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2012

Li J, Nina B, Lan C, Mary C, Hannenhalli S, Xiaohong Z, P. Thomas C, Parmacek MS. 2012. Myocardin-like Protein (MKL)-2 Regulates TGF-beta Signaling. Embryonic Stem Cells and the Developing Vasculature DevelopmentEmbryonic Stem Cells and the Developing Vasculature Development.

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.

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.

Khan Z, Bloom JS, Amini S, Singh M, Perlman DH, Caudy AA, Kruglyak L. 2012. Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS.. Mol Syst Biol. 8:602.

Khan Z, Bloom JS, Amini S, Singh M, Perlman DH, Caudy AA, Kruglyak L. 2012. Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS. Molecular Systems Biology. 8

Patro R., Dickerson J.P, Bista S., Gupta S.K, Varshney A. 2012. Speeding Up Particle Trajectory Simulations under Moving Force Fields using GPUs. Journal of Computing and Information Science in EngineeringJournal of Computing and Information Science in Engineering.

Pop M.. 2012. We are what we eat: how the diet of infants affects their gut microbiome. Genome BiologyGenome Biology. 13

Ricaldi JN, Fouts DE, Selengut JD, Harkins DM, Patra KP, Moreno A, Lehmann JS, Purushe J, Sanka R, Torres M et al.. 2012. Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity.. PLoS Negl Trop Dis. 6(10):e1853.

Ricaldi JN, Fouts DE, Selengut JD, Harkins DM, Patra KP, Moreno A, Lehmann JS, Purushe J, Sanka R, Torres M et al.. 2012. Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity.. PLoS Negl Trop Dis. 6(10):e1853.

Ricaldi JN, Fouts DE, Selengut J., Harkins DM, Patra KP, Moreno A, Lehmann JS, Purushe J, Sanka R, Torres M et al.. 2012. Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity. PLoS neglected tropical diseasesPLoS neglected tropical diseases. 6

Ricaldi JN, Fouts DE, Selengut J., Harkins DM, Patra KP, Moreno A, Lehmann JS, Purushe J, Sanka R, Torres M et al.. 2012. Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity. PLoS neglected tropical diseasesPLoS neglected tropical diseases. 6

2013

Ghodsi M, Hill CM, Astrovskaya I, Lin H, Sommer DD, Koren S, Pop M.. 2013. De novo likelihood-based measures for comparing genome assemblies. BMC research notes. 6

Hill CM, Astrovskaya I, Huang H, Koren S, Memon A, Treangen T, Pop M. 2013. De novo likelihood-based measures for comparing metagenomic assemblies. 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Boca SM, Bravo HCorrada, Caffo B, Leek JT, Parmigiani G. 2013. A decision-theory approach to interpretable set analysis for high-dimensional data. BiometricsBiometrics. 69

Paulson JN, O. Stine C, Bravo HCorrada, Pop M.. 2013. Differential abundance analysis for microbial marker-gene surveys. Nature methods. 10

Paulson JN, O. Stine C, Bravo HCorrada, Pop M.. 2013. Differential abundance analysis for microbial marker-gene surveys. Nature methods. 10

Nijkamp JF, Pop M., Reinders MJT, de Ridder D. 2013. Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold. Bioinformatics (Oxford, England)Bioinformatics (Oxford, England). 29

Takala-Harrison S, Clark TG, Jacob CG, Cummings MP, Miotto O, Dondorp AM, Fukuda MM, Nosten F, Noedl H, Imwong M et al.. 2013. Genetic loci associated with delayed clearance of Plasmodium falciparum following artemisinin treatment in Southeast Asia. Proceedings of the National Academy of Sciences of the United States of AmericaProceedings of the National Academy of Sciences of the United States of America. 110

Takala-Harrison S, Clark TG, Jacob CG, Cummings MP, Miotto O, Dondorp AM, Fukuda MM, Nosten F, Noedl H, Imwong M et al.. 2013. Genetic loci associated with delayed clearance of Plasmodium falciparum following artemisinin treatment in Southeast Asia. Proceedings of the National Academy of Sciences of the United States of AmericaProceedings of the National Academy of Sciences of the United States of America. 110

Takala-Harrison S, Clark TG, Jacob CG, Cummings MP, Miotto O, Dondorp AM, Fukuda MM, Nosten F, Noedl H, Imwong M et al.. 2013. Genetic loci associated with delayed clearance of Plasmodium falciparum following artemisinin treatment in Southeast Asia. Proceedings of the National Academy of Sciences of the United States of AmericaProceedings of the National Academy of Sciences of the United States of America. 110

Bishop-Lilly KA, Ge H, Butani A, Osborne B, Verratti K, Mokashi V, Nagarajan N, Pop M., Read TD, Richards AL. 2013. Genome sequencing of four strains of Rickettsia prowazekii, the causative agent of epidemic typhus, including one flying squirrel isolate. Genome announcementsGenome announcements. 1

Schatz MC, Phillippy AM, Sommer DD, Delcher AL, Puiu D, Narzisi G, Salzberg SL, Pop M.. 2013. Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. Briefings in bioinformaticsBriefings in bioinformatics. 14

Schatz MC, Phillippy AM, Sommer DD, Delcher AL, Puiu D, Narzisi G, Salzberg SL, Pop M.. 2013. Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. Briefings in bioinformaticsBriefings in bioinformatics. 14

Schatz MC, Phillippy AM, Sommer DD, Delcher AL, Puiu D, Narzisi G, Salzberg SL, Pop M.. 2013. Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. Briefings in bioinformaticsBriefings in bioinformatics. 14

Hill CM, Albach CH, Angel S, Pop M.. 2013. K-mulus: Strategies for BLAST in the cloud. 10th International Conference on Parallel Processing and Applied Mathematics (PPAM).

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