@article {49760,
	title = {Use and mis-use of supplementary material in science publications},
	journal = {BMC Bioinformatics},
	volume = {1632733845166},
	year = {2015},
	month = {Jan-12-2015},
	doi = {10.1186/s12859-015-0668-z},
	url = {http://www.biomedcentral.com/1471-2105/16/237http://link.springer.com/content/pdf/10.1186/s12859-015-0668-z},
	author = {Pop, Mihai and Salzberg, Steven L.}
}
@article {49778,
	title = {Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria.},
	journal = {J Bacteriol},
	volume = {192},
	year = {2010},
	month = {2010 Nov},
	pages = {5788-98},
	abstract = {<p>Regimens targeting Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), require long courses of treatment and a combination of three or more drugs. An increase in drug-resistant strains of M. tuberculosis demonstrates the need for additional TB-specific drugs. A notable feature of M. tuberculosis is coenzyme F(420), which is distributed sporadically and sparsely among prokaryotes. This distribution allows for comparative genomics-based investigations. Phylogenetic profiling (comparison of differential gene content) based on F(420) biosynthesis nominated many actinobacterial proteins as candidate F(420)-dependent enzymes. Three such families dominated the results: the luciferase-like monooxygenase (LLM), pyridoxamine 5{\textquoteright}-phosphate oxidase (PPOX), and deazaflavin-dependent nitroreductase (DDN) families. The DDN family was determined to be limited to F(420)-producing species. The LLM and PPOX families were observed in F(420)-producing species as well as species lacking F(420) but were particularly numerous in many actinobacterial species, including M. tuberculosis. Partitioning the LLM and PPOX families based on an organism{\textquoteright}s ability to make F(420) allowed the application of the SIMBAL (sites inferred by metabolic background assertion labeling) profiling method to identify F(420)-correlated subsequences. These regions were found to correspond to flavonoid cofactor binding sites. Significantly, these results showed that M. tuberculosis carries at least 28 separate F(420)-dependent enzymes, most of unknown function, and a paucity of flavin mononucleotide (FMN)-dependent proteins in these families. While prevalent in mycobacteria, markers of F(420) biosynthesis appeared to be absent from the normal human gut flora. These findings suggest that M. tuberculosis relies heavily on coenzyme F(420) for its redox reactions. This dependence and the cofactor{\textquoteright}s rarity may make F(420)-related proteins promising drug targets.</p>},
	keywords = {Actinobacteria, Amino Acid Sequence, Binding Sites, Coenzymes, Flavonoids, Gene Expression Profiling, Gene Expression Regulation, Bacterial, Genome, Bacterial, molecular biology, Molecular Sequence Data, Molecular Structure, Mycobacterium tuberculosis, Phylogeny, Protein Conformation, Riboflavin},
	issn = {1098-5530},
	doi = {10.1128/JB.00425-10},
	author = {Selengut, Jeremy D and Haft, Daniel H}
}
@article {38556,
	title = {Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria},
	journal = {Journal of bacteriologyJournal of bacteriology},
	volume = {192},
	year = {2010},
	note = {http://www.ncbi.nlm.nih.gov/pubmed/20675471?dopt=Abstract},
	type = {10.1128/JB.00425-10},
	abstract = {Regimens targeting Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), require long courses of treatment and a combination of three or more drugs. An increase in drug-resistant strains of M. tuberculosis demonstrates the need for additional TB-specific drugs. A notable feature of M. tuberculosis is coenzyme F(420), which is distributed sporadically and sparsely among prokaryotes. This distribution allows for comparative genomics-based investigations. Phylogenetic profiling (comparison of differential gene content) based on F(420) biosynthesis nominated many actinobacterial proteins as candidate F(420)-dependent enzymes. Three such families dominated the results: the luciferase-like monooxygenase (LLM), pyridoxamine 5{\textquoteright}-phosphate oxidase (PPOX), and deazaflavin-dependent nitroreductase (DDN) families. The DDN family was determined to be limited to F(420)-producing species. The LLM and PPOX families were observed in F(420)-producing species as well as species lacking F(420) but were particularly numerous in many actinobacterial species, including M. tuberculosis. Partitioning the LLM and PPOX families based on an organism{\textquoteright}s ability to make F(420) allowed the application of the SIMBAL (sites inferred by metabolic background assertion labeling) profiling method to identify F(420)-correlated subsequences. These regions were found to correspond to flavonoid cofactor binding sites. Significantly, these results showed that M. tuberculosis carries at least 28 separate F(420)-dependent enzymes, most of unknown function, and a paucity of flavin mononucleotide (FMN)-dependent proteins in these families. While prevalent in mycobacteria, markers of F(420) biosynthesis appeared to be absent from the normal human gut flora. These findings suggest that M. tuberculosis relies heavily on coenzyme F(420) for its redox reactions. This dependence and the cofactor{\textquoteright}s rarity may make F(420)-related proteins promising drug targets.},
	keywords = {Actinobacteria, Amino Acid Sequence, Binding Sites, Coenzymes, Flavonoids, Gene Expression Profiling, Gene Expression Regulation, Bacterial, Genome, Bacterial, molecular biology, Molecular Sequence Data, Molecular Structure, Mycobacterium tuberculosis, Phylogeny, Protein Conformation, Riboflavin},
	author = {J. Selengut and Haft, Daniel H.}
}
@article {38553,
	title = {Ultrafast and memory-efficient alignment of short DNA sequences to the human genome},
	journal = {Genome BiologyGenome Biology},
	volume = {10},
	year = {2009},
	type = {10.1186/gb-2009-10-3-r25},
	abstract = {Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of approximately 1.3 gigabytes. Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches. Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source http://bowtie.cbcb.umd.edu.},
	isbn = {1465-6906},
	author = {Langmead, Ben and Trapnell, Cole and M. Pop and Salzberg, Steven L.}
}
@article {38559,
	title = {Using Satellite Images of Environmental Changes to Predict Infectious Disease Outbreaks},
	journal = {Emerging Infectious DiseasesEmerg Infect DisEmerging Infectious DiseasesEmerg Infect Dis},
	volume = {15},
	year = {2009},
	type = {10.3201/eid/1509.081334},
	abstract = {A strong global satellite imaging system is essential for predicting outbreaks., Recent events clearly illustrate a continued vulnerability of large populations to infectious diseases, which is related to our changing human-constructed and natural environments. A single person with multidrug-resistant tuberculosis in 2007 provided a wake-up call to the United States and global public health infrastructure, as the health professionals and the public realized that today{\textquoteright}s ease of airline travel can potentially expose hundreds of persons to an untreatable disease associated with an infectious agent. Ease of travel, population increase, population displacement, pollution, agricultural activity, changing socioeconomic structures, and international conflicts worldwide have each contributed to infectious disease events. Today, however, nothing is larger in scale, has more potential for long-term effects, and is more uncertain than the effects of climate change on infectious disease outbreaks, epidemics, and pandemics. We discuss advances in our ability to predict these events and, in particular, the critical role that satellite imaging could play in mounting an effective response.},
	isbn = {1080-6040},
	author = {Ford, Timothy E. and Rita R. Colwell and Rose, Joan B. and Morse, Stephen S. and Rogers, David J. and Yates, Terry L.}
}
@proceedings {38555,
	title = {Uncovering Genomic Reassortments among Influenza Strains by Enumerating Maximal Bicliques},
	year = {2008},
	month = {2008},
	publisher = {IEEE},
	type = {10.1109/BIBM.2008.78},
	abstract = {The evolutionary histories of viral genomes have received significant recent attention due to their importance in understanding virulence and the corresponding ramifications to public health. We present a novel framework to detect reassortment events in influenza based on the comparison of two distributions of phylogenetic trees, rather than a pair of, possibly unreliable, consensus trees. We show how to detect all high-probability inconsistencies between two distributions of trees by enumerating maximal bicliques within a defined incompatibility graph. In the process, we give the first quadratic delay algorithm for enumerating maximal bicliques within general bipartite graphs. We demonstrate the utility of our approach by applying it to several sets of influenza genomes (both human- and avian-hosted) and successfully identify all known reassortment events and a few novel candidate reassortments. In addition, on simulated datasets, our approach correctly finds implanted reassortments and rarely detects reassortments where none were introduced.},
	keywords = {avian hosted influenza genome, Bioinformatics, Capacitive sensors, Delay, diseases, Event detection, general bipartite graphs, genomic reassortments, Genomics, graph theory, high probability inconsistencies, History, human hosted influenza genome, incompatibility graph, Influenza, influenza strain, maximal biclique, maximal biclique enumeration, microorganisms, phylogenetic trees, Phylogeny, Public healthcare, quadratic delay algorithm, reassortment, reassortment event detection, Tree graphs, viral genome evolutionary history, virulence},
	isbn = {978-0-7695-3452-7},
	author = {Nagarajan, N. and Kingsford, Carl}
}
@article {38554,
	title = {Ultrastructure of coccoid viable but non-culturable Vibrio cholerae},
	journal = {Environmental MicrobiologyEnvironmental Microbiology},
	volume = {9},
	year = {2007},
	type = {10.1111/j.1462-2920.2006.01150.x},
	abstract = {Morphology of viable but non-culturable Vibrio cholerae was monitored for 2~years by scanning and transmission electron microscopy. Morphological changes included very small coccoid forms, after extended incubation at 4{\textdegree}C and room temperature, and sequential transformation from curved rods to irregular (\~{}1~μm) rods to \~{}0.8~μm coccoid cells and, ultimately, to tiny coccoid forms (0.07{\textendash}0.4~μm). Irregular rod-shaped and coccoid cells were equally distributed in microcosms during the first 30{\textendash}60~days of incubation at both temperatures, but only coccoid cells were observed after incubation for 60~days at 4{\textdegree}C. When V.~cholerae O1 and O139, maintained for 30{\textendash}60~days at both temperatures, were heated to 45{\textdegree}C for 60~s, after serial passage through 0.45~μm and 0.1~μm filters, and plating on Luria{\textendash}Bertania (LB) agar, only cells larger than 1~μm yielded colonies on LB agar. Approximately 0.1\% of heat-treated cultures were culturable. Cell division in the smallest coccoid cells was observed, yielding daughter cells of equal size, whereas other coccoid cells revealed bleb-like, cell wall evagination, followed by transfer of nuclear material. Coccoid cells of V.~cholerae O1 and O139 incubated at 4{\textdegree}C for more than 1~year remained substrate responsive and antigenic.},
	isbn = {1462-2920},
	author = {Chaiyanan, Saipin and Chaiyanan, Sitthipan and Grim, Christopher and Maugel, Timothy and Huq, Anwar and Rita R. Colwell}
}
@article {38557,
	title = {A unified model explaining the offsets of overlapping and near-overlapping prokaryotic genes},
	journal = {Molecular biology and evolutionMolecular biology and evolution},
	volume = {24},
	year = {2007},
	author = {Kingsford, Carl and Delcher, A. L. and Salzberg, S. L.}
}
@article {38560,
	title = {Using the TIGR assembler in shotgun sequencing projects},
	journal = {METHODS IN MOLECULAR BIOLOGY-CLIFTON THEN TOTOWA-METHODS IN MOLECULAR BIOLOGY-CLIFTON THEN TOTOWA-},
	volume = {255},
	year = {2004},
	publisher = {Springer},
	author = {M. Pop and Kosack, D.}
}
@article {38558,
	title = {Unsupervised learning of disambiguation rules for part of speech tagging},
	journal = {Proceedings of the third workshop on very large corporaProceedings of the third workshop on very large corpora},
	volume = {30},
	year = {1995},
	publisher = {Somerset, New Jersey: Association for Computational Linguistics},
	author = {Brill, E. and M. Pop}
}
@article {49714,
	title = {The U1 small nuclear RNA-protein complex selectively binds a 5{\textquoteright} splice site in vitro.},
	journal = {Cell},
	volume = {33},
	year = {1983},
	month = {1983 Jun},
	pages = {509-18},
	abstract = {<p>The ability of purified U1 small nuclear RNA-protein complexes (U1 snRNPs) to bind in vitro to two RNAs transcribed from recombinant DNA clones by bacteriophage T7 RNA polymerase has been studied. A transcript which contains sequences corresponding to the small intron and flanking exons of the major mouse beta-globin gene is bound in marked preference to an RNA devoid of splice site sequences. The site of U1 snRNP binding to the globin RNA has been defined by T1 ribonuclease digestion of the RNA-U1 snRNP complex. A 15-17-nucleotide region, including the 5{\textquoteright} splice site, remains undigested and complexed with the snRNP such that it can be co-precipitated by antibodies directed against the U1 snRNP. Partial proteinase K digestion of the U1 snRNP abolishes interaction with the globin RNA, indicating that the snRNP proteins contribute significantly to RNA binding. No RNA cleavage, splicing, or recognition of the 3{\textquoteright} splice site by U1 snRNPs has been detected. Our results are discussed in terms of the probable role of U1 snRNPs in the messenger RNA splicing of eucaryotic cell nuclei.</p>},
	keywords = {Base Sequence, DNA-Directed RNA Polymerases, HUMANS, Nucleoproteins, Ribonuclease T1, Ribonucleoproteins, Ribonucleoproteins, Small Nuclear, RNA, RNA Splicing, T-Phages},
	issn = {0092-8674},
	author = {Mount, S M and Pettersson, I and Hinterberger, M and Karmas, A and Steitz, J A}
}
