Genome Research

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  Publication Venue For

  • Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans..  31:2035-2049. 2021
  • Linking the dynamics of chromatin occupancy and transcription with predictive models..  31:1035-1046. 2021
  • Genome-scale mutational signatures of aflatoxin in cells, mice, and human tumors..  27:1475-1486. 2017
  • Detecting differential growth of microbial populations with Gaussian process regression..  27:320-333. 2017
  • Bacterial infection remodels the DNA methylation landscape of human dendritic cells..  25:1801-1811. 2015
  • Enabling functional genomics with genome engineering..  25:1442-1455. 2015
  • Centromere reference models for human chromosomes X and Y satellite arrays..  24:697-707. 2014
  • Erratum: Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets (Genome Research (2012) 22 (386-397)).  23:905. 2013
  • Highly active zinc-finger nucleases by extended modular assembly..  23:530-538. 2013
  • Nutritional control of mRNA isoform expression during developmental arrest and recovery in C. elegans..  22:1920-1929. 2012
  • Comparative RNA sequencing reveals substantial genetic variation in endangered primates..  22:602-610. 2012
  • Cooperation between Polycomb and androgen receptor during oncogenic transformation.  22:322-331. 2012
  • Estrogen-mediated epigenetic repression of large chromosomal regions through DNA looping..  20:733-744. 2010
  • An ensemble model of competitive multi-factor binding of the genome..  19:2101-2112. 2009
  • Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver..  19:1044-1056. 2009
  • A transcription factor affinity-based code for mammalian transcription initiation..  19:644-656. 2009
  • Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns..  19:590-601. 2009
  • Human gamma-satellite DNA maintains open chromatin structure and protects a transgene from epigenetic silencing..  19:533-544. 2009
  • De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae..  19:294-305. 2009
  • Development and application of a phylogenomic toolkit: resolving the evolutionary history of Madagascar's lemurs..  18:489-499. 2008
  • Computational and experimental identification of novel human imprinted genes..  17:1723-1730. 2007
  • The anatomy of microbial cell state transitions in response to oxygen..  17:1399-1413. 2007
  • Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection..  16:1517-1528. 2006
  • Embracing the complexity of genomic data for personalized medicine..  16:559-566. 2006
  • Callipyge mutation affects gene expression in cis: a potential role for chromatin structure..  16:340-346. 2006
  • Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)..  16:123-131. 2006
  • The evolutionary dynamics of alpha-satellite..  16:88-96. 2006
  • Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects..  15:1023-1033. 2005
  • Genome-wide prediction of imprinted murine genes..  15:875-884. 2005
  • Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays.  15:284-291. 2005
  • Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution..  15:1-18. 2005
  • Properties of overlapping genes are conserved across microbial genomes..  14:2268-2272. 2004
  • Organization and evolution of a gene-rich region of the mouse genome: a 12.7-Mb region deleted in the Del(13)Svea36H mouse..  14:1888-1901. 2004
  • Phylogenetic footprint analysis of IGF2 in extant mammals..  14:1726-1732. 2004
  • Erratum: Applications of a rat multiple tissue gene expression data set (Genome Research (2004) vol. 14 (742-749)).  14:1444. 2004
  • Applications of a rat multiple tissue gene expression data set..  14:742-749. 2004
  • Developmental roles of pufferfish Hox clusters and genome evolution in ray-fin fish..  14:1-10. 2004
  • Comparative genome analysis of Vibrio vulnificus, a marine pathogen..  13:2577-2587. 2003
  • Development of human protein reference database as an initial platform for approaching systems biology in humans..  13:2363-2371. 2003
  • Assessment of Genome-Wide Protein Function Classification for Drosophila melanogaster.  13:2118-2128. 2003
  • Analysis of the mouse transcriptome for genes involved in the function of the nervous system..  13:1395-1401. 2003
  • Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana..  13:1250-1257. 2003
  • Identification of the single base change causing the callipyge muscle hypertrophy phenotype, the only known example of polar overdominance in mammals..  12:1496-1506. 2002
  • The Bioperl toolkit: Perl modules for the life sciences..  12:1611-1618. 2002
  • Physical maps for genome analysis of serotype A and D strains of the fungal pathogen Cryptococcus neoformans..  12:1445-1453. 2002
  • SGP-1: prediction and validation of homologous genes based on sequence alignments..  11:1574-1583. 2001
  • cis element/transcription factor analysis (cis/TF): a method for discovering transcription factor/cis element relationships..  11:1567-1573. 2001
  • Flexible use of high-density oligonucleotide arrays for single-nucleotide polymorphism discovery and validation..  11:1418-1424. 2001
  • High-throughput genotyping with single nucleotide polymorphisms..  11:1262-1268. 2001
  • Human and mouse alpha-synuclein genes: comparative genomic sequence analysis and identification of a novel gene regulatory element..  11:78-86. 2001
  • Novel imprinted DLK1/GTL2 domain on human chromosome 14 contains motifs that mimic those implicated in IGF2/H19 regulation..  10:1711-1718. 2000
  • Identifying potential tumor markers and antigens by database mining and rapid expression screening..  10:1393-1402. 2000
  • Genome annotation assessment in Drosophila melanogaster..  10:483-501. 2000
  • Promoter prediction on a genomic scale--the Adh experience..  10:539-542. 2000
  • A preliminary gene map for the Van der Woude syndrome critical region derived from 900 kb of genomic sequence at 1q32-q41..  10:81-94. 2000
  • A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat..  9:AP1-insert. 1999
  • The Sox10(Dom) mouse: modeling the genetic variation of Waardenburg-Shah (WS4) syndrome..  9:215-225. 1999
  • Erratum: A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat (Genome Research (1999) 9, (AP1-AP8)).  9:793. 1999
  • Less is more: compact genomes pay dividends..  8:683-685. 1998
  • A map of 75 human ribosomal protein genes..  8:509-523. 1998
  • Simultaneous genotyping and species identification using hybridization pattern recognition analysis of generic Mycobacterium DNA arrays..  8:435-448. 1998
  • Genome mapping by fluorescent fingerprinting..  7:1162-1168. 1997
  • Methods for precise sizing, automated binning of alleles, and reduction of error rates in large-scale genotyping using fluorescently labeled dinucleotide markers. FUSION (Finland-U.S. Investigation of NIDDM Genetics) Study Group..  7:165-178. 1997
  • An integrated YAC map of the human X chromosome..  6:943-955. 1996
  • Bacterial artificial chromosome cloning and mapping of a 630-kb human extrachromosomal structure..  6:612-619. 1996
  • Refined localization of the cerebral cavernous malformation gene (CCM1) to a 4-cM interval of chromosome 7q contained in a well-defined YAC contig..  5:368-380. 1995
  • A biometrical genome search in rats reveals the multigenic basis of blood pressure variation..  5:164-172. 1995
  • A second locus for hereditary hemorrhagic telangiectasia maps to chromosome 12..  5:21-28. 1995
  • Different methods of sample preparation influence sensitivity of mycobacterium tuberculosis and borrelia burgdorferi PCR.  3:301-304. 1993