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2013
Cummings MP.  2013.  AWTY, BAMBE, BEAGLE, BEAST, BEAUti, Bio++, DataMonkey, DendroPy, DnaSP, ENCprime/SeqCount, FigTree, GARLI, genealogical sorting index (gsi), HyPhy, IMa2, jModelTest, JELLYFISH, LAMARC, MacClade, MEGA, Mesquite .... Dictionary of Bioinformatics.
Mukherjee R, Singh LNS, Evans P, Hannenhalli S.  2013.  Correlated evolution of positions within mammalian cis elements PLoS ONE. PLoS ONE. in press:126.
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 America. 110:240-5.
Mahmoudabadi G, Rajagopalan K, Getzenberg RH, Hannenhalli S, Rangarajan G, Kulkarni P.  2013.  Intrinsically disordered proteins and conformational noise: Implications in cancer. Cell Cycle. 12(1):26-31.
Sohn J-C, Regier JC, Mitter C, Davis D, Landry J-\ F, Zwick A, Cummings MP.  2013.  A molecular phylogeny for Yponomeutoidea (Insecta, Lepido\ ptera, Ditrysia) and its implications for classification, biogeography and\ the evolution of host plant use.. PLoS One.
2012
Memon AM.  2012.  Advances in Computers.
Lin HC, Goldstein S, Mendelowitz L, Zhou S, Wetzel J, Schwartz DC, Pop M.  2012.  AGORA: Assembly Guided by Optical Restriction Alignment. BMC bioinformatics. 13:189.
Roy A, Halder B, Garain U, Doermann D.  2012.  Automatic Authentication of Banknotes. IEEE Transactions on Information Forensics & Security.
Ayres DL, Darling A, Zwickl DJ, Beerli P, Holder MT, Lewis PO, Huelsenbeck JP, Ronquist F, Swofford DL, Cummings MP et al..  2012.  BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics. Systematic BiologySyst Biol. 61(1):170-173.
Satinoff B, Boyd-Graber J.  2012.  Besting the Quiz Master: Crowdsourcing Incremental Classification Games. Empirical Methods in Natural Language Processing.
Lumezanu C, Feamster N, Klein H.  2012.  #bias: Measuring the Tweeting Behavior of Propagandists. Sixth International AAAI Conference on Weblogs and Social Media.
Gopalan R, Taheri S, Turaga P, Chellappa R.  2012.  A Blur-robust Descriptor with Applications to Face Recognition. IEEE Transactions on Pattern Analysis and Machine Intelligence. PP(99):1-1.
Zhuolin Jiang, Lin Z, Davis LS.  2012.  Class consistent k-means: Application to face and action recognition. Computer Vision and Image Understanding. 116(6):730-741.
Xie B, Tom Yeh, Walsh G, Watkins I, Huang M.  2012.  Co-designing an e-health tutorial for older adults. Proceedings of the 2012 iConference. :240-247.
Nikolova S, Boyd-Graber J, Fellbaum C.  2012.  Collecting Semantic Similarity Ratings to Connect Concepts in Assistive Communication Tools. Modeling, Learning, and Processing of Text Technological Data StructuresModeling, Learning, and Processing of Text Technological Data Structures. 370:81-93.
Bazinet AL, Cummings MP.  2012.  A comparative evaluation of sequence classification programs. BMC Bioinformatics. 13:92.
Wei Z, JaJa JF.  2012.  Constructing Inverted Files: To MapReduce or Not Revisited. UMIACS-TR-2012-03
Senoh M, Ghosh‐Banerjee J, Ramamurthy T, Colwell RR, Miyoshi S-ichi, Nair BG, Takeda Y.  2012.  Conversion of viable but nonculturable enteric bacteria to culturable by co‐culture with eukaryotic cells. Microbiology and Immunology. 56(5):342-345.
Liu B, Faller LL, Klitgord N, Mazumdar V, Ghodsi M, Sommer DD, Gibbons TR, Treangen TJ, Chang YC, Li S et al..  2012.  Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease. PloS one. 7:e37919.
Han B, Davis LS.  2012.  Density-Based Multifeature Background Subtraction with Support Vector Machine. Pattern Analysis and Machine Intelligence, IEEE Transactions on. 34(5):1017-1023.
Patel VM, Wu T, Biswas S, Phillips P, Chellappa R.  2012.  Dictionary-based Face Recognition Under Variable Lighting and Pose. IEEE Transactions on Information Forensics and Security. PP(99):1-1.
De Floriani L, Čomić L.  2012.  Dimension-independent multi-resolution morse complexes. Computers & Graphics.
Larson E, Froehlich J, Campbell T, Haggerty C, Atlas L, Fogarty J, Patel SN.  2012.  Disaggregated water sensing from a single, pressure-based sensor: An extended analysis of HydroSense using staged experiments. Pervasive and Mobile Computing. 8(1):82-102.
Rotman D, Preece J, Hammock J, Procita K, Hansen D, Parr C, Lewis D, Jacobs DW.  2012.  Dynamic changes in motivation in collaborative citizen-science projects. Proceedings of the ACM 2012 conference on Computer Supported Cooperative Work. :217-226.
Gumerov NA, Duraiswami R.  2012.  Efficient FMM accelerated vortex methods in three dimensions via the Lamb-Helmholtz decomposition. arXiv:1201.5430.

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