2016. Better Identification of Repeats in Metagenomic Scaffolding. 9838:174-184.
2016. Capturing the most wanted taxa through cross-sample correlations. The ISME Journal.
2016. Data-Driven Metabolic Pathway Compositions Enhance Cancer Survival Prediction. PLOS Computational Biology. 12(9):e1005125.
2016. Distinct genomic and epigenomic features demarcate hypomethylated blocks in colon cancer. BMC Cancer. 16447943582141728452710921541113181321912(17143623521101753416231113)
2016. Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers.. PLoS One. 11(9):e0160574.
2016. Dual Transcriptome Profiling of Leishmania-Infected Human Macrophages Reveals Distinct Reprogramming Signatures. mBio. 7(3):e00027-16.
2016. The fruRBA operon is necessary for Group A Streptococcal growth in fructose and for resistance to neutrophil killing during growth in whole human blood.. Infect Immun.
2016. Functional Alignment of Metabolic Networks.. J Comput Biol.
2016. Genome-scale study reveals reduced metabolic adaptability in patients with non-alcoholic fatty liver disease.. Nat Commun. 7:8994.
2016. Genome-scale study reveals reduced metabolic adaptability in patients with non-alcoholic fatty liver disease. Nature Communications. 7:8994.
2016. Heterogeneity of transcription factor binding specificity models within and across cell lines. Genome Research. :gr.199166.115.
2016. The fruRBA Operon Is Necessary for Group A Streptococcal Growth in Fructose and for Resistance to Neutrophil Killing during Growth in Whole Human Blood. Infection and Immunity. 84(4):1016-1031.
2016. Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment. BMC Genomics. 17183412111831230710512122489914142853341501081566039108377115651846133171373920352123327102188151723(1326124105778571763174155114260523Suppl 1611Suppl 26-7Suppl 197591Pt 11321131 Suppl241Database issue1612210375335)
2016. A joint analysis of transcriptomic and metabolomic data uncovers enhanced enzyme-metabolite coupling in breast cancer.. Sci Rep. 6:29662.
2016. Limitations of Current Approaches for Reference-Free, Graph-Based Variant Detection. the 7th ACM International ConferenceProceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics - BCB '16.
2016. Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection. Microbiome. 4320384718719152130282021211818418719223326578105723(158836212108125732558101131110121arXiv:1006.3316)
2016. Maligner: a fast ordered restriction map aligner.. Bioinformatics. 32(7):1016-22.
2016. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biology. 172151332403319158399361914131161021404177111215301354864643027202011311559929525133119(1Suppl 19)
2016. Metabolic Network Prediction of Drug Side Effects. Cell Systems. 2(3):209-213.
2016. Metagenomic Assembly: Overview, Challenges and Applications. Yale J Biol Med. 89(3)
2016. methylFlow: cell-specific methylation pattern reconstruction from high-throughput bisulfite-converted DNA sequencing. Bioinformatics. 32(11):1618-1624.
2016. A pathway-centric view of spatial proximity in the 3D nucleome across cell lines. Scientific Reports. 6:39279.
2016. A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity. npj Biofilms and Microbiomes. 2:16004.
2016. Positive and strongly relaxed purifying selection drive the evolution of repeats in proteins. Nature Communications. 7:13570.
2016. Privacy-Preserving Microbiome Analysis Using Secure Computation. Bioinformatics. :btw073.