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2014. Integrating Transcriptomics with Metabolic Modeling Predicts Biomarkers and Drug Targets for Alzheimer's Disease. PLoS ONE. 9(8):e105383.
2014. Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors.. Genome Med. 6(8):61.
2014. Maximal Sum of Metabolic Exchange Fluxes Outperforms Biomass Yield as a Predictor of Growth Rate of Microorganisms. PLoS ONE. 9(5):e98372.
2014. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays.. Bioinformatics. 30(10):1363-9.
2014. A molecular phylogeny and revised classification for the oldest ditrysian moth lineages (Lepidoptera: Tineoidea), with implications for ancestral feeding habits of the mega-diverse Ditrysia. Systematic Entomology. 40:409-432.
2014. Network-level architecture and the evolutionary potential of underground metabolism. Proceedings of the National Academy of Sciences. 111(32):11762-11767.
2014. A new rhesus macaque assembly and annotation for next-generation sequencing analyses. Biology direct. 9:20.
2014. A Novel Nutritional Predictor Links Microbial Fastidiousness with Lowered Ubiquity, Growth Rate, and Cooperativeness. PLoS Computational Biology. 10(7):e1003726.
2014. Phenotype-based cell-specific metabolic modeling reveals metabolic liabilities of cancer.. Elife. 3
2014. Predicting cancer-specific vulnerability via data-driven detection of synthetic lethality.. Cell. 158(5):1199-209.
2014. Quantitative 4D analyses of epithelial folding during Drosophila gastrulation.. Development. 141(14):2895-900.
2014. Removing batch effects for prediction problems with frozen surrogate variable analysis.. PeerJ. 2:e561.
2014. RNA-sequencing of the brain transcriptome implicates dysregulation of neuroplasticity, circadian rhythms and GTPase binding in bipolar disorder.. Mol Psychiatry. 19(11):1179-85.
2014. RNA-sequencing of the brain transcriptome implicates dysregulation of neuroplasticity, circadian rhythms and GTPase binding in bipolar disorder. Molecular psychiatry.
2014. Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms.. Nat Biotechnol. 32(5):462-4.
2014. Stable isotope labeling of phosphoproteins for large-scale phosphorylation rate determination.. Mol Cell Proteomics. 13(4):1106-18.
2014. Stoichiometry of site-specific lysine acetylation in an entire proteome.. J Biol Chem. 289(31):21326-38.
2015. Algorithms in Bioinformatics: 15th International Workshop, WABI 2015. Lecture Notes in Bioinformatics. :328.
2015. Bayesian integration of genetics and epigenetics detects causal regulatory SNPs underlying expression variability. Nature Communications. 6:8555.
2015. Chromatin and genomic determinants of alternative splicing. BCB '15 Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics .
2015. Computational challenges in microbiome research. 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).
2015. Diversion of aspartate in ASS1-deficient tumours fosters de novo pyrimidine synthesis. Nature. 527(7578):379-383.
2015. Drugs that reverse disease transcriptomic signatures are more effective in a mouse model of dyslipidemia.. Mol Syst Biol. 11(3):791.