@article {49606,
	title = {Orchestrating high-throughput genomic analysis with Bioconductor.},
	volume = {12},
	year = {2015},
	month = {2015 Feb},
	pages = {115-21},
	abstract = {<p>Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology. The project aims to enable interdisciplinary research, collaboration and rapid development of scientific software. Based on the statistical programming language R, Bioconductor comprises 934 interoperable packages contributed by a large, diverse community of scientists. Packages cover a range of bioinformatic and statistical applications. They undergo formal initial review and continuous automated testing. We present an overview for prospective users and contributors.</p>},
	keywords = {Computational Biology, Gene Expression Profiling, Genomics, High-Throughput Screening Assays, Programming Languages, software, User-Computer Interface},
	issn = {1548-7105},
	doi = {10.1038/nmeth.3252},
	author = {Huber, Wolfgang and Carey, Vincent J and Gentleman, Robert and Anders, Simon and Carlson, Marc and Carvalho, Benilton S and Bravo, H{\'e}ctor Corrada and Davis, Sean and Gatto, Laurent and Girke, Thomas and Gottardo, Raphael and Hahne, Florian and Hansen, Kasper D and Irizarry, Rafael A and Lawrence, Michael and Love, Michael I and MacDonald, James and Obenchain, Valerie and Ole{\'s}, Andrzej K and Pag{\`e}s, Herv{\'e} and Reyes, Alejandro and Shannon, Paul and Smyth, Gordon K and Tenenbaum, Dan and Waldron, Levi and Morgan, Martin}
}
@article {38412,
	title = {Occurrence of protozoans \& their limnological relationships in some ponds of Mathbaria, Bangladesh},
	journal = {University Journal of Zoology, Rajshahi UniversityUniversity Journal of Zoology, Rajshahi University},
	volume = {29},
	year = {2012},
	isbn = {1023-6104},
	author = {Mozumder, P. K. and Banu, M. A. and Naser, M. N. and Ali, M. S. and Alam, M. and Sack, R. B. and Rita R. Colwell and Huq, A.}
}
@article {38413,
	title = {Occurrence of the Vibrio cholerae seventh pandemic VSP-I island and a new variant},
	journal = {OMICS: A Journal of Integrative BiologyOMICS: A Journal of Integrative Biology},
	volume = {14},
	year = {2010},
	type = {10.1089/omi.2009.0087},
	isbn = {1536-2310, 1557-8100},
	author = {Grim, Christopher J. and Choi, Jinna and Jongsik, Chun and Jeon, Yoon-Seong and Taviani, Elisa and Hasan, Nur A. and Haley, Bradd and Huq, Anwar and Rita R. Colwell}
}
@article {38417,
	title = {Overcoming bias and systematic errors in next generation sequencing data},
	journal = {Genome medicineGenome medicine},
	volume = {2},
	year = {2010},
	note = {http://www.ncbi.nlm.nih.gov/pubmed/21144010?dopt=Abstract},
	type = {10.1186/gm208},
	abstract = {Considerable time and effort has been spent in developing analysis and quality assessment methods to allow the use of microarrays in a clinical setting. As is the case for microarrays and other high-throughput technologies, data from new high-throughput sequencing technologies are subject to technological and biological biases and systematic errors that can impact downstream analyses. Only when these issues can be readily identified and reliably adjusted for will clinical applications of these new technologies be feasible. Although much work remains to be done in this area, we describe consistently observed biases that should be taken into account when analyzing high-throughput sequencing data. In this article, we review current knowledge about these biases, discuss their impact on analysis results, and propose solutions.},
	author = {Taub, Margaret A. and H{\'e}ctor Corrada Bravo and Irizarry, Rafael A.}
}
@article {38411,
	title = {Occurrence and Expression of Luminescence in Vibrio Cholerae},
	journal = {Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol.},
	volume = {74},
	year = {2008},
	type = {10.1128/AEM.01537-07},
	abstract = {Several species of the genus Vibrio, including Vibrio cholerae, are bioluminescent or contain bioluminescent strains. Previous studies have reported that only 10\% of V. cholerae strains are luminescent. Analysis of 224 isolates of non-O1/non-O139 V. cholerae collected from Chesapeake Bay, MD, revealed that 52\% (116/224) were luminescent when an improved assay method was employed and 58\% (130/224) of isolates harbored the luxA gene. In contrast, 334 non-O1/non-O139 V. cholerae strains isolated from two rural provinces in Bangladesh yielded only 21 (6.3\%) luminescent and 35 (10.5\%) luxA+ isolates. An additional 270 clinical and environmental isolates of V. cholerae serogroups O1 and O139 were tested, and none were luminescent or harbored luxA. These results indicate that bioluminescence may be a trait specific for non-O1/non-O139 V. cholerae strains that frequently occur in certain environments. Luminescence expression patterns of V. cholerae were also investigated, and isolates could be grouped based on expression level. Several strains with defective expression of the lux operon, including natural K variants, were identified.},
	isbn = {0099-2240, 1098-5336},
	author = {Grim, Christopher J. and Taviani, Elisa and Alam, Munirul and Huq, Anwar and Sack, R. Bradley and Rita R. Colwell}
}
@proceedings {38416,
	title = {Optimizing mpf queries},
	year = {2007},
	month = {2007},
	type = {10.1145/1247480.1247558},
	address = {Beijing, China},
	author = {H{\'e}ctor Corrada Bravo and Ramakrishnan, Raghu}
}
@book {38414,
	title = {Oceans And Health: Pathogens In The Marine Environment},
	year = {2006},
	publisher = {Springer},
	organization = {Springer},
	abstract = {The release of non-disinfected wastewaters into the marine environment is a common worldwide practice, in under-developed as well as in highly developed countries. Consequently, the seas are constantly infused with wastewater bacteria, among them highly pathogenic ones. In view of the public health significance of this phenomenon, it is surprising how little is actually known concerning the fate of such bacteria once they enter the sea. While numerous studies have addressed the effects of various environmental parameters on colony formation, many of them actually ignore the fact that bacteria can retain viability and infectivity while losing colony-forming ability. Only in recent years have efforts also been directed at unraveling the mechanisms determining bacterial sensitivity or survival under these conditions. This, therefore, is one subject of Oceans and Health: Pathogens in the Marine Environment: the survival, infectivity, pathogenicity and viability of enteric bacteria in the sea. Chapters also detail the public health aspects of wastewater release, civil engineering and economic considerations, other sources of pathogens, and much more.},
	keywords = {Electronic books, Marine microbiology, Medical / Epidemiology, Medical / Microbiology, Nature / Animals / Marine Life, Pathogenic microorganisms, Science / Environmental Science, Science / Life Sciences / Biology, Science / Life Sciences / Marine Biology, Science / Life Sciences / Microbiology, Seawater/ microbiology},
	isbn = {9780387237084},
	author = {Belkin, Shimshon and Rita R. Colwell}
}
@article {38415,
	title = {An optimized system for expression and purification of secreted bacterial proteins},
	journal = {Protein Expression and PurificationProtein Expression and Purification},
	volume = {46},
	year = {2006},
	type = {10.1016/j.pep.2005.09.003},
	abstract = {In this report, we describe an optimized system for the efficient overexpression, purification, and refolding of secreted bacterial proteins. Candidate secreted proteins were produced recombinantly in Escherichia coli as Tobacco Etch Virus protease-cleavable hexahistidine-c-myc eptiope fusion proteins. Without regard to their initial solubility, recombinant fusion proteins were extracted from whole cells with guanidium chloride, purified under denaturing conditions by immobilized metal affinity chromatography, and refolded by rapid dilution into a solution containing only Tris buffer and sodium chloride. Following concentration on the same resin under native conditions, each protein was eluted for further purification and/or characterization. Preliminary studies on a test set of 12 secreted proteins ranging in size from 13 to 130\&$\#$xa0;kDa yielded between 10 and 50\&$\#$xa0;mg of fusion protein per liter of induced culture at greater than 90\% purity, as judged by Coomassie-stained SDS{\textendash}PAGE. Of the nine proteins further purified, analytical gel filtration chromatography indicated that each was a monomer in solution and circular dichroism spectroscopy revealed that each had adopted a well-defined secondary structure. While there are many potential applications for this system, the results presented here suggest that it will be particularly useful for investigators employing structural approaches to understand protein function, as attested to by the crystal structures of three proteins purified using this methodology (B.V. Geisbrecht, B.Y. Hamaoka, B. Perman, A. Zemla, D.J. Leahy, J. Biol. Chem. 280 (2005) 17243{\textendash}17250).},
	keywords = {Pathogens, Secreted proteins, Toxins, Virulence factors},
	isbn = {1046-5928},
	author = {Geisbrecht, Brian V. and Bouyain, Samuel and M. Pop}
}
@article {49563,
	title = {An outdoor 3-D visual tracking system for the study of spatial navigation and memory in rhesus monkeys.},
	volume = {37},
	year = {2005},
	month = {2005 Aug},
	pages = {453-63},
	abstract = {<p>Previous studies of the navigational abilities of nonhuman primates have largely been limited to what could be described by a human observer with a pen and paper. Consequently, we have developed a system that uses a pair of cameras to automatically obtain the three-dimensional trajectory of rhesus monkeys performing an outdoor spatial navigation and memory task. The system provides trajectories, path length, speed, and other variables that would be impossible for an unaided observer to note. From trajectory data, we computed and validated a path-length measurement. We use this measurement to compare the navigation abilities of several animals. In addition, we provide quantitative data on the accuracy of a method for automatic behavior detection. Currently, the system is being used to examine the sex differences in spatial navigation of rhesus monkeys. We expect that measures derived from the trajectory data will reveal strategies used by animals to solve spatial problems.</p>},
	keywords = {Animals, Behavior, Animal, Macaca mulatta, Memory, Models, Biological, Space Perception, Visual Perception},
	issn = {1554-351X},
	author = {Khan, Zia and Herman, Rebecca A and Wallen, Kim and Balch, Tucker}
}
@article {49753,
	title = {An Outdoor 3-d Visual Tracking System for the Study of Spatial Navigation and Memory in Rhesus Monkeys},
	journal = {Behavior Research Methods,Instruments \& Computers},
	volume = {37},
	year = {2005},
	month = {08/2005},
	pages = {453-463},
	author = {Zia Khan and Rebecca A. Herman and Kim Wallen and Tucker Balch}
}
@article {38410,
	title = {Occurrence and distribution of Vibrio cholerae in the coastal environment of Peru},
	journal = {Environmental MicrobiologyEnvironmental Microbiology},
	volume = {6},
	year = {2004},
	type = {10.1111/j.1462-2920.2004.00601.x},
	abstract = {The occurrence and distribution of Vibrio cholerae in sea water and plankton along the coast of Peru were studied from October 1997 to June 2000, and included the 1997{\textendash}98 El Ni{\~n}o event. Samples were collected at four sites in coastal waters off Peru at monthly intervals. Of 178 samples collected and tested, V. cholerae O1 was cultured from 10 (5.6\%) samples, and V. cholerae O1 was detected by direct fluorescent antibody assay in 26 out of 159 samples tested (16.4\%). Based on the number of cholera cases reported in Peru from 1997 to 2000, a significant correlation was observed between cholera incidence and elevated sea surface temperature (SST) along the coast of Peru (P~<~0.001). From the results of this study, coastal sea water and zooplankton are concluded to be a reservoir for V. cholerae in Peru. The climate{\textendash}cholera relationship observed for the 1997{\textendash}98 El Ni{\~n}o year suggests that an early warning system for cholera risk can be established for Peru and neighbouring Latin American countries.},
	isbn = {1462-2920},
	author = {Gil, Ana I. and Louis, Val{\'e}rie R. and Rivera, Irma N. G. and Lipp, Erin and Huq, Anwar and Lanata, Claudio F. and Taylor, David N. and Russek-Cohen, Estelle and Choopun, Nipa and Sack, R. Bradley and Rita R. Colwell}
}
