2015. Synthetic dosage lethality in the human metabolic network is highly predictive of tumor growth and cancer patient survival.. Proc Natl Acad Sci U S A.
2015. Systematics and biogeography of Pleurobranchus Cuvier, 1804, sea slugs (Heterobranchia: Nudipleura: Pleurobranchidae). Zoological Journal of the Linnean Society. :n/a-n/a.
2015. The Theory and Practice of Genome Sequence Assembly. Annu Rev Genomics Hum GenetAnnu Rev Genomics Hum Genet. 16:153-72.
2015. Transcriptomic profiling of gene expression and RNA processing during Leishmania major differentiation.. Nucleic Acids Res. 43(14):6799-813.
2015. Use and mis-use of supplementary material in science publications. BMC Bioinformatics. 1632733845166(1)
2014. Automated ensemble assembly and validation of microbial genomes.. BMC Bioinformatics. 15:126.
2014. BlindCall: ultra-fast base-calling of high-throughput sequencing data by blind deconvolution.. Bioinformatics. 30(9):1214-9.
2014. Computational methods for optical mapping. GigaScienceGigaScience. 3:33.
2014. A computational study of the Warburg effect identifies metabolic targets inhibiting cancer migration.. Mol Syst Biol. 10:744.
2014. Conservation in first introns is positively associated with the number of exons within genes and the presence of regulatory epigenetic signals. BMC Genomics. 15(1):526.
2014. Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products. BMC GenomicsBMC Genomics. 15:1101.
2014. CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation. Nucleic Acids ResNucleic Acids ResNucleic Acids Res. 42:774-89.
2014. Determinants of expression variability. Nucleic Acids Research. 42(6):3503-3514.
2014. Developmental expression of chicken FOXN1 and putative target genes during feather development.. Int J Dev Biol. 58(1):57-64.
2014. Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition.. Genome Biol. 15(6):R76.
2014. Epiviz: interactive visual analytics for functional genomics data.. Nat Methods. 11(9):938-40.
2014. An evaluation of Monte-Carlo logic and logicFS motivated by a study of the regulation of gene expression in heart failure. Journal of Applied Statistics. 41(9):1956-1975.
2014. Glycan Degradation (GlyDeR) Analysis Predicts Mammalian Gut Microbiota Abundance and Host Diet-Specific Adaptations. mBio. 5(4):e01526-14-e01526-14.
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.