics 20 (18): 3516-25.
    Reference Link
  • Bloom, Joshua S, Zia Khan, Leonid Kruglyak, Mona Singh, and Amy A Caudy. 2009. “Measuring Differential Gene Expression by Short Read Sequencing: Quantitative Comparison to 2-Channel Gene Expression Microarrays.”. BMC Genomics 10: 221.
    Reference Link
  • Dolinski, Kara, and David Botstein. (2005) 2005. “Changing Perspectives in Yeast Research Nearly a Decade After the Genome Sequence.”. Genome Res 15 (12): 1611-9.
    Reference Link
  • He, Bing, Amy A Caudy, Lance Parsons, Adam Rosebrock, Attilio Pane, Sandeep Raj, and Eric Wieschaus. (2012) 2012. “Mapping the Pericentric Heterochromatin by Comparative Genomic Hybridization Analysis and Chromosome Deletions in Drosophila Melanogaster.”. Genome Res 22 (12): 2507-19.
    Reference Link
  • Slotte, Tanja, Khaled M Hazzouri, Arvid Ågren, Daniel Koenig, Florian Maumus, Ya-Long Guo, Kim Steige, et al. (2013) 2013. “The Capsella Rubella Genome and the Genomic Consequences of Rapid Mating System Evolution.”. Nat Genet 45 (7): 831-5.
    Reference Link
  • Capra, John A, Katrin Paeschke, Mona Singh, and Virginia A Zakian. 2010. “G-Quadruplex DNA Sequences Are Evolutionarily Conserved and Associated With Distinct Genomic Features in Saccharomyces Cerevisiae.”. PLoS Comput Biol 6 (7): e1000861.
    Reference Link
  • Huttenhower, C, and O G Troyanskaya. (2008) 2008. “Assessing the Functional Structure of Genomic Data.”. Bioinformatics 24 (13).
    Reference Link
  • Botstein, David. (2011) 2011. “Genome-Sequencing Anniversary. Fruits of Genome Sequences for Biology.”. Science 331 (6020): 1025.
    Reference Link
  • Chen, Kathleen M, Evan M Cofer, Jian Zhou, and Olga G Troyanskaya. (2019) 2019. “Selene: A PyTorch-Based Deep Learning Library for Sequence Data.”. Nat Methods 16 (4): 315-18. doi:10.1038/s41592-019-0360-8.
    Reference Link
  • Hibbs, Matthew A, Nathaniel C Dirksen, Kai Li, and Olga G Troyanskaya. 2005. “Visualization Methods for Statistical Analysis of Microarray Clusters.”. BMC Bioinformatics 6: 115.
    Reference Link
  • Diehn, Maximilian, Ramona Bhattacharya, David Botstein, and Patrick O Brown. (2006) 2006. “Genome-Scale Identification of Membrane-Associated Human MRNAs.”. PLoS Genet 2 (1): e11.
    Reference Link
  • Wolf, Aaron B, and Joshua Akey. (2018) 2018. “Outstanding Questions in the Study of Archaic Hominin Admixture.”. PLoS Genet 14 (5): e1007349. doi:10.1371/journal.pgen.1007349.
    Reference Link

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