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GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases.
- Published in:
- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-31411-3
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- Article
MousiPLIER: A Mouse Pathway-Level Information Extractor Model.
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- eNeuro, 2024, v. 11, n. 6, p. 1, doi. 10.1523/ENEURO.0313-23.2024
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- Article
Sci-Hub provides access to nearly all scholarly literature.
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- eLife, 2018, p. 1, doi. 10.7554/eLife.32822
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- Article
IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.
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- Nucleic Acids Research, 2012, v. 40, p. W484, doi. 10.1093/nar/gks458
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- Article
PILGRM: an interactive data-driven discovery platform for expert biologists.
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- Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W368, doi. 10.1093/nar/gkr440
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- Article
PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia.
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- BioData Mining, 2018, v. 11, n. 1, p. N.PAG, doi. 10.1186/s13040-018-0175-7
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- Article
Network-based analysis of genetic variants associated with hippocampal volume in Alzheimer's disease: a study of ADNI cohorts.
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- BioData Mining, 2016, v. 9, p. 1, doi. 10.1186/s13040-016-0082-8
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- Article
Show me the models.
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- Nature Biotechnology, 2019, v. 37, n. 6, p. 623, doi. 10.1038/s41587-019-0143-x
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- Article
Reproducibility of computational workflows is automated using continuous analysis.
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- Nature Biotechnology, 2017, v. 35, n. 4, p. 342, doi. 10.1038/nbt.3780
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- Article
Understanding multicellular function and disease with human tissue-specific networks.
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- Nature Genetics, 2015, v. 47, n. 6, p. 569, doi. 10.1038/ng.3259
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Targeted exploration and analysis of large cross-platform human transcriptomic compendia.
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- Nature Methods, 2015, v. 12, n. 3, p. 211, doi. 10.1038/nmeth.3249
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Accurate evaluation and analysis of functional genomics data and methods.
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- Annals of the New York Academy of Sciences, 2012, v. 1260, n. 1, p. 95, doi. 10.1111/j.1749-6632.2011.06383.x
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- Article
wenda_gpu: fast domain adaptation for genomic data.
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- Bioinformatics, 2022, v. 38, n. 22, p. 5129, doi. 10.1093/bioinformatics/btac663
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- Article
Hetnet connectivity search provides rapid insights into how biomedical entities are related.
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- GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad047
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- Article
Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design.
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- GigaScience, 2021, v. 10, n. 9, p. 1, doi. 10.1093/gigascience/giab062
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- Article
Correcting for experiment-specific variability in expression compendia can remove underlying signals.
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- GigaScience, 2020, v. 9, n. 11, p. 1, doi. 10.1093/gigascience/giaa117
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- Article
A parasite's perspective on data sharing.
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- GigaScience, 2018, v. 7, n. 11, p. N.PAG, doi. 10.1093/gigascience/giy129
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- Article
Projecting genetic associations through gene expression patterns highlights disease etiology and drug mechanisms.
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- Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-41057-4
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- Article
Widespread redundancy in -omics profiles of cancer mutation states.
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- Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02705-y
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- Article
Failure to Replicate a Genetic Association May Provide Important Clues About Genetic Architecture.
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- PLoS ONE, 2009, v. 4, n. 6, p. 1, doi. 10.1371/journal.pone.0005639
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- Article
A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma.
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- BMC Genomics, 2017, v. 18, p. 1, doi. 10.1186/s12864-017-3519-7
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- Article
Leveraging global gene expression patterns to predict expression of unmeasured genes.
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- BMC Genomics, 2015, v. 16, p. 1, doi. 10.1186/s12864-015-2250-5
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- Article
Ten quick tips for deep learning in biology.
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- PLoS Computational Biology, 2022, v. 18, n. 3, p. 1, doi. 10.1371/journal.pcbi.1009803
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- Article
miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data.
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- PLoS Computational Biology, 2021, v. 17, n. 8, p. 1, doi. 10.1371/journal.pcbi.1009290
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A publishing infrastructure for Artificial Intelligence (AI)-assisted academic authoring.
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- Journal of the American Medical Informatics Association, 2024, v. 31, n. 9, p. 2103, doi. 10.1093/jamia/ocae139
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- Article
Analysis of science journalism reveals gender and regional disparities in coverage.
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- eLife, 2024, p. 1, doi. 10.7554/eLife.84855
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- Article
New Drosophila Long-Term Memory Genes Revealed by Assessing Computational Function Prediction Methods.
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- G3: Genes | Genomes | Genetics, 2019, v. 9, n. 1, p. 251, doi. 10.1534/g3.118.200867
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- Article
Machine Learning Analysis Identifies Drosophila Grunge/Atrophin as an Important Learning and Memory Gene Required for Memory Retention and Social Learning.
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- G3: Genes | Genomes | Genetics, 2017, v. 7, n. 11, p. 3705, doi. 10.1534/g3.117.300172
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- Article
Comprehensive Cross-Population Analysis of High-Grade Serous Ovarian Cancer Supports No More Than Three Subtypes.
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- G3: Genes | Genomes | Genetics, 2016, v. 6, n. 12, p. 4097, doi. 10.1534/g3.116.033514
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- Article
Systems Level Analysis of Systemic Sclerosis Shows a Network of Immune and Profibrotic Pathways Connected with Genetic Polymorphisms.
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- PLoS Computational Biology, 2015, v. 11, n. 1, p. 1, doi. 10.1371/journal.pcbi.1004005
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- Article
Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes.
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- PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002957
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- Article
Chapter 2: Data-Driven View of Disease Biology.
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- PLoS Computational Biology, 2012, v. 8, n. 12, p. 1, doi. 10.1371/journal.pcbi.1002816
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- Article
Examining linguistic shifts between preprints and publications.
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- PLoS Biology, 2022, v. 20, n. 2, p. 1, doi. 10.1371/journal.pbio.3001470
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A field guide to cultivating computational biology.
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- PLoS Biology, 2021, v. 19, n. 10, p. 1, doi. 10.1371/journal.pbio.3001419
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Adapting bioinformatics curricula for big data.
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- Briefings in Bioinformatics, 2016, v. 17, n. 1, p. 43, doi. 10.1093/bib/bbv018
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Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery.
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- Briefings in Bioinformatics, 2016, v. 17, n. 1, p. 33, doi. 10.1093/bib/bbv087
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- Article
International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways.
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- Nature Communications, 2015, v. 6, n. 9, p. 8019, doi. 10.1038/ncomms9019
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- Article
Performance of computational algorithms to deconvolve heterogeneous bulk ovarian tumor tissue depends on experimental factors.
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- Genome Biology, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s13059-023-03077-7
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- Article
Changing word meanings in biomedical literature reveal pandemics and new technologies.
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- BioData Mining, 2023, v. 16, n. 1, p. 1, doi. 10.1186/s13040-023-00332-2
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- Article
Expanding a database-derived biomedical knowledge graph via multi-relation extraction from biomedical abstracts.
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- BioData Mining, 2022, v. 15, n. 1, p. 1, doi. 10.1186/s13040-022-00311-z
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- Article
Pathway and network-based strategies to translate genetic discoveries into effective therapies.
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- Human Molecular Genetics, 2016, v. 25, n. R2, p. R94, doi. 10.1093/hmg/ddw160
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- Article
Identification of shared and unique susceptibility pathways among cancers of the lung, breast, and prostate from genome-wide association studies and issue-specific protein interactions.
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- Human Molecular Genetics, 2015, v. 24, n. 25, p. 7406, doi. 10.1093/hmg/ddv440
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- Article
The effect of non-linear signal in classification problems using gene expression.
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- PLoS Computational Biology, 2023, v. 19, n. 3, p. 1, doi. 10.1371/journal.pcbi.1010984
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Big Data Bioinformatics.
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- Journal of Cellular Physiology, 2014, v. 229, n. 12, p. 1896, doi. 10.1002/jcp.24662
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- Article
Specific histone modifications associate with alternative exon selection during mammalian development.
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- Nucleic Acids Research, 2020, v. 48, n. 9, p. 4709, doi. 10.1093/nar/gkaa248
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- Article
ADAGE signature analysis: differential expression analysis with data-defined gene sets.
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- BMC Bioinformatics, 2017, v. 18, p. 1, doi. 10.1186/s12859-017-1905-4
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- Article
Integrative Analysis Identifies Candidate Tumor Microenvironment and Intracellular Signaling Pathways that Define Tumor Heterogeneity in NF1.
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- Genes, 2020, v. 11, n. 2, p. 226, doi. 10.3390/genes11020226
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- Article
Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations.
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- Genome Biology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s13059-020-02021-3
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- Article
Predicting targeted drug combinations based on Pareto optimal patterns of coexpression network connectivity.
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- Genome Medicine, 2014, v. 6, n. 4, p. 63, doi. 10.1186/gm550
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Open collaborative writing with Manubot.
- Published in:
- PLoS Computational Biology, 2019, v. 15, n. 6, p. 1, doi. 10.1371/journal.pcbi.1007128
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- Article