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Journal Articles
Nelson KE, Fouts DE, Mongodin EF, Ravel J, DeBoy RT, Kolonay JF, Rasko DA, Angiuoli SV, Gill SR, Paulsen IT et al..  2004.  Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species. Nucleic acids researchNucleic Acids Research. 32
Cunningham CE, Li S, Vizeacoumar FS, Bhanumathy KKalyanasun, Lee JSang, Parameswaran S, Furber L, Abuhussein O, Paul JM, McDonald M et al..  2016.  Therapeutic relevance of the protein phosphatase 2A in cancer. Oncotarget.com.
Nierman WC, DeShazer D, H. Kim S, Tettelin H, Nelson KE, Feldblyum T, Ulrich RL, Ronning CM, Brinkac LM, Daugherty SC et al..  2004.  Structural flexibility in the Burkholderia mallei genome. 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. 101
el-Sayed NMA, Ghedin E, Song J, MacLeod A, Bringaud F, Larkin C, Wanless D, Peterson J, Hou L, Taylor S et al..  2003.  The sequence and analysis of Trypanosoma brucei chromosome II.. Nucleic Acids Res. 31(16):4856-63.
el-Sayed NMA, Ghedin E, Song J, MacLeod A, Bringaud F, Larkin C, Wanless D, Peterson J, Hou L, Taylor S et al..  2003.  The sequence and analysis of Trypanosoma brucei chromosome II.. Nucleic Acids Res. 31(16):4856-63.
el-Sayed NMA, Ghedin E, Song J, MacLeod A, Bringaud F, Larkin C, Wanless D, Peterson J, Hou L, Taylor S et al..  2003.  The sequence and analysis of Trypanosoma brucei chromosome II.. Nucleic Acids Res. 31(16):4856-63.
Simola D.F, Dalva M., Hannenhalli S, Liebhaber S., Bucan M., Ungar L..  2005.  Post-transcriptional Control in Mammalian Dendrites.
Hadley D., Murphy T., Valladares O., Hannenhalli S, Ungar L., Kim J., Bucan M.,.  2006.  Patterns of sequence conservation in presynaptic neural genes. Genome BiolGenome Biol. 7
Field D, Garrity G, Gray T, Morrison N, Selengut J., Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV et al..  2008.  The minimum information about a genome sequence (MIGS) specification. Nature biotechnologyNature biotechnology. 26
Wang J., Ungar L.H, Tseng H., Hannenhalli S.  2007.  MetaProm: a neural network based meta-predictor for alternative human promoter prediction. BMC genomicsBMC Genomics. 8
Heidelberg JF, Seshadri R, Haveman SA, Hemme CL, Paulsen IT, Kolonay JF, Eisen JA, Ward N, Methe B, Brinkac LM et al..  2004.  The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Nature biotechnologyNature biotechnology. 22
Methé B.A, Nelson K.E, Eisen J.A, Paulsen I.T, Nelson W., Heidelberg J.F, Wu D., Wu M., Ward N., Beanan M.J et al..  2003.  Genome of Geobacter sulfurreducens: metal reduction in subsurface environments. Science (New York, N.Y.)Science (New York, N.Y.). 302
Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, A. Durkin S et al..  2005.  Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". 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. 102
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.
C. Buell R, Joardar V, Lindeberg M, Selengut J., Paulsen IT, Gwinn ML, Dodson RJ, DeBoy RT, A. Durkin S, Kolonay JF et al..  2003.  The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. 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. 100
Hotopp JCDunning, Lin M, Madupu R, Crabtree J, Angiuoli SV, Eisen JA, Eisen J, Seshadri R, Ren Q, Wu M et al..  2006.  Comparative genomics of emerging human ehrlichiosis agents. PLoS geneticsPLoS genetics. 2
Read TD, Salzberg SL, Pop M., Shumway M, Umayam L, Jiang L, Holtzapple E, Busch JD, Smith KL, Schupp JM et al..  2002.  Comparative Genome Sequencing for Discovery of Novel Polymorphisms in Bacillus Anthracis. ScienceScienceScienceScience. 296
Simola D.F, Bucan M., Dalva M., Hannenhalli S, Liebhaber S., Ungar L..  2005.  Bioinformatic Prediction of mRNA Targets of the Fragile X Mental Retardation Protein.
Journal Article
Timp W, Bravo HCorrada, McDonald OG, Goggins M, Umbricht C, Zeiger M, Feinberg AP, Irizarry RA.  2014.  Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors.. Genome Med. 6(8):61.
Eilam O., Zarecki R., Oberhardt M., Ursell L.K, Kupiec M., Knight R., Gophna U., Ruppin E..  2014.  Glycan Degradation (GlyDeR) Analysis Predicts Mammalian Gut Microbiota Abundance and Host Diet-Specific Adaptations. mBio. 5(4):e01526-14-e01526-14.
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.
Books
Goodheart J, University P.Department.  2013.  Sea Slug Systematics: Using Molecular and Morphological Tools to Infer Species Relationships in Opisthobracnchs.
Book Chapters
Hannenhalli S, Hubbell E, Lipshutz R, Pevzner P.  2002.  Combinatorial Algorithms for Design of DNA Arrays. Chip TechnologyChip Technology. 77

Publications