@article {19724,
	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 = {Jeremy D Selengut and Haft, Daniel H}
}
@article {18695,
	title = {Avid interactions underlie the Lys63-linked polyubiquitin binding specificities observed for UBA domains},
	journal = {Nature Structural \& Molecular Biology},
	volume = {16},
	year = {2009},
	month = {2009///},
	pages = {883 - 889},
	abstract = {Ubiquitin (denoted Ub) receptor proteins as a group must contain a diverse set of binding specificities to distinguish the many forms of polyubiquitin (polyUb) signals. Previous studies suggested that the large class of ubiquitin-associated (UBA) domains contains members with intrinsic specificity for Lys63-linked polyUb or Lys48-linked polyUb, thus explaining how UBA-containing proteins can mediate diverse signaling events. Here we show that previously observed Lys63-polyUb selectivity in UBA domains is the result of an artifact in which the dimeric fusion partner, glutathione S-transferase (GST), positions two UBAs for higher affinity, avid interactions with Lys63-polyUb, but not with Lys48-polyUb. Freed from GST, these UBAs are either nonselective or prefer Lys48-polyUb. Accordingly, NMR experiments reveal no Lys63-polyUb{\textendash}specific binding epitopes for these UBAs. We reexamine previous conclusions based on GST-UBAs and present an alternative model for how UBAs achieve a diverse range of linkage specificities.},
	keywords = {apoptosis, basic cellular processes, Biochemistry, biophysics, cell biology, cell cycle, cell surface proteins, cell-cell interactions, checkpoints, chromatin, chromatin remodeling, chromatin structure, content, DNA recombination, DNA repair, DNA replication, Gene expression, Genetics, intracellular signaling, journal, macromolecules, mechanism, membrane processes, molecular, molecular basis of disease, molecular biology, molecular interactions, multi-component complexes, nature publishing group, nature structural molecular biology, nucleic acids, protein degradation, protein folding, protein processing, Proteins, regulation of transcription, regulation of translation, RNA, RNA processing, RNAi, signal transduction, single molecule studies, structure and function of proteins, transcription, translation},
	isbn = {1545-9993},
	doi = {10.1038/nsmb.1637},
	url = {http://www.nature.com/nsmb/journal/v16/n8/abs/nsmb.1637.html},
	author = {Sims,Joshua J. and Haririnia,Aydin and Dickinson,Bryan C. and Fushman, David and Cohen,Robert E.}
}
@article {12888,
	title = {Microbial oceanography in a sea of opportunity},
	journal = {Nature},
	volume = {459},
	year = {2009},
	month = {2009/05/13/},
	pages = {180 - 184},
	abstract = {Plankton use solar energy to drive the nutrient cycles that make the planet habitable for larger organisms. We can now explore the diversity and functions of plankton using genomics, revealing the gene repertoires associated with survival in the oceans. Such studies will help us to appreciate the sensitivity of ocean systems and of the ocean{\textquoteright}s response to climate change, improving the predictive power of climate models.},
	keywords = {Astronomy, astrophysics, Biochemistry, Bioinformatics, Biology, biotechnology, cancer, cell cycle, cell signalling, climate change, Computational Biology, development, developmental biology, DNA, drug discovery, earth science, ecology, environmental science, Evolution, evolutionary biology, functional genomics, Genetics, Genomics, geophysics, immunology, interdisciplinary science, life, marine biology, materials science, medical research, medicine, metabolomics, molecular biology, molecular interactions, nanotechnology, Nature, neurobiology, neuroscience, palaeobiology, pharmacology, Physics, proteomics, quantum physics, RNA, Science, science news, science policy, signal transduction, structural biology, systems biology, transcriptomics},
	isbn = {0028-0836},
	doi = {10.1038/nature08056},
	url = {http://www.nature.com/nature/journal/v459/n7244/abs/nature08056.html},
	author = {Bowler,Chris and Karl,David M. and Rita R Colwell}
}
@article {18717,
	title = {Structural Biology: Analysis of {\textquoteright}downhill{\textquoteright} protein folding; Analysis of protein-folding cooperativity (Reply)},
	journal = {Nature},
	volume = {445},
	year = {2007},
	month = {2007/02/15/},
	pages = {E17-E18 - E17-E18},
	abstract = {Ferguson et al. and Zhou and Bai criticize the quality of our nuclear magnetic resonance (NMR) data and atom-by-atom analysis of global {\textquoteright}downhill{\textquoteright} folding, also claiming that the data are compatible with two-state folding.},
	keywords = {Astronomy, astrophysics, Biochemistry, Bioinformatics, Biology, biotechnology, cancer, cell cycle, cell signalling., climate change, Computational Biology, development, developmental biology, DNA, drug discovery, earth science, ecology, environmental science, Evolution, evolutionary biology, functional genomics, Genetics, Genomics, geophysics, immunology, interdisciplinary science, life, marine biology, materials science, medical research, medicine, metabolomics, molecular biology, molecular interactions, nanotechnology, Nature, neurobiology, neuroscience, palaeobiology, pharmacology, Physics, proteomics, quantum physics, RNA, Science, science news, science policy, signal transduction, structural biology, systems biology, transcriptomics},
	isbn = {0028-0836},
	doi = {10.1038/nature05645},
	url = {http://www.nature.com/nature/journal/v445/n7129/full/nature05645.html?lang=en},
	author = {Sadqi,Mourad and Fushman, David and Mu{\~n}oz,Victor}
}
@article {18699,
	title = {Diverse polyubiquitin interaction properties of ubiquitin-associated domains},
	journal = {Nature Structural \& Molecular Biology},
	volume = {12},
	year = {2005},
	month = {2005///},
	pages = {708 - 714},
	abstract = {The ubiquitin-associated (UBA) domain occurs frequently in proteins involved in ubiquitin-dependent signaling pathways. Although polyubiquitin chain binding is considered to be a defining feature of the UBA domain family, the generality of this property has not been established. Here we have surveyed the polyubiquitin interaction properties of 30 UBA domains, including 16 of 17 occurrences in budding yeast. The UBA domains sort into four classes that include linkage-selective polyubiquitin binders and domains that bind different chains (and monoubiquitin) in a nondiscriminatory manner; one notable class (30\%) did not bind any ubiquitin ligand surveyed. The properties of a given UBA domain are conserved from yeast to mammals. Their functional relevance is further suggested by the ability of an ectopic UBA domain to alter the specificity of a deubiquitylating enzyme in a predictable manner. Conversely, non-UBA sequences can modulate the interaction properties of a UBA domain.},
	keywords = {apoptosis, basic cellular processes, Biochemistry, biophysics, cell biology, cell cycle, cell surface proteins, cell-cell interactions, checkpoints, chromatin, chromatin remodeling, chromatin structure, content, DNA recombination, DNA repair, DNA replication, Gene expression, Genetics, intracellular signaling, journal, macromolecules, mechanism, membrane processes, molecular, molecular basis of disease, molecular biology, molecular interactions, multi-component complexes, nature publishing group, nature structural molecular biology, nucleic acids, protein degradation, protein folding, protein processing, Proteins, regulation of transcription, regulation of translation, RNA, RNA processing, RNAi, signal transduction, single molecule studies, structure and function of proteins, transcription, translation},
	isbn = {1545-9993},
	doi = {10.1038/nsmb962},
	url = {http://www.nature.com/nsmb/journal/v12/n8/full/nsmb962.html},
	author = {Raasi,Shahri and Varadan,Ranjani and Fushman, David and Pickart,Cecile M.}
}
@article {15541,
	title = {Algorithmic issues in modeling motion},
	journal = {ACM Comput. Surv.},
	volume = {34},
	year = {2002},
	month = {2002/12//},
	pages = {550 - 572},
	abstract = {This article is a survey of research areas in which motion plays a pivotal role. The aim of the article is to review current approaches to modeling motion together with related data structures and algorithms, and to summarize the challenges that lie ahead in producing a more unified theory of motion representation that would be useful across several disciplines.},
	keywords = {computational geometry, Computer vision, mobile networks, modeling, molecular biology, motion modeling, physical simulation, robotoics, spatio-temporal databases},
	isbn = {0360-0300},
	doi = {10.1145/592642.592647},
	url = {http://doi.acm.org/10.1145/592642.592647},
	author = {Agarwal,Pankaj K. and Guibas,Leonidas J. and Edelsbrunner,Herbert and Erickson,Jeff and Isard,Michael and Har-Peled,Sariel and Hershberger,John and Jensen,Christian and Kavraki,Lydia and Koehl,Patrice and Lin,Ming and Manocha,Dinesh and Metaxas,Dimitris and Mirtich,Brian and Mount, Dave and Muthukrishnan,S. and Pai,Dinesh and Sacks,Elisha and Snoeyink,Jack and Suri,Subhash and Wolefson,Ouri}
}
@conference {14621,
	title = {Hardness of flip-cut problems from optical mapping [DNA molecules application]},
	booktitle = {Compression and Complexity of Sequences 1997. Proceedings},
	year = {1997},
	month = {1997/06/11/13},
	pages = {275 - 284},
	publisher = {IEEE},
	organization = {IEEE},
	abstract = {Optical mapping is a new technology for constructing restriction maps. Associated computational problems include aligning multiple partial restriction maps into a single {\textquotedblleft}consensus{\textquotedblright} restriction map, and determining the correct orientation of each molecule, which was formalized as the exclusive binary flip cut (EBFC) problem by Muthukrishnan and Parida (see Proc. of the First ACM Conference on Computational Molecular Biology (RECOMB), Santa Fe, p.209-19, 1997). Here, the authors prove that the EBFC problem, as well as a number of its variants, are NP-complete. They also identify another problem formalized as binary shift cut (BSC) problem motivated by the fact that there might be missing fragments at the beginnings and/or the ends of the molecules, and prove it to be NP-complete. Therefore, they do not have efficient, that is, polynomial time solutions unless P=NP},
	keywords = {binary shift cut, Biochemistry, Bioinformatics, biological techniques, Biology, biomedical optical imaging, combinatorial mathematics, combinatorial problem, computational complexity, computational problems, DNA, DNA molecule, exclusive binary flip cut, flip-cut problem hardness, Genetic engineering, Genomics, MATHEMATICS, molecular biology, molecular biophysics, molecule orientation, multiple partial restriction maps, NP-complete problem, optical mapping, polynomial time solutions, Polynomials, sequences},
	isbn = {0-8186-8132-2},
	doi = {10.1109/SEQUEN.1997.666922},
	author = {Dancik,V. and Hannenhalli, Sridhar and Muthukrishnan,S.}
}
@conference {14579,
	title = {A SIMD solution to the sequence comparison problem on the MGAP},
	booktitle = {International Conference on Application Specific Array Processors, 1994. Proceedings},
	year = {1994},
	month = {1994/08/22/24},
	pages = {336 - 345},
	publisher = {IEEE},
	organization = {IEEE},
	abstract = {Molecular biologists frequently compare an unknown biosequence with a set of other known biosequences to find the sequence which is maximally similar, with the hope that what is true of one sequence, either physically or functionally, could be true of its analogue. Even though efficient dynamic programming algorithms exist for the problem, when the size of the database is large, the time required is quite long, even for moderate length sequences. In this paper, we present an efficient pipelined SIMD solution to the sequence alignment problem on the Micro-Grain Array Processor (MGAP), a fine-grained massively parallel array of processors with nearest-neighbor connections. The algorithm compares K sequences of length O(M) with the actual sequence of length N, in O(M+N+K) time with O(MN) processors, which is AT-optimal. The implementation on the MGAP computes at the rate of about 0.1 million comparisons per second for sequences of length 128},
	keywords = {AT-optimal algorithm, Biological information theory, biology computing, biosequence comparison problem, computational complexity, Computer science, Costs, database size, Databases, DNA computing, dynamic programming, dynamic programming algorithms, fine-grained massively parallel processor array, Genetics, Heuristic algorithms, maximally similar sequence, MGAP parallel computer, Micro-Grain Array Processor, Military computing, molecular biology, molecular biophysics, Nearest neighbor searches, nearest-neighbor connections, Parallel algorithms, pipeline processing, pipelined SIMD solution, sequence alignment problem, sequences},
	isbn = {0-8186-6517-3},
	doi = {10.1109/ASAP.1994.331791},
	author = {Borah,M. and Bajwa,R. S and Hannenhalli, Sridhar and Irwin,M. J}
}
