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Almeida M, Pop M, Le Chatelier E, Prifti E, Pons N, Ghozlane A, S Ehrlich D.  2016.  Capturing the most wanted taxa through cross-sample correlations. The ISME Journal.
Sharmin M, Bravo éctorCorrada, Hannenhalli S.  2016.  Distinct genomic and epigenomic features demarcate hypomethylated blocks in colon cancer. BMC Cancer. 16447943582141728452710921541113181321912(17143623521101753416231113)
Davison M, Treangen TJ, Koren S, Pop M, Bhaya D.  2016.  Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers.. PLoS One. 11(9):e0160574.
Valdes KM, Sundar GS, Vega LA, Belew AT, Islam E, Binet R, El-Sayed NM, Le Breton Y, McIver KS.  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.
Mazza A, Wagner A, Ruppin E, Sharan R.  2016.  Functional Alignment of Metabolic Networks.. J Comput Biol.
tyläinen Tö, Jerby L, jä EM ä, Mattila I, ntti Sä, Auvinen P, Gastaldelli A, rvinen Hä, Ruppin E, ič Mš.  2016.  Genome-scale study reveals reduced metabolic adaptability in patients with non-alcoholic fatty liver disease. Nature Communications. 7:8994.
Hyötyläinen T, Jerby L, Petäjä EM, Mattila I, Jäntti S, Auvinen P, Gastaldelli A, Yki-Järvinen H, Ruppin E, Orešič M.  2016.  Genome-scale study reveals reduced metabolic adaptability in patients with non-alcoholic fatty liver disease.. Nat Commun. 7:8994.
Sharmin M, Bravo éctorCorrada, Hannenhalli S.  2016.  Heterogeneity of transcription factor binding specificity models within and across cell lines. Genome Research. :gr.199166.115.
Valdes KM, Sundar GS, Vega LA, Belew AT, Islam E, Binet R, El-Sayed NM, Le Breton Y, McIver KS.  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.
Pop M, Paulson JN, Chakraborty S, Astrovskaya I, Lindsay BR, Li S, Bravo éctorCorrada, Harro C, Parkhill J, Walker AW et al..  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)
Auslander N, Yizhak K, Weinstock A, Budhu A, Tang W, Wang XWei, Ambs S, Ruppin E.  2016.  A joint analysis of transcriptomic and metabolomic data uncovers enhanced enzyme-metabolite coupling in breast cancer.. Sci Rep. 6:29662.
Mendelowitz LM, Schwartz DC, Pop M.  2016.  Maligner: a fast ordered restriction map aligner.. Bioinformatics. 32(7):1016-22.
Ondov BD, Treangen TJ, Melsted áll, Mallonee AB, Bergman NH, Koren S, Phillippy AM.  2016.  Mash: fast genome and metagenome distance estimation using MinHash. Genome Biology. 172151332403319158399361914131161021404177111215301354864643027202011311559929525133119(1Suppl 19)
Shaked I, Oberhardt  A., Atias N, Sharan R, Ruppin E.  2016.  Metabolic Network Prediction of Drug Side Effects. Cell Systems. 2(3):209-213.
Nguyen N-phuong, Warnow T, Pop M, White B.  2016.  A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity. npj Biofilms and Microbiomes. 2:16004.
Wagner J, Paulson JN, Wang X, Bhattacharjee B, Bravo éctorCorrada.  2016.  Privacy-Preserving Microbiome Analysis Using Secure Computation. Bioinformatics. :btw073.
Mokryn O, Wagner A, Blattner M, Ruppin E, Shavitt Y.  2016.  The Role of Temporal Trends in Growing Networks.. PLoS One. 11(8):e0156505.
Oberhardt MA, Zarecki R, Reshef L, Xia F, Duran-Frigola M, Schreiber R, Henry CS, Ben-Tal N, Dwyer DJ, Gophna U et al..  2016.  Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5'-Phosphate Production in E. coli.. PLoS Comput Biol. 12(1):e1004705.
Pozniak Y, Balint-Lahat N, Rudolph JDaniel, Lindskog C, Katzir R, Avivi C, Pontén F, Ruppin E, Barshack I, Geiger T.  2016.  System-wide Clinical Proteomics of Breast Cancer Reveals Global Remodeling of Tissue Homeostasis.. Cell Syst. 2(3):172-84.
Li Y, Shah-Simpson S, Okrah K, A Belew T, Choi J, Caradonna KL, Padmanabhan P, Ndegwa DM, M Temanni R, Bravo HCorrada et al..  2016.  Transcriptome Remodeling in Trypanosoma cruzi and Human Cells during Intracellular Infection.. PLoS Pathog. 12(4):e1005511.
Pop M, Touzet H.  2015.  Algorithms in Bioinformatics: 15th International Workshop, WABI 2015. Lecture Notes in Bioinformatics. :328.
Das A, Morley M, Moravec CS, Tang W.HW, Hakonarson H, Ashley EA, Brandimarto J, Hu R, Li M, Li H et al..  2015.  Bayesian integration of genetics and epigenetics detects causal regulatory SNPs underlying expression variability. Nature Communications. 6:8555.
Wang K, Cao K, Hannenhalli S.  2015.  Chromatin and genomic determinants of alternative splicing. BCB '15 Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics .
Pop M.  2015.  Computational challenges in microbiome research. 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).
Rabinovich S, Adler L, Yizhak K, Sarver A, Silberman A, Agron S, Stettner N, Sun Q, Brandis A, Helbling D et al..  2015.  Diversion of aspartate in ASS1-deficient tumours fosters de novo pyrimidine synthesis. Nature. 527(7578):379-383.