Publications
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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.
2013. AWTY, BAMBE, BEAGLE, BEAST, BEAUti, Bio++, DataMonkey, DendroPy, DnaSP, ENCprime/SeqCount, FigTree, GARLI, genealogical sorting index (gsi), HyPhy, IMa2, jModelTest, JELLYFISH, LAMARC, MacClade, MEGA, Mesquite. Dictionary of Bioinformatics.
2013. Can RNA-Seq resolve the rapid radiation of advanced moths and butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An exploratory study PLoS One. 8
2013. Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding. BMC Genomics. 14(1):428.
2013. De novo likelihood-based measures for comparing metagenomic assemblies. 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).
2013. A decision-theory approach to interpretable set analysis for high-dimensional data. BiometricsBiometrics. 69
2013. Derepression of Cancer/testis antigens in cancer is associated with distinct patterns of DNA hypomethylation. BMC CancerBMC CancerBMC Cancer. 13:144.