publication venue for
- SurvBal: compositional microbiome balances for survival outcomes.. 40. 2024
- Ragas: integration and enhanced visualization for single cell subcluster analysis. 2024
- ArCH: improving the performance of clonal hematopoiesis variant calling and interpretation.. 40. 2024
- cloudrnaSPAdes: Isoform assembly using bulk barcoded RNA sequencing data. 2024
- Cell type matching across species using protein embeddings and transfer learning.. 39. 2023
- Multiscale model of the different modes of cancer cell invasion.. 39. 2023
- MultiNEP: a Multi-omics Network Enhancement framework for Prioritizing disease genes and metabolites simultaneously. 2023
- Biomedical Evidence Engineering for Data-Driven Discovery. 2022
- ScisorWiz: Visualizing Differential Isoform Expression in Single-Cell Long-Read Data. 2022
- Testing microbiome association using integrated quantile regression models.. 38. 2022
- maplet: An extensible R toolbox for modular and reproducible metabolomics pipelines. 2021
- SGI: Automatic clinical subgroup identification in omics datasets. 2021
- coronaSPAdes: from biosynthetic gene clusters to RNA viral assemblies. 2021
- Peel Learning for Pathway-Related Outcome Prediction. 2021
- Omics community detection using multi-resolution clustering.. 37. 2021
- Inferring cancer progression from Single-Cell Sequencing while allowing mutation losses.. 37. 2021
- Chemical-protein interaction extraction via Gaussian probability distribution and external biomedical knowledge.. 36. 2020
- aPCoA: covariate adjusted principal coordinates analysis.. 36. 2020
- A Bayesian approach to accurate and robust signature detection on LINCS L1000 data.. 36. 2020
- ABEMUS: platform-specific and data-informed detection of somatic SNVs in cfDNA.. 36. 2020
- Meltos: multi-sample tumor phylogeny reconstruction for structural variants.. 36. 2020
- Testing clonal relatedness of two tumors from the same patient based on their mutational profiles: update of the Clonality R package.. 35. 2019
- Driver network as a biomarker: systematic integration and network modeling of multi-omics data to derive driver signaling pathways for drug combination prediction.. 35. 2019
- Breaking the paradigm: Dr Insight empowers signature-free, enhanced drug repurposing.. 35. 2019
- Integrating hypertension phenotype and genotype with hybrid non-negative matrix factorization.. 35. 2019
- Characterizing protein-DNA binding event subtypes in ChIP-exo data.. 35. 2019
- MoDentify: phenotype-driven module identification in metabolomics networks at different resolutions.. 35. 2019
- CRNET: an efficient sampling approach to infer functional regulatory networks by integrating large-scale ChIP-seq and time-course RNA-seq data.. 34. 2018
- Aether: leveraging linear programming for optimal cloud computing in genomics.. 34. 2018
- Phantom: investigating heterogeneous gene sets in time-course data.. 33. 2017
- EthSEQ: ethnicity annotation from whole exome sequencing data.. 33. 2017
- PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF.. 33. 2017
- MetaPlotR: a Perl/R pipeline for plotting metagenes of nucleotide modifications and other transcriptomic sites.. 33. 2017
- BASIC: BCR assembly from single cells.. 33. 2017
- DM-BLD: differential methylation detection using a hierarchical Bayesian model exploiting local dependency.. 33. 2016
- Visual Omics Explorer (VOE): a cross-platform portal for interactive data visualization.. 32. 2016
- phylogeo: an R package for geographic analysis and visualization of microbiome data.. 31. 2015
- Deep sequencing analysis of viral infection and evolution allows rapid and detailed characterization of viral mutant spectrum.. 31. 2015
- SNiPA: an interactive, genetic variant-centered annotation browser.. 31. 2014
- Genomation: a toolkit to summarize, annotate and visualize genomic intervals.. 31. 2014
- Characterization of structural variants with single molecule and hybrid sequencing approaches.. 30. 2014
- switchBox: an R package for k-Top Scoring Pairs classifier development.. 31. 2014
- The Ensembl REST API: Ensembl Data for Any Language.. 31. 2014
- lrgpr: interactive linear mixed model analysis of genome-wide association studies with composite hypothesis testing and regression diagnostics in R.. 30. 2014
- A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data.. 30. 2014
- Detecting independent and recurrent copy number aberrations using interval graphs.. 30. 2014
- DrugComboRanker: drug combination discovery based on target network analysis.. 30. 2014
- PRADA: pipeline for RNA sequencing data analysis.. 30. 2014
- HEFT: eQTL analysis of many thousands of expressed genes while simultaneously controlling for hidden factors.. 30. 2013
- MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels.. 29. 2013
- DrugMap Central: an on-line query and visualization tool to facilitate drug repositioning studies.. 29. 2013
- VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment.. 28. 2012
- Empirical Bayes conditional independence graphs for regulatory network recovery.. 28. 2012
- Robust identification of transcriptional regulatory networks using a Gibbs sampler on outlier sum statistic.. 28. 2012
- Mirroring co-evolving trees in the light of their topologies.. 28. 2012
- An enhanced Petri-net model to predict synergistic effects of pairwise drug combinations from gene microarray data.. 27. 2011
- Clonality: an R package for testing clonal relatedness of two tumors from the same patient based on their genomic profiles.. 27. 2011
- Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data.. 27. 2011
- Predicting in vitro drug sensitivity using Random Forests.. 27. 2010
- RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries.. 27. 2010
- Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery.. 26. 2010
- Reconstruction of the neuromuscular junction connectome.. 26. 2010
- Using semantic web rules to reason on an ontology of pseudogenes.. 26. 2010
- FastMEDUSA: a parallelized tool to infer gene regulatory networks.. 26. 2010
- GPCR-OKB: the G Protein Coupled Receptor Oligomer Knowledge Base.. 26. 2010
- Detection and characterization of novel sequence insertions using paired-end next-generation sequencing.. 26. 2010
- A modified LOESS normalization applied to microRNA arrays: a comparative evaluation.. 25. 2009
- Predicting the binding preference of transcription factors to individual DNA k-mers.. 25. 2008
- Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment.. 25. 2008
- Conditional random pattern algorithm for LOH inference and segmentation.. 25. 2008
- ProCope--protein complex prediction and evaluation.. 24. 2008
- Biomolecular network motif counting and discovery by color coding.. 24. 2008
- Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies.. 24. 2008
- Reversible jump MCMC approach for peak identification for stroke SELDI mass spectrometry using mixture model.. 24. 2008
- GeneTrack--a genomic data processing and visualization framework.. 24. 2008
- Model-based Bayesian clustering (MBBC).. 24. 2008
- ZFIQ: a software package for zebrafish biology.. 24. 2007
- Novel cell segmentation and online SVM for cell cycle phase identification in automated microscopy.. 24. 2007
- Gepard: a rapid and sensitive tool for creating dotplots on genome scale.. 23. 2007
- R/qtlbim: QTL with Bayesian Interval Mapping in experimental crosses.. 23. 2007
- PAWE-3D: visualizing power for association with error in case-control genetic studies of complex traits.. 21. 2005
- A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins.. 20. 2004
- An XML message broker framework for exchange and integration of microarray data.. 19. 2003
- Batch mode generation of residue-based diagrams of proteins.. 19. 2003
- Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data.. 19. 2003
- Annotation of bacterial genomes using improved phylogenomic profiles.. 19 Suppl 1. 2003