Volume 13; Issue 1

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BMC Bioinformatics
Volume 13; Issue 1

BMC Bioinformatics

Volume 13; Issue 1

1

Readjoiner: a fast and memory efficient string graph-based sequence assembler

Giorgio Gonnella, Stefan Kurtz

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 477 KB

english, 2012

2

Analysis of energy-based algorithms for RNA secondary structure prediction

Monir Hajiaghayi, Anne Condon, Holger H Hoos

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 540 KB

english, 2012

3

Deterministic global optimization algorithm based on outer approximation for the parameter estimation of nonlinear dynamic biological systems

Anton Miró, Carlos Pozo, Gonzalo Guillén-Gosálbez, Jose A Egea, Laureano Jiménez

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 954 KB

english, 2012

4

Predicting protein-ATP binding sites from primary sequence through fusing bi-profile sampling of multi-view features

Ya-Nan Zhang, Dong-Jun Yu, Shu-Sen Li, Yong-Xian Fan, Yan Huang, Hong-Bin Shen

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 482 KB

english, 2012

5

Role of long- and short-range hydrophobic, hydrophilic and charged residues contact network in protein’s structural organization

Dhriti Sengupta, Sudip Kundu

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 260 KB

english, 2012

6

Inferring high-confidence human protein-protein interactions

Xueping Yu, Anders Wallqvist, Jaques Reifman

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 676 KB

english, 2012

7

TAPDANCE: An automated tool to identify and annotate transposon insertion CISs and associations between CISs from next generation sequence data

Aaron L Sarver, Jesse Erdman, Tim Starr, David A Largaespada, Kevin A T Silverstein

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 867 KB

english, 2012

8

Minimalist ensemble algorithms for genome-wide protein localization prediction

Jhih-Rong Lin, Ananda Mohan Mondal, Rong Liu, Jianjun Hu

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 996 KB

english, 2012

9

Developing a powerfulIn Silicotool for the discovery of novel caspase-3 substrates: a preliminary screening of the human proteome

Muneef Ayyash, Hashem Tamimi, Yaqoub Ashhab

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 399 KB

english, 2012

10

Markov Chain Ontology Analysis (MCOA)

H Robert Frost, Alexa T McCray

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 796 KB

english, 2012

11

Model-based peak alignment of metabolomic profiling from comprehensive two-dimensional gas chromatography mass spectrometry

Jaesik Jeong, Xue Shi, Xiang Zhang, Seongho Kim, Changyu Shen

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 311 KB

english, 2012

12

PANDAseq: paired-end assembler for illumina sequences

Andre P Masella, Andrea K Bartram, Jakub M Truszkowski, Daniel G Brown, Josh D Neufeld

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 181 KB

english, 2012

13

PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity

Bhakti Dwivedi, Robert Schmieder, Dawn B Goldsmith, Robert A Edwards, Mya Breitbart

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.28 MB

english, 2012

14

PupDB: a database of pupylated proteins

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 702 KB

english, 2012

15

Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer

Pierre Peterlongo, Rayan Chikhi

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 11.24 MB

english, 2012

16

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

Chaisson, Mark J, Tesler, Glenn

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 2.58 MB

english, 2012

17

Quality assessment of protein model-structures based on structural and functional similarities

Bogumil M Konopka, Jean-Christophe Nebel, Malgorzata Kotulska

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 2.87 MB

english, 2012

18

Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community

Konstantinos Krampis, Tim Booth, Brad Chapman, Bela Tiwari, Mesude Bicak, Dawn Field, Karen E Nelson

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.23 MB

english, 2012

19

TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks

Cyrille Lepoivre, Aurélie Bergon, Fabrice Lopez, Narayanan B Perumal, Catherine Nguyen, Jean Imbert, Denis Puthier

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 2.75 MB

english, 2012

20

CYPSI: a structure-based interface for cytochrome P450s and ligands inArabidopsis thaliana

Zhang, Gaihua, Zhang, Yijing, Su, Zhen

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 4.26 MB

english, 2012

21

Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures

Andrew F Neuwald,Christopher J Lanczycki,Aron Marchler-Bauer

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 2.43 MB

english, 2012

22

GuiTope: an application for mapping random-sequence peptides to protein sequences

Rebecca F Halperin, Phillip Stafford, Jack S Emery, Krupa Arun Navalkar, Stephen Albert Johnston

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 675 KB

english, 2012

23

MIPHENO: data normalization for high throughput metabolite analysis

Shannon M Bell, Lyle D Burgoon, Robert L Last

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 388 KB

english, 2012

24

Handling the data management needs of high-throughput sequencing data: SpeedGene, a compression algorithm for the efficient storage of genetic data

Dandi Qiao, Wai-Ki Yip, Christoph Lange

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 262 KB

english, 2012

25

MELTING, a flexible platform to predict the melting temperatures of nucleic acids

Marine Dumousseau, Nicolas Rodriguez, Nick Juty, Nicolas Le Novère

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 589 KB

english, 2012

26

Workflows for microarray data processing in the Kepler environment

Thomas Stropp, Timothy McPhillips, Bertram Ludäscher, Mark Bieda

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 908 KB

english, 2012

27

rCUR: an R package for CUR matrix decomposition

András Bodor, István Csabai, Michael W Mahoney, Norbert Solymosi

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 595 KB

english, 2012

28

Profile-based short linear protein motif discovery

Niall J Haslam, Denis C Shields

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 229 KB

english, 2012

29

Multiple structure alignment with msTALI

Paul Shealy, Homayoun Valafar

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 896 KB

english, 2012

30

Natural product-likeness score revisited: an open-source, open-data implementation

Kalai Vanii Jayaseelan, Pablo Moreno, Andreas Truszkowski, Peter Ertl, Christoph Steinbeck

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 316 KB

english, 2012

31

Learning Sparse Representations for Fruit-Fly Gene Expression Pattern Image Annotation and Retrieval

Lei Yuan, Alexander Woodard, Shuiwang Ji, Yuan Jiang, Zhi-Hua Zhou, Sudhir Kumar, Jieping Ye

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 4.44 MB

english, 2012

32

Extracting semantically enriched events from biomedical literature

Makoto Miwa, Paul Thompson, John McNaught, Douglas B Kell, Sophia Ananiadou

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.35 MB

english, 2012

33

Towards the identification of protein complexes and functional modules by integrating PPI network and gene expression data

Min Li, Xuehong Wu, Jianxin Wang, Yi Pan

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 746 KB

english, 2012

34

Convergent evolution in structural elements of proteins investigated using cross profile analysis

Kentaro Tomii, Yoshito Sawada, Shinya Honda

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.10 MB

english, 2012

35

TreeSnatcher plus: capturing phylogenetic trees from images

Thomas Laubach, Arndt von Haeseler, Martin J Lercher

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 290 KB

english, 2012

36

MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins

Lukasz P Kozlowski, Janusz M Bujnicki

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 378 KB

english, 2012

37

Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs

Suleiman A Khan, Ali Faisal, John Patrick Mpindi, Juuso A Parkkinen, Tuomo Kalliokoski, Antti Poso, Olli P Kallioniemi, Krister Wennerberg, Samuel Kaski

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 2.22 MB

english, 2012

38

Molecular ecological network analyses

Ye Deng, Yi-Huei Jiang, Yunfeng Yang, Zhili He, Feng Luo, Jizhong Zhou

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1004 KB

english, 2012

39

Detection and correction of probe-level artefacts on microarrays

Tobias Petri, Evi Berchtold, Ralf Zimmer, Caroline C Friedel

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 704 KB

english, 2012

40

PyMS: a Python toolkit for processing of gas chromatography-mass spectrometry (GC-MS) data. Application and comparative study of selected tools

Sean O’Callaghan, David P De Souza, Andrew Isaac, Qiao Wang, Luke Hodkinson, Moshe Olshansky, Tim Erwin, Bill Appelbe, Dedreia L Tull, Ute Roessner, Antony Bacic, Malcolm J McConville, Vladimir A Liki

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 708 KB

english, 2012

41

OLSVis: an animated, interactive visual browser for bio-ontologies

Steven Vercruysse, Aravind Venkatesan, Martin Kuiper

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 473 KB

english, 2012

42

MergeAlign: improving multiple sequence alignment performance by dynamic reconstruction of consensus multiple sequence alignments

Peter W Collingridge, Steven Kelly

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 398 KB

english, 2012

43

Biomine: predicting links between biological entities using network models of heterogeneous databases

Lauri Eronen, Hannu Toivonen

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 502 KB

english, 2012

44

Core module biomarker identification with network exploration for breast cancer metastasis

Ruoting Yang, Bernie J Daigle Jr, Linda R Petzold, Francis J Doyle III

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.07 MB

english, 2012

45

On the hypothesis-free testing of metabolite ratios in genome-wide and metabolome-wide association studies

Ann-Kristin Petersen, Jan Krumsiek, Brigitte Wägele, Fabian J Theis, H-Erich Wichmann, Christian Gieger, Karsten Suhre

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 210 KB

english, 2012

46

Detection of identity by descent using next-generation whole genome sequencing data

Shu-Yi Su, Jay Kasberger, Sergio Baranzini, William Byerley, Wilson Liao, Jorge Oksenberg, Elliott Sherr, Eric Jorgenson

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 587 KB

english, 2012

47

Quartet decomposition server: a platform for analyzing phylogenetic trees

Fenglou Mao, David Williams, Olga Zhaxybayeva, Maria Poptsova, Pascal Lapierre, J Peter Gogarten, Ying Xu

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 472 KB

english, 2012

48

BioWord: A sequence manipulation suite for Microsoft Word

Laura J Anzaldi, Daniel Muñoz-Fernández, Ivan Erill

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 493 KB

english, 2012

49

PollenCALC: Software for estimation of pollen compatibility of self-incompatible allo- and autotetraploid species

Andrea Arias Aguirre, Bernd Wollenweber, Ursula K Frei, Thomas Lübberstedt

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 568 KB

english, 2012

50

Identifying dysregulated pathways in cancers from pathway interaction networks

Ke-Qin Liu, Zhi-Ping Liu, Jin-Kao Hao, Luonan Chen, Xing-Ming Zhao

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 931 KB

english, 2012

51

The language of gene ontology: a Zipf’s law analysis

Leila Ranandeh Kalankesh, Robert Stevens, Andy Brass

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 284 KB

english, 2012

52

Fast and robust multiple sequence alignment with phylogeny-aware gap placement

Adam M Szalkowski

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 459 KB

english, 2012

53

TDT-HET: A new transmission disequilibrium test that incorporates locus heterogeneity into the analysis of family-based association data

Douglas Londono, Steven Buyske, Stephen J Finch, Swarkar Sharma, Carol A Wise, Derek Gordon

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 397 KB

english, 2012

54

Gene regulatory network modeling via global optimization of high-order dynamic Bayesian network

Nguyen Xuan Vinh, Madhu Chetty, Ross Coppel, Pramod P Wangikar

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 968 KB

english, 2012

55

Simulating gene-gene and gene-environment interactions in complex diseases: Gene-Environment iNteraction Simulator 2

Michele Pinelli, Giovanni Scala, Roberto Amato, Sergio Cocozza, Gennaro Miele

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 345 KB

english, 2012

56

Bios2mds: an R package for comparing orthologous protein families by metric multidimensional scaling

Julien Pelé, Jean-Michel Bécu, Hervé Abdi, Marie Chabbert

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 562 KB

english, 2012

57

Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction

Jian Ye, George Coulouris, Irena Zaretskaya, Ioana Cutcutache, Steve Rozen, Thomas L Madden

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 853 KB

english, 2012

58

β-empirical Bayes inference and model diagnosis of microarray data

Mohammad Manir Hossain Mollah, M Nurul Haque Mollah, Hirohisa Kishino

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.03 MB

english, 2012

59

Down-weighting overlapping genes improves gene set analysis

Adi Laurentiu Tarca, Sorin Draghici, Gaurav Bhatti, Roberto Romero

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 503 KB

english, 2012

60

A Bayesian model for classifying all differentially expressed proteins simultaneously in 2D PAGE gels

Steven H Wu, Michael A Black, Robyn A North, Allen G Rodrigo

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 442 KB

english, 2012

61

EGNAS: an exhaustive DNA sequence design algorithm

Alfred Kick, Martin Bönsch, Michael Mertig

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 773 KB

english, 2012

62

Comparative study of classification algorithms for immunosignaturing data

Muskan Kukreja, Stephen Albert Johnston, Phillip Stafford

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 419 KB

english, 2012

63

miREvo: an integrative microRNA evolutionary analysis platform for next-generation sequencing experiments

Ming Wen, Yang Shen, Suhua Shi, Tian Tang

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 714 KB

english, 2012

64

The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools

Andreas Wilke, Travis Harrison, Jared Wilkening, Dawn Field, Elizabeth M Glass, Nikos Kyrpides, Konstantinos Mavrommatis, Folker Meyer

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 358 KB

english, 2012

65

QuartetS-DB: a large-scale orthology database for prokaryotes and eukaryotes inferred by evolutionary evidence

Chenggang Yu, Valmik Desai, Li Cheng, Jaques Reifman

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 892 KB

english, 2012

66

Error-correcting properties of the SOLiD Exact Call Chemistry

Tim Massingham, Nick Goldman

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 286 KB

english, 2012

67

Identifying mutation regions for closely related individuals without a known pedigree

Wenjuan Cui, Lusheng Wang

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 483 KB

english, 2012

68

Arrow plot: a new graphical tool for selecting up and down regulated genes and genes differentially expressed on sample subgroups

Carina Silva-Fortes, Maria Antónia Amaral Turkman, Lisete Sousa

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 881 KB

english, 2012

69

Surprising results on phylogenetic tree building methods based on molecular sequences

Gaston H Gonnet

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 294 KB

english, 2012

70

PREMIM and EMIM: tools for estimation of maternal, imprinting and interaction effects using multinomial modelling

Richard Howey, Heather J Cordell

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 7.10 MB

english, 2012

71

The EnzymeTracker: an open-source laboratory information management system for sample tracking

Thomas Triplet, Gregory Butler

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.25 MB

english, 2012

72

A statistical approach to selecting and confirming validation targets in -omics experiments

Jeffrey T Leek, Margaret A Taub, Jason L Rasgon

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.14 MB

english, 2012

73

Towards a theoretical understanding of false positives in DNA motif finding

Amin Zia, Alan M Moses

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 732 KB

english, 2012

74

Detecting sequence dependent transcriptional pauses from RNA and protein number time series

Frank Emmert-Streib, Antti Häkkinen, Andre S Ribeiro

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 435 KB

english, 2012

75

Molecular evolution of dihydrouridine synthases

Joanna M Kasprzak, Anna Czerwoniec, Janusz M Bujnicki

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.08 MB

english, 2012

76

A fast tool for minimum hybridization networks

Zhi-Zhong Chen, Lusheng Wang, Satoshi Yamanaka

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 262 KB

english, 2012

77

Genes2FANs: connecting genes through functional association networks

Ruth Dannenfelser, Neil R Clark, Avi Ma’ayan

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.64 MB

english, 2012

78

Protein-protein binding site identification by enumerating the configurations

Fei Guo, Shuai Cheng Li, Lusheng Wang, Daming Zhu

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.01 MB

english, 2012

79

Automatic categorization of diverse experimental information in the bioscience literature

Ruihua Fang, Gary Schindelman, Kimberly Van Auken, Jolene Fernandes, Wen Chen, Xiaodong Wang, Paul Davis, Mary Ann Tuli, Steven J Marygold, Gillian Millburn, Beverley Matthews, Haiyan Zhang, Nick Brow

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 210 KB

english, 2012

80

ParticleCall: A particle filter for base calling in next-generation sequencing systems

Xiaohu Shen, Haris Vikalo

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 239 KB

english, 2012

81

Concept annotation in the CRAFT corpus

Michael Bada, Miriam Eckert, Donald Evans, Kristin Garcia, Krista Shipley, Dmitry Sitnikov, William A Baumgartner Jr, K Bretonnel Cohen, Karin Verspoor, Judith A Blake, Lawrence E Hunter

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 442 KB

english, 2012

82

Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study

Jose C A Santos, Houssam Nassif, David Page, Stephen H Muggleton, Michael J E Sternberg

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 256 KB

english, 2012

83

A graph-based approach for designing extensible pipelines

Maíra R Rodrigues, Wagner CS Magalhães, Moara Machado, Eduardo Tarazona-Santos

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 652 KB

english, 2012

84

SNP interaction detection with Random Forests in high-dimensional genetic data

Stacey J Winham, Colin L Colby, Robert R Freimuth, Xin Wang, Mariza de Andrade, Marianne Huebner, Joanna M Biernacka

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 553 KB

english, 2012

85

Re-visiting protein-centric two-tier classification of existing DNA-protein complexes

Sony Malhotra, Ramanathan Sowdhamini

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 961 KB

english, 2012

86

Slim-Filter: an interactive windows-based application for illumina genome analyzer data assessment and manipulation

Georgiy Golovko, Kamil Khanipov, Mark Rojas, Antonio Martinez-Alcántara, Jesse J Howard, Efren Ballesteros, Sharu Gupta, William Widger, Yuriy Fofanov

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 343 KB

english, 2012

87

Integrative prescreening in analysis of multiple cancer genomic studies

Rui Song, Jian Huang, Shuangge Ma

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 194 KB

english, 2012

88

Detecting pore-lining regions in transmembrane protein sequences

Timothy Nugent, David T Jones

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 383 KB

english, 2012

89

Training text chunkers on a silver standard corpus: can silver replace gold?

Ning Kang, Erik M van Mulligen, Jan A Kors

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 121 KB

english, 2012

90

Optimization ofde novotranscriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms

Berat Z Haznedaroglu, Darryl Reeves, Hamid Rismani-Yazdi, Jordan Peccia

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 656 KB

english, 2012

91

An image classification approach to analyze the suppression of plant immunity by the human pathogenSalmonellaTyphimurium

Marek Schikora, Balram Neupane, Satish Madhogaria, Wolfgang Koch, Daniel Cremers, Heribert Hirt, Karl-Heinz Kogel, Adam Schikora

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 647 KB

english, 2012

92

A text-mining system for extracting metabolic reactions from full-text articles

Jan Czarnecki, Irene Nobeli, Adrian M Smith, Adrian J Shepherd

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 641 KB

english, 2012

93

Defining and searching for structural motifs using DeepView/Swiss-PdbViewer

Maria U Johansson, Vincent Zoete, Olivier Michielin, Nicolas Guex

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.22 MB

english, 2012

94

A novel hierarchical clustering algorithm for gene sequences

Dan Wei, Qingshan Jiang, Yanjie Wei, Shengrui Wang

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.21 MB

english, 2012

95

Seqcrawler: biological data indexing and browsing platform

Olivier Sallou, Anthony Bretaudeau, Aurelien Roult

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 279 KB

english, 2012

96

The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding

Karl Kornacker, Morten Beck Rye, Tony Håndstad, Finn Drabløs

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 719 KB

english, 2012

97

Analysis of high dimensional data using pre-defined set and subset information, with applications to genomic data

Wenge Guo, Mingan Yang, Chuanhua Xing, Shyamal D Peddada

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 197 KB

english, 2012

98

Finding minimum gene subsets with heuristic breadth-first search algorithm for robust tumor classification

Shu-Lin Wang, Xue-Ling Li, Jianwen Fang

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.54 MB

english, 2012

99

A Bayesian method for comparing and combining binary classifiers in the absence of a gold standard

Jonathan M Keith, Christian M Davey, Sarah E Boyd

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 282 KB

english, 2012

100

Propagating semantic information in biochemical network models

Marvin Schulz, Edda Klipp, Wolfram Liebermeister

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 981 KB

english, 2012

101

Correction: A linear classifier based on entity recognition tools and a statistical approach to method extraction in the protein-protein interaction literature

Anália Lourenço, Michael Conover, Andrew Wong, Azadeh Nematzadeh, Fengxia Pan, Hagit Shatkay, Luis M Rocha

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 141 KB

english, 2012

102

Optimal experiment selection for parameter estimation in biological differential equation models

Mark K Transtrum, Peng Qiu

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 360 KB

english, 2012

103

Integrating gene expression and protein-protein interaction network to prioritize cancer-associated genes

Chao Wu, Jun Zhu, Xuegong Zhang

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 540 KB

english, 2012

104

Short-read reading-frame predictors are not created equal: sequence error causes loss of signal

William L Trimble, Kevin P Keegan, Mark D’Souza, Andreas Wilke, Jared Wilkening, Jack Gilbert, Folker Meyer

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 427 KB

english, 2012

105

Computational modeling of the bHLH domain of the transcription factor TWIST1 and R118C, S144R and K145E mutants

Amanda M Maia, João HM da Silva, André L Mencalha, Ernesto R Caffarena, Eliana Abdelhay

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 2.02 MB

english, 2012

106

Estimation of sequencing error rates in short reads

Xin Victoria Wang, Natalie Blades, Jie Ding, Razvan Sultana, Giovanni Parmigiani

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 299 KB

english, 2012

107

ParsEval: parallel comparison and analysis of gene structure annotations

Daniel S Standage, Volker P Brendel

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 312 KB

english, 2012

108

A resource for benchmarking the usefulness of protein structure models

Daniel Carbajo, Anna Tramontano

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 469 KB

english, 2012

109

AGORA: Assembly Guided by Optical Restriction Alignment

Henry C Lin, Steve Goldstein, Lee Mendelowitz, Shiguo Zhou, Joshua Wetzel, David C Schwartz, Mihai Pop

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 484 KB

english, 2012

110

A web-based multi-genome synteny viewer for customized data

Kashi V Revanna, Daniel Munro, Alvin Gao, Chi-Chen Chiu, Anil Pathak, Qunfeng Dong

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 578 KB

english, 2012

111

Pairwise protein expression classifier for candidate biomarker discovery for early detection of human disease prognosis

Parminder Kaur, Daniela Schlatzer, Kenneth Cooke, Mark R Chance

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 588 KB

english, 2012

112

Comparison of methods to detect copy number alterations in cancer using simulated and real genotyping data

David Mosén-Ansorena, Ana María Aransay, Naiara Rodríguez-Ezpeleta

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.86 MB

english, 2012

113

Evaluating the consistency of gene sets used in the analysis of bacterial gene expression data

Nathan L Tintle, Alexandra Sitarik, Benjamin Boerema, Kylie Young, Aaron A Best, Matthew DeJongh

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 449 KB

english, 2012

114

CLAG: an unsupervised non hierarchical clustering algorithm handling biological data

Linda Dib, Alessandra Carbone

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.01 MB

english, 2012

115

Early classification of multivariate temporal observations by extraction of interpretable shapelets

Mohamed F Ghalwash, Zoran Obradovic

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 248 KB

english, 2012

116

Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel

Nikolaos Alachiotis, Simon A Berger, Alexandros Stamatakis

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 232 KB

english, 2012

117

GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions

Junsu Ko, Hahnbeom Park, Chaok Seok

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 286 KB

english, 2012

118

Normalization of ChIP-seq data with control

Kun Liang, Sündüz Keleş

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 371 KB

english, 2012

119

ABrowse - a customizable next-generation genome browser framework

Lei Kong, Jun Wang, Shuqi Zhao, Xiaocheng Gu, Jingchu Luo, Ge Gao

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 551 KB

english, 2012

120

graphite- a Bioconductor package to convert pathway topology to gene network

Gabriele Sales, Enrica Calura, Duccio Cavalieri, Chiara Romualdi

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 681 KB

english, 2012

121

Cloudgene: A graphical execution platform for MapReduce programs on private and public clouds

Sebastian Schönherr, Lukas Forer, Hansi Weißensteiner, Florian Kronenberg, Günther Specht, Anita Kloss-Brandstätter

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 674 KB

english, 2012

122

SDAR: a practical tool for graphical analysis of two-dimensional data

Saroja Weeratunga, Nien-Jen Hu, Anne Simon, Andreas Hofmann

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 352 KB

english, 2012

123

An integrative computational approach to effectively guide experimental identification of regulatory elements in promoters

Igor V Deyneko, Siegfried Weiss, Sara Leschner

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 315 KB

english, 2012

124

Stepwise kinetic equilibrium models of quantitative polymerase chain reaction

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 595 KB

english, 2012

125

Enabling dynamic network analysis through visualization in TVNViewer

Ross E Curtis, Jing Xiang, Ankur Parikh, Peter Kinnaird, Eric P Xing

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.30 MB

english, 2012

126

Reconstructing DNA copy number by joint segmentation of multiple sequences

Zhongyang Zhang, Kenneth Lange, Chiara Sabatti

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 545 KB

english, 2012

127

CaPSID: A bioinformatics platform for computational pathogen sequence identification in human genomes and transcriptomes

Ivan Borozan, Shane Wilson, Paola Blanchette, Philippe Laflamme, Stuart N Watt, Paul M Krzyzanowski, Fabrice Sircoulomb, Robert Rottapel, Philip E Branton, Vincent Ferretti

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 918 KB

english, 2012

128

A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools

Karin Verspoor, Kevin Bretonnel Cohen, Arrick Lanfranchi, Colin Warner, Helen L Johnson, Christophe Roeder, Jinho D Choi, Christopher Funk, Yuriy Malenkiy, Miriam Eckert, Nianwen Xue, William A Baumga

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 383 KB

english, 2012

129

FluShuffle and FluResort: new algorithms to identify reassorted strains of the influenza virus by mass spectrometry

Aaron TL Lun, Jason WH Wong, Kevin M Downard

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 568 KB

english, 2012

130

Fast automatic quantitative cell replication with fluorescent live cell imaging

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.21 MB

english, 2012

131

A support vector machine based test for incongruence between sets of trees in tree space

David C Haws, Peter Huggins, Eric M O’Neill, David W Weisrock, Ruriko Yoshida

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 352 KB

english, 2012

132

NetiNeti: discovery of scientific names from text using machine learning methods

Lakshmi Manohar Akella, Catherine N Norton, Holly Miller

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 463 KB

english, 2012

133

Screening of selective histone deacetylase inhibitors by proteochemometric modeling

Dingfeng Wu, Qi Huang, Yida Zhang, Qingchen Zhang, Qi Liu, Jun Gao, Zhiwei Cao, Ruixin Zhu

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 290 KB

english, 2012

134

Sampling issues in quantitative analysis of dendritic spines morphology

Błażej Ruszczycki, Zsuzsanna Szepesi, Grzegorz M Wilczynski, Monika Bijata, Katarzyna Kalita, Leszek Kaczmarek, Jakub Wlodarczyk

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 461 KB

english, 2012

135

Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets

Nils Hoffmann, Matthias Keck, Heiko Neuweger, Mathias Wilhelm, Petra Högy, Karsten Niehaus, Jens Stoye

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.63 MB

english, 2012

136

Searching for transcription factor binding sites in vector spaces

Chih Lee, Chun-Hsi Huang

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 5.81 MB

english, 2012

137

GenNon-h: Generating multiple sequence alignments on nonhomogeneous phylogenetic trees

Anna M Kedzierska, Marta Casanellas

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 149 KB

english, 2012

138

Multi-scale agent-based brain cancer modeling and prediction of TKI treatment response: Incorporating EGFR signaling pathway and angiogenesis

Xiaoqiang Sun, Le Zhang, Hua Tan, Jiguang Bao, Costas Strouthos, Xiaobo Zhou

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.14 MB

english, 2012

139

CerealsDB 2.0: an integrated resource for plant breeders and scientists

Paul A Wilkinson, Mark O Winfield, Gary LA Barker, Alexandra M Allen, Amanda Burridge, Jane A Coghill, Keith J Edwards

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 422 KB

english, 2012

140

TFinDit: transcription factor-DNA interaction data depository

Daniel Turner, RyangGuk Kim, Jun-tao Guo

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 459 KB

english, 2012

141

ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data

Christopher R Cabanski, Keary Cavin, Chris Bizon, Matthew D Wilkerson, Joel S Parker, Kirk C Wilhelmsen, Charles M Perou, JS Marron, D Neil Hayes

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 337 KB

english, 2012

142

ANCAC: amino acid, nucleotide, and codon analysis of COGs – a tool for sequence bias analysis in microbial orthologs

Arno Meiler, Claudia Klinger, Michael Kaufmann

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 644 KB

english, 2012

143

Network enrichment analysis: extension of gene-set enrichment analysis to gene networks

Andrey Alexeyenko, Woojoo Lee, Maria Pernemalm, Justin Guegan, Philippe Dessen, Vladimir Lazar, Janne Lehtiö, Yudi Pawitan

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 517 KB

english, 2012

144

The top-scoring ‘N’ algorithm: a generalized relative expression classification method from small numbers of biomolecules

Andrew T Magis, Nathan D Price

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 250 KB

english, 2012

145

Protein-DNA docking with a coarse-grained force field

Piotr Setny, Ranjit Prasad Bahadur, Martin Zacharias

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 339 KB

english, 2012

146

AbsIDconvert: An absolute approach for converting genetic identifiers at different granularities

Fahim Mohammad, Robert M Flight, Benjamin J Harrison, Jeffrey C Petruska, Eric C Rouchka

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 925 KB

english, 2012

147

Quick, “Imputation-free” meta-analysis with proxy-SNPs

Christian Meesters, Markus Leber, Christine Herold, Marina Angisch, Manuel Mattheisen, Dmitriy Drichel, André Lacour, Tim Becker

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 365 KB

english, 2012

148

Ranked retrieval of segmented nuclei for objective assessment of cancer gene repositioning

William J Cukierski, Kaustav Nandy, Prabhakar Gudla, Karen J Meaburn, Tom Misteli, David J Foran, Stephen J Lockett

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 968 KB

english, 2012

149

Automatic classification of protein structures relying on similarities between alignments

Guillaume Santini, Henry Soldano, Joël Pothier

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1012 KB

english, 2012

150

Disentangling evolutionary signals: conservation, specificity determining positions and coevolution. Implication for catalytic residue prediction

Elin Teppa, Angela D Wilkins, Morten Nielsen, Cristina Marino Buslje

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 303 KB

english, 2012

151

Correlation analysis of the side-chains conformational distribution in bound and unbound proteins

Tatsiana Kirys, Anatoly M Ruvinsky, Alexander V Tuzikov, Ilya A Vakser

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 301 KB

english, 2012

152

A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approach

Estelle Proux-Wéra, David Armisén, Kevin P Byrne, Kenneth H Wolfe

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 405 KB

english, 2012

153

SNP calling by sequencing pooled samples

Emanuele Raineri, Luca Ferretti, Anna Esteve-Codina, Bruno Nevado, Simon Heath, Miguel Pérez-Enciso

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 228 KB

english, 2012

154

Independent Principal Component Analysis for biologically meaningful dimension reduction of large biological data sets

Fangzhou Yao, Jeff Coquery, Kim-Anh Lê Cao

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 412 KB

english, 2012

155

The Ruby UCSC API: accessing the UCSC genome database using Ruby

Hiroyuki Mishima, Jan Aerts, Toshiaki Katayama, Raoul J P Bonnal, Koh-ichiro Yoshiura

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 625 KB

english, 2012

156

Regulatory network operations in the Pathway Tools software

Suzanne M Paley, Mario Latendresse, Peter D Karp

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.24 MB

english, 2012

157

The LO-BaFL method and ALS microarray expression analysis

Cristina Baciu, Kevin J Thompson, Jean-Luc Mougeot, Benjamin R Brooks, Jennifer W Weller

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 620 KB

english, 2012

158

ncRNAclassifier: a tool for detection and classification of transposable element sequences in RNA hairpins

Sébastien Tempel, Nicolas Pollet, Fariza Tahi

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 893 KB

english, 2012

159

Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs

Hani Z Girgis, Ivan Ovcharenko

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 475 KB

english, 2012

160

QUAliFiER: An automated pipeline for quality assessment of gated flow cytometry data

Greg Finak, Wenxin Jiang, Jorge Pardo, Adam Asare, Raphael Gottardo

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.10 MB

english, 2012

161

VarioML framework for comprehensive variation data representation and exchange

Myles Byrne, Ivo FAC Fokkema, Owen Lancaster, Tomasz Adamusiak, Anni Ahonen-Bishopp, David Atlan, Christophe Béroud, Michael Cornell, Raymond Dalgleish, Andrew Devereau, George P Patrinos, Morris A Sw

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 436 KB

english, 2012

162

A scalable method for identifying frequent subtrees in sets of large phylogenetic trees

Avinash Ramu, Tamer Kahveci, J Gordon Burleigh

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 303 KB

english, 2012

163

DMET-Analyzer: automatic analysis of Affymetrix DMET Data

Pietro Hiram Guzzi, Giuseppe Agapito, Maria Teresa Di Martino, Mariamena Arbitrio, Pierfrancesco Tassone, Pierosandro Tagliaferri, Mario Cannataro

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 503 KB

english, 2012

164

Consensus embedding: theory, algorithms and application to segmentation and classification of biomedical data

Satish Viswanath, Anant Madabhushi

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 2.72 MB

english, 2012

165

Frnakenstein: multiple target inverse RNA folding

Rune B Lyngsø, James WJ Anderson, Elena Sizikova, Amarendra Badugu, Tomas Hyland, Jotun Hein

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 265 KB

english, 2012

166

Semantic similarity in the biomedical domain: an evaluation across knowledge sources

Vijay N Garla, Cynthia Brandt

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 266 KB

english, 2012

167

Cluster-based assessment of protein-protein interaction confidence

Atanas Kamburov, Arndt Grossmann, Ralf Herwig, Ulrich Stelzl

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 659 KB

english, 2012

168

Improving the thermostability of alpha-amylase by combinatorial coevolving-site saturation mutagenesis

Chenghua Wang, Ribo Huang, Bingfang He, Qishi Du

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 533 KB

english, 2012

169

Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource

Thomas J Sharpton, Guillaume Jospin, Dongying Wu, Morgan GI Langille, Katherine S Pollard, Jonathan A Eisen

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 611 KB

english, 2012

170

Supervised segmentation of phenotype descriptions for the human skeletal phenome using hybrid methods

Tudor Groza, Jane Hunter, Andreas Zankl

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 227 KB

english, 2012

171

MetNet Online: a novel integrated resource for plant systems biology

Yves Sucaet, Yi Wang, Jie Li, Eve Syrkin Wurtele

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 587 KB

english, 2012

172

Simple regression models as a threshold for selecting AFLP loci with reduced error rates

David L Price, Michael D Casler

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 299 KB

english, 2012

173

dsPIG: a tool to predict imprinted genes from the deep sequencing of whole transcriptomes

Hua Li, Xiao Su, Juan Gallegos, Yue Lu, Yuan Ji, Jeffrey J Molldrem, Shoudan Liang

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 610 KB

english, 2012

174

Gene expression anti-profiles as a basis for accurate universal cancer signatures

Héctor Corrada Bravo, Vasyl Pihur, Matthew McCall, Rafael A Irizarry, Jeffrey T Leek

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.58 MB

english, 2012

175

Identification of polymorphic inversions from genotypes

Alejandro Cáceres, Suzanne S Sindi, Benjamin J Raphael, Mario Cáceres, Juan R González

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 589 KB

english, 2012

176

Identifying structural domains of proteins using clustering

Howard J Feldman

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 601 KB

english, 2012

177

PAnalyzer: A software tool for protein inference in shotgun proteomics

Gorka Prieto, Kerman Aloria, Nerea Osinalde, Asier Fullaondo, Jesus M Arizmendi, Rune Matthiesen

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 813 KB

english, 2012

178

The utility of comparative models and the local model quality for protein crystal structure determination by Molecular Replacement

Marcin Pawlowski, Janusz M Bujnicki

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 329 KB

english, 2012

179

Method: automatic segmentation of mitochondria utilizing patch classification, contour pair classification, and automatically seeded level sets

Richard J Giuly, Maryann E Martone, Mark H Ellisman

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.42 MB

english, 2012

180

Effective inter-residue contact definitions for accurate protein fold recognition

Chao Yuan, Hao Chen, Daisuke Kihara

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.38 MB

english, 2012

181

Effects of protein interaction data integration, representation and reliability on the use of network properties for drug target prediction

Antonio Mora, Ian M Donaldson

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 293 KB

english, 2012

182

Oculus: faster sequence alignment by streaming read compression

Brendan A Veeneman, Matthew K Iyer, Arul M Chinnaiyan

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 215 KB

english, 2012

183

Human-specific protein isoforms produced by novel splice sites in the human genome after the human-chimpanzee divergence

Dong Seon Kim, Yoonsoo Hahn

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 411 KB

english, 2012

184

Self-organizing ontology of biochemically relevant small molecules

Leonid L Chepelev, Janna Hastings, Marcus Ennis, Christoph Steinbeck, Michel Dumontier

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 798 KB

english, 2012

185

ICGE: anRpackage for detecting relevant clusters and atypical units in gene expression

Itziar Irigoien, Basilio Sierra, Concepcion Arenas

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 275 KB

english, 2012

186

NRE: a tool for exploring neutral loci in the human genome

Leonardo Arbiza, Elaine Zhong, Alon Keinan

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 192 KB

english, 2012

187

PolySac3DB: an annotated data base of 3 dimensional structures of polysaccharides

Anita Sarkar, Serge Pérez

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 955 KB

english, 2012

188

Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model

Kristof De Beuf, Joachim De Schrijver, Olivier Thas, Wim Van Criekinge, Rafael A Irizarry, Lieven Clement

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 289 KB

english, 2012

189

An assessment on epitope prediction methods for protozoa genomes

Daniela M Resende, Antônio M Rezende, Nesley JD Oliveira, Izabella CA Batista, Rodrigo Corrêa-Oliveira, Alexandre B Reis, Jeronimo C Ruiz

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 544 KB

english, 2012

190

Automatic design of decision-tree induction algorithms tailored to flexible-receptor docking data

Rodrigo C Barros, Ana T Winck, Karina S Machado, Márcio P Basgalupp, André CPLF de Carvalho, Duncan D Ruiz, Osmar Norberto de Souza

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 538 KB

english, 2012

191

Bioinformatics resource manager v2.3: an integrated software environment for systems biology with microRNA and cross-species analysis tools

Susan C Tilton, Tamara L Tal, Sheena M Scroggins, Jill A Franzosa, Elena S Peterson, Robert L Tanguay, Katrina M Waters

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.52 MB

english, 2012

192

Core Hunter II: fast core subset selection based on multiple genetic diversity measures using Mixed Replica search

Herman De Beukelaer, Petr Smýkal, Guy F Davenport, Veerle Fack

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.93 MB

english, 2012

193

EpicCapo: epitope prediction using combined information of amino acid pairwise contact potentials and HLA-peptide contact site information

Thammakorn Saethang, Osamu Hirose, Ingorn Kimkong, Vu Anh Tran, Xuan Tho Dang, Lan Anh T Nguyen, Tu Kien T Le, Mamoru Kubo, Yoichi Yamada, Kenji Satou

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 428 KB

english, 2012

194

A Monte Carlo-based framework enhances the discovery and interpretation of regulatory sequence motifs

Phillip Seitzer, Elizabeth G Wilbanks, David J Larsen, Marc T Facciotti

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 847 KB

english, 2012

195

On the contributions of topological features to transcriptional regulatory network robustness

Faiyaz Al Zamal, Derek Ruths

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 570 KB

english, 2012

196

SNPEVG: a graphical tool for GWAS graphing with mouse clicks

Shengwen Wang, Daniel Dvorkin, Yang Da

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 568 KB

english, 2012

197

CodingMotif: exact determination of overrepresented nucleotide motifs in coding sequences

Yang Ding, William A Lorenz, Jeffrey H Chuang

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 602 KB

english, 2012

198

Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework

Steven Lewis, Attila Csordas, Sarah Killcoyne, Henning Hermjakob, Michael R Hoopmann, Robert L Moritz, Eric W Deutsch, John Boyle

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 345 KB

english, 2012

199

BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins

Matti Kankainen, Teija Ojala, Liisa Holm

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.17 MB

english, 2012

200

A Computational model for compressed sensing RNAi cellular screening

Hua Tan, Jing Fan, Jiguang Bao, Jennifer G Dy, Xiaobo Zhou

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.02 MB

english, 2012

201

PPINGUIN: Peptide Profiling Guided Identification of Proteins improves quantitation of iTRAQ ratios

Chris Bauer, Frank Kleinjung, Dorothea Rutishauser, Christian Panse, Alexandra Chadt, Tanja Dreja, Hadi Al-Hasani, Knut Reinert, Ralph Schlapbach, Johannes Schuchhardt

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 324 KB

english, 2012

202

Assessing statistical significance in causal graphs

Leonid Chindelevitch, Po-Ru Loh, Ahmed Enayetallah, Bonnie Berger, Daniel Ziemek

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 402 KB

english, 2012

203

miRTrail - a comprehensive webserver for analyzing gene and miRNA patterns to enhance the understanding of regulatory mechanisms in diseases

Cedric Laczny, Petra Leidinger, Jan Haas, Nicole Ludwig, Christina Backes, Andreas Gerasch, Michael Kaufmann, Britta Vogel, Hugo A Katus, Benjamin Meder, Cord Stähler, Eckart Meese, Hans-Peter Lenhof,

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.13 MB

english, 2012

204

Non-negative matrix factorisation methods for the spectral decomposition of MRS data from human brain tumours

Sandra Ortega-Martorell, Paulo JG Lisboa, Alfredo Vellido, Margarida Julià-Sapé, Carles Arús

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 471 KB

english, 2012

205

Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets

Paul Ashford, David S Moss, Alexander Alex, Siew K Yeap, Alice Povia, Irene Nobeli, Mark A Williams

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.20 MB

english, 2012

206

A comparison study on feature selection of DNA structural properties for promoter prediction

Yanglan Gan, Jihong Guan, Shuigeng Zhou

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 552 KB

english, 2012

207

Predicting protein-protein interface residues using local surface structural similarity

Rafael A Jordan, Yasser EL-Manzalawy, Drena Dobbs, Vasant Honavar

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.93 MB

english, 2012

208

Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance

Zhang Zhang, Jun Li, Peng Cui, Feng Ding, Ang Li, Jeffrey P Townsend, Jun Yu

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 283 KB

english, 2012

209

Grading amino acid properties increased accuracies of single point mutation on protein stability prediction

Jianguo Liu, Xianjiang Kang

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 277 KB

english, 2012

210

Arena3D: visualizing time-driven phenotypic differences in biological systems

Maria Secrier, Georgios A Pavlopoulos, Jan Aerts, Reinhard Schneider

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 722 KB

english, 2012

211

Correlation set analysis: detecting active regulators in disease populations using prior causal knowledge

Chia-Ling Huang, John Lamb, Leonid Chindelevitch, Jarek Kostrowicki, Justin Guinney, Charles DeLisi, Daniel Ziemek

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 954 KB

english, 2012

212

Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II

John Archer, Greg Baillie, Simon J Watson, Paul Kellam, Andrew Rambaut, David L Robertson

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.06 MB

english, 2012

213

Structural features based genome-wide characterization and prediction of nucleosome organization

Yanglan Gan, Jihong Guan, Shuigeng Zhou, Weixiong Zhang

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 579 KB

english, 2012

214

proTRAC - a software for probabilistic piRNA cluster detection, visualization and analysis

David Rosenkranz, Hans Zischler

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 506 KB

english, 2012

215

The Bone Dysplasia Ontology: integrating genotype and phenotype information in the skeletal dysplasia domain

Tudor Groza, Jane Hunter, Andreas Zankl

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 507 KB

english, 2012

216

Progressive dry-core-wet-rim hydration trend in a nested-ring topology of protein binding interfaces

Zhenhua Li, Ying He, Limsoon Wong, Jinyan Li

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 714 KB

english, 2012

217

Detecting disease-associated genes with confounding variable adjustment and the impact on genomic meta-analysis: With application to major depressive disorder

Xingbin Wang, Yan Lin, Chi Song, Etienne Sibille, George C Tseng

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.06 MB

english, 2012

218

Mouse obesity network reconstruction with a variational Bayes algorithm to employ aggressive false positive control

Benjamin A Logsdon, Gabriel E Hoffman, Jason G Mezey

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.35 MB

english, 2012

219

Mining biological information from 3D short time-series gene expression data: the OPTricluster algorithm

Alain B Tchagang, Sieu Phan, Fazel Famili, Heather Shearer, Pierre Fobert, Yi Huang, Jitao Zou, Daiqing Huang, Adrian Cutler, Ziying Liu, Youlian Pan

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 951 KB

english, 2012

220

CLIPS-1D: analysis of multiple sequence alignments to deduce for residue-positions a role in catalysis, ligand-binding, or protein structure

Jan-Oliver Janda, Markus Busch, Fabian Kück, Mikhail Porfenenko, Rainer Merkl

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 404 KB

english, 2012

221

'maskBAD' - a package to detect and remove Affymetrix probes with binding affinity differences

Michael Dannemann, Michael Lachmann, Anna Lorenc

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 301 KB

english, 2012

222

F2C2: a fast tool for the computation of flux coupling in genome-scale metabolic networks

Abdelhalim Larhlimi, Laszlo David, Joachim Selbig, Alexander Bockmayr

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 321 KB

english, 2012

223

Methods for visual mining of genomic and proteomic data atlases

John Boyle, Richard Kreisberg, Ryan Bressler, Sarah Killcoyne

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.39 MB

english, 2012

224

A comparison of feature selection and classification methods in DNA methylation studies using the Illumina Infinium platform

Joanna Zhuang, Martin Widschwendter, Andrew E Teschendorff

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 481 KB

english, 2012

225

MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases

Akhil Kumar, Patrick F Suthers, Costas D Maranas

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 558 KB

english, 2012

226

Is EC class predictable from reaction mechanism?

Neetika Nath, John BO Mitchell

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 528 KB

english, 2012

227

EnzML: multi-label prediction of enzyme classes using InterPro signatures

Luna De Ferrari, Stuart Aitken, Jano van Hemert, Igor Goryanin

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 699 KB

english, 2012

228

CBDB: The codon bias database

Adam Hilterbrand, Joseph Saelens, Catherine Putonti

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 321 KB

english, 2012

229

Predicting the outer membrane proteome ofPasteurella multocidabased on consensus prediction enhanced by results integration and manual confirmation

Teerasak E-komon, Richard Burchmore, Pawel Herzyk, Robert Davies

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 924 KB

english, 2012

230

Comprehensive comparison of graph based multiple protein sequence alignment strategies

Ilya Plyusnin, Liisa Holm

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 258 KB

english, 2012

231

The MULTICOM toolbox for protein structure prediction

Jianlin Cheng, Jilong Li, Zheng Wang, Jesse Eickholt, Xin Deng

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 690 KB

english, 2012

232

T3DB: an integrated database for bacterial type III secretion system

Yejun Wang, He Huang, Ming’an Sun, Qing Zhang, Dianjing Guo

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 283 KB

english, 2012

233

Fitting hidden Markov models of protein domains to a target species: application toPlasmodium falciparum

Nicolas Terrapon, Olivier Gascuel, Éric Maréchal, Laurent Bréhélin

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 498 KB

english, 2012

234

Accelerated maximum likelihood parameter estimation for stochastic biochemical systems

Bernie J Daigle Jr, Min K Roh, Linda R Petzold, Jarad Niemi

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 664 KB

english, 2012

235

Prognostic gene signatures for patient stratification in breast cancer - accuracy, stability and interpretability of gene selection approaches using prior knowledge on protein-protein interactions

Yupeng Cun, Holger FröhlichHolger Fröhlich

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.20 MB

english, 2012

236

Protein docking prediction using predicted protein-protein interface

Bin Li, Daisuke Kihara

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.85 MB

english, 2012

237

A unified computational model for revealing and predicting subtle subtypes of cancers

Xianwen Ren, Yong Wang, Jiguang Wang, Xiang-Sun Zhang

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 300 KB

english, 2012

238

Cancer bioinformatics: A new approach to systems clinical medicine

Duojiao Wu, Catherine M Rice, Xiangdong Wang

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 139 KB

english, 2012

239

Ultrahigh-dimensional variable selection method for whole-genome gene-gene interaction analysis

Masao Ueki, Gen Tamiya

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 693 KB

english, 2012

240

A Bayesian variable selection procedure to rank overlapping gene sets

Axel Skarman, Mohammad Shariati, Luc Jans, Li Jiang, Peter Sørensen

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 343 KB

english, 2012

241

Metaprotein expression modeling for label-free quantitative proteomics

Joseph E Lucas, J Will Thompson, Laura G Dubois, Jeanette McCarthy, Hans Tillmann, Alexander Thompson, Norah Shire, Ron Hendrickson, Francisco Dieguez, Phyllis Goldman, Kathleen Schwarz, Keyur Patel,

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.25 MB

english, 2012

242

Quantitatively integrating molecular structure and bioactivity profile evidence into drug-target relationship analysis

Tianlei Xu, Ruixin Zhu, Qi Liu, Zhiwei Cao

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 594 KB

english, 2012

243

EpiFire: An open source C++ library and application for contact network epidemiology

Thomas Hladish, Eugene Melamud, Luis Alberto Barrera, Alison Galvani, Lauren Ancel Meyers

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 552 KB

english, 2012

244

Tavaxy: Integrating Taverna and Galaxy workflows with cloud computing support

Mohamed Abouelhoda, Shadi Alaa Issa, Moustafa Ghanem

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.52 MB

english, 2012

245

An integrative variant analysis suite for whole exome next-generation sequencing data

Danny Challis, Jin Yu, Uday S Evani, Andrew R Jackson, Sameer Paithankar, Cristian Coarfa, Aleksandar Milosavljevic, Richard A Gibbs, Fuli Yu

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 557 KB

english, 2012

246

Matching of array CGH and gene expression microarray features for the purpose of integrative genomic analyses

Wessel N van Wieringen, Kristian Unger, Gwenaël GR Leday, Oscar Krijgsman, Renée X de Menezes, Bauke Ylstra, Mark A van de Wiel

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 337 KB

english, 2012

247

Detecting long tandem duplications in genomic sequences

Eric Audemard, Thomas Schiex, Thomas Faraut

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 403 KB

english, 2012

248

Augmented annotation and orthologue analysis forOryctolagus cuniculus: Better Bunny

Douglas B Craig, Sujatha Kannan, Alan A Dombkowski

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 483 KB

english, 2012

249

DIPSBC - data integration platform for systems biology collaborations

Felix Dreher, Thomas Kreitler, Christopher Hardt, Atanas Kamburov, Reha Yildirimman, Karl Schellander, Hans Lehrach, Bodo MH Lange, Ralf Herwig

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.22 MB

english, 2012

250

DNA methylation arrays as surrogate measures of cell mixture distribution

Eugene Andres Houseman, William P Accomando, Devin C Koestler, Brock C Christensen, Carmen J Marsit, Heather H Nelson, John K Wiencke, Karl T Kelsey

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 548 KB

english, 2012

251

PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods

Alexandre P Francisco, Ctia Vaz, Pedro T Monteiro, José Melo-Cristino, Mário Ramirez, Joo A Carrio

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 2.46 MB

english, 2012

252

SparSNP: Fast and memory-efficient analysis of all SNPs for phenotype prediction

Gad Abraham, Adam Kowalczyk, Justin Zobel, Michael Inouye

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 228 KB

english, 2012

253

Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art

Rasna R Walia, Cornelia Caragea, Benjamin A Lewis, Fadi Towfic, Michael Terribilini, Yasser El-Manzalawy, Drena Dobbs, Vasant Honavar

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 820 KB

english, 2012

254

PyElph - a software tool for gel images analysis and phylogenetics

Ana Brânduşa Pavel, Cristian Ioan Vasile

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 570 KB

english, 2012

255

GeVaDSs – decision support system for novel Genetic Vaccine development process

Jacek Blazewicz, Marcin Borowski, Wahiba Chaara, Pawel Kedziora, David Klatzmann, Piotr Lukasiak, Adrien Six, Pawel Wojciechowski

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.98 MB

english, 2012

256

A comparative evaluation of sequence classification programs

Adam L Bazinet, Michael P Cummings

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 309 KB

english, 2012

257

Anin silicoplatform for the design of heterologous pathways in nonnative metabolite production

Sunisa Chatsurachai, Chikara Furusawa, Hiroshi Shimizu

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 438 KB

english, 2012

258

Integrating biological knowledge into variable selection: an empirical Bayes approach with an application in cancer biology

Steven M Hill, Richard M Neve, Nora Bayani, Wen-Lin Kuo, Safiyyah Ziyad, Paul T Spellman, Joe W Gray, Sach Mukherjee

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 578 KB

english, 2012

259

3DMolNavi: A web-based retrieval and navigation tool for flexible molecular shape comparison

Yu-Shen Liu, Meng Wang, Jean-Claude Paul, Karthik Ramani

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 318 KB

english, 2012

260

SIS: a program to generate draft genome sequence scaffolds for prokaryotes

Zanoni Dias, Ulisses Dias, João C Setubal

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 467 KB

english, 2012

261

Exploration of multivariate analysis in microbial coding sequence modeling

Tahir Mehmood, Jon Bohlin, Anja Bråthen Kristoffersen, Solve Sæbø, Jonas Warringer, Lars Snipen

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 251 KB

english, 2012

262

The partitioned LASSO-patternsearch algorithm with application to gene expression data

Weiliang Shi, Grace Wahba, Rafael A Irizarry, Hector Corrada Bravo, Stephen J Wright

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 340 KB

english, 2012

263

MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity

Dinesh K Barupal, Pradeep K Haldiya, Gert Wohlgemuth, Tobias Kind, Shanker L Kothari, Kent E Pinkerton, Oliver Fiehn

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.28 MB

english, 2012

264

Protein interface classification by evolutionary analysis

Duarte, Jose M, Srebniak, Adam, SchÃ¤rer, Martin A, Capitani, Guido

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 2.39 MB

english, 2012

265

G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes

Lemay, Danielle G, Martin, William F, Hinrichs, Angie S, Rijnkels, Monique, German, J Bruce, Korf, Ian, Pollard, Katherine S

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 2.26 MB

english, 2012

266

Copy number variation signature to predict human ancestry

Melissa Pronold, Marzieh Vali, Roger Pique-Regi, Shahab Asgharzadeh

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 520 KB

english, 2012

267

Unlocking the potential of publicly available microarray data using inSilicoDb and inSilicoMerging R/Bioconductor packages

Jonatan Taminau, Stijn Meganck, Cosmin Lazar, David Steenhoff…

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 234 KB

english, 2012

268

RNAmap2D – calculation, visualization and analysis of contact and distance maps for RNA and protein-RNA complex structures

Michal J Pietal, Natalia Szostak, Kristian M Rother…

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.28 MB

english, 2012

269

Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study

Lei Sun, Zhihua Zhang, Timothy L Bailey, Andrew C Perkins…

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.10 MB

english, 2012

270

Fast detection of de novo copy number variants from SNP arrays for case-parent trios

Robert B Scharpf, Terri H Beaty, Holger Schwender, Samuel G Younkin…

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1020 KB

english, 2012

271

Generalization of the normal-exponential model: exploration of a more accurate parametrisation for the signal distribution on Illumina BeadArrays

Sandra Plancade, Yves Rozenholc, Eiliv Lund

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 696 KB

english, 2012

272

Comparison of co-expression measures: mutual information, correlation, and model based indices

Lin Song, Peter Langfelder, Steve Horvath

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.64 MB

english, 2012

273

Improving stability and understandability of genotype-phenotype mapping inSaccharomycesusing regularized variable selection in L-PLS regression

Tahir Mehmood, Jonas Warringer, Lars Snipen, Solve Sæbø

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 281 KB

english, 2012

274

A computational pipeline for the development of multi-marker bio-signature panels and ensemble classifiers

Oliver P Günther, Virginia Chen, Gabriela Cohen Freue…

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 560 KB

english, 2012

275

A novel approach for biomarker selection and the integration of repeated measures experiments from two assays

Benoit Liquet, Kim-Anh Lê Cao, Hakim Hocini, Rodolphe Thiébaut

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.69 MB

english, 2012

276

Flexible and efficient genome tiling design with penalized uniqueness score

Yang Du, Eduard Murani, Siriluck Ponsuksili, Klaus Wimmers

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 575 KB

english, 2012

277

Finding quasi-modules of human and viral miRNAs: a case study of human cytomegalovirus (HCMV)

Isana Veksler-Lublinsky, Yonat Shemer-Avni, Eti Meiri, Zvi Bentwich…

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.35 MB

english, 2012

278

Learning virulent proteins from integrated query networks

Eithon Cadag, Peter Tarczy-Hornoch, Peter J Myler

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 927 KB

english, 2012

279

Multiple-platform data integration method with application to combined analysis of microarray and proteomic data

Shicheng Wu, Yawen Xu, Zeny Feng, Xiaojian Yang, Xiaogang Wang…

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.10 MB

english, 2012

280

TeraStitcher - A tool for fast automatic 3D-stitching of teravoxel-sized microscopy images

Alessandro Bria, Giulio Iannello

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.27 MB

english, 2012

281

CloudMan as a platform for tool, data, and analysis distribution

Enis Afgan, Brad Chapman, James Taylor

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 315 KB

english, 2012

282

Local functional descriptors for surface comparison based binding prediction

Gregory M Cipriano, George N Phillips Jr, Michael Gleicher

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.26 MB

english, 2012

283

Estimating relative abundances of proteins from shotgun proteomics data

Sean McIlwain, Michael Mathews, Michael S Bereman, Edwin W Rubel…

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.18 MB

english, 2012

284

Multiple graph regularized protein domain ranking

Jim Jing-Yan Wang, Halima Bensmail, Xin Gao

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 445 KB

english, 2012

285

Gains of ubiquitylation sites in highly conserved proteins in the human lineage

Dong Seon Kim, Yoonsoo Hahn

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 231 KB

english, 2012

286

Copy Number Variation detection from 1000 Genomes project exon capture sequencing data

Jiantao Wu, Krzysztof R Grzeda, Chip Stewart, Fabian Grubert…

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.11 MB

english, 2012

287

Improving protein coreference resolution by simple semantic classification

Ngan Nguyen, Jin-Dong Kim, Makoto Miwa, Takuya Matsuzaki…

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 433 KB

english, 2012

288

Clustering of time-course gene expression profiles using normal mixture models with autoregressive random effects

Kui Wang, Shu Kay Ng, Geoffrey J McLachlan

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 651 KB

english, 2012

289

Improving accuracy for cancer classification with a new algorithm for genes selection

Hongyan Zhang, Haiyan Wang, Zhijun Dai, Ming-shun Chen, Zheming Yuan

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 906 KB

english, 2012

290

Quantitative fluorescence loss in photobleaching for analysis of protein transport and aggregation

Daniel Wüstner, Lukasz M Solanko, Frederik W Lund, Daniel Sage…

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.36 MB

english, 2012

291

iMS2Flux– a high–throughput processing tool for stable isotope labeled mass spectrometric data used for metabolic flux analysis

C Hart Poskar, Jan Huege, Christian Krach, Mathias Franke…

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 387 KB

english, 2012

292

The tree alignment problem

Andrés Varón, Ward C Wheeler

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 761 KB

english, 2012

293

Isotope pattern deconvolution for peptide mass spectrometry by non-negative least squares/least absolute deviation template matching

Martin Slawski, Rene Hussong, Andreas Tholey, Thomas Jakoby…

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 572 KB

english, 2012

294

mGOASVM: Multi-label protein subcellular localization based on gene ontology and support vector machines

Shibiao Wan, Man-Wai Mak, Sun-Yuan Kung

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 351 KB

english, 2012

295

MCMC-ODPR: Primer design optimization using Markov Chain Monte Carlo sampling

James L Kitchen, Jonathan D Moore, Sarah A Palmer, Robin G Allaby

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 220 KB

english, 2012

296

Dynamic changes in the secondary structure of ECE-1 and XCE account for their different substrate specificities

Zaheer Ul-Haq, Sadaf Iqbal, Syed Tarique Moin

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.49 MB

english, 2012

297

A novel algorithm for simultaneous SNP selection in high-dimensional genome-wide association studies

Verena Zuber, A Pedro Duarte Silva, Korbinian Strimmer

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 238 KB

english, 2012

298

Denoising PCR-amplified metagenome data

Michael J Rosen, Benjamin J Callahan, Daniel S Fisher, Susan P Holmes

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 467 KB

english, 2012

299

Cascaded discrimination of normal, abnormal, and confounder classes in histopathology: Gleason grading of prostate cancer

Scott Doyle, Michael D Feldman, Natalie Shih, John Tomaszewski…

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.88 MB

english, 2012

300

Efficient reconstruction of biological networks via transitive reduction on general purpose graphics processors

Dragan Bošnački, Maximilian R Odenbrett, Anton Wijs…

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 362 KB

english, 2012

301

Multi-scale RNA comparison based on RNA triple vector curve representation

Ying Li, Ming Duan, Yanchun Liang

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 971 KB

english, 2012

302

ChopSticks: High-resolution analysis of homozygous deletions by exploiting concordant read pairs

Tomohiro Yasuda, Shin Suzuki, Masao Nagasaki, Satoru Miyano

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 422 KB

english, 2012

303

Bayesian semiparametric regression models to characterize molecular evolution

Saheli Datta, Abel Rodriguez, Raquel Prado

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 484 KB

english, 2012

304

Simple binary segmentation frameworks for identifying variation in DNA copy number

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.50 MB

english, 2012

305

Coral: an integrated suite of visualizations for comparing clusterings

Darya Filippova, Aashish Gadani, Carl Kingsford

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 3.24 MB

english, 2012

306

Combing the hairball with BioFabric: a new approach for visualization of large networks

William JR Longabaugh

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.40 MB

english, 2012

307

A quantitative genetic and epigenetic model of complex traits

Zhong Wang, Zuoheng Wang, Jianxin Wang, Yihan Sui, Jian Zhang…

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 394 KB

english, 2012

308

Exploiting protein flexibility to predict the location of allosteric sites

Alejandro Panjkovich, Xavier Daura

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 459 KB

english, 2012

309

Combining multiple hypothesis testing and affinity propagation clustering leads to accurate, robust and sample size independent classification on gene expression data

Argiris Sakellariou, Despina Sanoudou, George Spyrou

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 557 KB

english, 2012

310

Gene Fusion Markup Language: a prototype for exchanging gene fusion data

Shanker Kalyana-Sundaram, Achiraman Shanmugam, Arul M Chinnaiyan

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 224 KB

english, 2012

311

Tissue-based Alzheimer gene expression markers–comparison of multiple machine learning approaches and investigation of redundancy in small biomarker sets

Lena Scheubert, Mitja Luštrek, Rainer Schmidt, Dirk Repsilber…

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.07 MB

english, 2012

312

Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment

Noah M Daniels, Shilpa Nadimpalli, Lenore J Cowen

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 273 KB

english, 2012

313

Coalescent: an open-source and scalable framework for exact calculations in coalescent theory

Susanta Tewari, John L Spouge

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 749 KB

english, 2012

314

Normalized N50 assembly metric using gap-restricted co-linear chaining

Veli Mäkinen, Leena Salmela, Johannes Ylinen

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 162 KB

english, 2012

315

The Process-Interaction-Model: a common representation of rule-based and logical models allows studying signal transduction on different levels of detail

Katrin Kolczyk, Regina Samaga, Holger Conzelmann, Sebastian Mirschel…

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.16 MB

english, 2012

316

HIDEN: Hierarchical decomposition of regulatory networks

Günhan Gülsoy, Nirmalya Bandhyopadhyay, Tamer Kahveci

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.15 MB

english, 2012

317

Quantitative biomedical annotation using medical subject heading over-representation profiles (MeSHOPs)

Warren A Cheung, BF Francis Ouellette, Wyeth W Wasserman

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.30 MB

english, 2012

318

The simulation of meiosis in diploid and tetraploid organisms using various genetic models

Roeland E Voorrips, Chris A Maliepaard

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 319 KB

english, 2012

319

ESTclean: a cleaning tool for next-gen transcriptome shotgun sequencing

Hongseok Tae, Dongsung Ryu, Suhas Sureshchandra, Jeong-Hyeon Choi

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 965 KB

english, 2012

320

An algorithm for chemical genomic profiling that minimizes batch effects: bucket evaluations

Daniel Shabtai, Guri Giaever, Corey Nislow

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.34 MB

english, 2012

321

Graph rigidity reveals well-constrained regions of chromosome conformation embeddings

Geet Duggal, Carl Kingsford

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 619 KB

english, 2012

322

Analysis of tiling array expression studies with flexible designs in Bioconductor (waveTiling)

Kristof De Beuf, Peter Pipelers, Megan Andriankaja, Olivier Thas…

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.03 MB

english, 2012

323

Highly improved homopolymer aware nucleotide-protein alignments with 454 data

Fredrik Lysholm

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 960 KB

english, 2012

324

Coupled mutation finder: A new entropy-based method quantifying phylogenetic noise for the detection of compensatory mutations

Mehmet Gültas, Martin Haubrock, Nesrin Tüysüz, Stephan Waack

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.01 MB

english, 2012

325

Improved model quality assessment using ProQ2

Arjun Ray, Erik Lindahl, Björn Wallner

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 291 KB

english, 2012

326

Wavelet-based detection of transcriptional activity on a novelStaphylococcus aureustiling microarray

Víctor Segura, Alejandro Toledo-Arana, Maite Uzqueda, Iñigo Lasa…

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.66 MB

english, 2012

327

Process attributes in bio-ontologies

André Q Andrade, Ward Blondé, Janna Hastings, Stefan Schulz

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 380 KB

english, 2012

328

Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython

Eric Talevich, Brandon M Invergo, Peter JA Cock, Brad A Chapman

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 321 KB

english, 2012

329

GSA-PCA: gene set generation by principal component analysis of the Laplacian matrix of a metabolic network

Dan Jacobson, Guy Emerton

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.09 MB

english, 2012

330

Network-enabled gene expression analysis

David Edwards, Lei Wang, Peter Sørensen

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 459 KB

english, 2012

331

Evaluating the effect of disturbed ensemble distributions on SCFG based statistical sampling of RNA secondary structures

Anika Scheid, Markus E Nebel

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 756 KB

english, 2012

332

Bayesian model to detect phenotype-specific genes for copy number data

Juan R González, Carlos Abellán, Juan J Abellán

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.28 MB

english, 2012

333

ROCS: a Reproducibility Index and Confidence Score for Interaction Proteomics Studies

Jean-Eudes Dazard, Sudipto Saha, Rob M Ewing

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 960 KB

english, 2012

334

Web tools for large-scale 3D biological images and atlases

Zsolt L Husz, Nicholas Burton, Bill Hill, Nestor Milyaev…

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.74 MB

english, 2012

335

False discovery rate control in two-stage designs

Zehetmayer, Sonja, Posch, Martin

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 238 KB

english, 2012

336

Integrated QSAR study for inhibitors of hedgehog signal pathway against multiple cell lines:a collaborative filtering method

Gao, Jun, Che, Dongsheng, Zheng, Vincent W, Zhu, Ruixin, Liu, Qi

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 3.35 MB

english, 2012

337

Evolving stochastic context--free grammars for RNA secondary structure prediction

WJ Anderson, James, Tataru, Paula, Staines, Joe, Hein, Jotun, Lyngsø, Rune

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 718 KB

english, 2012