publication venue for
- Author Correction: Mutational signatures reveal the role of RAD52 in p53-independent p21-driven genomic instability. 2022
- RExPRT: a machine learning tool to predict pathogenicity of tandem repeat loci.. 25. 2024
- Ariadne: synthetic long read deconvolution using assembly graphs.. 24. 2023
- BamQuery: a proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens.. 24. 2023
- Back in 3D-a report on Genome Informatics 2022.. 24. 2023
- REPAC: analysis of alternative polyadenylation from RNA-sequencing data.. 24. 2023
- β-actin mediated H3K27ac changes demonstrate the link between compartment switching and enhancer-dependent transcriptional regulation.. 24. 2023
- Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies.. 23. 2022
- Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples.. 23. 2022
- PEGR: a flexible management platform for reproducible epigenomic and genomic research.. 23. 2022
- The SEQC2 epigenomics quality control (EpiQC) study.. 22. 2021
- recount3: summaries and queries for large-scale RNA-seq expression and splicing.. 22. 2021
- DNA methylation-calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation.. 22. 2021
- A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency.. 22. 2021
- Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions.. 22. 2021
- High throughput single-cell detection of multiplex CRISPR-edited gene modifications.. 21. 2020
- Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae.. 21. 2020
- TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription.. 21. 2020
- DeepMILO: a deep learning approach to predict the impact of non-coding sequence variants on 3D chromatin structure.. 21. 2020
- VALOR2: characterization of large-scale structural variants using linked-reads.. 21. 2020
- EpiMethylTag: simultaneous detection of ATAC-seq or ChIP-seq signals with DNA methylation.. 20. 2019
- DNMT3A and TET1 cooperate to regulate promoter epigenetic landscapes in mouse embryonic stem cells.. 19. 2018
- Mutational signatures reveal the role of RAD52 in p53-independent p21-driven genomic instability.. 19. 2018
- Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications.. 19. 2018
- Comprehensive benchmarking and ensemble approaches for metagenomic classifiers.. 18. 2017
- Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network.. 18. 2017
- Methicillin-resistant Staphylococcus aureus emerged long before the introduction of methicillin into clinical practice.. 18. 2017
- Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures.. 17. 2016
- A benchmark for RNA-seq quantification pipelines.. 17. 2016
- Expanding the diversity of DNA base modifications with N⁶-methyldeoxyadenosine.. 17. 2016
- Identification of low abundance microbiome in clinical samples using whole genome sequencing.. 16. 2015
- Promoter-like epigenetic signatures in exons displaying cell type-specific splicing.. 16. 2015
- The impact of read length on quantification of differentially expressed genes and splice junction detection.. 16. 2015
- Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation.. 16. 2015
- Intra-tumor genetic heterogeneity and alternative driver genetic alterations in breast cancers with heterogeneous HER2 gene amplification.. 16. 2015
- Fast and scalable inference of multi-sample cancer lineages.. 16. 2015
- Benchmarking mutation effect prediction algorithms using functionally validated cancer-related missense mutations.. 15. 2014
- Dynamic evolution of clonal epialleles revealed by methclone.. 15. 2014
- Comparative sequencing analysis reveals high genomic concordance between matched primary and metastatic colorectal cancer lesions.. 15. 2014
- Unraveling the clonal hierarchy of somatic genomic aberrations.. 15. 2014
- Deep sequencing reveals clonal evolution patterns and mutation events associated with relapse in B-cell lymphomas.. 15. 2014
- Advancing clinical oncology through genome biology and technology.. 15. 2014
- Global regulation of mRNA translation and stability in the early Drosophila embryo by the Smaug RNA-binding protein.. 15. 2014
- FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer.. 15. 2014
- Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data.. 14. 2013
- Crowdfunding genomics and bioinformatics.. 14. 2013
- A microRNA network regulates proliferative timing and extracellular matrix synthesis during cellular quiescence in fibroblasts.. 13. 2012
- Assessing telomeric DNA content in pediatric cancers using whole-genome sequencing data.. 13. 2012
- The birth of the Epitranscriptome: deciphering the function of RNA modifications.. 13. 2012
- Hypothesis-driven genomics pays off.. 13. 2012
- methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles.. 13. 2012
- Analysis of variation at transcription factor binding sites in Drosophila and humans.. 13. 2012
- A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples.. 13. 2012
- Faster sequencers, larger datasets, new challenges.. 13. 2012
- Integrating diverse genomic data using gene sets.. 12. 2011
- The one new journal we might actually need.. 12. 2011
- Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.. 12. 2011
- The real cost of sequencing: higher than you think!. 12. 2011
- FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data.. 11. 2010
- Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites.. 11. 2010
- Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts.. 10. 2009
- A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome.. 10. 2009
- ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads.. 10. 2009
- Wimps? What wimps?. 10. 2009
- What my genome told me--and what it didn't.. 10. 2009
- Render unto Darwin.. 10. 2009
- Guilt by association.. 10. 2009
- Life is a Ponzi scheme.. 10. 2009
- The wisdom, and madness, of crowds.. 9. 2008
- Meta-morphosis.. 9. 2008
- When bubbles burst.. 9. 2008
- The story they missed.. 9. 2008
- A seat at the table.. 9. 2008
- A TATA binding protein regulatory network that governs transcription complex assembly.. 8. 2007
- Co-localization of CENP-C and CENP-H to discontinuous domains of CENP-A chromatin at human neocentromeres.. 8. 2007
- siRNA screen of the human signaling proteome identifies the PtdIns(3,4,5)P3-mTOR signaling pathway as a primary regulator of transferrin uptake.. 8. 2007
- Independent centromere formation in a capricious, gene-free domain of chromosome 13q21 in Old World monkeys and pigs.. 7. 2006
- Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics.. 7. 2006
- Changes in gene expression during the development of mammary tumors in MMTV-Wnt-1 transgenic mice.. 6. 2005
- Eighty years ago.. 6. 2005
- A matter of life and death.. 6. 2005
- Tsunami.. 6. 2005
- Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach.. 6. 2005
- Profiling of pathway-specific changes in gene expression following growth of human cancer cell lines transplanted into mice.. 4. 2003
- A piece of the action.. 2. 2001
- Abundant protein domains occur in proportion to proteome size.. 2. 2001
- Count me out.. 1. 2000
- Seek and ye shall maybe find.. 1. 2000
- Perpetual motion of the worst kind.. 1. 2000
- The dark side.. 1. 2000
- Dog eat dogma.. 1. 2000
- The grail problem.. 1. 2000
- Response to Zhou and Robinson.. 16. 2015
- Rising from the crypt: decreasing DNA methylation during differentiation of the small intestine. 2013
- Rising in the East. 2010
- The guards themselves. 2002
- An issue to remember. 2009
- The tech for the next decade: promises and challenges in genome biology. 2019
- Chromatin meets RNA polymerase II. 2007
- Developing a systems-level understanding of gene expression. 2007
- Recent advances in Drosophila genomics. 2004
- The Sequencing Quality Control 2 study: establishing community standards for sequencing in precision medicine.. 22. 2021
- Too big to succeed?. 10. 2009
- Spatial omics technologies at multimodal and single cell/subcellular level. 2022
- Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin. 2022
- Experimental design and quantitative analysis of microbial community multiomics. 2017
- Predicting preferential DNA vector insertion sites: implications for functional genomics and gene therapy. 2007
- Genome-wide analysis of protein-DNA interactions in living cells. 2001