publication venue for
- Controlled Noise: Evidence of epigenetic regulation of Single-Cell expression variability.. 40:btae457. 2024
- ISRES+: an improved evolutionary strategy for function minimization to estimate the free parameters of systems biology models.. 39:btad403. 2023
- Advanced graph and sequence neural networks for molecular property prediction and drug discovery.. 38:2579-2586. 2022
- Deep graph representations embed network information for robust disease marker identification.. 38:1075-1086. 2022
- ClassifyTE: a stacking-based prediction of hierarchical classification of transposable elements.. 37:2529-2536. 2021
- rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database 2021
- Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA-sequencing data quality control.. 37:963-967. 2021
- Bayesian structural equation modeling in multiple omics data with application to circadian genes.. 36:3951-3958. 2020
- scGEAToolbox: a Matlab toolbox for single-cell RNA sequencing data analysis.. 36:1948-1949. 2019
- Computational modeling of cellular structures using conditional deep generative networks.. 35:2141-2149. 2019
- RNAdetect: efficient computational detection of novel non-coding RNAs.. 35:1133-1141. 2019
- StackDPPred: a stacking based prediction of DNA-binding protein from sequence.. 35:433-441. 2019
- Driver network as a biomarker: systematic integration and network modeling of multi-omics data to derive driver signaling pathways for drug combination prediction.. 35:3709-3717. 2019
- GWASinlps: non-local prior based iterative SNP selection tool for genome-wide association studies.. 35:1-11. 2019
- Quantifying the notions of canalizing and master genes in a gene regulatory network-a Boolean network modeling perspective.. 35:643-649. 2019
- Bayesian negative binomial regression for differential expression with confounding factors.. 34:3349-3356. 2018
- RaMWAS: fast methylome-wide association study pipeline for enrichment platforms.. 34:2283-2285. 2018
- AEGS: identifying aberrantly expressed gene sets for differential variability analysis.. 34:881-883. 2018
- DeepEM3D: approaching human-level performance on 3D anisotropic EM image segmentation.. 33:2555-2562. 2017
- GppFst: genomic posterior predictive simulations of FST and dXY for identifying outlier loci from population genomic data.. 33:1414-1415. 2017
- Deep models for brain EM image segmentation: novel insights and improved performance.. 32:2352-2358. 2016
- Bayesian variable selection for binary outcomes in high-dimensional genomic studies using non-local priors.. 32:1338-1345. 2016
- Cross-validation under separate sampling: strong bias and how to correct it.. 30:3349-3355. 2014
- Identification of important regressor groups, subgroups and individuals via regularization methods: application to gut microbiome data.. 30:831-837. 2014
- Automated annotation of developmental stages of Drosophila embryos in images containing spatial patterns of expression.. 30:266-273. 2014
- Development of a domain-specific genetic language to design Chlamydomonas reinhardtii expression vectors.. 30:251-257. 2014
- Effect of separate sampling on classification accuracy.. 30:242-250. 2014
- Functional module identification in protein interaction networks by interaction patterns.. 30:81-93. 2014
- ROBNCA: robust network component analysis for recovering transcription factor activities.. 29:2410-2418. 2013
- Intervention in gene regulatory networks with maximal phenotype alteration.. 29:1758-1767. 2013
- Bayesian analysis of gene essentiality based on sequencing of transposon insertion libraries.. 29:695-703. 2013
- ToxPi GUI: an interactive visualization tool for transparent integration of data from diverse sources of evidence.. 29:402-403. 2013
- Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing.. 29:2096-2102. 2013
- Performance reproducibility index for classification.. 28:2824-2833. 2012
- Application of survival analysis methodology to the quantitative analysis of LC-MS proteomics data.. 28:1998-2003. 2012
- RESQUE: network reduction using semi-Markov random walk scores for efficient querying of biological networks.. 28:2129-2136. 2012
- Identifying mechanistic similarities in drug responses.. 28:1902-1910. 2012
- BPDA2d--a 2D global optimization-based Bayesian peptide detection algorithm for liquid chromatograph-mass spectrometry.. 28:564-572. 2012
- A hybrid approach to protein differential expression in mass spectrometry-based proteomics.. 28:1586-1591. 2012
- DanteR: an extensible R-based tool for quantitative analysis of -omics data.. 28:2404-2406. 2012
- Computational network analysis of the anatomical and genetic organizations in the mouse brain.. 27:3293-3299. 2011
- FlyExpress: visual mining of spatiotemporal patterns for genes and publications in Drosophila embryogenesis.. 27:3319-3320. 2011
- High-dimensional bolstered error estimation.. 27:3056-3064. 2011
- Application of the Bayesian MMSE estimator for classification error to gene expression microarray data.. 27:1822-1831. 2011
- Multiple-rule bias in the comparison of classification rules.. 27:1675-1683. 2011
- Cancer therapy design based on pathway logic.. 27:548-555. 2011
- State reduction for network intervention in probabilistic Boolean networks.. 26:3098-3104. 2010
- A CoD-based reduction algorithm for designing stationary control policies on Boolean networks.. 26:1556-1563. 2010
- A soft kinetic data structure for lesion border detection.. 26:i21-i28. 2010
- Small-sample precision of ROC-related estimates.. 26:822-830. 2010
- Reporting bias when using real data sets to analyze classification performance.. 26:68-76. 2010
- Adaptive intervention in probabilistic boolean networks.. 25:2042-2048. 2009
- SAFEGUI: resampling-based tests of categorical significance in gene expression data made easy.. 25:541-542. 2009
- FastMap: fast eQTL mapping in homozygous populations.. 25:482-489. 2009
- A statistical framework for protein quantitation in bottom-up MS-based proteomics.. 25:2028-2034. 2009
- Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition.. 25:2573-2580. 2009
- Automated annotation of Drosophila gene expression patterns using a controlled vocabulary.. 24:1881-1888. 2008
- Classification with reject option in gene expression data.. 24:1889-1895. 2008
- A model of higher accuracy for the individual haplotyping problem based on weighted SNP fragments and genotype with errors.. 24:i105-i113. 2008
- Structural systems identification of genetic regulatory networks.. 24:553-560. 2008
- Structural systems identification of genetic regulatory networks. 24:553-560. 2008
- Inferring missing genotypes in large SNP panels using fast nearest-neighbor searches over sliding windows.. 23:i401-i407. 2007
- Identifying clusters of functionally related genes in genomes.. 23:1053-1060. 2007
- The impact of function perturbations in Boolean networks.. 23:1265-1273. 2007
- Crystallographic protein model-building on the web.. 23:375-377. 2007
- SNiPer-HD: improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays.. 23:57-63. 2007
- What should be expected from feature selection in small-sample settings.. 22:2430-2436. 2006
- Inferring gene regulatory networks from time series data using the minimum description length principle.. 22:2129-2135. 2006
- EDGE: extraction and analysis of differential gene expression (vol 22, pg 507, 2006). 22:1412-1412. 2006
- Genetic test bed for feature selection.. 22:837-842. 2006
- EDGE: extraction and analysis of differential gene expression.. 22:507-508. 2006
- Intervention in a family of Boolean networks.. 22:226-232. 2006
- ClaNC: point-and-click software for classifying microarrays to nearest centroids.. 22:122-123. 2006
- A two-stage normalization method for partially degraded mRNA microarray data.. 21:4000-4006. 2005
- Generating Boolean networks with a prescribed attractor structure.. 21:4021-4025. 2005
- Estimating misclassification error with small samples via bootstrap cross-validation.. 21:1979-1986. 2005
- Optimal number of features as a function of sample size for various classification rules.. 21:1509-1515. 2005
- Boolean relationships among genes responsive to ionizing radiation in the NCI 60 ACDS.. 21:1542-1549. 2005
- Intervention in context-sensitive probabilistic Boolean networks.. 21:1211-1218. 2005
- Superior feature-set ranking for small samples using bolstered error estimation.. 21:1046-1054. 2005
- How many samples are needed to build a classifier: a general sequential approach.. 21:63-70. 2005
- Gene selection using a two-level hierarchical Bayesian model.. 20:3423-3430. 2004
- A Bayesian connectivity-based approach to constructing probabilistic gene regulatory networks.. 20:2918-2927. 2004
- Which is better for cDNA-microarray-based classification: ratios or direct intensities.. 20:2513-2520. 2004
- Growing genetic regulatory networks from seed genes.. 20:1241-1247. 2004
- External control in Markovian genetic regulatory networks: the imperfect information case.. 20:924-930. 2004
- Is cross-validation valid for small-sample microarray classification?. 20:374-380. 2004
- Is cross-validation better than resubstitution for ranking genes?. 20:253-258. 2004
- Missing-value estimation using linear and non-linear regression with Bayesian gene selection.. 19:2302-2307. 2003
- An XML message broker framework for exchange and integration of microarray data.. 19:1844-1845. 2003
- Corrected small-sample estimation of the Bayes error.. 19:944-951. 2003
- Gene selection: a Bayesian variable selection approach.. 19:90-97. 2003
- Transformation and normalization of oligonucleotide microarray data.. 19:1817-1823. 2003
- Gene perturbation and intervention in probabilistic Boolean networks.. 18:1319-1331. 2002
- Ratio statistics of gene expression levels and applications to microarray data analysis.. 18:1207-1215. 2002
- Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks.. 18:261-274. 2002
- Splicing graphs and EST assembly problem.. 18 Suppl 1:S181-S188. 2002
- Algorithms and software for support of gene identification experiments.. 14:14-19. 1998
- BioABACUS: a database of abbreviations and acronyms in biotechnology and computer science.. 14:888-889. 1998
- Covariate-dependent negative binomial factor analysis of RNA sequencing data. 2018
- Kinetics analysis methods for approximate folding landscapes. 2007