@article {49583, title = {Network-level architecture and the evolutionary potential of underground metabolism}, volume = {111}, year = {2014}, month = {Dec-08-2014}, pages = {11762 - 11767}, issn = {0027-8424}, doi = {10.1073/pnas.1406102111}, url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1406102111}, author = {Notebaart, R. A. and Szappanos, B. and Kintses, B. and Pal, F. and Gyorkei, A. and Bogos, B. and Lazar, V. and Spohn, R. and Bogos, B. and Wagner, A. and Ruppin, E. and Pal, C. and Papp, B.} } @article {49862, title = {A new rhesus macaque assembly and annotation for next-generation sequencing analyses}, journal = {Biology direct}, volume = {9}, year = {2014}, pages = {20}, author = {Zimin, Aleksey V and Cornish, Adam S and Maudhoo, Mnirnal D and Gibbs, Robert M and Zhang, Xiongfei and Pandey, Sanjit and Meehan, Daniel T and Wipfler, Kristin and Bosinger, Steven E and Johnson, Zachary P and Todd Treangen} } @article {49587, title = {A Novel Nutritional Predictor Links Microbial Fastidiousness with Lowered Ubiquity, Growth Rate, and Cooperativeness}, journal = {PLoS Computational Biology}, volume = {10}, year = {2014}, month = {May-07-2015}, pages = {e1003726}, doi = {10.1371/journal.pcbi.1003726}, url = {http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003726}, author = {Zarecki, Raphy and Oberhardt, Matthew A. and Reshef, Leah and Gophna, Uri and Ruppin, Eytan}, editor = {Maranas, Costas D.} } @article {38407, title = {Next Generation Sequence Assembly with AMOS}, journal = {Current Protocols in BioinformaticsCurrent Protocols in Bioinformatics}, volume = {11}, year = {2011}, publisher = {Wiley Online Library}, author = {Todd Treangen and Sommer, D. D. and Angly, F. E. and Koren, S. and M. Pop} } @article {38404, title = {New records of phytoplankton for Bangladesh. 9. Some rare and a new species}, journal = {Bangladesh Journal of Plant TaxonomyBangladesh Journal of Plant Taxonomy}, volume = {16}, year = {2009}, type = {10.3329/bjpt.v16i1.2734}, abstract = {Ten taxa belonging to Chlorophyceae, Cyanophyceae, Bacillariophyceae and Euglenophyceae, and one with an uncertain taxonomic position have been described in this paper. Of these, 10 taxa have been found to be globally rare and new records for Bangladesh, whereas Strombomonas islamii Khondker sp. nov. has been described as new to science.}, isbn = {1028-2092}, author = {Khondker, Moniruzzaman and Bhuiyan, Rauf Ahmed and Yeasmin, Jenat and Alam, Munirul and Sack, R. Bradley and Huq, Anwar and Rita R. Colwell} } @conference {49856, title = {Novel computational methods for large scale genome comparison}, booktitle = {2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2008)}, year = {2009}, publisher = {Springer}, organization = {Springer}, author = {Todd Treangen and Messeguer, Xavier} } @article {49869, title = {A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats}, journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {6}, year = {2009}, month = {Jan-04-2009}, pages = {180 - 189}, issn = {1545-5963}, doi = {10.1109/TCBB.2009.9}, url = {http://ieeexplore.ieee.org/document/4770094/http://xplorestaging.ieee.org/ielx5/8857/4907697/04770094.pdf?arnumber=4770094}, author = {Todd Treangen and Darling, A.E. and Achaz, G. and Ragan, M.A. and Messeguer, X. and Rocha, E.P.C.} } @article {49853, title = {A novel heuristic for local multiple alignment of interspersed DNA repeats}, journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)}, volume = {6}, year = {2009}, pages = {180{\textendash}189}, author = {Todd Treangen and Darling, Aaron E and Achaz, Guillaume and Ragan, Mark A and Messeguer, Xavier and Rocha, Eduardo PC} } @article {38398, title = {New records of phytoplankton for Bangladesh. 2. Cryptophyceae and Synurophyceae}, journal = {Bangladesh Journal of BotanyBangladesh Journal of Botany}, volume = {36}, year = {2008}, type = {10.3329/bjb.v36i1.1549}, abstract = {This study presents two species of Rhodomonas, four species of Chroomonas, six species of Cryptomonas and Cryptochrysis minor, Cyanomonas coeruleus, Chrysodidymus synuroideus and Mallomonas akrokomos. These species have been reported from some ponds of Mathbaria in Pirojpur and Bakerganj of Barisal district in Bangladesh.}, isbn = {0253-5416}, author = {Khondker, Moniruzzaman and Bhuiyan, Rauf Ahmed and Yeasmin, Jenat and Alam, Munirul and Sack, R. Bradley and Huq, Anwar and Rita R. Colwell} } @article {38401, title = {New records of phytoplankton for Bangladesh. 5. Euglena, Euglenocapsa}, journal = {Bangladesh Journal of Plant TaxonomyBangladesh Journal of Plant Taxonomy}, volume = {15}, year = {2008}, type = {10.3329/bjpt.v15i1.910}, abstract = {This study presents 20 taxa of the genus Euglena and one species of the rare euglenoid genus Euglenocapsa. All these taxa are reported for the first time from some pond ecosystems of Mathbaria in Pirojpur and Bakerganj of Barisal districts of Bangladesh.}, isbn = {1028-2092}, author = {Khondker, Moniruzzaman and Bhuiyan, Rauf Ahmed and Yeasmin, Jenat and Alam, Munirul and Sack, R. Bradley and Huq, Anwar and Rita R. Colwell} } @article {38402, title = {New records of phytoplankton for Bangladesh. 7. Phacus spp}, journal = {Bangladesh Journal of BotanyBangladesh Journal of Botany}, volume = {37}, year = {2008}, type = {10.3329/bjb.v37i1.1564}, abstract = {Thirteen species of Phacus hitherto not reported from Bangladesh have been described and illustrated. Freshwater ponds at southern districts of Pirojpur and Barisal revealed these presence of the species.}, isbn = {0253-5416}, author = {Khondker, Moniruzzaman and Bhuiyan, Rauf Ahmed and Yeasmin, Jenat and Alam, Munirul and Sack, R. Bradley and Huq, Anwar and Rita R. Colwell} } @article {38403, title = {New records of phytoplankton for Bangladesh. 8. Trachelomonas Ehr. (Euglenophyceae)}, journal = {Bangladesh Journal of BotanyBangladesh Journal of Botany}, volume = {37}, year = {2008}, type = {10.3329/bjb.v37i2.1719}, abstract = {Investigation of pelagic plankton communities from some freshwater ponds of Pirojpur and Barisal districts revealed the presence of 17 species under the genus Trachelomonas Ehr. for the first time in Bangladesh.}, isbn = {0253-5416}, author = {Khondker, Moniruzzaman and Bhuiyan, Rauf Ahmed and Yeasmin, Jenat and Alam, Munirul and Sack, R. Bradley and Huq, Anwar and Rita R. Colwell} } @article {49783, title = {New developments in the InterPro database.}, journal = {Nucleic Acids Res}, volume = {35}, year = {2007}, month = {2007 Jan}, pages = {D224-8}, abstract = {

InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following protein signature databases: PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs, PIRSF, SUPERFAMILY, Gene3D and PANTHER. The latter two new member databases have been integrated since the last publication in this journal. There have been several new developments in InterPro, including an additional reading field, new database links, extensions to the web interface and additional match XML files. InterPro has always provided matches to UniProtKB proteins on the website and in the match XML file on the FTP site. Additional matches to proteins in UniParc (UniProt archive) are now available for download in the new match XML files only. The latest InterPro release (13.0) contains more than 13 000 entries, covering over 78\% of all proteins in UniProtKB. The database is available for text- and sequence-based searches via a webserver (http://www.ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro). The InterProScan search tool is now also available via a web service at http://www.ebi.ac.uk/Tools/webservices/WSInterProScan.html.

}, keywords = {Databases, Protein, Internet, Protein Structure, Tertiary, Proteins, Sequence Analysis, Protein, Systems Integration, User-Computer Interface}, issn = {1362-4962}, doi = {10.1093/nar/gkl841}, author = {Mulder, Nicola J and Apweiler, Rolf and Attwood, Teresa K and Bairoch, Amos and Bateman, Alex and Binns, David and Bork, Peer and Buillard, Virginie and Cerutti, Lorenzo and Copley, Richard and Courcelle, Emmanuel and Das, Ujjwal and Daugherty, Louise and Dibley, Mark and Finn, Robert and Fleischmann, Wolfgang and Gough, Julian and Haft, Daniel and Hulo, Nicolas and Hunter, Sarah and Kahn, Daniel and Kanapin, Alexander and Kejariwal, Anish and Labarga, Alberto and Langendijk-Genevaux, Petra S and Lonsdale, David and Lopez, Rodrigo and Letunic, Ivica and Madera, Martin and Maslen, John and McAnulla, Craig and McDowall, Jennifer and Mistry, Jaina and Mitchell, Alex and Nikolskaya, Anastasia N and Orchard, Sandra and Orengo, Christine and Petryszak, Robert and Selengut, Jeremy D and Sigrist, Christian J A and Thomas, Paul D and Valentin, Franck and Wilson, Derek and Wu, Cathy H and Yeats, Corin} } @article {38399, title = {New records of phytoplankton for Bangladesh. 3. Volvocales}, journal = {Bangladesh Journal of Plant TaxonomyBangladesh Journal of Plant Taxonomy}, volume = {14}, year = {2007}, type = {10.3329/bjpt.v14i1.518}, abstract = {This study presents 21 species of Chlamydomonas, four species of Carteria, two species of each of Nephroselmis, Pyramidomonas and Scherffelia, and Collodictyon triciliatum, Polytoma minus, Tetrachloridium ? allorgei and Tetraselmis cordiformis. These species have been reported from some ponds of Mathbaria of Pirojpur and Bakerganj of Barisal districts in Bangladesh.}, isbn = {1028-2092}, author = {Khondker, Moniruzzaman and Bhuiyan, Rauf Ahmed and Yeasmin, Jenat and Alam, Munirul and Sack, R. Bradley and Huq, Anwar and Rita R. Colwell} } @article {38400, title = {New records of phytoplankton for Bangladesh. 4. Chlorococcales}, journal = {Bangladesh Journal of Plant TaxonomyBangladesh Journal of Plant Taxonomy}, volume = {14}, year = {2007}, type = {10.3329/bjpt.v14i2.528}, abstract = {This study presents three species from each of Schroederia, Monoraphidium and Ankistrodesmus, two species and one variety of Dictyosphaerium, two varieties of Pediastrum, and Tetraedron arthrodesmiforme var. contorta, Chlorotetraedron polymorphum, Myrmecia aquatica, Oocystis tainoensis, Nephrocytium spirale, Kirchneriella irregularis, Coelastrum indicum and Scenedesmus similagineus. These taxa have been reported from some ponds of Mathbaria of Pirojpur and Bakerganj of Barisal Districts in Bangladesh.}, isbn = {1028-2092}, author = {Khondker, Moniruzzaman and Bhuiyan, Rauf Ahmed and Yeasim, Jenat and Alam, Munirul and Sack, R. Bradley and Huq, Anwar and Rita R. Colwell} } @article {38405, title = {New Trypanosoma cruzi Repeated Element That Shows Site Specificity for Insertion}, journal = {Eukaryotic CellEukaryotic Cell}, volume = {6}, year = {2007}, type = {

10.1128/EC.00036-07

}, abstract = {A new family of site-specific repeated elements identified in Trypanosoma cruzi, which we named TcTREZO, is described here. TcTREZO appears to be a composite repeated element, since three subregions may be defined within it on the basis of sequence similarities with other T. cruzi sequences. Analysis of the distribution of TcTREZO in the genome clearly indicates that it displays site specificity for insertion. Most TcTREZO elements are flanked by conserved sequences. There is a highly conserved 68-bp sequence at the 5{\textquoteright} end of the element and a sequence domain of [~]500 bp without a well-defined borderline at the 3{\textquoteright} end. Northern blot hybridization and reverse transcriptase PCR analyses showed that TcTREZO transcripts are expressed as oligo(A)-terminated transcripts whose length corresponds to the unit size of the element (1.6 kb). Transcripts of [~]0.2 kb derived from a small part of TcTREZO are also detected in steady-state RNA. TcTREZO transcripts are unspliced and not translated. The copy number of TcTREZO sequences was estimated to be [~]173 copies per haploid genome. TcTREZO appears to have been assembled by insertions of sequences into a progenitor element. Once associated with each other, these subunits were amplified as a new transposable element. TcTREZO shows site specificity for insertion, suggesting that a sequence-specific endonuclease could be responsible for its insertion at a unique site.}, author = {Souza, Renata T. and Santos, Marcia R. M. and Lima, Fabio M. and Najib M. El-Sayed and Myler, Peter J. and Ruiz, Jeronimo C. and da Silveira, Jose Franco} } @article {38408, title = {A Note on Efficient Computation of Haplotypes via Perfect Phylogeny}, journal = {Journal of Computational BiologyJournal of Computational Biology}, volume = {11}, year = {2004}, type = {10.1089/cmb.2004.11.858}, abstract = {The problem of inferring haplotype phase from a population of genotypes has received a lot of attention recently. This is partly due to the observation that there are many regions on human genomic DNA where genetic recombination is rare (Helmuth, 2001; Daly et al., 2001; Stephens et al., 2001; Friss et al., 2001). A Haplotype Map project has been announced by NIH to identify and characterize populations in terms of these haplotypes. Recently, Gusfield introduced the perfect phylogeny haplotyping problem, as an algorithmic implication of the no-recombination in long blocks observation, together with the standard population-genetic assumption of infinite sites. Gusfield{\textquoteright}s solution based on matroid theory was followed by direct θ(nm2 ) solutions that use simpler techniques (Bafna et al., 2003; Eskin et al., 2003), and also bound the number of solutions to the PPH problem. In this short note, we address two questions that were left open. First, can the algorithms of Bafna et al. (2003) and Eskin et al. (2003) be sped-up to O(nm + m2 ) time, which would imply an O(nm) time-bound for the PPH problem? Second, if there are multiple solutions, can we find one that is most parsimonious in terms of the number of distinct haplotypes.We give reductions that suggests that the answer to both questions is "no." For the first problem, we show that computing the output of the first step (in either method) is equivalent to Boolean matrix multiplication. Therefore, the best bound we can presently achieve is O(nmω{\textendash}1), where ω <= 2.52 is the exponent of matrix multiplication. Thus, any linear time solution to the PPH problem likely requires a different approach. For the second problem of computing a PPH solution that minimizes the number of distinct haplotypes, we show that the problem is NP-hard using a reduction from Vertex Cover (Garey and Johnson, 1979).}, isbn = {1066-5277, 1557-8666}, author = {Bafna, Vineet and Gusfield, Dan and Sridhar Hannenhalli and Yooseph, Shibu} } @article {38394, title = {Necessity is the mother of invention: a simple grid computing system using commodity tools}, journal = {J Parallel Distr ComJ Parallel Distr Com}, volume = {63}, year = {2003}, type = {DOI 10.1016/S0743-7315(03)00004-2}, abstract = {Access to sufficient resources is a barrier to scientific progress for many researchers facing large computational problems. Gaining access to large-scale resources (i.e., university-wide or federally supported computer centers) can be difficult, given their limited availability, particular architectures, and request/review/approval cycles. Simultaneously, researchers often find themselves with access to workstations and older clusters overlooked by their owners in favor of newer hardware. Software to tie these resources into a coherent Grid, however, has been problematic. Here, we describe our experiences building a Grid computing system to conduct a large-scale simulation study using "borrowed" computing resources distributed over a wide area. Using standard software components, we have produced a Grid computing system capable of coupling several hundred processors spanning multiple continents and administrative domains. We believe that this system fills an important niche between a closely coupled local system and a heavyweight, highly customized wide area system. (C) 2003 Elsevier Science (USA). All rights reserved.}, keywords = {Apache, computing, distributed, Grid, HTTP, java, Linux, Perl, SQL, Unix, XML-RPC}, author = {Myers, D. S. and Michael P. Cummings} } @article {49631, title = {A new, expressed multigene family containing a hot spot for insertion of retroelements is associated with polymorphic subtelomeric regions of Trypanosoma brucei.}, journal = {Eukaryot Cell}, volume = {1}, year = {2002}, month = {2002 Feb}, pages = {137-51}, abstract = {

We describe a novel gene family that forms clusters in subtelomeric regions of Trypanosoma brucei chromosomes and partially accounts for the observed clustering of retrotransposons. The ingi and ribosomal inserted mobile element (RIME) non-LTR retrotransposons share 250 bp at both extremities and are the most abundant putatively mobile elements, with about 500 copies per haploid genome. From cDNA clones and subsequently in the T. brucei genomic DNA databases, we identified 52 homologous gene and pseudogene sequences, 16 of which contain a RIME and/or ingi retrotransposon inserted at exactly the same relative position. Here these genes are called the RHS family, for retrotransposon hot spot. Comparison of the protein sequences encoded by RHS genes (21 copies) and pseudogenes (24 copies) revealed a conserved central region containing an ATP/GTP-binding motif and the RIME/ingi insertion site. The RHS proteins share between 13 and 96\% identity, and six subfamilies, RHS1 to RHS6, can be defined on the basis of their divergent C-terminal domains. Immunofluorescence and Western blot analyses using RHS subfamily-specific immune sera show that RHS proteins are constitutively expressed and occur mainly in the nucleus. Analysis of Genome Survey Sequence databases indicated that the Trypanosoma brucei diploid genome contains about 280 RHS (pseudo)genes. Among the 52 identified RHS (pseudo)genes, 48 copies are in three RHS clusters located in subtelomeric regions of chromosomes Ia and II and adjacent to the active bloodstream form expression site in T. brucei strain TREU927/4 GUTat10.1. RHS genes comprise the remaining sequence of the size-polymorphic "repetitive region" described for T. brucei chromosome I, and a homologous gene family is present in the Trypanosoma cruzi genome.

}, keywords = {Amino Acid Sequence, Animals, Base Sequence, Cloning, Molecular, DNA Primers, DNA, Protozoan, Escherichia coli, Genes, Protozoan, Molecular Sequence Data, Multigene Family, Mutagenesis, Insertional, Phylogeny, Polymorphism, Genetic, Protozoan Proteins, Pseudogenes, Retroelements, sequence alignment, Sequence Homology, Amino Acid, Telomere, Trypanosoma brucei brucei, Trypanosoma cruzi}, issn = {1535-9778}, author = {Bringaud, Frederic and Biteau, Nicolas and Melville, Sara E and Hez, St{\'e}phanie and El-Sayed, Najib M and Leech, Vanessa and Berriman, Matthew and Hall, Neil and Donelson, John E and Baltz, Th{\'e}o} } @article {38406, title = {A new, expressed multigene family containing a hot spot for insertion of retroelements is associated with polymorphic subtelomeric regions of Trypanosoma brucei}, journal = {Eukaryotic cellEukaryotic Cell}, volume = {1}, year = {2002}, author = {Bringaud, F. and Biteau, N. and Melville, S. E. and Hez, S. and Najib M. El-Sayed and Leech, V. and Berriman, M. and Hall, N. and Donelson, J. E. and Baltz, T.} } @article {38409, title = {Nucleotide sequence diversity at the alcohol dehydrogenase 1 locus in wild barley ({\i}t Hordeum vulgare ssp. {\i}t spontaneum): an evaluation of the background selection hypothesis}, journal = {Proc Natl Acad Sci USAProc Natl Acad Sci USA}, volume = {95}, year = {1998}, abstract = {The background selection hypothesis predicts a reduction in nucleotide site diversity and an excess of rare variants, owing to linkage associations with deleterious alleles. This effect is expected to be amplified in species that are predominantly self-fertilizing. To examine the predictions of the background selection hypothesis in self-fertilizing species, we sequenced 1,362 bp of adh1, a gene for alcohol dehydrogenase (Adh; alcohol:NAD+ oxidoreductase, EC 1.1.1.1), in a sample of 45 accessions of wild barley, Hordeum vulgare ssp. spontaneum, drawn from throughout the species range. The region sequenced included 786 bp of exon sequence (part of exon 4, all of exons 5-9, and part of exon 10) and 576 bp of intron sequence (all of introns 4-9). There were 19 sites polymorphic for nucleotide substitutions, 8 in introns, and 11 in exons. Of the 11 nucleotide substitutions in codons, 4 were synonymous and 7 were nonsynonymous, occurring uniquely in the sample. There was no evidence of recombination in the region studied, and the estimated effective population size (Ne) based on synonymous sites was approximately 1.8-4.2 x 10(5). Several tests reveal that the pattern of nonsynonymous substitutions departs significantly from neutral expectations. However, the data do not appear to be consistent with recovery from a population bottleneck, recent population expansion, selective sweep, or strong positive selection. Though several features of the data are consistent with background selection, the distributions of polymorphic synonymous and intron sites are not perturbed toward a significant excess of rare alleles as would be predicted by background selection.}, author = {Michael P. Cummings and Clegg, M. T.} } @article {38397, title = {A neural model of positive schizophrenic symptoms}, journal = {Schizophrenia BulletinSchizophrenia Bulletin}, volume = {22}, year = {1996}, author = {Ruppin, E. and Reggia, James A. and Horn, D.} } @article {38395, title = {A neural model of delusions and hallucinations in schizophrenia}, journal = {Advances in Neural Information Processing SystemsAdvances in Neural Information Processing Systems}, year = {1995}, author = {Ruppin, E. and Reggia, James A. and Horn, D.} } @article {38396, title = {A neural model of memory impairment in diffuse cerebral atrophy}, journal = {The British Journal of PsychiatryThe British Journal of Psychiatry}, volume = {166}, year = {1995}, author = {Ruppin, E. and Reggia, James A.} }