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From biomedical cloud platforms to microservices: next steps in FAIR data and analysis.
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- Scientific Data, 2022, v. 9, n. 1, p. 1, doi. 10.1038/s41597-022-01619-5
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- Article
Methods for evaluating unsupervised vector representations of genomic regions.
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- NAR Genomics & Bioinformatics, 2024, v. 6, n. 3, p. 1, doi. 10.1093/nargab/lqae086
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- Article
Fast clustering and cell-type annotation of scATAC data using pre-trained embeddings.
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- NAR Genomics & Bioinformatics, 2024, v. 6, n. 3, p. 1, doi. 10.1093/nargab/lqae073
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- Article
PEPATAC: an optimized pipeline for ATAC-seq data analysis with serial alignments.
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- NAR Genomics & Bioinformatics, 2021, v. 3, n. 4, p. 1, doi. 10.1093/nargab/lqab101
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- Article
LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis.
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- Nucleic Acids Research, 2018, v. 46, n. W1, p. W194, doi. 10.1093/nar/gky464
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- Article
Coloc-stats: a unified web interface to perform colocalization analysis of genomic features.
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- Nucleic Acids Research, 2018, v. 46, n. W1, p. W186, doi. 10.1093/nar/gky474
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- Article
Multimodal analysis of cell-free DNA whole-genome sequencing for pediatric cancers with low mutational burden.
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- Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-23445-w
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- Article
ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors.
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- Nature Methods, 2015, v. 12, n. 10, p. 963, doi. 10.1038/nmeth.3542
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- Article
DeepGSEA: explainable deep gene set enrichment analysis for single-cell transcriptomic data.
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- Bioinformatics, 2024, v. 40, n. 7, p. 1, doi. 10.1093/bioinformatics/btae434
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- Article
GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA.
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- Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad069
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- Article
Refget: standardized access to reference sequences.
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- Bioinformatics, 2022, v. 38, n. 1, p. 299, doi. 10.1093/bioinformatics/btab524
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- Article
Embeddings of genomic region sets capture rich biological associations in lower dimensions.
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- Bioinformatics, 2021, v. 37, n. 23, p. 4299, doi. 10.1093/bioinformatics/btab439
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- Article
IGD: high-performance search for large-scale genomic interval datasets.
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- Bioinformatics, 2021, v. 37, n. 1, p. 118, doi. 10.1093/bioinformatics/btaa1062
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- Article
Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects.
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- GigaScience, 2021, v. 10, n. 12, p. 1, doi. 10.1093/gigascience/giab077
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- Article
Chromatin conformation capture (Hi-C) sequencing of patient-derived xenografts: analysis guidelines.
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- GigaScience, 2021, v. 10, n. 4, p. 1, doi. 10.1093/gigascience/giab022
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- Article
Bedshift: perturbation of genomic interval sets.
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- Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02440-w
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- Article
PEPPRO: quality control and processing of nascent RNA profiling data.
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- Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02349-4
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- Article
COCOA: coordinate covariation analysis of epigenetic heterogeneity.
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- Genome Biology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s13059-020-02139-4
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- Article
When phylogenetic assumptions are violated: base compositional heterogeneity and among-site rate variation in beetle mitochondrial phylogenomics.
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- Systematic Entomology, 2010, v. 35, n. 3, p. 429, doi. 10.1111/j.1365-3113.2009.00517.x
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- Article
Joint Representation Learning for Retrieval and Annotation of Genomic Interval Sets.
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- Bioengineering (Basel), 2024, v. 11, n. 3, p. 263, doi. 10.3390/bioengineering11030263
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- Article
Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity.
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- Genome Biology, 2012, v. 13, n. 10, p. 1, doi. 10.1186/gb-2012-13-10-R88
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- Article
Nonstationary Evolution and Compositional Heterogeneity in Beetle Mitochondrial Phylogenomics.
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- Systematic Biology, 2009, v. 58, n. 4, p. 381, doi. 10.1093/sysbio/syp037
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The accessible chromatin landscape of the human genome.
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- Nature, 2012, v. 489, n. 7414, p. 75, doi. 10.1038/nature11232
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Methods for constructing and evaluating consensus genomic interval sets.
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- Nucleic Acids Research, 2024, v. 52, n. 17, p. 10119, doi. 10.1093/nar/gkae685
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- Article
Single-cell epigenomic variability reveals functional cancer heterogeneity.
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- Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-016-1133-7
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Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection.
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- PLoS Genetics, 2012, v. 8, n. 6, p. 1, doi. 10.1371/journal.pgen.1002789
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Expanding the Galaxy's reference data.
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- Bioinformatics Advances, 2022, v. 2, n. 1, p. 1, doi. 10.1093/bioadv/vbac030
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- Article
Challenges to sharing sample metadata in computational genomics.
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- Frontiers in Genetics, 2023, p. 1, doi. 10.3389/fgene.2023.1154198
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Opportunities and challenges in sharing and reusing genomic interval data.
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- Frontiers in Genetics, 2023, v. 14, p. 1, doi. 10.3389/fgene.2023.1155809
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- Article
Augmented Interval List: a novel data structure for efficient genomic interval search.
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- Bioinformatics, 2019, v. 35, n. 23, p. 4907, doi. 10.1093/bioinformatics/btz407
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- Article
MIRA: an R package for DNA methylation-based inference of regulatory activity.
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- Bioinformatics, 2018, v. 34, n. 15, p. 2649, doi. 10.1093/bioinformatics/bty083
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- Article
LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor.
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- Bioinformatics, 2016, v. 32, n. 4, p. 587, doi. 10.1093/bioinformatics/btv612
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- Article
Identifying and Characterizing Regulatory Sequences in the Human Genome with Chromatin Accessibility Assays.
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- Genes, 2012, v. 3, n. 4, p. 651, doi. 10.3390/genes3040651
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GenomicDistributions: fast analysis of genomic intervals with Bioconductor.
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- BMC Genomics, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s12864-022-08467-y
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- Article