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Ema's library [328 articles]

Recent papers added to Ema's library.
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  • AluGene: a database of Alu elements incorporated within protein-coding genes
    Nucl. Acids Res., Vol. 32, No. suppl_1. (1 January 2004), pp. D489-492.
    by Tal Dagan, Rotem Sorek, Eilon Sharon, Gil Ast, Dan Graur
    posted to no-tag by Ema on 2008-12-03 23:05:36 as **
  • Structural Relationships between Highly Conserved Elements and Genes in Vertebrate Genomes
    PLoS ONE, Vol. 3, No. 11. (14 November 2008), e3727.
    by Hong Sun, Geir Skogerbø, Zhen Wang, Wei Liu, Yixue Li
    posted to no-tag by Ema on 2008-11-16 00:57:09 as ** along with 3 people and 1 group hpaces bpcusack sameetmehta Bioinformatics
  • The Origins of Eukaryotic Gene Structure
    Mol Biol Evol, Vol. 23, No. 2. (1 February 2006), pp. 450-468.
    by Michael Lynch
    posted to no-tag by Ema on 2008-11-10 23:32:13 as ** along with 23 people and 9 groups karbak stevanspringer dayjm Ayest indigoviolet tny xwbcn dchughes petecl penka mtagaya madhadron cmm brixtonmc zhangli msierk brettc web20student BioNica krishnaJCSG timflutre jwestbrook ArtemPankin EisenLab Computational_Systems_Biology Nie FAB-lab G4ID Bioinformatics_MDACC evo-devo King_Lab Genetics-of-Gambling
  • Tree of Life Based on Genome Context Networks
    PLoS ONE, Vol. 3, No. 10. (October 2008), e3357.
    by Guohui Ding, Zhonghao Yu, Jing Zhao, Zhen Wang, Yun Li, Xiaobin Xing, Chuan Wang, Lei Liu, Yixue Li
    posted to no-tag by Ema on 2008-11-09 13:09:54 as ** along with 1 person fhsantanna
  • Electrostatic potentials of E.coli genome DNA.
    Journal of biomolecular structure & dynamics, Vol. 23, No. 3. (December 2005), pp. 341-345.
    by SG Kamzolova, AA Sorokin, TD Dzhelyadin, PM Beskaravainy, AA Osypov
    posted to no-tag by Ema on 2008-10-18 10:21:30 as **
  • Electrostatic properties of promoter recognized by E. coli RNA polymerase Esigma70.
    Journal of bioinformatics and computational biology, Vol. 4, No. 2. (April 2006), pp. 455-467.
    by AA Sorokin, AA Osypov, TR Dzhelyadin, PM Beskaravainy, SG Kamzolova
    posted to no-tag by Ema on 2008-10-18 10:20:54 as **
  • An RNA gene expressed during cortical development evolved rapidly in humans
    Nature (16 August 2006)
    by Katherine S Pollard, Sofie R Salama, Nelle Lambert, Marie-Alexandra Lambot, Sandra Coppens, Jakob S Pedersen, Sol Katzman, Bryan King, Courtney Onodera, Adam Siepel, Andrew D Kern, Colette Dehay, Haller Igel, Manuel Ares, Pierre Vanderhaeghen, David Haussler
    posted to no-tag by Ema on 2008-10-10 16:30:33 as ** along with 14 people and 3 groups sriesenfeld carlfulp brian bpb marcius nickluscombe larios joshuashen ealloza ce2benna lusk bpcusack nolodie rrhudson EBI-regulation BioinfoCIPF SGU-CIPF
  • Ultraconserved elements in the human genome.
    Science, Vol. 304, No. 5675. (28 May 2004), pp. 1321-1325.
    by G Bejerano, M Pheasant, I Makunin, S Stephen, WJ Kent, JS Mattick, D Haussler
    posted to no-tag by Ema on 2008-10-10 16:30:15 as ** along with 16 people and 5 groups treangen carlfulp karbak barry ujh alexisgallagher bpb aprasad balicea dchughes pradiptaray djkt sujaikumar blobbybirdman cisevol fpattyn structural_bioinformatics Bioinformatics G4ID Genetics-of-Gambling cis-regulatory-evolution
  • Efficient and Accurate Construction of Genetic Linkage Maps from the Minimum Spanning Tree of a Graph
    PLoS Genet, Vol. 4, No. 10. (10 October 2008), e1000212.
    by Yonghui Wu, Prasanna R Bhat, Timothy J Close, Stefano Lonardi
    posted to no-tag by Ema on 2008-10-10 13:59:47 as ** along with 2 people zwang djkt
  • Fast and Accurate Search for Non-coding RNA Pseudoknot Structures in Genomes.
    Bioinformatics (Oxford, England) (7 August 2008)
    by Zhibin Huang, Yong Wu, Joseph Robertson, Liang Feng, Russell L L Malmberg, Liming Cai
    posted to no-tag by Ema on 2008-10-06 15:14:05 as ** along with 3 people samgj djkt papamicd
  • Integrated detection and population-genetic analysis of SNPs and copy number variation.
    Nature genetics (7 September 2008)
    by Steven A A McCarroll, Finny G G Kuruvilla, Joshua M M Korn, Simon Cawley, James Nemesh, Alec Wysoker, Michael H H Shapero, Paul I W I de Bakker, Julian B B Maller, Andrew Kirby, Amanda L L Elliott, Melissa Parkin, Earl Hubbell, Teresa Webster, Rui Mei, James Veitch, Patrick J J Collins, Robert Handsaker, Steve Lincoln, Marcia Nizzari, John Blume, Keith W W Jones, Rich Rava, Mark J J Daly, Stacey B B Gabriel, David Altshuler
    posted to no-tag by Ema on 2008-10-01 14:29:45 as ** along with 14 people and 1 group Hans45 pdexheimer madreach waszak caseybrown rsantana Zephyrus psique jbsaltz misonneh djkt daed rdiaz guhjy Roswell Cancer Crosstalk
  • nature07325.pdf (application/pdf Object)
    posted to no-tag by Ema on 2008-10-01 14:29:05 as **
  • Advancing Science through Conversations: Bridging the Gap between Blogs and the Academy
    PLoS Biology, Vol. 6, No. 9. (1 September 2008), e240.
    by Shelley A Batts, Nicholas J Anthis, Tara C Smith
    posted to no-tag by Ema on 2008-09-22 23:53:24 as ** along with 13 people Gaetan Scis0000002 silberbauer jrw fheintz fgibson nuin amarois hpiwowar druvus bcondon dullhunk Enro
  • Strategies for Identifying RNA Splicing Regulatory Motifs and Predicting Alternative Splicing Events
    PLoS Comput Biol, Vol. 4, No. 1. (25 January 2008), e21.
    by Dirk Holste, Uwe Ohler
    posted to no-tag by Ema on 2008-09-18 13:42:24 as ** along with 4 people natstreet druvus giovenko xili03
  • ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles.
    Bioinformatics (Oxford, England), Vol. 24, No. 13. (1 July 2008)
    by T Abeel, Y Saeys, P Rouzé, Y Van de Peer
    posted to no-tag by Ema on 2008-09-18 13:41:48 as ** along with 3 people and 1 group gdb druvus Auger Dead 60's
  • Mining prokaryotic genomes for unknown amino acids: a stop-codon-based approach
    BMC Bioinformatics, Vol. 8 (28 June 2007), 225.
    by Masashi Fujita, Hisaaki Mihara, Susumu Goto, Nobuyoshi Esaki, Minoru Kanehisa
    posted to motif by Ema on 2008-09-14 20:45:51 as ** along with 4 people raft Cortel wenhan rsandie
  • Shadow Enhancers as a Source of Evolutionary Novelty
    Science, Vol. 321, No. 5894. (5 September 2008), 1314.
    by Joung-Woo Hong, David A Hendrix, Michael S Levine
    posted to no-tag by Ema on 2008-09-14 20:45:33 as ** along with 14 people and 2 groups jfr rouault emptyhb dlobo sebastien_vigneau Stew bpcusack carlfulp Zephyrus djkt natstreet isimpson maximilianh caseybrown GEB Roswell Cancer Crosstalk
  • GENETICS: Enhancing Gene Regulation
    Science, Vol. 321, No. 5894. (5 September 2008), pp. 1300-1301.
    by Gregory A Wray, Courtney C Babbitt
    posted to no-tag by Ema on 2008-09-14 20:45:18 as ** along with 7 people and 1 group jfr huiminC oelemento sebastien_vigneau bpcusack gracio isimpson BenosLab
  • The short-sequence designs of isochores from the human genome — PNAS
    posted to no-tag by Ema on 2008-09-14 20:45:03 as **
  • Prevolutionary dynamics and the origin of evolution — PNAS
    posted to no-tag by Ema on 2008-09-14 20:35:31 as **
  • Identifying the Important HIV-1 Recombination Breakpoints
    PLoS Comput Biol, Vol. 4, No. 9. (2008), e1000178.
    by John Archer, John W Pinney, Jun Fan, Etienne Simon-Loriere, Eric J Arts, Matteo Negroni, David L Robertson
    posted to no-tag by Ema on 2008-09-14 20:24:58 as ** along with 2 people friendpine oelemento
  • Top-Down Analysis of Temporal Hierarchy in Biochemical Reaction Networks
    PLoS Comput Biol, Vol. 4, No. 9. (2008), e1000177.
    by Neema Jamshidi, Bernhard Palsson
    posted to no-tag by Ema on 2008-09-14 20:24:44 as ** along with 2 people aramesh2 raik
  • Preferentially Quantized Linker DNA Lengths in Saccharomyces cerevisiae
    PLoS Comput Biol, Vol. 4, No. 9. (2008), e1000175.
    by Ji-Ping Wang, Yvonne Fondufe-Mittendorf, Liqun Xi, Guei-Feng Tsai, Eran Segal, Jonathan Widom
    posted to no-tag by Ema on 2008-09-14 20:24:35 as ** along with 1 person aalibes
  • Identifying Cognate Binding Pairs among a Large Set of Paralogs: The Case of PE/PPE Proteins of Mycobacterium tuberculosis
    PLoS Comput Biol, Vol. 4, No. 9. (2008), e1000174.
    by Robert Riley, Matteo Pellegrini, David Eisenberg
    posted to no-tag by Ema on 2008-09-14 20:24:24 as ** along with 1 person chad_davis
  • Sizing Up Allometric Scaling Theory
    PLoS Comput Biol, Vol. 4, No. 9. (2008), e1000171.
    by Van M Savage, Eric J Deeds, Walter Fontana
    posted to no-tag by Ema on 2008-09-14 20:23:56 as **
  • Insights into Protein–DNA Interactions through Structure Network Analysis
    PLoS Comput Biol, Vol. 4, No. 9. (2008), e1000170.
    by R Sathyapriya, MS Vijayabaskar, Saraswathi Vishveshwara
    posted to no-tag by Ema on 2008-09-12 14:41:48 as ** along with 7 people and 1 group Zephyrus emptyhb aalibes AbnerCYH Totobox zwang hmk Roswell Cancer Crosstalk
  • Trends between gene content and genome size in prokaryotic species with larger genomes
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 9. (2 March 2004), pp. 3160-3165.
    by Konstantinos T Konstantinidis, James M Tiedje
    posted to no-tag by Ema on 2008-09-11 21:25:40 as **
  • The Dynamic Brain: From Spiking Neurons to Neural Masses and Cortical Fields
    PLoS Comput Biol, Vol. 4, No. 8. (2008), e1000092.
    by Gustavo Deco, Viktor K Jirsa, Peter A Robinson, Michael Breakspear, Karl Friston
    posted to no-tag by Ema on 2008-09-11 19:00:34 as ** along with 3 people robotact fgibson flieder
  • Understanding the limits to generalizability of experimental evolutionary models
    Nature, Vol. 455, No. 7210. (2008), pp. 220-223.
    by Samantha E Forde, Robert E Beardmore, Ivana Gudelj, Sinan S Arkin, John N Thompson, Laurence D Hurst
    posted to evolution by Ema on 2008-09-11 17:54:39 as ** along with 10 people and 1 group qwermish pradiptaray jasonn DanHodson druvus Zephyrus zwang Katje skoddet tmmurali Roswell Cancer Crosstalk
  • Rewiring of the Yeast Transcriptional Network Through the Evolution of Motif Usage
    Science, Vol. 309, No. 5736. (05 August 2005), pp. 938-940.
    by Jan Ihmels, Sven Bergmann, Maryam Gerami-Nejad, Itai Yanai, Mark Mcclellan, Judith Berman, Naama Barkai
    posted to no-tag by Ema on 2008-09-10 18:20:02 as ** along with 11 people and 3 groups hge balabu roys aalibes monod arve marcius adepace entropy janek04 emptyhb EisenLab BioinfoCIPF SGU-CIPF
  • Reconstruction of ancestral protein sequences and its applications
    BMC Evolutionary Biology, Vol. 4, No. 1. (2004)
    by Wei Cai, Jimin Pei, Nick Grishin
    posted to no-tag by Ema on 2008-09-09 13:38:35 as ** along with 1 person druvus
  • Just-in-time assembly of cell-cycle protein complexes : Nature Precedings
    posted to no-tag by Ema on 2008-09-09 13:38:22 as **
  • A General Definition and Nomenclature for Alternative Splicing Events
    PLoS Comput Biol, Vol. 4, No. 8. (2008), e1000147.
    by Michael Sammeth, Sylvain Foissac, Roderic Guigó
    posted to no-tag by Ema on 2008-09-05 15:56:08 as ** along with 8 people and 1 group malcook treangen madreach sabahkadri bootsy jm12 brianb wutongbin BenosLab
  • Classifying RNA-Binding Proteins Based on Electrostatic Properties
    PLoS Comput Biol, Vol. 4, No. 8. (2008), e1000146.
    by Shula Shazman, Yael Mandel-Gutfreund
    posted to no-tag by Ema on 2008-09-05 15:55:50 as ** along with 1 person zwang
  • Integrating Metabolic, Transcriptional Regulatory and Signal Transduction Models in Escherichia coli.
    Bioinformatics (Oxford, England) (10 July 2008)
    by Markus W W Covert, Nan Xiao, Tiffany J J Chen, Jonathan R R Karr
    posted to no-tag by Ema on 2008-09-05 15:45:10 as ** along with 2 people guhjy nuin
  • Local graph alignment and motif search in biological networks.
    Proc Natl Acad Sci U S A, Vol. 101, No. 41. (12 October 2004), pp. 14689-14694.
    by J Berg, M Lässig
    posted to no-tag by Ema on 2008-09-05 15:41:55 as ** along with 3 people and 1 group camster alexisgallagher ssb dbk-lab
  • A critique of the molecular target-based drug discovery paradigm based on principles of metabolic control: Advantages of pathway-based discovery.
    Metab Eng (20 September 2007)
    by Marc K K Hellerstein
    posted to no-tag by Ema on 2008-09-05 15:12:29 as ** along with 5 people and 2 groups guhjy Zephyrus barry msierk cmmorel Roswell Cancer Crosstalk McCammon
  • The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins — PNAS
    posted to no-tag by Ema on 2008-08-21 19:27:31 as **
  • A Dynamic Stochastic Model for DNA Replication Initiation in Early Embryos
    PLoS ONE, Vol. 3, No. 8. (2008), e2919.
    by Arach Goldar, Hélène Labit, Kathrin Marheineke, Olivier Hyrien
    posted to no-tag by Ema on 2008-08-21 19:26:26 as **
  • Bioinformatics and cancer target discovery.
    Drug discovery today, Vol. 9, No. 18. (15 September 2004), pp. 795-802.
    by B Desany, Z Zhang
    posted to no-tag by Ema on 2008-08-21 03:14:04 as **
  • Genetic Variation in an Individual Human Exome
    PLoS Genet, Vol. 4, No. 8. (2008), e1000160.
    by Pauline C Ng, Samuel Levy, Jiaqi Huang, Timothy B Stockwell, Brian P Walenz, Kelvin Li, Nelson Axelrod, Dana A Busam, Robert L Strausberg, Craig J Venter
    posted to no-tag by Ema on 2008-08-16 18:58:43 as ** along with 8 people xingxu madreach misonneh djkt bpcusack caseybrown guhjy reyez
  • Regulatory Control and the Costs and Benefits of Biochemical Noise
    PLoS Comput Biol, Vol. 4, No. 8. (2008), e1000125.
    by Sorin Tănase-Nicola, Ten
    posted to no-tag by Ema on 2008-08-16 18:58:28 as ** along with 2 people klo jjray
  • Geometric Interpretation of Gene Coexpression Network Analysis
    PLoS Comput Biol, Vol. 4, No. 8. (2008), e1000117.
    by Steve Horvath, Jun Dong
    posted to no-tag by Ema on 2008-08-16 18:58:11 as ** along with 15 people cswinburne jfr ptrobajo pengchy nolodie druvus aramesh2 kengg roys tmmurali Borelli Totobox AbnerCYH davidchavalarias caseybrown
  • Lakeside Cemeteries in the Sahara: 5000 Years of Holocene Population and Environmental Change
    PLoS ONE, Vol. 3, No. 8. (2008), e2995.
    by Paul C Sereno, Elena A Garcea, Hélène Jousse, Christopher M Stojanowski, Jean-François Saliège, Abdoulaye Maga, Oumarou A Ide, Kelly J Knudson, Anna M Mercuri, Thomas W Stafford, Thomas G Kaye, Carlo Giraudi, Isabella M N'siala, Enzo Cocca, Hannah M Moots, Didier B Dutheil, Jeffrey P Stivers
    posted to no-tag by Ema on 2008-08-15 13:29:57 as **
  • Segment-based multiple sequence alignment
    Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i187-192.
    by Tobias Rausch, Anne-Katrin Emde, David Weese, Andreas Doring, Cedric Notredame, Knut Reinert
    posted to no-tag by Ema on 2008-08-12 13:15:44 as ** along with 6 people Md_2007 zwang APRegier djkt aprasad groepl
  • Optimal spliced alignments of short sequence reads
    Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i174-180.
    by Fabio De Bona, Stephan Ossowski, Korbinian Schneeberger, Gunnar Ratsch
    posted to no-tag by Ema on 2008-08-12 13:15:31 as ** along with 7 people and 1 group lukaswindhager malcook jmcq nmohelli caseybrown cthachuk Neeperando SIMR bioinformatics
  • PAML 4: Phylogenetic Analysis by Maximum Likelihood
    Mol Biol Evol (4 May 2007), msm088.
    by Ziheng Yang
    posted to no-tag by Ema on 2008-08-12 08:26:48 as ** along with 9 people and 1 group druvus operon akifumi hdopazo BioNica stajich ryanraaum RamuAnandakrishnan CharlesM Berkeley Mycology
  • Toward Automatic Reconstruction of a Highly Resolved Tree of Life
    Science, Vol. 311, No. 5765. (3 March 2006), pp. 1283-1287.
    by Francesca D Ciccarelli, Tobias Doerks, Christian von Mering, Christopher J Creevey, Berend Snel, Peer Bork
    posted to no-tag by Ema on 2008-08-12 08:07:45 as ** along with 16 people and 6 groups fhsantanna kinestetika dparks Retchless knaseanka dpollard tny dchughes nirfriedman cmm azazello wenhan maximilianh cmzmasek lonshy diamantis microbiology_nijmegen EisenLab FAB-lab G4ID Genetics-of-Gambling MBLAB
  • The incoherent feed-forward loop can generate non-monotonic input functions for genes
    Mol Syst Biol, Vol. 4 (15 July 2008)
    by Shai Kaplan, Anat Bren, Erez Dekel, Uri Alon
    posted to no-tag by Ema on 2008-08-06 18:02:20 as ** along with 1 person austin
  • Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size
    Mol Syst Biol, Vol. 4 (2008)
    by Jingshan Zhang, Sergei Maslov, Eugene I Shakhnovich
    posted to no-tag by Ema on 2008-08-06 18:02:07 as ** along with 3 people grahamc zwang biehl
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