Genome research

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ZSWIM8 destabilizes many murine microRNAs and is required for proper embryonic growth and development. 2023
Genome-wide promoter assembly in E. coli measured at single-base resolution.. 32. 2022
Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore technologies reveals platform-specific error patterns. 2022
A full-proteome, interaction-specific characterization of mutational hotspots across human cancers. 2021
A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells.. 31. 2021
Haplotype diversity and sequence heterogeneity of human telomeres. 2021
SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission.. 31. 2021
Chromatin activation as a unifying principle underlying pathogenic mechanisms in multiple myeloma.. 30. 2020
Comparative transcriptomics of primary cells in vertebrates.. 30. 2020
Functional annotation of human long noncoding RNAs via molecular phenotyping.. 30. 2020
Recounting the FANTOM CAGE-Associated Transcriptome.. 30. 2020
Copolymerization of single-cell nucleic acids into balls of acrylamide gel.. 30. 2019
PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data.. 29. 2019
BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs.. 29. 2019
Minerva: an alignment- and reference-free approach to deconvolve Linked-Reads for metagenomics.. 29. 2018
Genome-wide determinants of sequence-specific DNA binding of general regulatory factors.. 28. 2018
Widespread and precise reprogramming of yeast protein-genome interactions in response to heat shock.. 28. 2018
Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis.. 28. 2017
Microfluidic isoform sequencing shows widespread splicing coordination in the human transcriptome.. 28. 2017
The identification and functional annotation of RNA structures conserved in vertebrates.. 27. 2017
Integrated genomic analyses reveal frequent TERT aberrations in acral melanoma.. 27. 2017
Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations.. 27. 2017
Genome-wide uniformity of human 'open' pre-initiation complexes.. 27. 2016
Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations.. 26. 2016
The pig X and Y Chromosomes: structure, sequence, and evolution.. 26. 2015
Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans.. 25. 2015
Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers.. 25. 2015
Alignathon: a competitive assessment of whole-genome alignment methods.. 24. 2014
Linking signaling pathways to transcriptional programs in breast cancer.. 24. 2014
DNA methylation profiling in human B cells reveals immune regulatory elements and epigenetic plasticity at Alu elements during B-cell activation.. 23. 2013
Pathoscope: species identification and strain attribution with unassembled sequencing data.. 23. 2013
Enhancer transcripts mark active estrogen receptor binding sites.. 23. 2013
Inferring chromatin-bound protein complexes from genome-wide binding assays.. 23. 2013
DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing.. 23. 2012
Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs.. 22. 2012
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.. 22. 2012
Unusual combinatorial involvement of poly-A/T tracts in organizing genes and chromatin in Dictyostelium.. 22. 2012
Simultaneous structural variation discovery among multiple paired-end sequenced genomes.. 21. 2011
Variety of genomic DNA patterns for nucleosome positioning.. 21. 2011
Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development.. 21. 2011
A DNA methylation fingerprint of 1628 human samples.. 22. 2011
Stable and dynamic nucleosome states during a meiotic developmental process.. 21. 2011
Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data.. 21. 2010
Alu repeat discovery and characterization within human genomes.. 21. 2010
Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing.. 21. 2010
Integrative analysis of the melanoma transcriptome.. 20. 2010
Sex-specific and lineage-specific alternative splicing in primates.. 20. 2009
Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding.. 19. 2009
Genomic mapping of binding regions for the Ecdysone receptor protein complex.. 19. 2009
High-resolution DNA-binding specificity analysis of yeast transcription factors.. 19. 2009
A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome.. 19. 2009
Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs.. 18. 2008
Genome-wide nucleotide-level mammalian ancestor reconstruction.. 18. 2008
Rapid whole-genome mutational profiling using next-generation sequencing technologies.. 18. 2008
A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome.. 18. 2008
RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays.. 18. 2008
A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning.. 18. 2008
Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae.. 17. 2007
Novel patterns of genome rearrangement and their association with survival in breast cancer.. 16. 2006
Comparative isoschizomer profiling of cytosine methylation: the HELP assay.. 16. 2006
Multiplexed profiling of candidate genes for CpG island methylation status using a flexible PCR/LDR/Universal Array assay.. 16. 2005
DNA amplification method tolerant to sample degradation.. 14. 2004
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).. 14. 2004
High-throughput selection of effective RNAi probes for gene silencing.. 13. 2003
Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation.. 13. 2003
Tropheryma whipplei Twist: a human pathogenic Actinobacteria with a reduced genome.. 13. 2003
Mouse BAC ends quality assessment and sequence analyses.. 11. 2001
Detecting gene copy number fluctuations in tumor cells by microarray analysis of genomic representations.. 10. 2000
A 3-Mb high-resolution BAC/PAC contig of 12q22 encompassing the 830-kb consensus minimal deletion in male germ cell tumors.. 9. 1999
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. 1995
Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics. 2024

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