Publications

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2015
Cardone A, Chalfoun J, Peskin A, Bajcsy P, Kociolek M, Bhadriraju K, Brady M.  2015.  Segmentation and sub-cellular feature-based analysis of microscopy images. BioImage Informatics Conference .
Bajcsy P, Cardone A, Chalfoun J, Halter M, Juba D, Kociolek M, Majurski M, Peskin A, Simon C, Simon M et al..  2015.  Survey statistics of automated segmentations applied to optical imaging of mammalian cells. BMC bioinformatics. 16:1.
Alivisatos A.P, Blaser M.J, Brodie E.L, Chun M., Dangl J.L, Donohue T.J, Dorrestein P.C, Gilbert J.A, Green J.L, Jansson J.K et al..  2015.  A unified initiative to harness Earth's microbiomes. Science. (62607551614341176):507-508.
Alivisatos A.P, Blaser M.J, Brodie E.L, Chun M., Dangl J.L, Donohue T.J, Dorrestein P.C, Gilbert J.A, Green J.L, Jansson J.K et al..  2015.  A unified initiative to harness Earth's microbiomes. Science. (62607551614341176):507-508.
Zaitchik B.F, Guikema S.D, Haley B.J, Taviani E., Chen A., Brown M.E., Huq A., Colwell RR.  2015.  Use of Environmental Parameters to Model Pathogenic Vibrios in Chesapeake Bay. Journal of Environmental Informatics.
2014
Kirchberger P.C, Turnsek M., Hunt D.E, Haley B.J, Colwell RR, Polz M.F, Tarr C.L, Boucher Y..  2014.  Vibrio metoecus sp. nov., a close relative of Vibrio cholerae isolated from coastal brackish ponds and clinical specimens. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY. (Pt 95616795215116120545121):3208-3214.
Hasan NA, Young BA, Minard-Smith AT, Saeed K, Li H, Heizer EM, McMillan NJ, Isom R, Abdullah AShakur, Bornman DM et al..  2014.  Microbial Community Profiling of Human Saliva Using Shotgun Metagenomic Sequencing. PLoS ONE. (5):e97699.
Alam M, Rashed SM, Bin Mannan S, Islam T, Lizarraga-Partida ML, Delgado G, Morales-Espinosa R, Mendez JLuis, Navarro A, Watanabe H et al..  2014.  Occurrence in Mexico, 1998–2008, of Vibrio cholerae CTX + El Tor carrying an additional truncated CTX prophage. Proceedings of the National Academy of Sciences. 111(27):9917-9922.
Budowle B, Connell ND, Bielecka-Oder A, Colwell RR, Corbett CR, Fletcher J, Forsman M, Kadavy DR, Markotic A, Morse SA et al..  2014.  Validation of high throughput sequencing and microbial forensics applications. Investigative Genetics. 5(1):9.
Budowle B, Connell ND, Bielecka-Oder A, Colwell RR, Corbett CR, Fletcher J, Forsman M, Kadavy DR, Markotic A, Morse SA et al..  2014.  Validation of high throughput sequencing and microbial forensics applications. Investigative Genetics. 5(1):9.
D. Grimes J, Ford TE, Colwell RR, Baker-Austin C, Martinez-Urtaza J, Subramaniam A, Capone DG.  2014.  Viewing Marine Bacteria, Their Activity and Response to Environmental Drivers from Orbit. Microbial Ecology. (38):489-500.
2013
Nguyen VA, Hu Y, Boyd-Graber J.  2013.  Argviz: Interactive Visualization of Topic Dynamics in Multi-party Conversations. Human Language Technologies: The 2013 Annual Conference of the North American Chapter of the Association for Computational Linguistics.
Hu Y, Boyd-Graber J, III HDaume, Z Ying I.  2013.  Binary to Bushy: Bayesian Hierarchical Clustering with the Beta Coalescent. :1079-1087.
Nguyen V-A, Boyd-Graber J, Altschul SF.  2013.  Dirichlet Mixtures, the Dirichlet Process, and the Structure of Protein Space. Journal of Computational Biology. 20PDF icon cmb%2E2012%2E0244.pdf (292.43 KB)
Clements JD, Connell ND, Dirks C, El-Faham M, Hay A, Heitman E, Stith JH, Bond EC, Colwell RR, Anestidou L et al..  2013.  Engaging Actively with Issues in the Responsible Conduct of Science: Lessons from International Efforts Are Relevant for Undergraduate Education in the United States. CBE—Life Sciences Education. (4):596-603.
Bozo-Hurtado L, García-Amado M, Chistoserdov A, Varela R, Narvaez J, Colwell RR, Suárez P.  2013.  Identification of bacteria in enrichment cultures of sulfate reducers in the Cariaco Basin water column employing Denaturing Gradient Gel Electrophoresis of 16S ribosomal RNA gene fragments. Aquatic Biosystems. 9(1):17.
Hara K, Azenkot S, Campbell M, Bennett CL, Le V, Pannella S, Moore R, Minckler K, Ng RH, Froehlich J.  2013.  Improving public transit accessibility for blind riders by crowdsourcing bus stop landmark locations with Google street view. The 15th International ACM SIGACCESS Conference. :16-8.
Nguyen V-A, Boyd-Graber J, Resnik P.  2013.  Lexical and Hierarchical Topic Regression. :1106-1114.
Hekler EB, Klasnja P, Froehlich J, Buman MP.  2013.  Mind the Theoretical Gap: Interpreting, Using, and Developing Behavioral Theory in HCI Research. CHI 2013 To Appear.
Nguyen V-A, Boyd-Graber J, Resnik P, Cai DA, Midberry JE, Wang Y.  2013.  Modeling topic control to detect influence in conversations using nonparametric topic models. Machine Learning. :1-41.
Zhai K, Boyd-Graber J.  2013.  Online Latent Dirichlet Allocation with Infinite Vocabulary. International Conference on Machine Learning. PDF icon 2013_icml_infvoc.pdf (985.1 KB)
Juba D, Cardone A, Ip C Y, Simon Jr CG, K Tison C, Kumar G, Brady M, Varshney A.  2013.  Parallel geometric classification of stem cells by their three-dimensional morphology. Computational Science & Discovery. 6(1):015007.
Chalfoun J, Kociolek M, Dima A, Halter M, Cardone A, Peskin A, Bajcsy P, Brady M.  2013.  Segmenting time-lapse phase contrast images of adjacent NIH 3T3 cells.. Journal of microscopy. 249(1):41-52.
Chalfoun J, Kociolek M, Dima A, Halter M, Cardone A, Peskin A, Bajcsy P, Brady M.  2013.  Segmenting time-lapse phase contrast images of adjacent NIH 3T3 cells.. Journal of microscopy. 249(1):41-52.
Boyd-Graber J, Glasgow K, Zajac JS.  2013.  Spoiler Alert: Machine Learning Approaches to Detect Social Media Posts with Revelatory Information.

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