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Journal Article

Khan Z., Bloom J.S, Kruglyak L., Singh M.. 2009. A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays. Bioinformatics. 25(13):1609-1616.

Waisberg M, Cerqueira GC, Yager SB, Francischetti IMB, Lu J, Gera N, Srinivasan P, Miura K, Rada B, Lukszo J et al.. 2012. Plasmodium falciparum merozoite surface protein 1 blocks the proinflammatory protein S100P.. Proc Natl Acad Sci U S A. 109(14):5429-34.

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HCorrada, Davis S, Gatto L, Girke T et al.. 2015. Orchestrating high-throughput genomic analysis with Bioconductor.. Nat Methods. 12(2):115-21.

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HCorrada, Davis S, Gatto L, Girke T et al.. 2015. Orchestrating high-throughput genomic analysis with Bioconductor.. Nat Methods. 12(2):115-21.

Notebaart R.A, Szappanos B., Kintses B., Pal F., Gyorkei A., Bogos B., Lazar V., Spohn R., Bogos B., Wagner A. et al.. 2014. Network-level architecture and the evolutionary potential of underground metabolism. Proceedings of the National Academy of Sciences. 111(32):11762-11767.

Notebaart R.A, Szappanos B., Kintses B., Pal F., Gyorkei A., Bogos B., Lazar V., Spohn R., Bogos B., Wagner A. et al.. 2014. Network-level architecture and the evolutionary potential of underground metabolism. Proceedings of the National Academy of Sciences. 111(32):11762-11767.

Bloom JS, Khan Z, Kruglyak L, Singh M, Caudy AA. 2009. Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays. BMC Genomics. 10(1):221.

Zarecki R, Oberhardt MA, Yizhak K, Wagner A, Segal EShtifman, Freilich S, Henry CS, Gophna U, Ruppin E. 2014. Maximal Sum of Metabolic Exchange Fluxes Outperforms Biomass Yield as a Predictor of Growth Rate of Microorganisms. PLoS ONE. 9(5):e98372.

Stempler S, Yizhak K, Ruppin E. 2014. Integrating Transcriptomics with Metabolic Modeling Predicts Biomarkers and Drug Targets for Alzheimer's Disease. PLoS ONE. 9(8):e105383.

Seaver SMD, Bradbury LMT, Frelin O, Zarecki R, Ruppin E, Hanson AD, Henry CS. 2015. Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm.. Front Plant Sci. 6:142.

Balch T., Dellaert F., Feldman A., Guillory A., Isbell C.L., Khan Z., Pratt S.C., Stein A.N., Wilde H.. 2006. How Multirobot Systems Research will Accelerate our Understanding of Social Animal Behavior. Proceedings of the IEEE. 94(7):1445-1463.

Balch T, Dellaert F, Feldman A, Guillory A, Isbell C, Khan Z, Stein A, Wilde H. 2006. How A.I. and multi-robot systems research will accelerate our understanding of social animal behavior. Proceedings of the IEEE. 94(7):1445-1463.

Smircich P, Forteza D, El-Sayed NM, Garat B. 2013. Genomic analysis of sequence-dependent DNA curvature in Leishmania.. PLoS One. 8(4):e63068.

Fleming BD, Chandrasekaran P, Dillon LAL, Dalby E, Suresh R, Sarkar A, El-Sayed NM, Mosser DM. 2015. The generation of macrophages with anti-inflammatory activity in the absence of STAT6 signaling.. J Leukoc Biol. 98(3):395-407.

Fleming BD, Chandrasekaran P, Dillon LAL, Dalby E, Suresh R, Sarkar A, El-Sayed NM, Mosser DM. 2015. The generation of macrophages with anti-inflammatory activity in the absence of STAT6 signaling.. J Leukoc Biol. 98(3):395-407.

Zheng L, Cardaci S, Jerby L, MacKenzie ED, Sciacovelli M, T Johnson I, Gaude E, King A, Leach JDG, Edrada-Ebel RA et al.. 2015. Fumarate induces redox-dependent senescence by modifying glutathione metabolism.. Nat Commun. 6:6001.

Chelaru F, Smith L, Goldstein N, Bravo HCorrada. 2014. Epiviz: interactive visual analytics for functional genomics data.. Nat Methods. 11(9):938-40.

Uziel O, Yosef N, Sharan R, Ruppin E, Kupiec M, Kushnir M, Beery E, Cohen-Diker T, Nordenberg J, Lahav M. 2015. The effects of telomere shortening on cancer cells: a network model of proteomic and microRNA analysis.. Genomics. 105(1):5-16.

Pop M, Walker AW, Paulson J, Lindsay B, Antonio M, M Hossain A, Oundo J, Tamboura B, Mai V, Astrovskaya I et al.. 2014. Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition.. Genome Biol. 15(6):R76.

Pop M, Walker AW, Paulson J, Lindsay B, Antonio M, M Hossain A, Oundo J, Tamboura B, Mai V, Astrovskaya I et al.. 2014. Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition.. Genome Biol. 15(6):R76.

Pop M, Walker AW, Paulson J, Lindsay B, Antonio M, M Hossain A, Oundo J, Tamboura B, Mai V, Astrovskaya I et al.. 2014. Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition.. Genome Biol. 15(6):R76.

Pop M, Walker AW, Paulson J, Lindsay B, Antonio M, M Hossain A, Oundo J, Tamboura B, Mai V, Astrovskaya I et al.. 2014. Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition.. Genome Biol. 15(6):R76.

Mukherjee R., Singh L.NS, Evans P., Hannenhalli S. 2013. Correlated evolution of positions within mammalian cis elements . Plos One. 8:e55521.

Kanodia J.S, Kim Y., Tomer R., Khan Z., Chung K., Storey J.D, Lu H., Keller P.J, Shvartsman S.Y. 2011. A computational statistics approach for estimating the spatial range of morphogen gradients. Development. 138(22):4867-4874.

Kanodia J.S, Kim Y., Tomer R., Khan Z., Chung K., Storey J.D, Lu H., Keller P.J, Shvartsman S.Y. 2011. A computational statistics approach for estimating the spatial range of morphogen gradients. Development. 138(22):4867-4874.

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