Not all tickets are equal and we know it: Guiding pruning with domain-specific knowledge.
CoRR, 2024
SpaCeNet: Spatial Cellular Networks from Omics Data.
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Proceedings of the Research in Computational Molecular Biology, 2024
BONOBO: Bayesian Optimized Sample-Specific Networks Obtained by Omics Data.
Proceedings of the Research in Computational Molecular Biology, 2024
Pruning neural network models for gene regulatory dynamics using data and domain knowledge.
Proceedings of the Advances in Neural Information Processing Systems 38: Annual Conference on Neural Information Processing Systems 2024, 2024
Looking back at the first twenty years of genomics.
Quant. Biol., 2022
GRAND: a database of gene regulatory network models across human conditions.
Nucleic Acids Res., 2022
Scaling up Continuous-Time Markov Chains Helps Resolve Underspecification.
Proceedings of the Advances in Neural Information Processing Systems 34: Annual Conference on Neural Information Processing Systems 2021, 2021
Gene Regulatory Network Inference as Relaxed Graph Matching.
Proceedings of the Thirty-Fifth AAAI Conference on Artificial Intelligence, 2021
Cascade Size Distributions: Why They Matter and How to Compute Them Efficiently.
Proceedings of the Thirty-Fifth AAAI Conference on Artificial Intelligence, 2021
PUMA: PANDA Using MicroRNA Associations.
Bioinform., 2020
Clustering Sparse Data With Feature Correlation With Application to Discover Subtypes in Cancer.
IEEE Access, 2020
A Novel Deep Learning Model by Stacking Conditional Restricted Boltzmann Machine and Deep Neural Network.
Proceedings of the KDD '20: The 26th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, 2020
Catalysis Clustering with GAN by Incorporating Domain Knowledge.
Proceedings of the KDD '20: The 26th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, 2020
Cascade Size Distributions and Why They Matter.
CoRR, 2019
Identification of differentially expressed gene sets using the Generalized Berk-Jones statistic.
Bioinform., 2019
Proceedings of the Biocomputing 2019: Proceedings of the Pacific Symposium, 2019
Clustering on Sparse Data in Non-overlapping Feature Space with Applications to Cancer Subtyping.
Proceedings of the IEEE International Conference on Data Mining, 2018
Network-based Distance Metric with Application to Discover Disease Subtypes in Cancer.
CoRR, 2017
Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data.
BMC Bioinform., 2017
Biomarker correlation network in colorectal carcinoma by tumor anatomic location.
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BMC Bioinform., 2017
Estimating gene regulatory networks with pandaR.
Bioinform., 2017
Bipartite Community Structure of eQTLs.
PLoS Comput. Biol., 2016
BatchQC: interactive software for evaluating sample and batch effects in genomic data.
Bioinform., 2016
PyPanda: a Python package for gene regulatory network reconstruction.
Bioinform., 2016
Integrating transcriptional and protein interaction networks to prioritize condition-specific master regulators.
BMC Syst. Biol., 2015
A network model for angiogenesis in ovarian cancer.
BMC Bioinform., 2015
High performance computing of gene regulatory networks using a message-passing model.
Proceedings of the 2015 IEEE High Performance Extreme Computing Conference, 2015
Sexually-dimorphic targeting of functionally-related genes in COPD.
BMC Syst. Biol., 2014
Analyzing networks of phenotypes in complex diseases: methodology and applications in COPD.
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BMC Syst. Biol., 2014
Significance Analysis of Prognostic Signatures.
PLoS Comput. Biol., 2013
Inconsistency in large pharmacogenomic studies.
Nat., 2013
Research and applications: Comparison and validation of genomic predictors for anticancer drug sensitivity.
J. Am. Medical Informatics Assoc., 2013
RamiGO: an R/Bioconductor package providing an AmiGO Visualize interface.
Bioinform., 2013
Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks.
Nucleic Acids Res., 2012
GeneSigDB: a manually curated database and resource for analysis of gene expression signatures.
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Nucleic Acids Res., 2012
iBBiG: iterative binary bi-clustering of gene sets.
Bioinform., 2012
nEASE: a method for gene ontology subclassification of high-throughput gene expression data.
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Bioinform., 2012
GCOD - GeneChip Oncology Database.
BMC Bioinform., 2011
Multiple-input multiple-output causal strategies for gene selection.
BMC Bioinform., 2011
<i>survcomp</i>: an R/Bioconductor package for performance assessment and comparison of survival models.
Bioinform., 2011
Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV.
Bioinform., 2011
Defining an informativeness metric for clustering gene expression data.
Bioinform., 2011
GeneSigDB - a curated database of gene expression signatures.
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Nucleic Acids Res., 2010
AI Methods for Analyzing Microarray Data.
Proceedings of the Encyclopedia of Artificial Intelligence (3 Volumes), 2009
Decomposition of Gene Expression State Space Trajectories.
PLoS Comput. Biol., 2009
Data-driven normalization strategies for high-throughput quantitative RT-PCR.
BMC Bioinform., 2009
An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation).
BMC Bioinform., 2009
Papers on normalization, variable selection, classification or clustering of microarray data.
Bioinform., 2009
Proceedings of the Biocomputing 2009: Proceedings of the Pacific Symposium, 2009
Seeded Bayesian Networks: Constructing genetic networks from microarray data.
BMC Syst. Biol., 2008
Proceedings of the Biocomputing 2008, 2008
Microarray blob-defect removal improves array analysis.
Bioinform., 2007
Stochasticity and Networks in Genomic Data.
Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007
It is time to end the patenting of software.
Bioinform., 2006
The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.
Nucleic Acids Res., 2005
CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data.
Bioinform., 2005
MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH terms.
Bioinform., 2005
The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists.
Nucleic Acids Res., 2003
TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets.
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Bioinform., 2003
Knowledge-Based Access to the Bio-Medical Literature, Ontologically-Grounded Experiments for the TREC 2003 Genomics Track.
Proceedings of The Twelfth Text REtrieval Conference, 2003
Microarray gene expression data analysis - a beginner's guide.
Blackwell, ISBN: 978-1-40510-682-5, 2003
Genesis: cluster analysis of microarray data.
Bioinform., 2002
The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species.
Nucleic Acids Res., 2001
The TIGR Gene Indices: reconstruction and representation of expressed gene sequences.
Nucleic Acids Res., 2000