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nuin's library [502 articles]

Recent papers added to nuin's library.
  • An environmental perspective on large-scale genome clustering based on metabolic capabilities.
    Bioinformatics (Oxford, England), Vol. 24, No. 16. (15 August 2008)
    by G Kastenmüller, J Gasteiger, HW Mewes
    posted to genome clustering by nuin on 2008-08-12 18:14:19 as **
  • Towards de novo identification of metabolites by analyzing tandem mass spectra.
    Bioinformatics (Oxford, England), Vol. 24, No. 16. (15 August 2008)
    by S Böcker, F Rasche
    posted to ms metabolites by nuin on 2008-08-12 18:11:04 as **
  • Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry.
    Bioinformatics (Oxford, England), Vol. 24, No. 16. (15 August 2008)
    by L Käll, JD Storey, WS Noble
    posted to peptides ms identification by nuin on 2008-08-12 18:10:46 as **
  • Segment-based multiple sequence alignment.
    Bioinformatics (Oxford, England), Vol. 24, No. 16. (15 August 2008)
    by T Rausch, AK Emde, D Weese, A Döring, C Notredame, K Reinert
    posted to sequence alignment by nuin on 2008-08-12 18:10:24 as **
  • Efficient representation and P-value computation for high-order Markov motifs.
    Bioinformatics (Oxford, England), Vol. 24, No. 16. (15 August 2008)
    by PG da Fonseca, KS Guimarães, MF Sagot
    posted to motifs markov by nuin on 2008-08-12 18:10:09 as **
  • A fast and flexible method for the segmentation of aCGH data.
    Bioinformatics (Oxford, England), Vol. 24, No. 16. (15 August 2008)
    by E Ben-Yaacov, YC Eldar
    posted to data analysis acgh by nuin on 2008-08-12 18:09:48 as ** along with 1 person aviad_work
  • Analysis of segmental duplications via duplication distance.
    Bioinformatics (Oxford, England), Vol. 24, No. 16. (15 August 2008)
    by CL Kahn, BJ Raphael
    posted to duplicons distance by nuin on 2008-08-12 18:09:11 as **
  • Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis
    Science, Vol. 320, No. 5883. (20 June 2008), pp. 1632-1635.
    by Ari Loytynoja, Nick Goldman
    posted to phylogenetics alignment by nuin on 2008-08-01 11:17:02 as ** along with 22 people and 3 groups marti emptyhb michaelbarton jlgreen AbnerCYH bpcusack bmaust gulsacan Schmidtc bpb zwang aprasad imtechnology marck ArtemPankin djkt gjuggler hpaces dinnes chad_davis jago phoenixzxl iSEEM Green Lab Khavkin's lab
  • A machine learning approach to explore the spectra intensity pattern of peptides using tandem mass spectrometry data
    BMC Bioinformatics, Vol. 9 (30 July 2008), 325.
    by Cong Zhou, Lucas D Bowler, Jianfeng Feng
    posted to proteomics ocbn ms by nuin on 2008-07-30 19:28:15 as **
  • Calculating SPR distances between trees
    Cladistics, Vol. 9999, No. 9999. (2007)
    by Pablo A Goloboff
    posted to tree distance by nuin on 2008-07-30 19:13:24 as **
  • Classification and feature selection algorithms for multi-class CGH data.
    Bioinformatics (Oxford, England), Vol. 24, No. 13. (1 July 2008)
    by J Liu, S Ranka, T Kahveci
    posted to classification cgh by nuin on 2008-07-30 19:13:05 as **
  • MACHOS: Markov clusters of homologous subsequences.
    Bioinformatics (Oxford, England), Vol. 24, No. 13. (1 July 2008)
    by S Wong, MA Ragan
    posted to proteins markov clusters by nuin on 2008-07-30 19:12:47 as ** along with 1 person gulkur
  • Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space
    Bioinformatics, Vol. 24, No. 13. (1 July 2008), pp. i41-49.
    by Yaniv Loewenstein, Elon Portugaly, Menachem Fromer, Michal Linial
    posted to protein clustering by nuin on 2008-07-30 19:12:18 as ** along with 2 people sconlan chad_davis
  • Classification of arrayCGH data using fused SVM.
    Bioinformatics (Oxford, England), Vol. 24, No. 13. (1 July 2008)
    by F Rapaport, E Barillot, JP Vert
    posted to classification arraycgh by nuin on 2008-07-30 19:11:53 as **
  • Estimating true evolutionary distances under the DCJ model.
    Bioinformatics (Oxford, England), Vol. 24, No. 13. (1 July 2008)
    by Y Lin, BM Moret
    posted to evolutionary distance by nuin on 2008-07-30 19:10:59 as **
  • Likelihood Based Clustering (LiBaC) for Codon Models, a method for grouping sites according to similarities in the underlying process of evolution.
    Molecular biology and evolution (26 June 2008)
    by Le Bao, Hong Gu, Katherine A A Dunn, Joseph P P Bielawski
    posted to similarities evolution by nuin on 2008-07-30 19:10:39 as **
  • Investigating selection on viruses: a statistical alignment approach
    BMC Bioinformatics, Vol. 9 (10 July 2008), 304.
    by Saskia de Groot, Thomas Mailund, Gerton Lunter, Jotun Hein
    posted to virus selection alignment by nuin on 2008-07-30 19:09:57 as ** along with 1 person Ema
  • Grammar-based distance in progressive multiple sequence alignment
    BMC Bioinformatics, Vol. 9 (10 July 2008), 306.
    by David J Russell, Hasan H Otu, Khalid Sayood
    posted to grammar alignment by nuin on 2008-07-30 19:09:28 as ** along with 1 person Neeperando
  • The complete nucleotide sequences of the five genetically distinct plastid genomes of Oenothera, subsection Oenothera: II. A microevolutionary view using bioinformatics and formal genetic data.
    Molecular biology and evolution (8 July 2008)
    by Stephan Greiner, Xi Wang, Reinhold G G Herrmann, Uwe Rauwolf, Klaus Mayer, Georg Haberer, Jörg Meurer
    posted to bioinformatics by nuin on 2008-07-30 19:09:05 as **
  • Metagenomics reveals our incomplete knowledge of global diversity.
    Bioinformatics (Oxford, England) (13 July 2008)
    by Miguel Pignatelli, Gabriel Aparicio, Ignacio Blanquer, Vicente Hernández, Andrés Moya, Javier Tamames
    posted to metagenomics by nuin on 2008-07-30 19:05:41 as ** along with 1 person bootsy
  • 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 transcription by nuin on 2008-07-30 19:05:21 as **
  • Experience using web services for biological sequence analysis.
    Briefings in bioinformatics (11 July 2008)
    by Heinz Stockinger, Teresa Attwood, Shahid Nadeem N Chohan, Richard Côté, Philippe Cudré-Mauroux, Laurent Falquet, Pedro Fernandes, Robert D D Finn, Taavi Hupponen, Eija Korpelainen, Alberto Labarga, Aurelie Laugraud, Tania Lima, Evangelos Pafilis, Marco Pagni, Steve Pettifer, Isabelle Phan, Nazim Rahman
    posted to webservices sequence analysis by nuin on 2008-07-30 19:04:32 as ** along with 1 person dullhunk
  • Detecting short tandem repeats from genome data: opening the software black box.
    Briefings in bioinformatics (10 July 2008)
    by Angelika Merkel, Neil Gemmell
    posted to str genome detection by nuin on 2008-07-30 19:04:07 as **
  • PathCluster: a framework for gene set-based hierarchical clustering.
    Bioinformatics (Oxford, England) (15 July 2008)
    by Tae-Min M Kim, Seon-Hee H Yim, Yong-Bok B Jeong, Yu-Chae C Jung, Yeun-Jun J Chung
    posted to gene clustering by nuin on 2008-07-30 19:02:48 as ** along with 2 people shigepong maralena
  • The Wisdom of the Commons: Ensemble Tree Classifiers for Prostate Cancer Prognosis.
    Bioinformatics (Oxford, England) (15 July 2008)
    by James A A Koziol, Anne C C Feng, Zhenyu Jia, Yipeng Wang, Michael McClelland, Dan Mercola
    posted to prostate cancer by nuin on 2008-07-30 19:02:28 as **
  • Computational biology resources lack persistence and usability.
    PLoS computational biology, Vol. 4, No. 7. (July 2008)
    by S Veretnik, JL Fink, PE Bourne
    posted to bioinformatics by nuin on 2008-07-30 19:00:59 as ** along with 5 people and 1 group maximilianh fgibson hpiwowar dullhunk xjlibod BergmanLab
  • The Protein Information and Property Explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data.
    Bioinformatics (Oxford, England) (16 July 2008)
    by H Ramos, P Shannon, R Aebersold
    posted to proteomics protein ms by nuin on 2008-07-30 18:57:59 as ** along with 1 person jyuh
  • An exact algorithm for the geodesic distance between phylogenetic trees.
    Journal of computational biology : a journal of computational molecular cell biology, Vol. 15, No. 6. (g 2008), pp. 577-591.
    by A Kupczok, AV Haeseler, S Klaere
    posted to trees phylogenetics by nuin on 2008-07-30 18:57:01 as **
  • EPoS: a modular software framework for phylogenetic analysis.
    Bioinformatics (Oxford, England) (16 July 2008)
    by Thasso Griebel, Malte Brinkmeyer, Sebastian Böcker
    posted to phylogenetics bioinformatics by nuin on 2008-07-30 18:54:16 as **
  • BioBayes: A Software Package for Bayesian Inference in Systems Biology
    Bioinformatics (16 July 2008), btn338.
    by Vladislav Vyshemirsky, Mark Girolami
    posted to bioinformatics bayes by nuin on 2008-07-30 18:53:56 as ** along with 2 people jyuh renatomilani
  • Frequent and Widespread Parallel Evolution of Protein Sequences.
    Molecular biology and evolution (25 June 2008)
    by Antonis Rokas, Sean B B Carroll
    posted to protein evolution by nuin on 2008-07-30 18:51:57 as ** along with 2 people zwang david_mcclellan
  • iFoldRNA: Three-dimensional RNA Structure Prediction and Folding.
    Bioinformatics (Oxford, England) (25 June 2008)
    by Shantanu Sharma, Feng Ding, Nikolay V V Dokholyan
    posted to structural rna prediction by nuin on 2008-07-30 17:57:41 as **
  • Evaluating Statistical Methods Using Plasmode Data Sets in the Age of Massive Public Databases: An Illustration Using False Discovery Rates
    PLoS Genet, Vol. 4, No. 6. (20 June 2008), e1000098.
    by Gary L Gadbury, Qinfang Xiang, Lin Yang, Stephen Barnes, Grier P Page, David B Allison
    posted to statistics fdr by nuin on 2008-07-30 17:52:51 as ** along with 2 people jyuh djkt
  • Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models
    Bioinformatics (18 June 2008), btn313.
    by Art F Poon, Fraser I Lewis, Simon D Frost, Sergei L Pond
    posted to detection co-evolving bayes by nuin on 2008-07-30 17:50:08 as ** along with 1 person marck
  • Impact of whole genome amplification on analysis of copy number variants.
    Nucleic acids research, Vol. 36, No. 13. (August 2008)
    by TJ Pugh, AD Delaney, N Farnoud, S Flibotte, M Griffith, HI Li, H Qian, P Farinha, RD Gascoyne, MA Marra
    posted to number genome copy amplification by nuin on 2008-07-30 17:48:52 as ** along with 2 people and 1 group jyuh stajich Berkeley Mycology
  • Memory-efficient dynamic programming backtrace and pairwise local sequence alignment.
    Bioinformatics (Oxford, England) (17 June 2008)
    by Lee A A Newberg
    posted to programming dynamic alignment by nuin on 2008-07-30 17:47:41 as ** along with 2 people chad_davis stajich
  • Precise detection of rearrangement breakpoints in mammalian chromosomes
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Claire Lemaitre, Eric Tannier, Christian Gautier, Marie F Sagot
    posted to detection chromosomes breakpoints by nuin on 2008-07-30 17:45:43 as ** along with 3 people and 1 group timflutre Neeperando cisevol BergmanLab
  • TiGER: a database for tissue-specific gene expression and regulation
    BMC Bioinformatics, Vol. 9 (09 June 2008), 271.
    by Xiong Liu, Xueping Yu, Donald J Zack, Heng Zhu, Jiang Qian
    posted to regulation gene expression database by nuin on 2008-07-30 17:36:08 as ** along with 3 people jyuh reyez bootsy
  • Efficient analysis and extraction of MS/MS result data from Mascot result files.
    BMC bioinformatics, Vol. 6 (2005)
    by F Grosse-Coosmann, AM Boehm, A Sickmann
    posted to proteomics ocbn bjarnason by nuin on 2008-07-28 21:24:56 as **
  • A quantitative analysis software tool for mass spectrometry–based proteomics
    Nature Methods, Vol. 5, No. 4. (16 March 2008), pp. 319-322.
    by Sung K Park, John D Venable, Tao Xu, John R Yates
    posted to proteomics ocbn bjarnason by nuin on 2008-07-28 14:31:48 as ** along with 2 people jyuh olberd
  • Label-free protein quantification using LC-coupled ion trap or FT mass spectrometry: Reproducibility, linearity, and application with complex proteomes.
    Journal of proteome research, Vol. 5, No. 5. (May 2006), pp. 1214-1223.
    by G Wang, WW Wu, W Zeng, CL Chou, RF Shen
    posted to proteomics ocbn bjarnason by nuin on 2008-07-24 19:24:44 as **
  • Improved Validation of Peptide MS/MS Assignments Using Spectral Intensity Prediction
    Mol Cell Proteomics, Vol. 6, No. 1. (1 January 2007), pp. 1-17.
    by Shaojun Sun, Karen Meyer-Arendt, Brian Eichelberger, Robert Brown, Chia-Yu Yen, William M Old, Kevin Pierce, Krzysztof J Cios, Natalie G Ahn, Katheryn A Resing
    posted to proteomics ocbn bjarnason by nuin on 2008-07-24 18:45:40 as **
  • Quantitative Profile of Five Murine Core Proteomes Using Label-free Functional Proteomics.
    Mol Cell Proteomics, Vol. 6, No. 9. (September 2007), pp. 1560-1573.
    by PR Cutillas, B Vanhaesebroeck
    posted to proteomics ocbn bjarnason by nuin on 2008-07-24 17:06:04 as ** along with 3 people jyuh nedwards js7814
  • Comprehensive Label-Free Method for the Relative Quantification of Proteins from Biological Samples
    J. Proteome Res., Vol. 4, No. 4. (8 August 2005), pp. 1442-1450.
    by RE Higgs, MD Knierman, V Gelfanova, JP Butler, JE Hale
    posted to proteomics ocbn bjarnason by nuin on 2008-07-24 16:58:07 as **
  • Identifying differences in protein expression levels by spectral counting and feature selection.
    Genetics and molecular research : GMR, Vol. 7, No. 2. (2008), pp. 342-356.
    by PC Carvalho, J Hewel, VC Barbosa, JR Yates
    posted to proteomics ocbn bjarnason by nuin on 2008-07-24 16:22:02 as **
  • Statistical models for protein validation using tandem mass spectral data and protein amino acid sequence databases.
    Anal Chem, Vol. 76, No. 6. (15 March 2004), pp. 1664-1671.
    by RG Sadygov, H Liu, JR Yates
    posted to proteomics ocbn bjarnason by nuin on 2008-07-23 16:08:56 as ** along with 2 people fishtank nedwards
  • Comparison of Label-free Methods for Quantifying Human Proteins by Shotgun Proteomics
    Mol Cell Proteomics, Vol. 4, No. 10. (1 October 2005), pp. 1487-1502.
    by William M Old, Karen Meyer-Arendt, Lauren Aveline-Wolf, Kevin G Pierce, Alex Mendoza, Joel R Sevinsky, Katheryn A Resing, Natalie G Ahn
    posted to proteomics ocbn bjarnason by nuin on 2008-07-23 16:06:59 as ** along with 3 people kentsis nedwards js7814
  • <B><I>In vitro</I></B> and <B><I>in silico</I></B> processes to identify differentially expressed proteins
    PROTEOMICS, Vol. 4, No. 8. (2004), pp. 2333-2351.
    by Nadia Allet, Nicolas Barrillat, Thierry Baussant, Celia Boiteau, Paolo Botti, Lydie Bougueleret, Nicolas Budin, Denis Canet, Stéphanie Carraud, Diego Chiappe, Nicolas Christmann, Jacques Colinge, Isabelle Cusin, Nicolas Dafflon, Benoît Depresle, Irène Fasso, Pascal Frauchiger, Hubert Gaertner, Anne Gleizes, Eduardo Gonzalez-Couto, Catherine Jeandenans, Abderrahim Karmime, Thomas Kowall, Sophie Lagache, Eve Mahé, Alexandre Masselot, Hassan Mattou, Marc Moniatte, Anne Niknejad, Marianne Paolini, Frédéric Perret, Nicolas Pinaud, Frédéric Ranno, Sylvain Raimondi, Samia Reffas, Pierre-Olivier Regamey, Pierre-Antoine Rey, Patricia Rodriguez-Tomé, Keith Rose, Gérald Rossellat, Cédric Saudrais, Camille Schmidt, Matteo Villain, Catherine Zwahlen
    posted to bjarnason proteomics ocbn by nuin on 2008-07-23 16:05:14 as **
  • An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data.
    J Proteome Res, Vol. 7, No. 1. (January 2008), pp. 51-61.
    by LN Mueller, MY Brusniak, DR Mani, R Aebersold
    posted to proteomics ocbn bjarnason by nuin on 2008-07-23 16:02:03 as ** along with 4 people jyuh raiyar nedwards olberd
  • Exponentially Modified Protein Abundance Index (emPAI) for Estimation of Absolute Protein Amount in Proteomics by the Number of Sequenced Peptides per Protein
    Mol Cell Proteomics, Vol. 4, No. 9. (1 September 2005), pp. 1265-1272.
    by Yasushi Ishihama, Yoshiya Oda, Tsuyoshi Tabata, Toshitaka Sato, Takeshi Nagasu, Juri Rappsilber, Matthias Mann
    posted to proteomics ocbn bjarnason by nuin on 2008-07-23 15:56:31 as ** along with 1 person nedwards
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