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2005
El‐Sayed NM, Myler P.J, Bartholomeu D.C, Nilsson D., Aggarwal G., Tran A.N, Ghedin E., Worthey E.A, Delcher A.L, Blandin G. et al..  2005.  The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease. ScienceScience. 309
Lewinski M.K, Bisgrove D., Shinn P., Chen H., Hoffmann C., Hannenhalli S, Verdin E., Berry C.C, Ecker J.R, Bushman F.D.  2005.  Genome-Wide Analysis of Chromosomal Features Repressing Human Immunodeficiency Virus Transcription. Journal of VirologyJ. Virol.Journal of VirologyJ. Virol.. 79
Bushman F, Lewinski M, Ciuffi A, Barr S, Leipzig J, Hannenhalli S, Hoffmann C.  2005.  Genome-wide analysis of retroviral DNA integration. Nat Rev MicroNat Rev MicroNat Rev MicroNat Rev Micro. 3
Colwell RR.  2005.  Global microbial ecology of Vibrio cholerae. Oceans and health: pathogens in the marine environmentOceans and health: pathogens in the marine environment.
Cummings MP, Huskamp J.C.  2005.  Grid computing. EDUCAUSE ReviewEDUCAUSE Review. 40
Haft DH, Selengut J., Mongodin EF, Nelson KE.  2005.  A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS computational biologyPLOS Computational Biology. 1
2007
Zhang Y, Rath N, Hannenhalli S, Wang Z, Cappola T, Kimura S, Atochina-Vasserman E, Lu MMin, Beers MF, Morrisey EE.  2007.  GATA and Nkx factors synergistically regulate tissue-specific gene expression and development in vivo. DevelopmentDevelopment. 134
Salzberg SL, Kingsford C, Cattoli G, Spiro DJ, Janies DA, Aly MMehrez, Brown IH, Couacy-Hymann E, De Mia GMario, Dung DHuu et al..  2007.  Genome Analysis Linking Recent European and African Influenza (H5N1) Viruses. Emerging Infectious DiseasesEmerg Infect DisEmerging Infectious DiseasesEmerg Infect Dis. 13
Myers GSA, Parker D, Al-Hasani K, Kennan RM, Seemann T, Ren Q, Badger JH, Selengut JD, DeBoy RT, Tettelin H et al..  2007.  Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus.. Nat Biotechnol. 25(5):569-75.
Myers GSA, Parker D, Al-Hasani K, Kennan RM, Seemann T, Ren Q, Badger JH, Selengut J., DeBoy RT, Tettelin H et al..  2007.  Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus. Nature biotechnologyNature biotechnology. 25
Yang S., Wang K., Valladares O., Hannenhalli S, Bucan M.,.  2007.  Genome-wide expression profiling and bioinformatics analysis of diurnally regulated genes in the mouse prefrontal cortex. Genome BiolGenome Biol. 8
Shahri HHaidarian, Namata G, Navlakha S, Deshpande A, Roussopoulos N.  2007.  A graph-based approach to vehicle tracking in traffic camera video streams. Proceedings of the 4th workshop on Data management for sensor networks: in conjunction with 33rd International Conference on Very Large Data Bases.
Bazinet AL, Myers D.S, Fuetsch J., Cummings MP.  2007.  Grid Services Base Library: A high-level, procedural application programming interface for writing Globus-based Grid services. Future Generation Comp SystFuture Generation Comp Syst. 23
2008
Cummings MP, Neel MC, Shaw KL.  2008.  A GENEALOGICAL APPROACH TO QUANTIFYING LINEAGE DIVERGENCE. EvolutionEvolution. 62
Phillippy AM, Schatz MC, Pop M..  2008.  Genome assembly forensics: finding the elusive mis-assembly. Genome BiologyGenome Biology. 9
Sethupathy P, Giang H, Plotkin JB, Hannenhalli S.  2008.  Genome-Wide Analysis of Natural Selection on Human Cis-Elements. PLoS ONEPLoS ONEPLoS ONEPLoS ONE. 3
Nagarajan N., Navajas-Pérez R., Pop M., Alam M., Ming R., Paterson A.H, Salzberg S.L.  2008.  Genome-wide analysis of repetitive elements in papaya. Tropical Plant BiologyTropical Plant Biology. 1
Pruzzo C, Vezzulli L, Colwell RR.  2008.  Global impact of Vibrio cholerae interactions with chitin. Environmental MicrobiologyEnvironmental Microbiology. 10
Giancarlo R., Hannenhalli S.  2008.  Guest Editors' Introduction to the Special Section on Algorithms in Bioinformatics (WABI'07). IEEE/ACM Transactions on Computational Biology and BioinformaticsIEEE/ACM Transactions on Computational Biology and Bioinformatics.
2009
Shah R, Lu Y, Hinkle CC, McGillicuddy FC, Kim R, Hannenhalli S, Cappola TP, Heffron S, Wang XM, Mehta NN et al..  2009.  Gene Profiling of Human Adipose Tissue During Evoked Inflammation In Vivo. DiabetesDiabetesDiabetesDiabetes. 58
Treangen T, Abraham A-L, Touchon M, Rocha EPC.  2009.  Genesis, effects and fates of repeats in prokaryotic genomes. FEMS microbiology reviews. 33:539–571.
Pop M..  2009.  Genome Assembly Reborn: Recent Computational Challenges. Briefings in BioinformaticsBrief BioinformBriefings in BioinformaticsBrief Bioinform. 10
Brettin TS, Bruce DC, Challacombe JF, Detter JC, Han CS, Munik A.C, Chertkov O, Meincke L, Saunders E, Choi SY et al..  2009.  Genome assortment, not serogroup, defines Vibrio cholerae pandemic strains. NatureNature.
Berriman M, Haas BJ, LoVerde PT, R Wilson A, Dillon GP, Cerqueira GC, Mashiyama ST, Al-Lazikani B, Andrade LF, Ashton PD et al..  2009.  The genome of the blood fluke Schistosoma mansoni.. Nature. 460(7253):352-8.
Bartholomeu DC, Cerqueira GC, Leão ACarolina A, daRocha WD, Pais FS, Macedo C, Djikeng A, Teixeira SMR, El-Sayed NM.  2009.  Genomic organization and expression profile of the mucin-associated surface protein (masp) family of the human pathogen Trypanosoma cruzi.. Nucleic Acids Res. 37(10):3407-17.

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