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Low-variance RNAs identify Parkinson's disease molecular signature in blood.
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- Movement Disorders, 2015, v. 30, n. 6, p. 813, doi. 10.1002/mds.26205
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- Article
Accurate detection of aneuploidies in array CGH and gene expression microarray data.
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- Bioinformatics, 2004, v. 20, n. 18, p. 3533, doi. 10.1093/bioinformatics/bth440
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- Article
Nonparametric methods for identifying differentially expressed genes in microarray data.
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- Bioinformatics, 2002, v. 18, n. 11, p. 1454, doi. 10.1093/bioinformatics/18.11.1454
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- Article
Sequence complexity profiles of prokaryotic genomic sequences: A fast algorithm for calculating linguistic complexity.
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- Bioinformatics, 2002, v. 18, n. 5, p. 679, doi. 10.1093/bioinformatics/18.5.679
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- Article
Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana.
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- BMC Systems Biology, 2010, v. 4, p. 180, doi. 10.1186/1752-0509-4-180
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- Article
Comparative gene expression between two yeast species.
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- BMC Genomics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2164-14-33
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- Article
Peak-agnostic high-resolution cis-regulatory circuitry mapping using single cell multiome data.
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- Nucleic Acids Research, 2024, v. 52, n. 2, p. 572, doi. 10.1093/nar/gkad1166
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- Article
Probabilistic modelling of chromatin code landscape reveals functional diversity of enhancer-like chromatin states.
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- Nature Communications, 2016, v. 7, n. 2, p. 10528, doi. 10.1038/ncomms10528
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- Article
Systems-level dynamic analyses of fate change in murine embryonic stem cells.
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- Nature, 2009, v. 462, n. 7271, p. 358, doi. 10.1038/nature08575
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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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- Article
Computationally Driven, Quantitative Experiments Discover Genes Required for Mitochondrial Biogenesis.
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- PLoS Genetics, 2009, v. 5, n. 3, p. 1, doi. 10.1371/journal.pgen.1000407
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- Article
Putting microarrays in a context: Integrated analysis of diverse biological data.
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- Briefings in Bioinformatics, 2005, v. 6, n. 1, p. 34, doi. 10.1093/bib/6.1.34
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- Article
Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans.
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- eLife, 2016, p. 1, doi. 10.7554/eLife.17670
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- Article
Nearest Neighbor Networks: clustering expression data based on gene neighborhoods.
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- BMC Bioinformatics, 2007, v. 8, p. 250, doi. 10.1186/1471-2105-8-250
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- Article
Visualization-based discovery and analysis of genomic aberrations in microarray data.
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- BMC Bioinformatics, 2005, v. 6, p. 146, doi. 10.1186/1471-2105-6-146
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- Article
Visualization methods for statistical analysis of microarray clusters.
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- BMC Bioinformatics, 2005, v. 6, p. 115, doi. 10.1186/1471-2105-6-115
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- Article
Global Quantitative Modeling of Chromatin Factor Interactions.
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- PLoS Computational Biology, 2014, v. 10, n. 3, p. 1, doi. 10.1371/journal.pcbi.1003525
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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
Tissue-Specific Functional Networks for Prioritizing Phenotype and Disease Genes.
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- PLoS Computational Biology, 2012, v. 8, n. 9, p. 1, doi. 10.1371/journal.pcbi.1002694
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- Article
Accurate Quantification of Functional Analogy among Close Homologs.
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- PLoS Computational Biology, 2011, v. 7, n. 2, p. 1, doi. 10.1371/journal.pcbi.1001074
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- Article
Mapping Dynamic Histone Acetylation Patterns to Gene Expression in Nanog-Depleted Murine Embryonic Stem Cells.
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- PLoS Computational Biology, 2010, v. 6, n. 12, p. 1, doi. 10.1371/journal.pcbi.1001034
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- Article
Simultaneous Genome-Wide Inference of Physical, Genetic, Regulatory, and Functional Pathway Components.
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- PLoS Computational Biology, 2010, v. 6, n. 11, p. 1, doi. 10.1371/journal.pcbi.1001009
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- Article
Functional Genomics Complements Quantitative Genetics in Identifying Disease-Gene Associations.
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- PLoS Computational Biology, 2010, v. 6, n. 11, p. 1, doi. 10.1371/journal.pcbi.1000991
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- Publication type:
- Article
Global Prediction of Tissue-Specific Gene Expression and Context-Dependent Gene Networks in Caenorhabditis.
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- PLoS Computational Biology, 2009, v. 5, n. 6, p. 1, doi. 10.1371/journal.pcbi.1000417
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- Article
Directing Experimental Biology: A Case Study in Mitochondrial Biogenesis.
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- PLoS Computational Biology, 2009, v. 5, n. 3, p. 1, doi. 10.1371/journal.pcbi.1000322
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- Article
Coordinated Concentration Changes of Transcripts and Metabolites in Saccharomyces cerevisiae.
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- PLoS Computational Biology, 2009, v. 5, n. 1, p. 1, doi. 10.1371/journal.pcbi.1000270
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- Article
Predicting Cellular Growth from Gene Expression Signatures.
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- PLoS Computational Biology, 2009, v. 5, n. 1, p. 1, doi. 10.1371/journal.pcbi.1000257
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- Article
A Genomewide Functional Network for the Laboratory Mouse.
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- PLoS Computational Biology, 2008, v. 4, n. 9, p. 1, doi. 10.1371/journal.pcbi.1000165
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- Article
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
CROTON: an automated and variant-aware deep learning framework for predicting CRISPR/Cas9 editing outcomes.
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- Bioinformatics, 2021, v. 37, p. i342, doi. 10.1093/bioinformatics/btab268
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- Article
Subtype-specific transcriptional regulators in breast tumors subjected to genetic and epigenetic alterations.
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- Bioinformatics, 2020, v. 36, n. 4, p. 994, doi. 10.1093/bioinformatics/btz709
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- Article
Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development.
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- PLoS Genetics, 2019, v. 15, n. 9, p. 1, doi. 10.1371/journal.pgen.1008382
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- Article
Correction: Lack of a site-specific phosphorylation of Presenilin 1 disrupts microglial gene networks and progenitors during development.
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- 2021
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- Correction Notice
Lack of a site-specific phosphorylation of Presenilin 1 disrupts microglial gene networks and progenitors during development.
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- PLoS ONE, 2020, v. 15, n. 8, p. 1, doi. 10.1371/journal.pone.0237773
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- Article
Predicting effects of noncoding variants with deep learning-based sequence model.
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- Nature Methods, 2015, v. 12, n. 10, p. 931, doi. 10.1038/nmeth.3547
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- Article
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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- Article
Quantitative analysis of fitness and genetic interactions in yeast on a genome scale.
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- Nature Methods, 2010, v. 7, n. 12, p. 1017, doi. 10.1038/nmeth.1534
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- Article
Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures.
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- Nucleic Acids Research, 2022, v. 50, n. 14, p. 8168, doi. 10.1093/nar/gkac596
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- Article
GIANT 2.0: genome-scale integrated analysis of gene networks in tissues.
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- Nucleic Acids Research, 2018, v. 46, n. W1, p. W65, doi. 10.1093/nar/gky408
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- Article
GIANT API: an application programming interface for functional genomics.
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- Nucleic Acids Research, 2016, v. 44, n. W1, p. W587, doi. 10.1093/nar/gkw289
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- Article
IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.
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- Nucleic Acids Research, 2015, v. 43, n. W1, p. W128, doi. 10.1093/nar/gkv486
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- Article
FNTM: a server for predicting functional networks of tissues in mouse.
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- Nucleic Acids Research, 2015, v. 43, n. W1, p. W182, doi. 10.1093/nar/gkv443
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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
Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies.
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- Bioinformatics, 2013, v. 29, n. 23, p. 3036, doi. 10.1093/bioinformatics/btt529
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- Article
An effective statistical evaluation of ChIPseq dataset similarity.
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- Bioinformatics, 2012, v. 28, n. 5, p. 607, doi. 10.1093/bioinformatics/bts009
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- Article
Detailing regulatory networks through large scale data integration.
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- Bioinformatics, 2009, v. 25, n. 24, p. 3267, doi. 10.1093/bioinformatics/btp588
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- Article
The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction.
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- Bioinformatics, 2009, v. 25, n. 18, p. 2404, doi. 10.1093/bioinformatics/btp397
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- Article
Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields.
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- Bioinformatics, 2009, v. 25, n. 10, p. 1307, doi. 10.1093/bioinformatics/btn585
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- Article