papamicd's watchlist [more than 800 articles] Export

Recent papers matching papamicd's watchlist criteria

	RNA folding on the 3D triangular lattice [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (05 November 2009), 369. by Joel Gillespie, Martin Mayne, Minghui Jiang posted by 1 person reyez
	A biosegmentation benchmark for evaluation of bioimage analysis methods [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 368. by Elisa D. Gelasca, Boguslaw Obara, Dmitry Fedorov, Kristian Kvilekval, B. Manjunath posted by 1 person erexhepa
	GLIDERS - A web-based search engine for genome-wide linkage disequilibrium between HapMap SNPs [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 367. by Robert Lawrence, Aaron D. Williams, Richard Mott, John Broxholme, Lon Cardon, Eleftheria Zeggini posted by 2 people kshameer daforerog
	(PS)2-v2: template-based protein structure prediction server [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (31 October 2009), 366. by Chih C. Chen, Jenn K. Hwang, Jinn M. Yang posted by 2 people Orengo Group Journal Picks sillitoe
	Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (30 October 2009), 365. by Stefano Lise, Cedric Archambeau, Massimiliano Pontil, David Jones posted by 8 people Orengo Group Journal Picks sillitoe apaydin kshameer zwang phoenixzxl higueruelo neils
	iTriplet, a rule-based nucleic acid sequence motif finder [My Copy] Algorithms for Molecular Biology, Vol. 4 (29 October 2009), 14. by Eric Ho, Christopher Jakubowski, Samuel Gunderson
	multiplierz: an extensible API based desktop environment for proteomics data analysis [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (29 October 2009), 364. by Jignesh Parikh, Manor Askenazi, Scott Ficarro, et al.Tanya Cashorali, James Webber, Nathaniel Blank, Yi Zhang, Jarrod Marto posted by 3 people davidmam renatomilani neilswainston
	A novel R-package graphic user interface for the analysis of metabonomic profiles. [My Copy] BMC bioinformatics, Vol. 10, No. 1. (29 October 2009), 363. by Jose L. Izquierdo-Garcia, Ignacio Rodriguez, Angelos Kyriazis, et al.Palmira Villa, Pilar Barreiro, Manuel Desco, Jesus Ruiz-Cabello
	BARCRAWL and BARTAB: Software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (29 October 2009), 362. by Daniel Frank posted by 6 people natstreet druvus MarkFiers Journal picks ppgardne heliopais
	Predicting sulfotyrosine sites using the random forest algorithm with significantly improved prediction accuracy [My Copy] BMC Bioinformatics, Vol. 10 (29 October 2009), 361. by Zheng R. Yang
	Inferring within-patient HIV-1 evolutionary dynamics under anti-HIV therapy using serial virus samples with vSPA. [My Copy] BMC bioinformatics, Vol. 10, No. 1. (29 October 2009), 360. by Naoki Hasegawa, Wataru Sugiura, Junko Shibata, Masakazu Matsuda, Fengrong Ren, Hiroshi Tanaka posted by 2 people Orengo Group Journal Picks sillitoe
	Analysis and comparison of very large metagenomes with fast clustering and functional annotation [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 359. by Weizhong Li posted by 7 people Orengo Group Journal Picks sillitoe ramonvidal Journal picks ppgardne kshameer neils
	ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 358. by Enrico Glaab, Jonathan Garibaldi, Natalio Krasnogor posted by 6 people Orengo Group Journal Picks sillitoe Bioinformatics dswan heliopais neils
	AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses [My Copy] BMC Bioinformatics, Vol. 10 (28 October 2009), 357. by Surendra Kumar, Asmund Skjaeveland, Russell Orr, et al.Pal Enger, Torgeir Ruden, Bjorn-Helge Mevik, Fabien Burki, Andreas Botnen, Kamran Shalchian-Tabrizi
	phyloXML: XML for evolutionary biology and comparative genomics [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 356. by Mira Han, Christian Zmasek posted by 8 people operon BergmanLab cisevol kshameer Geknitics druvus phoenixzxl cmzmasek
	Stratification of co-evolving genomic groups using ranked phylogenetic profiles [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 355. by Shiri Freilich, Leon Goldovsky, Assaf Gottlieb, Eric Blanc, Sophia Tsoka, Christos Ouzounis posted by 4 people CLH_1865 Mycology stajich druvus
	Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics Applications [My Copy] Algorithms for Molecular Biology, Vol. 4 (22 October 2009), 13. by Piero Fariselli, Castrense Savojardo, Pier L. Martelli, Rita Casadio
	Breaking the hierarchy - a new cluster selection mechanism for hierarchical clustering methods [My Copy] Algorithms for Molecular Biology, Vol. 4, No. 1. (2009), 12. by Laszlo Zahoranszky, Gyula Katona, Peter Hari, Andras M. Csizmadia, Katharina Zweig, Gergely Z. Kohalmi posted by 2 people reyez walshtp
	Gene silencing in the marine diatom Phaeodactylum tricornutum [My Copy] Nucleic Acids Research, Vol. 37, No. 14., pp. e96-e96. by Valentina De Riso, Raffaella Raniello, Florian Maumus, Alessandra Rogato, Chris Bowler, Angela Falciatore
	From Corynebacterium glutamicum to Mycobacterium tuberculosis--towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet. [My Copy] Nucleic acids research, Vol. 37, No. 14. (August 2009) by Justina Krawczyk, Thomas A. Kohl, Alexander Goesmann, Jörn Kalinowski, Jan Baumbach posted by 2 people Orengo Group Journal Picks davidalee
	Studying vertebrate topoisomerase 2 function using a conditional knockdown system in DT40 cells [My Copy] Nucleic Acids Research, Vol. 37, No. 14., pp. e98-e98. by Mark Johnson, Hui Hui H. Phua, Sophia C. Bennett, Jennifer M. Spence, Christine J. Farr
	Kinetic and thermodynamic characterization of single-mismatch discrimination using single-molecule imaging [My Copy] Nucleic Acids Research, Vol. 37, No. 14., pp. e99-e99. by Anders Gunnarsson, Peter Jnsson, Vladimir P. Zhdanov, Fredrik Hk
	Imaging individual microRNAs in single mammalian cells in situ. [My Copy] Nucleic acids research, Vol. 37, No. 14. (1 August 2009), e100. by Jing Lu, Andrew Tsourkas posted by 3 people guhjy reyez ealloza
	Modulation of alternative splicing by long-range RNA structures in Drosophila [My Copy] Nucl. Acids Res., Vol. 37, No. 14. (1 August 2009), pp. 4533-4544. by Veronica A. Raker, Andrei A. Mironov, Mikhail S. Gelfand, Dmitri D. Pervouchine posted by 1 person cajunsushi
	The structure of CrgA from Neisseria meningitidis reveals a new octameric assembly state for LysR transcriptional regulators [My Copy] Nucleic Acids Research, Vol. 37, No. 14., pp. 4545-4558. by Sarah Sainsbury, Laura A. Lane, Jingshan Ren, et al.Robert J. Gilbert, Nigel J. Saunders, Carol V. Robinson, David I. Stuart, Raymond J. Owens
	Targeting cyclin B1 through peptide-based delivery of siRNA prevents tumour growth [My Copy] Nucleic Acids Research, Vol. 37, No. 14., pp. 4559-4569. by Laurence Crombez, May Catherine C. Morris, Sandrine Dufort, et al.Gudrun Aldrian-Herrada, Quan Nguyen, Gary Mc Master, Jean-Luc Coll, Frederic Heitz, Gilles Divita
	Sexy gene conversions: locating gene conversions on the X-chromosome [My Copy] Nucleic Acids Research, Vol. 37, No. 14., pp. 4570-4579. by Mark J. Lawson, Liqing Zhang
	The flexibility of locally melted DNA [My Copy] Nucleic Acids Research, Vol. 37, No. 14., pp. 4580-4586. by Robert A. Forties, Ralf Bundschuh, Michael G. Poirier
	An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia. [My Copy] Nucleic acids research, Vol. 37, No. 14. (August 2009), pp. 4587-4602. by Yair Benita, Hirotoshi Kikuchi, Andrew D. Smith, Michael Q. Zhang, Daniel C. Chung, Ramnik J. Xavier posted by 2 people rcr1991 guhjy
	Intra-tumor heterogeneity of MLH1 promoter methylation revealed by deep single molecule bisulfite sequencing [My Copy] Nucleic Acids Research, Vol. 37, No. 14., pp. 4603-4612. by Katherine E. Varley, David G. Mutch, Tina B. Edmonston, Paul J. Goodfellow, Robi D. Mitra
	Cavities in protein-DNA and protein-RNA interfaces [My Copy] Nucl. Acids Res., Vol. 37, No. 14. (1 August 2009), pp. 4613-4620. by Shrihari Sonavane, Pinak Chakrabarti posted by 2 people reyez higueruelo
	Combining use of a panel of ssDNA aptamers in the detection of Staphylococcus aureus [My Copy] Nucleic Acids Research, Vol. 37, No. 14., pp. 4621-4628. by Xiaoxiao Cao, Shaohua Li, Liucun Chen, et al.Hongmei Ding, Hua Xu, Yanping Huang, Jie Li, Nongle Liu, Weihong Cao, Yanjun Zhu, Beifen Shen, Ningsheng Shao
	Using genome-wide measurements for computational prediction of SH2-peptide interactions. [My Copy] Nucleic acids research, Vol. 37, No. 14. (1 August 2009), pp. 4629-4641. by Zeba Wunderlich, Leonid A. Mirny posted by 2 people Orengo Group Journal Picks davidalee
	Conferring a template-dependent polymerase activity to terminal deoxynucleotidyltransferase by mutations in the Loop1 region [My Copy] Nucleic Acids Research, Vol. 37, No. 14., pp. 4642-4656. by Flix Romain, Isabelle Barbosa, Jrme Gouge, Franois Rougeon, Marc Delarue
	Activation of alternative Jdp2 promoters and functional protein isoforms in T-cell lymphomas by retroviral insertion mutagenesis [My Copy] Nucleic Acids Research, Vol. 37, No. 14., pp. 4657-4671. by Mads Heilskov H. Rasmussen, Bruce Wang, Matthias Wabl, Anders Lade L. Nielsen, Finn Skou S. Pedersen
	A physical and functional link between splicing factors promotes pre-mRNA 3' end processing [My Copy] Nucl. Acids Res. (8 June 2009), gkp470. by Stefania Millevoi, Adrien Decorsiere, Clarisse Loulergue, et al.Jason Iacovoni, Sandra Bernat, Michael Antoniou, Stephan Vagner posted by 1 person cajunsushi
	The incorporation of the novel histone variant H2AL2 confers unusual structural and functional properties of the nucleosome [My Copy] Nucleic Acids Research, Vol. 37, No. 14., pp. 4684-4695. by Sajad Hussain H. Syed, Mathieu Boulard, Manu Shubhdarshan S. Shukla, et al.Thierry Gautier, Andrew Travers, Jan Bednar, Cendrine Faivre-Moskalenko, Stefan Dimitrov, Dimitar Angelov
	Thermodynamic characterization of tandem mismatches found in naturally occurring RNA [My Copy] Nucl. Acids Res., Vol. 37, No. 14. (1 August 2009), pp. 4696-4706. by Martha E. Christiansen, Brent M. Znosko posted by 1 person reyez
	Using DNA mechanics to predict in vitro nucleosome positions and formation energies [My Copy] Nucleic Acids Research, Vol. 37, No. 14., pp. 4707-4722. by Alexandre V. Morozov, Karissa Fortney, Daria A. Gaykalova, Vasily M. Studitsky, Jonathan Widom, Eric D. Siggia
	ST1710DNA complex crystal structure reveals the DNA binding mechanism of the MarR family of regulators [My Copy] Nucleic Acids Research, Vol. 37, No. 14., pp. 4723-4735. by Thirumananseri Kumarevel, Tomoyuki Tanaka, Takashi Umehara, Shigeyuki Yokoyama
	RNA-binding specificity of E. coli NusA [My Copy] Nucleic Acids Research, Vol. 37, No. 14., pp. 4736-4742. by Stefan Prasch, Marcel Jurk, Robert S. Washburn, Max E. Gottesman, Birgitta M. Whrl, Paul Rsch
	The Hin recombinase assembles a tetrameric protein swivel that exchanges DNA strands [My Copy] Nucleic Acids Research, Vol. 37, No. 14., pp. 4743-4756. by Gautam Dhar, Meghan M. McLean, John K. Heiss, Reid C. Johnson
	The effects of unnatural base pairs and mispairs on DNA duplex stability and solvation [My Copy] Nucleic Acids Research, Vol. 37, No. 14., pp. 4757-4763. by Gil Tae T. Hwang, Yoshiyuki Hari, Floyd E. Romesberg
	DNA binding and synapsis by the large C-terminal domain of phiC31 integrase. [My Copy] Nucleic acids research, Vol. 37, No. 14. (August 2009), pp. 4764-4773. by Andrew R. McEwan, Paul A. Rowley, Margaret C. Smith posted by 1 person sockington
	Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch [My Copy] Nucleic Acids Research, Vol. 37, No. 14., pp. 4774-4786. by Alessandra Villa, Jens Whnert, Gerhard Stock
	Functional importance of Crenarchaea-specific extra-loop revealed by an X-ray structure of a heterotetrameric crenarchaeal splicing endonuclease [My Copy] Nucleic Acids Research, Vol. 37, No. 14., pp. 4787-4798. by Shigeo Yoshinari, Tomoo Shiba, Daniel-Ken Inaoka, et al.Takashi Itoh, Genji Kurisu, Shigeharu Harada, Kiyoshi Kita, Yoh-ichi Watanabe
	Repressor CopG prevents access of RNA polymerase to promoter and actively dissociates open complexes [My Copy] Nucleic Acids Research, Vol. 37, No. 14., pp. 4799-4811. by Ana M. Hernndez-Arriaga, Tania S. Rubio-Lepe, Manuel Espinosa, Gloria del Solar
	Fur controls iron homeostasis and oxidative stress defense in the oligotrophic alpha-proteobacterium Caulobacter crescentus [My Copy] Nucleic Acids Research, Vol. 37, No. 14., pp. 4812-4825. by Jos F. da Silva Neto, Vnia S. Braz, Valria C. S. Italiani, Marilis V. Marques
	A novel androgen receptor-binding element modulates Cdc6 transcription in prostate cancer cells during cell-cycle progression [My Copy] Nucleic Acids Research, Vol. 37, No. 14., pp. 4826-4838. by Feng Jin, Joseph D. Fondell
	Developmentally regulated MAPK pathways modulate heterochromatin in Saccharomyces cerevisiae [My Copy] Nucleic Acids Research, Vol. 37, No. 14., pp. 4839-4849. by Yuval Mazor, Martin Kupiec

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phylogeny	2
16s	1
alignment	1
analysis	1
annotation	1
bias	1
buillotine	1
citations	1
codon	1
comparison	1
design	1
distance	1
download	1
geometric	1
interaction	1
kernel	1
k-mer	1
learning	1
networks	1
non-coding	1
protein	1
rna	1
sequence	1
sequencing	1
sites	1
splice	1
structure	1
subdivisions	1
tool	1
tsp	1

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