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interFLOW: maximum flow framework for the identification of factors mediating the signaling convergence of multiple receptors.
- Published in:
- NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00391-z
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- Publication type:
- Article
A network-based method for associating genes with autism spectrum disorder.
- Published in:
- Frontiers in Bioinformatics, 2024, p. 1, doi. 10.3389/fbinf.2024.1295600
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- Publication type:
- Article
A mutation-level covariate model for mutational signatures.
- Published in:
- PLoS Computational Biology, 2023, v. 19, n. 6, p. 1, doi. 10.1371/journal.pcbi.1011195
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- Publication type:
- Article
A Biterm Topic Model for Sparse Mutation Data.
- Published in:
- Cancers, 2023, v. 15, n. 5, p. 1601, doi. 10.3390/cancers15051601
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- Publication type:
- Article
A comparative analysis of telomere length maintenance circuits in fission and budding yeast.
- Published in:
- Frontiers in Genetics, 2022, v. 13, p. 1, doi. 10.3389/fgene.2022.1033113
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- Publication type:
- Article
Exosomal telomerase transcripts reprogram the microRNA transcriptome profile of fibroblasts and partially contribute to CAF formation.
- Published in:
- Scientific Reports, 2022, v. 11, n. 1, p. 1, doi. 10.1038/s41598-022-20186-8
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- Publication type:
- Article
Multi-task learning for predicting SARS-CoV-2 antibody escape.
- Published in:
- Frontiers in Genetics, 2022, v. 13, p. 1, doi. 10.3389/fgene.2022.886649
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- Publication type:
- Article
A mixture model for signature discovery from sparse mutation data.
- Published in:
- Genome Medicine, 2021, v. 13, n. 1, p. 1, doi. 10.1186/s13073-021-00988-7
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- Publication type:
- Article
Effect of SARS-CoV-2 proteins on vascular permeability.
- Published in:
- eLife, 2021, p. 1, doi. 10.7554/eLife.69314
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- Publication type:
- Article
A data-driven approach for constructing mutation categories for mutational signature analysis.
- Published in:
- PLoS Computational Biology, 2021, v. 17, n. 10, p. 1, doi. 10.1371/journal.pcbi.1009542
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- Publication type:
- Article
Poster: CLL-283: CLL-Derived Exosomes Turn Endothelial Cells into CLL-Supportive Cells.
- Published in:
- Clinical Lymphoma, Myeloma & Leukemia, 2021, v. 21, p. S222, doi. 10.1016/S2152-2650(21)01400-2
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- Publication type:
- Article
CLL-283: CLL-Derived Exosomes Turn Endothelial Cells into CLL-Supportive Cells.
- Published in:
- Clinical Lymphoma, Myeloma & Leukemia, 2021, v. 21, p. S321, doi. 10.1016/S2152-2650(21)01757-2
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- Publication type:
- Article
Evolution of fibroblasts in the lung metastatic microenvironment is driven by stage-specific transcriptional plasticity.
- Published in:
- eLife, 2021, p. 1, doi. 10.7554/eLife.60745
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- Publication type:
- Article
Long reads capture simultaneous enhancer–promoter methylation status for cell-type deconvolution.
- Published in:
- Bioinformatics, 2021, v. 37, p. i327, doi. 10.1093/bioinformatics/btab306
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- Publication type:
- Article
Comparing the utility of in vivo transposon mutagenesis approaches in yeast species to infer gene essentiality.
- Published in:
- Current Genetics, 2020, v. 66, n. 6, p. 1117, doi. 10.1007/s00294-020-01096-6
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- Publication type:
- Article
Identification of Essential Genes and Fluconazole Susceptibility Genes in Candida glabrata by Profiling Hermes Transposon Insertions.
- Published in:
- G3: Genes | Genomes | Genetics, 2020, v. 10, n. 10, p. 3859, doi. 10.1534/g3.120.401595
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- Publication type:
- Article
Network-based approaches elucidate differences within APOBEC and clock-like signatures in breast cancer.
- Published in:
- Genome Medicine, 2020, v. 12, n. 1, p. 1, doi. 10.1186/s13073-020-00745-2
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- Publication type:
- Article
The first enhancer in an enhancer chain safeguards subsequent enhancer-promoter contacts from a distance.
- Published in:
- Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1808-y
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- Publication type:
- Article
Hidden Markov models lead to higher resolution maps of mutation signature activity in cancer.
- Published in:
- Genome Medicine, 2019, v. 11, n. 1, p. N.PAG, doi. 10.1186/s13073-019-0659-1
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- Publication type:
- Article
Modeling clinical and molecular covariates of mutational process activity in cancer.
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- Bioinformatics, 2019, v. 35, n. 14, p. i492, doi. 10.1093/bioinformatics/btz340
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- Publication type:
- Article
A systematic approach to orient the human protein–protein interaction network.
- Published in:
- Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-10887-6
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- Publication type:
- Article
To Embed or Not: Network Embedding as a Paradigm in Computational Biology.
- Published in:
- Frontiers in Genetics, 2019, p. N.PAG, doi. 10.3389/fgene.2019.00381
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- Publication type:
- Article
Comparative Analysis of Normalization Methods for Network Propagation.
- Published in:
- Frontiers in Genetics, 2019, p. N.PAG, doi. 10.3389/fgene.2019.00004
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- Publication type:
- Article
An optimization framework for network annotation.
- Published in:
- Bioinformatics, 2018, v. 34, n. 13, p. i502, doi. 10.1093/bioinformatics/bty236
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- Publication type:
- Article
A network diffusion approach to inferring sample-specific function reveals functional changes associated with breast cancer.
- Published in:
- PLoS Computational Biology, 2017, v. 13, n. 11, p. 1, doi. 10.1371/journal.pcbi.1005793
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- Publication type:
- Article
ANAT 2.0: reconstructing functional protein subnetworks.
- Published in:
- BMC Bioinformatics, 2017, v. 18, p. 1, doi. 10.1186/s12859-017-1932-1
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- Publication type:
- Article
BeWith: A Between-Within method to discover relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions.
- Published in:
- PLoS Computational Biology, 2017, v. 13, n. 10, p. 1, doi. 10.1371/journal.pcbi.1005695
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- Publication type:
- Article
GLADIATOR: a global approach for elucidating disease modules.
- Published in:
- Genome Medicine, 2017, v. 9, p. 1, doi. 10.1186/s13073-017-0435-z
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- Publication type:
- Article
Complexity and algorithms for copy-number evolution problems.
- Published in:
- Algorithms for Molecular Biology, 2017, v. 12, p. 1, doi. 10.1186/s13015-017-0103-2
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- Publication type:
- Article
Quantifying deleterious effects of regulatory variants.
- Published in:
- Nucleic Acids Research, 2017, v. 45, n. 5, p. 2307, doi. 10.1093/nar/gkw1263
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- Publication type:
- Article
An integer programming framework for inferring disease complexes from network data.
- Published in:
- Bioinformatics, 2016, v. 32, n. 12, p. i271, doi. 10.1093/bioinformatics/btw263
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- Publication type:
- Article
Utilizing yeast chemogenomic profiles for the prediction of pharmacogenomic associations in humans.
- Published in:
- Scientific Reports, 2016, p. 23703, doi. 10.1038/srep23703
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- Publication type:
- Article
Systematic identification and correction of annotation errors in the genetic interaction map of Saccharomyces cerevisiae.
- Published in:
- Nucleic Acids Research, 2016, v. 44, n. 5, p. 1, doi. 10.1093/nar/gkv1284
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- Publication type:
- Article
Network-Based Integration of Disparate Omic Data To Identify "Silent Players" in Cancer.
- Published in:
- PLoS Computational Biology, 2015, v. 11, n. 12, p. 1, doi. 10.1371/journal.pcbi.1004595
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- Publication type:
- Article
Human protein interaction networks across tissues and diseases.
- Published in:
- Frontiers in Genetics, 2015, p. 1, doi. 10.3389/fgene.2015.00257
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- Publication type:
- Article
Human protein interaction networks across tissues and diseases.
- Published in:
- Frontiers in Genetics, 2015, p. 1
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- Publication type:
- Article
Experimental design schemes for learning Boolean network models.
- Published in:
- Bioinformatics, 2014, v. 30, n. 17, p. i445, doi. 10.1093/bioinformatics/btu451
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- Publication type:
- Article
Network orientation via shortest paths.
- Published in:
- Bioinformatics, 2014, v. 30, n. 10, p. 1449, doi. 10.1093/bioinformatics/btu043
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- Publication type:
- Article
Modelling the Yeast Interactome.
- Published in:
- Scientific Reports, 2014, p. 1, doi. 10.1038/srep04273
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- Publication type:
- Article
A Method for Predicting Protein-Protein Interaction Types.
- Published in:
- PLoS ONE, 2014, v. 9, n. 3, p. 1, doi. 10.1371/journal.pone.0090904
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- Publication type:
- Article
A minimum-labeling approach for reconstructing protein networks across multiple conditions.
- Published in:
- Algorithms for Molecular Biology, 2014, v. 9, n. 1, p. 1, doi. 10.1186/1748-7188-9-1
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- Publication type:
- Article
Pathways of Toxicity.
- Published in:
- Altex, 2014, p. 53, doi. 10.14573/altex.1309261
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- Article
Toward a role model.
- Published in:
- EMBO Reports, 2013, v. 14, n. 11, p. 948, doi. 10.1038/embor.2013.161
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- Publication type:
- Article
A method for inferring medical diagnoses from patient similarities.
- Published in:
- BMC Medicine, 2013, v. 11, n. 1, p. 1, doi. 10.1186/1741-7015-11-194
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- Publication type:
- Article
Environmental Stresses Disrupt Telomere Length Homeostasis.
- Published in:
- PLoS Genetics, 2013, v. 9, n. 9, p. 1, doi. 10.1371/journal.pgen.1003721
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- Publication type:
- Article
Estimating population size via line graph reconstruction.
- Published in:
- Algorithms for Molecular Biology, 2013, v. 8, n. 1, p. 1, doi. 10.1186/1748-7188-8-17
- By:
- Publication type:
- Article
Simultaneous Identification of Multiple Driver Pathways in Cancer
- Published in:
- PLoS Computational Biology, 2013, v. 9, n. 5, p. 1, doi. 10.1371/journal.pcbi.1003054
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- Publication type:
- Article
A method for inferring medical diagnoses from patient similarities.
- Published in:
- 2013
- By:
- Publication type:
- journal article
Enhancing the Prioritization of Disease-Causing Genes through Tissue Specific Protein Interaction Networks.
- Published in:
- PLoS Computational Biology, 2012, v. 8, n. 9, p. 1, doi. 10.1371/journal.pcbi.1002690
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- Publication type:
- Article
Met Kinetic Signature Derived from the Response to HGF/SF in a Cellular Model Predicts Breast Cancer Patient Survival.
- Published in:
- PLoS ONE, 2012, v. 7, n. 9, p. 1, doi. 10.1371/journal.pone.0045969
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- Publication type:
- Article