neils's library 1118 articles Export Sort

	Shewanella spp. Genomic Evolution for a Cold Marine Lifestyle and In-Situ Explosive Biodegradation PLoS ONE, Vol. 5, No. 2. (8 February 2010), e9109. by Jian-Shen Zhao, Yinghai Deng, Dominic Manno, Jalal Hawari posted to shewanella psychrophily pollution metabolism marine genomics biodegradation bactera by neils on 2010-02-06 07:08:27
	Extracting consistent knowledge from highly inconsistent cancer gene data sources BMC Bioinformatics, Vol. 11, No. 1. (05 February 2010), 76. by Xue Gong, Ruihong Wu, Yuannv Zhang, et al.Wenyuan Zhao, Lixin Cheng, Yunyan Gu, Lin Zhang, Jing Wang, Jing Zhu, Zheng Guo posted to integration dataset database consistency cancer by neils on 2010-02-06 04:35:03 along with 1 person renatomilani
	Overexpression of SUGT1 in human colorectal cancer and its clinicopathological significance. International journal of oncology, Vol. 36, No. 3. (March 2010), pp. 569-575. by Masaaki Iwatsuki, Koshi Mimori, Tetsuya Sato, et al.Hiroyuki Toh, Takehiko Yokobori, Fumiaki Tanaka, Koichi Ishikawa, Hideo Baba, Masaki Mori posted to sugt1 overexpression microarray human disease colorectal cancer by neils on 2010-02-04 12:42:54
	A conserved mechanism of autoinhibition for the AMPK kinase domain: ATP-binding site and catalytic loop refolding as a means of regulation. Acta crystallographica. Section F, Structural biology and crystallization communications, Vol. 66, No. Pt 2. (1 February 2010), pp. 143-151. by Dene R. Littler, John R. Walker, Tara Davis, et al.Leanne E. Wybenga-Groot, Patrick J. Finerty, Elena Newman, Farell Mackenzie, Sirano Dhe-Paganon posted to regulation protein-serine-threonine mechanism kinase inhibition ampk by neils on 2010-02-04 11:55:28
	Cascleave: towards more accurate prediction of caspase substrate cleavage sites Bioinformatics (3 February 2010), btq043. by Jiangning Song, Hao Tan, Hongbin Shen, et al.Khalid Mahmood, Sarah E. Boyd, Geoffrey I. Webb, Tatsuya Akutsu, James C. Whisstock posted to substrate specificity prediction caspase accuracy by neils on 2010-02-04 04:45:07
	Identifying biologically relevant differences between metagenomic communities Bioinformatics (3 February 2010), btq041. by Donovan H. Parks, Robert G. Beiko posted to statistics software metagenomics comparison community by neils on 2010-02-04 04:44:47 along with 1 person jmeppley
	BABAR: an R package to simplify the normalisation of common reference design microarray-based transcriptomic datasets BMC Bioinformatics, Vol. 11, No. 1. (2010), 73. by Mark Alston, John Seers, Jay Hinton, Sacha Lucchini posted to statistics software r-project normalization microarray dataset by neils on 2010-02-03 23:40:58
	The structure of DdrB from Deinococcus: a new fold for single-stranded DNA binding proteins Nucl. Acids Res. (2 February 2010), gkq036. by Seiji Sugiman-Marangos, Murray S. Junop posted to structure radiation protein extremophile dna-binding deinococcus bacteria by neils on 2010-02-03 07:42:55 along with 1 person spabit
	Cloning, sequence analysis and studies on the expression of the nirS gene, encoding cytochrome cd1 nitrite reductase, from Thiosphaera pantotropha. (1997) by Neil F. W. Saunders posted to thiosphaera thesis metabolism denitrification cytochrome cd1 bacteria by neils on 2010-02-03 04:57:29
	A temporal precedence based clustering method for gene expression microarray data BMC Bioinformatics, Vol. 11, No. 1. (30 January 2010), 68. by Ritesh Krishna, Chang T. Li, Vicky B. Wollaston posted to time-course statistics microarray expression clustering by neils on 2010-02-03 01:10:59 along with 1 person tag
	Joint Genome-Wide Profiling of miRNA and mRNA Expression in Alzheimer's Disease Cortex Reveals Altered miRNA Regulation. PloS one, Vol. 5, No. 2. (1 February 2010), e8898. by Juan Nunez-Iglesias, Chun-Chi C. Liu, Todd E. Morgan, Caleb E. Finch, Xianghong Jasmine J. Zhou posted to transcriptomics regulation mrna mirna expression disease cortex alzheimers by neils on 2010-02-03 01:06:40 along with 3 people and 1 group daforerog lp2 ppgardne Journal picks
	Unusual binding interactions in PDZ domain crystal structures help explain binding mechanisms. Protein science : a publication of the Protein Society (29 January 2010) by Jonathan M. Elkins, Carina Gileadi, Leela Shrestha, et al.Claire Phillips, Jing Wang, Joao Muniz, Declan A. Doyle posted to structure pdz mechanism domain crystallography binding by neils on 2010-02-03 01:05:01
	Evolutionary dynamics of CRISPR systems in the Ocean metagenome. Applied and environmental microbiology (29 January 2010) by Valery A. Sorokin, Mikhail S. Gelfand, Irena I. Artamonova posted to ocean metagenomics evolution crispr classification by neils on 2010-02-03 00:25:14
	Archaeal eukaryote-like serine/threonine protein kinase interacts with and phosphorylates a forkhead-associated domain-containing protein. Journal of bacteriology (29 January 2010) by Bin Wang, Shifan Yang, Lei Zhang, Zheng-Guo G. He posted to substrate protein-serine-threonine phosphorylation kinase forkhead archaea by neils on 2010-02-03 00:24:00
	Gene3D: merging structure and function for a Thousand genomes Nucl. Acids Res., Vol. 38, No. suppl_1. (1 January 2010), pp. D296-300. by Jonathan Lees, Corin Yeats, Oliver Redfern, Andrew Clegg, Christine Orengo posted to structure protein genomics database classification by neils on 2010-02-03 00:23:31 along with 2 people and 1 group flbarroso CorinYeats Orengo Group Journal Picks
	Estimating DNA coverage and abundance in metagenomes using a gamma approximation Bioinformatics, Vol. 26, No. 3. (1 February 2010), pp. 295-301. by Sean D. Hooper, Daniel Dalevi, Amrita Pati, Konstantinos Mavromatis, Natalia N. Ivanova, Nikos C. Kyrpides posted to statistics sequencing metagenomics estimation coverage by neils on 2010-02-03 00:13:08 along with 1 person and 1 group CorinYeats Orengo Group Journal Picks
	FoldAmyloid: a method of prediction of amyloidogenic regions from protein sequence Bioinformatics, Vol. 26, No. 3. (1 February 2010), pp. 326-332. by Sergiy O. Garbuzynskiy, Michail Y. Lobanov, Oxana V. Galzitskaya posted to structure sequence protein prediction folding amyloid by neils on 2010-02-03 00:12:21 along with 2 people flbarroso pfluffernuugen
	Protein complex prediction based on simultaneous protein interaction network Bioinformatics In Bioinformatics, Vol. 26, No. 3. (1 February 2010), pp. 385-391. by Suk H. Jung, Bora Hyun, Woo-Hyuk Jang, Hee-Young Hur, Dong-Soo Han posted to protein-protein prediction network interaction complex clustering by neils on 2010-02-03 00:11:36 along with 3 people jjray zwang phoenixzxl
	Robust biomarker identification for cancer diagnosis with ensemble feature selection methods Bioinformatics, Vol. 26, No. 3. (1 February 2010), pp. 392-398. by Thomas Abeel, Thibault Helleputte, Yves Van de Peer, Pierre Dupont, Yvan Saeys posted to svm statistics selection feature cancer biomarker by neils on 2010-02-03 00:10:45 along with 6 people and 1 group zufar TRHvidsten nosbod ptrobajo bedo torfinnnome kclbioinf
	Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus Genome Research, Vol. 20, No. 2. (22 February 2010), pp. 170-179. by Biola M. Javierre, Agustin F. Fernandez, Julia Richter, et al.Fatima Al-Shahrour, J. Ignacio Martin-Subero, Javier Rodriguez-Ubreva, Maria Berdasco, Mario F. Fraga, Terrance P. O'Hanlon, Lisa G. Rider, Filipe V. Jacinto, F. Javier Lopez-Longo, Joaquin Dopazo, Marta Forn, Miguel A. Peinado, Luis Carreño, Amr H. Sawalha, John B. Harley, Reiner Siebert, Manel Esteller, Frederick W. Miller, Esteban Ballestar posted to methylation lupus human dna disease autoimmune by neils on 2010-02-01 22:52:02
	Identification of novel non-coding RNAs using profiles of short sequence reads from next generation sequencing data BMC Genomics, Vol. 11, No. 1. (1 February 2010), 77. by Chol H. Jung, Martin Hansen, Igor Makunin, Darren Korbie, John Mattick posted to short-read sequencing next-generation ncrna identification by neils on 2010-02-01 01:18:56 along with 4 people guhjy samgj natstreet druvus
	PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae Database, Vol. 2010, No. 0. (28 January 2010), bap026. by Chris Stark, Ting-Cheng Su, Ashton Breitkreutz, et al.Pedro Lourenco, Matthew Dahabieh, Bobby-Joe Breitkreutz, Mike Tyers, Ivan Sadowski posted to yeast verification substrate saccharomyces phosphorylation experimental database by neils on 2010-01-30 03:30:38 along with 1 person coela
	Live Coverage of Scientific Conferences Using Web Technologies PLoS Comput Biol, Vol. 6, No. 1. (29 January 2010), e1000563. by Allyson L. Lister, Ruchira S. Datta, Oliver Hofmann, et al.Roland Krause, Michael Kuhn, Bettina Roth, Reinhard Schneider posted to web20 twitter reporting microblogging ismb friendfeed conference by neils on 2010-01-30 00:48:13 along with 18 people and 2 groups huizee erinmr lyss Schopfel LyHoang gthorisson jrennstich dswan haiku perbohner AJCann carolh12 CameronNeylon Enro druvus sjcockell allysonlister Yanno Bioinformatics eLearning in Leicester
	Live Coverage of Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) 2009 PLoS Comput Biol, Vol. 6, No. 1. (29 January 2010), e1000640. by Allyson L. Lister, Ruchira S. Datta, Oliver Hofmann, et al.Roland Krause, Michael Kuhn, Bettina Roth, Reinhard Schneider posted to twitter report microblogging ismb friendfeed conference by neils on 2010-01-30 00:39:10 along with 4 people and 1 group dullhunk sjcockell allysonlister Yanno Journal picks
	Assembling genomes using short-read sequencing technology Genome Biology, Vol. 11, No. 1. (2010), 202. by Shaun Jackman, Inanc Birol posted to short-read sequencing review genome assembly by neils on 2010-01-28 22:17:59 along with 9 people jamselem GustavoLacerda idonaldson seb1 junehlee natstreet druvus robsyme dgu
	Validation of differential gene expression algorithms: Application comparing fold-change estimation to hypothesis testing BMC Bioinformatics, Vol. 11, No. 1. (2010), 63. by Corey Yanofsky, David Bickel posted to validation statistics expression differential algorithms by neils on 2010-01-28 22:15:11 along with 5 people GustavoLacerda chriscole shikin sgsfak brianb
	The phosphoproteome of the minimal bacterium Mycoplasma pneumoniae: Analysis of the complete known Ser/ Thr kinome suggests the existence of novel kinases. Molecular & cellular proteomics : MCP (22 January 2010), M900267-MCP200. by Sebastian R. Schmidl, Katrin Gronau, Nico Pietack, Michael Hecker, Dörte Becher, Jörg Stülke posted to proteomics protein-serine-threonine phosphorylation mycobacterium kinases bacteria by neils on 2010-01-27 00:15:45 along with 1 group Journal picks
	MicroRNA-145 Targets YES and STAT1 in Colon Cancer Cells PLoS ONE, Vol. 5, No. 1. (21 January 2010), e8836. by Lea H. Gregersen, Anders B. Jacobsen, Lisa B. Frankel, Jiayu Wen, Anders Krogh, Anders H. Lund posted to targets mirna colon cancer by neils on 2010-01-27 00:13:52 along with 1 person torfinnnome
	The novel mouse Polo-like kinase 5 responds to DNA damage and localizes in the nucleolus Nucl. Acids Res. (25 January 2010), gkq011. by Zdenek Andrysik, William Z. Bernstein, Li Deng, et al.David L. Myer, Ya-Qin Li, Jay A. Tischfield, Peter J. Stambrook, El M. Bahassi posted to polo nucleolus kinase dna damage by neils on 2010-01-27 00:13:07
	Identification of RACK1 and Protein Kinase Calpha as Integral Components of the Mammalian Circadian Clock Science, Vol. 327, No. 5964. (22 January 2010), pp. 463-466. by Maria S. Robles, Cyril Boyault, Darko Knutti, Kiran Padmanabhan, Charles J. Weitz posted to transcription regulation rack1 protein pkc mammals kinase circadian by neils on 2010-01-21 22:28:13 along with 2 people JoramJvR samubernard
	Prediction of the binding affinities of peptides to class II MHC using a regularized thermodynamic model BMC Bioinformatics, Vol. 11, No. 1. (2010), 41. by Andrew Bordner, Hans Mittelmann posted to thermodynamics protein-ligand prediction peptide mhc interaction class-ii by neils on 2010-01-21 01:38:56
	Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome BMC Genomics, Vol. 11, No. 1. (2010), 46. by Brian Jones, Funing Sun, Julian Marchesi posted to plasmids microbiome metagenomics human gut by neils on 2010-01-19 11:20:11 along with 3 people and 1 group elipapa skennedy8 sharpton iSEEM
	Evolution of electron transfer out of the cell: comparative genomics of six Geobacter genomes BMC Genomics, Vol. 11, No. 1. (2010), 40. by Jessica Butler, Nelson Young, Derek Lovley posted to geobacter genomics electron_transport_chain bioenergetics bacteria by neils on 2010-01-17 22:57:32
	Multiple Imputations Applied to the DREAM3 Phosphoproteomics Challenge: A Winning Strategy PLoS ONE, Vol. 5, No. 1. (18 January 2010), e8012. by Nicolas Guex, Eugenia Migliavacca, Ioannis Xenarios posted to prediction phosphorylation network interaction dream3 by neils on 2010-01-16 07:28:15
	An Integrative -omics Approach to Identify Functional Sub-Networks in Human Colorectal Cancer PLoS Comput Biol, Vol. 6, No. 1. (15 January 2010), e1000639. by Rod K. Nibbe, Mehmet Koyutürk, Mark R. Chance posted to protein-protein prediction networks interaction integration human colorectal cancer by neils on 2010-01-15 07:54:19 along with 6 people poirel ptrobajo chasmand minostro frohike karthikraman
	Associating Genes and Protein Complexes with Disease via Network Propagation PLoS Comput Biol, Vol. 6, No. 1. (15 January 2010), e1000641. by Oron Vanunu, Oded Magger, Eytan Ruppin, Tomer Shlomi, Roded Sharan posted to prediction network genes disease complex association alzheimers by neils on 2010-01-15 07:51:17 along with 6 people dakelley cdsouthan phoenixzxl poirel pedrobeltrao karthikraman
	High-content siRNA screening of the kinome identifies kinases involved in Alzheimer's disease-related tau hyperphosphorylation BMC Genomics, Vol. 11, No. 1. (2010), 25. by David Azorsa, RiLee Robeson, Danielle Frost, et al.Bessie Meechoovet, Gillian Brautigam, Chad Dickey, Christian Beaudry, Gargi Basu, David Holz, Joseph Hernandez, Kristen Bisanz, Leslie Gwinn, Andrew Grover, Joseph Rogers, Eric Reiman, Michael Hutton, Dietrich Stephan, Spyro Mousses, Travis Dunckley posted to sirna screening phosphorylation kinome identification disease alzheimers by neils on 2010-01-12 22:43:40
	Thermus thermophilus Proteins That Are Differentially Expressed in Response to Growth Temperature and Their Implication in Thermoadaptation Journal of Proteome Research, Vol. 0, No. 0. (0000) by Hebin Li, Xinglai Ji, Zhidong Zhou, Yiqian Wang, Xiaobo Zhang posted to thermus thermophily temperature proteomics proteins growth expression by neils on 2010-01-11 22:40:12
	Combining Structure and Sequence Information Allows Automated Prediction of Substrate Specificities within Enzyme Families PLoS Comput Biol, Vol. 6, No. 1. (2010) by Marc Röttig, Christian Rausch, Oliver Kohlbacher posted to structure specificity sequence prediction enzyme by neils on 2010-01-08 08:02:03
	Bioinformatics analysis of microarray data. Methods in molecular biology (Clifton, N.J.) In Cardiovascular Genomics , Vol. 573 (2009), pp. 259-284. by Yunyu Zhang, Joseph Szustakowski, Martina Schinke posted to tutorial r-project microarray introduction data bioconductor analysis by neils on 2010-01-08 03:11:14 along with 2 people torfinnnome guhjy
	Shifting the genomic gold standard for the prokaryotic species definition Proceedings of the National Academy of Sciences, Vol. 106, No. 45. (10 November 2009), pp. 19126-19131. by Michael Richter, Ramon Rosselló-Móra posted to species similarity sequencing prokaryote phylogenetics hybridization dna-dna by neils on 2010-01-07 22:38:56 along with 5 people and 1 group journalwatch bethshank skato_toyaku Katje pyilmaz microbiology_nijmegen
	Comparing the substrate specificities of cytochrome c biogenesis Systems I and II. The FEBS journal (29 December 2009) by Alan D. Goddard, Julie M. Stevens, Arnaud Rondelet, Elena Nomerotskaia, James W. Allen, Stuart J. Ferguson posted to cytochrome c-type biogenesis biochemistry bacteria by neils on 2010-01-07 22:36:40
	PyMix - The Python mixture package - a tool for clustering of heterogeneous biological data BMC Bioinformatics, Vol. 11, No. 1. (6 January 2010), 9. by Benjamin Georgi, Ivan G. Costa, Alexander Schliep posted to statistics software python heterogeneous data clustering by neils on 2010-01-06 23:06:41 along with 9 people nickolay meanerelk operon erexhepa druvus rvidal kshameer torfinnnome karthikraman
	Failure to Detect the Novel Retrovirus XMRV in Chronic Fatigue Syndrome PLoS ONE, Vol. 5, No. 1. (6 January 2010), e8519. by Otto Erlwein, Steve Kaye, Myra O. McClure, et al.Jonathan Weber, Gillian Wills, David Collier, Simon Wessely, Anthony Cleare posted to xmrv virus retrovirus human disease cfs by neils on 2010-01-06 02:05:22
	Normal colon epithelium: a dataset for the analysis of gene expression and alternative splicing events in colon disease. BMC Genomics, Vol. 11, No. 1. (2010), 5. by Wilfrido Mojica, Lesleyann Hawthorn posted to splicing microarray gene expression disease dataset colon affymetrix by neils on 2010-01-04 22:19:16 along with 1 person torfinnnome
	Adaptation of Hansenula polymorpha to methanol: a transcriptome analysis BMC Genomics, Vol. 11, No. 1. (2010), 1. by Tim van Zutphen, Richard Baerends, Kim Susanna, et al.Anne de Jong, Oscar Kuipers, Marten Veenhuis, Ida van der Klei posted to yeast transcriptomics methanol metabolism hansenula c1 by neils on 2010-01-04 09:09:38
	The Tasmanian Devil Transcriptome Reveals Schwann Cell Origins of a Clonally Transmissible Cancer Science, Vol. 327, No. 5961. (1 January 2010), pp. 84-87. by Elizabeth P. Murchison, Cesar Tovar, Arthur Hsu, et al.Hannah S. Bender, Pouya Kheradpour, Clare A. Rebbeck, David Obendorf, Carly Conlan, Melanie Bahlo, Catherine A. Blizzard, Stephen Pyecroft, Alexandre Kreiss, Manolis Kellis, Alexander Stark, Timothy T. Harkins, Jennifer A. Graves, Gregory M. Woods, Gregory J. Hannon, Anthony T. Papenfuss posted to transmissible transcriptomics tasmanian-devil schwann cell cancer by neils on 2010-01-02 01:22:54 along with 1 person and 1 group robertrentzsch Orengo Group Journal Picks
	Skittle: A 2-Dimensional Genome Visualization Tool BMC Bioinformatics, Vol. 10, No. 1. (2009), 452. by Josiah Seaman, John Sanford posted to visualisation software pattern genomics by neils on 2010-01-02 01:19:14 along with 2 people druvus kshameer
	Identification of Networks of Co-Occurring, Tumor-Related DNA Copy Number Changes Using a Genome-Wide Scoring Approach PLoS Comput Biol, Vol. 6, No. 1. (1 January 2010), e1000631. by Christiaan Klijn, Jan Bot, David J. Adams, Marcel Reinders, Lodewyk Wessels, Jos Jonkers posted to tumour statistics scoring network genomics copy-number by neils on 2010-01-02 01:16:36 along with 2 people shikin frohike
	A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea Nature, Vol. 462, No. 7276. (24 December 2009), pp. 1056-1060. by Dongying Wu, Philip Hugenholtz, Konstantinos Mavromatis, et al.Rudiger Pukall, Eileen Dalin, Natalia N. Ivanova, Victor Kunin, Lynne Goodwin, Martin Wu, Brian J. Tindall, Sean D. Hooper, Amrita Pati, Athanasios Lykidis, Stefan Spring, Iain J. Anderson, Patrik D/'haeseleer, Adam Zemla, Mitchell Singer, Alla Lapidus, Matt Nolan, Alex Copeland, Cliff Han, Feng Chen, Jan-Fang Cheng, Susan Lucas, Cheryl Kerfeld, Elke Lang, Sabine Gronow, Patrick Chain, David Bruce, Edward M. Rubin, Nikos C. Kyrpides, Hans-Peter Klenk, Jonathan A. Eisen posted to phylogenetics genomics bacteria archaea by neils on 2009-12-24 06:01:08 along with 22 people and 4 groups jjray elipapa mamoru setubal yuifu robertrentzsch haruo rvosa meriemelkaroui skennedy8 yyfwuhan druvus dutilh chriswillmott ppgardne djkt GeeSharpMinor operon TRHvidsten jonathaneisen michaelbarton skembel Orengo Group Journal Picks FAB-lab Journal picks iSEEM

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