Academic Journals Database
Disseminating quality controlled scientific knowledge

BMC Bioinformatics

ISSN: 1471--2105
Publisher: BioMed Central


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Detecting genomic regions associated with a disease using variability functions and Adjusted Rand Index

Author(s): Badescu Dunarel | Boc Alix | Diallo Abdoulaye | Makarenkov Vladimir
Volume: 12
Issue: Suppl 9
Year: 2011
Genomic distance under gene substitutions

Author(s): Braga Marília | Machado Raphael | Ribeiro Leonardo | Stoye Jens
Volume: 12
Issue: Suppl 9
Year: 2011
A method for computing an inventory of metazoan mitochondrial gene order rearrangements

Author(s): Bernt Matthias | Middendorf Martin
Volume: 12
Issue: Suppl 9
Year: 2011
Fractionation statistics

Author(s): Wang Baoyong | Zheng Chunfang | Sankoff David
Volume: 12
Issue: Suppl 9
Year: 2011
Fast and accurate methods for phylogenomic analyses

Author(s): Yang Jimmy | Warnow Tandy
Volume: 12
Issue: Suppl 9
Year: 2011
The genomic features that affect the lengths of 5’ untranslated regions in multicellular eukaryotes

Author(s): Chen Chun-Hsi | Lin Hsuan-Yu | Pan Chia-Lin | Chen Feng-Chi
Volume: 12
Issue: Suppl 9
Year: 2011
Consistency-based detection of potential tumor-specific deletions in matched normal/tumor genomes

Author(s): Wittler Roland | Chauve Cedric
Volume: 12
Issue: Suppl 9
Year: 2011
Genome dedoubling by DCJ and reversal

Author(s): Thomas Antoine | Varré Jean-Stéphane | Ouangraoua Aïda
Volume: 12
Issue: Suppl 9
Year: 2011
Evolution of orthologous tandemly arrayed gene clusters

Author(s): Tremblay Savard Olivier | Bertrand Denis | El-Mabrouk Nadia
Volume: 12
Issue: Suppl 9
Year: 2011
Changes in transcriptional orientation are associated with increases in evolutionary rates of enterobacterial genes

Author(s): Lin Chieh-Hua | Lian Chun-Yi | Hsiung Chao | Chen Feng-Chi
Volume: 12
Issue: Suppl 9
Year: 2011
Identification of conserved gene clusters in multiple genomes based on synteny and homology

Author(s): Sarkar Anasua | Soueidan Hayssam | Nikolski Macha
Volume: 12
Issue: Suppl 9
Year: 2011
Approximating the double-cut-and-join distance between unsigned genomes

Author(s): Chen Xin | Sun Ruimin | Yu Jiadong
Volume: 12
Issue: Suppl 9
Year: 2011
Evidence for intron length conservation in a set of mammalian genes associated with embryonic development

Author(s): Seoighe Cathal | Korir Paul
Volume: 12
Issue: Suppl 9
Year: 2011
STELLAR: fast and exact local alignments

Author(s): Kehr Birte | Weese David | Reinert Knut
Volume: 12
Issue: Suppl 9
Year: 2011
Origin and evolution of gene families in Bacteria and Archaea

Author(s): Collins R | Merz Hugh | Higgs Paul
Volume: 12
Issue: Suppl 9
Year: 2011
On the weight of indels in genomic distances

Author(s): Braga Marília | Machado Raphael | Ribeiro Leonardo | Stoye Jens
Volume: 12
Issue: Suppl 9
Year: 2011
Efficient algorithms for reconstructing gene content by co-evolution

Author(s): Birin Hadas | Tuller Tamir
Volume: 12
Issue: Suppl 9
Year: 2011
Constraints on genes shape long-term conservation of macro-synteny in metazoan genomes

Author(s): Lv Jie | Havlak Paul | Putnam Nicholas
Volume: 12
Issue: Suppl 9
Year: 2011
The evolution of the tape measure protein: units, duplications and losses

Author(s): Belcaid Mahdi | Bergeron Anne | Poisson Guylaine
Volume: 12
Issue: Suppl 9
Year: 2011
The rise and fall of breakpoint reuse depending on genome resolution

Author(s): Attie Oliver | Darling Aaron | Yancopoulos Sophia
Volume: 12
Issue: Suppl 9
Year: 2011
ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining

Author(s): Huan Tianxiao | Sivachenko Andrey | Harrison Scott | Chen Jake
Volume: 9
Issue: Suppl 9
Year: 2008
From microarray to biology: an integrated experimental, statistical and in silico analysis of how the extracellular matrix modulates the phenotype of cancer cells

Author(s): Dozmorov Mikhail | Kyker Kimberly | Hauser Paul | Saban Ricardo | Buethe David | Dozmorov Igor | Centola Michael | Culkin Daniel | Hurst Robert
Volume: 9
Issue: Suppl 9
Year: 2008
A structural approach for finding functional modules from large biological networks

Author(s): Mete Mutlu | Tang Fusheng | Xu Xiaowei | Yuruk Nurcan
Volume: 9
Issue: Suppl 9
Year: 2008
Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples

Author(s): Hong Huixiao | Su Zhenqiang | Ge Weigong | Shi Leming | Perkins Roger | Fang Hong | Xu Joshua | Chen James | Han Tao | Kaput Jim | Fuscoe James | Tong Weida
Volume: 9
Issue: Suppl 9
Year: 2008
Time-dependent ARMA modeling of genomic sequences

Author(s): Zielinski Jerzy | Bouaynaya Nidhal | Schonfeld Dan | O'Neill William
Volume: 9
Issue: Suppl 9
Year: 2008
Clustering ionic flow blockade toggles with a Mixture of HMMs

Author(s): Churbanov Alexander | Winters-Hilt Stephen
Volume: 9
Issue: Suppl 9
Year: 2008
The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies

Author(s): Shi Leming | Jones Wendell | Jensen Roderick | Harris Stephen | Perkins Roger | Goodsaid Federico | Guo Lei | Croner Lisa | Boysen Cecilie | Fang Hong | Qian Feng | Amur Shashi | Bao Wenjun | Barbacioru Catalin | Bertholet Vincent | Cao Xiaoxi | Chu Tzu-Ming | Collins Patrick | Fan Xiao-hui | Frueh Felix | Fuscoe James | Guo Xu | Han Jing | Herman Damir | Hong Huixiao | Kawasaki Ernest | Li Quan-Zhen | Luo Yuling | Ma Yunqing | Mei Nan | Peterson Ron | Puri Raj | Shippy Richard | Su Zhenqiang | Sun Yongming | Sun Hongmei | Thorn Brett | Turpaz Yaron | Wang Charles | Wang Sue | Warrington Janet | Willey James | Wu Jie | Xie Qian | Zhang Liang | Zhang Lu | Zhong Sheng | Wolfinger Russell | Tong Weida
Volume: 9
Issue: Suppl 9
Year: 2008
Very Important Pool (VIP) genes – an application for microarray-based molecular signatures

Author(s): Su Zhenqiang | Hong Huixiao | Fang Hong | Shi Leming | Perkins Roger | Tong Weida
Volume: 9
Issue: Suppl 9
Year: 2008
Systems biology approach to identification of biomarkers for metastatic progression in cancer

Author(s): Ptitsyn Andrey | Weil Michael | Thamm Douglas
Volume: 9
Issue: Suppl 9
Year: 2008
A comparison study on algorithms of detecting long forms for short forms in biomedical text

Author(s): Torii Manabu | Hu Zhang-zhi | Song Min | Wu Cathy | Liu Hongfang
Volume: 8
Issue: Suppl 9
Year: 2007
GO for gene documents

Author(s): Srinivasan Padmini | Qiu Xin Ying
Volume: 8
Issue: Suppl 9
Year: 2007
BioCAD: an information fusion platform for bio-network inference and analysis

Author(s): Lee Doheon | Kim Sangwoo | Kim Younghoon
Volume: 8
Issue: Suppl 9
Year: 2007
An integrative method for scoring candidate genes from association studies: application to warfarin dosing

Author(s): Tatonetti Nicholas | Dudley Joel | Sagreiya Hersh | Butte Atul | Altman Russ
Volume: 11
Issue: Suppl 9
Year: 2010
Mining multi-item drug adverse effect associations in spontaneous reporting systems

Author(s): Harpaz Rave | Chase Herbert | Friedman Carol
Volume: 11
Issue: Suppl 9
Year: 2010
Using gene co-expression network analysis to predict biomarkers for chronic lymphocytic leukemia

Author(s): Zhang Jie | Xiang Yang | Ding Liya | Keen-Circle Kristin | Borlawsky Tara | Ozer Hatice | Jin Ruoming | Payne Philip | Huang Kun
Volume: 11
Issue: Suppl 9
Year: 2010
Multi-dimensional discovery of biomarker and phenotype complexes

Author(s): Payne Philip | Huang Kun | Keen-Circle Kristin | Kundu Abhisek | Zhang Jie | Borlawsky Tara
Volume: 11
Issue: Suppl 9
Year: 2010
Structural similarity assessment for drug sensitivity prediction in cancer PDF available

Author(s): Shivakumar Pavithra | Krauthammer Michael
Volume: 10
Issue: Suppl 9
Year: 2009
Feature selection for fMRI-based deception detection PDF available

Author(s): Jin Bo | Strasburger Alvin | Laken Steven | Kozel F Andrew | Johnson Kevin | George Mark | Lu Xinghua
Volume: 10
Issue: Suppl 9
Year: 2009
Developing a manually annotated clinical document corpus to identify phenotypic information for inflammatory bowel disease PDF available

Author(s): South Brett | Shen Shuying | Jones Makoto | Garvin Jennifer | Samore Matthew | Chapman Wendy | Gundlapalli Adi
Volume: 10
Issue: Suppl 9
Year: 2009
Transcriptional network classifiers PDF available

Author(s): Chang Hsun-Hsien | Ramoni Marco
Volume: 10
Issue: Suppl 9
Year: 2009
PAPAyA: a platform for breast cancer biomarker signature discovery, evaluation and assessment PDF available

Author(s): Janevski Angel | Kamalakaran Sitharthan | Banerjee Nilanjana | Varadan Vinay | Dimitrova Nevenka
Volume: 10
Issue: Suppl 9
Year: 2009
Mechanism-anchored profiling derived from epigenetic networks predicts outcome in acute lymphoblastic leukemia PDF available

Author(s): Yang Xinan | Huang Yong | Chen James | Xie Jianming | Sun Xiao | Lussier Yves
Volume: 10
Issue: Suppl 9
Year: 2009
Network analysis of genes regulated in renal diseases: implications for a molecular-based classification PDF available

Author(s): Bhavnani Suresh | Eichinger Felix | Martini Sebastian | Saxman Paul | Jagadish HV | Kretzler Matthias
Volume: 10
Issue: Suppl 9
Year: 2009
Analysis of AML genes in dysregulated molecular networks PDF available

Author(s): Lee Eunjung | Jung Hyunchul | Radivojac Predrag | Kim Jong-Won | Lee Doheon
Volume: 10
Issue: Suppl 9
Year: 2009
Assessing the quality of annotations in asthma gene expression experiments

Author(s): Lacson Ronilda | Mbagwu Michael | Yousif Hisham | Ohno-Machado Lucila
Volume: 11
Issue: Suppl 9
Year: 2010
Comparison of multiplex meta analysis techniques for understanding the acute rejection of solid organ transplants

Author(s): Morgan Alexander | Khatri Purvesh | Jones Richard | Sarwal Minnie | Butte Atul
Volume: 11
Issue: Suppl 9
Year: 2010
Assessment of genetic variation for the LINE-1 retrotransposon from next generation sequence data

Author(s): Rouchka Eric | Montoya-Durango Diego E | Stribinskis Vilius | Ramos Kenneth | Kalbfleisch Ted
Volume: 11
Issue: Suppl 9
Year: 2010
Feasibility of incorporating genomic knowledge into electronic medical records for pharmacogenomic clinical decision support

Author(s): Overby Casey | Tarczy-Hornoch Peter | Hoath James | Kalet Ira | Veenstra David
Volume: 11
Issue: Suppl 9
Year: 2010
Knowledge-based variable selection for learning rules from proteomic data PDF available

Author(s): Lustgarten Jonathan | Visweswaran Shyam | Bowser Robert | Hogan William | Gopalakrishnan Vanathi
Volume: 10
Issue: Suppl 9
Year: 2009
Evaluation of a large-scale biomedical data annotation initiative PDF available

Author(s): Lacson Ronilda | Pitzer Erik | Hinske Christian | Galante Pedro | Ohno-Machado Lucila
Volume: 10
Issue: Suppl 9
Year: 2009
Towards large-scale sample annotation in gene expression repositories PDF available

Author(s): Pitzer Erik | Lacson Ronilda | Hinske Christian | Kim Jihoon | Galante Pedro | Ohno-Machado Lucila
Volume: 10
Issue: Suppl 9
Year: 2009
The potential for automated question answering in the context of genomic medicine: an assessment of existing resources and properties of answers PDF available

Author(s): Overby Casey | Tarczy-Hornoch Peter | Demner-Fushman Dina
Volume: 10
Issue: Suppl 9
Year: 2009
A systems biology approach to the identification and analysis of transcriptional regulatory networks in osteocytes PDF available

Author(s): Dean Angela | Harris Stephen | Kalajzic Ivo | Ruan Jianhua
Volume: 10
Issue: Suppl 9
Year: 2009
Infection in the intensive care unit alters physiological networks PDF available

Author(s): Grossman Adam | Cohen Mitchell | Manley Geoffrey | Butte Atul
Volume: 10
Issue: Suppl 9
Year: 2009
Validation of an NSP-based (negative selection pattern) gene family identification strategy

Author(s): Frank Ronald | Kandoth Cyriac | Ercal Fikret
Volume: 9
Issue: Suppl 9
Year: 2008
Comprehensive analysis of circadian periodic pattern in plant transcriptome

Author(s): Ptitsyn Andrey
Volume: 9
Issue: Suppl 9
Year: 2008
Hybrid MM/SVM structural sensors for stochastic sequential data

Author(s): Roux Brian | Winters-Hilt Stephen
Volume: 9
Issue: Suppl 9
Year: 2008
Large-scale directional relationship extraction and resolution

Author(s): Giles Cory | Wren Jonathan
Volume: 9
Issue: Suppl 9
Year: 2008
Extracting unrecognized gene relationships from the biomedical literature via matrix factorizations

Author(s): Kim Hyunsoo | Park Haesun | Drake Barry
Volume: 8
Issue: Suppl 9
Year: 2007
Framework for a Protein Ontology

Author(s): Natale Darren | Arighi Cecilia | Barker Winona | Blake Judith | Chang Ti-Cheng | Hu Zhangzhi | Liu Hongfang | Smith Barry | Wu Cathy
Volume: 8
Issue: Suppl 9
Year: 2007
MTAP: The Motif Tool Assessment Platform

Author(s): Quest Daniel | Dempsey Kathryn | Shafiullah Mohammad | Bastola Dhundy | Ali Hesham
Volume: 9
Issue: Suppl 9
Year: 2008
Exhaustive prediction of disease susceptibility to coding base changes in the human genome

Author(s): Kulkarni Vinayak | Errami Mounir | Barber Robert | Garner Harold
Volume: 9
Issue: Suppl 9
Year: 2008
Testing for treatment effects on gene ontology

Author(s): Lee Taewon | Desai Varsha | Velasco Cruz | Reis Robert | Delongchamp Robert
Volume: 9
Issue: Suppl 9
Year: 2008
Latent physiological factors of complex human diseases revealed by independent component analysis of clinarrays

Author(s): Chen David | Dudley Joel | Butte Atul
Volume: 11
Issue: Suppl 9
Year: 2010
Mapping transcription mechanisms from multimodal genomic data

Author(s): Chang Hsun-Hsien | McGeachie Michael | Alterovitz Gil | Ramoni Marco
Volume: 11
Issue: Suppl 9
Year: 2010
Stromal microenvironment processes unveiled by biological component analysis of gene expression in xenograft tumor models

Author(s): Yang Xinan | Lee Younghee | Huang Yong | Chen James | Xing Rosie | Lussier Yves
Volume: 11
Issue: Suppl 9
Year: 2010
Comparison of concept recognizers for building the Open Biomedical Annotator PDF available

Author(s): Shah Nigam | Bhatia Nipun | Jonquet Clement | Rubin Daniel | Chiang Annie | Musen Mark
Volume: 10
Issue: Suppl 9
Year: 2009
Characterizing environmental and phenotypic associations using information theory and electronic health records PDF available

Author(s): Wang Xiaoyan | Hripcsak George | Friedman Carol
Volume: 10
Issue: Suppl 9
Year: 2009
Selected proceedings of the 2010 Summit on Translational Bioinformatics

Author(s): Mendonça Eneida | Tarczy-Hornoch Peter
Volume: 11
Issue: Suppl 9
Year: 2010
Evaluating the accuracy of a functional SNP annotation system PDF available

Author(s): Shen Terry | Carlson Christopher | Tarczy-Hornoch Peter
Volume: 10
Issue: Suppl 9
Year: 2009
Selected proceedings of the 2009 Summit on Translational Bioinformatics PDF available

Author(s): Lussier Yves | Sarkar Indra
Volume: 10
Issue: Suppl 9
Year: 2009
Proceedings of the 2008 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference

Author(s): Wren Jonathan | Wilkins Dawn | Fuscoe James | Bridges Susan | Winters-Hilt Stephen | Gusev Yuriy
Volume: 9
Issue: Suppl 9
Year: 2008
Classifying protein-protein interaction articles using word and syntactic features

Author(s): Kim Sun | Wilbur W
Volume: 12
Issue: Suppl 8
Year: 2011
Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases

Author(s): Chatr-aryamontri Andrew | Winter Andrew | Perfetto Livia | Briganti Leonardo | Licata Luana | Iannuccelli Marta | Castagnoli Luisa | Cesareni Gianni | Tyers Mike
Volume: 12
Issue: Suppl 8
Year: 2011
Soft tagging of overlapping high confidence gene mention variants for cross-species full-text gene normalization

Author(s): Kuo Cheng-Ju | Ling Maurice | Hsu Chun-Nan
Volume: 12
Issue: Suppl 8
Year: 2011
Cross-species gene normalization by species inference

Author(s): Wei Chih-Hsuan | Kao Hung-Yu
Volume: 12
Issue: Suppl 8
Year: 2011
BioCreative III interactive task: an overview

Author(s): Arighi Cecilia | Roberts Phoebe | Agarwal Shashank | Bhattacharya Sanmitra | Cesareni Gianni | Chatr-aryamontri Andrew | Clematide Simon | Gaudet Pascale | Giglio Michelle | Harrow Ian | Huala Eva | Krallinger Martin | Leser Ulf | Li Donghui | Liu Feifan | Lu Zhiyong | Maltais Lois | Okazaki Naoaki | Perfetto Livia | Rinaldi Fabio | Sætre Rune | Salgado David | Srinivasan Padmini | Thomas Philippe | Toldo Luca | Hirschman Lynette | Wu Cathy
Volume: 12
Issue: Suppl 8
Year: 2011
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text

Author(s): Krallinger Martin | Vazquez Miguel | Leitner Florian | Salgado David | Chatr-aryamontri Andrew | Winter Andrew | Perfetto Livia | Briganti Leonardo | Licata Luana | Iannuccelli Marta | Castagnoli Luisa | Cesareni Gianni | Tyers Mike | Schneider Gerold | Rinaldi Fabio | Leaman Robert | Gonzalez Graciela | Matos Sergio | Kim Sun | Wilbur W | Rocha Luis | Shatkay Hagit | Tendulkar Ashish | Agarwal Shashank | Liu Feifan | Wang Xinglong | Rak Rafal | Noto Keith | Elkan Charles | Lu Zhiyong | Dogan Rezarta | Fontaine Jean-Fred | Andrade-Navarro Miguel | Valencia Alfonso
Volume: 12
Issue: Suppl 8
Year: 2011
The gene normalization task in BioCreative III

Author(s): Lu Zhiyong | Kao Hung-Yu | Wei Chih-Hsuan | Huang Minlie | Liu Jingchen | Kuo Cheng-Ju | Hsu Chun-Nan | Tsai Richard | Dai Hong-Jie | Okazaki Naoaki | Cho Han-Cheol | Gerner Martin | Solt Illes | Agarwal Shashank | Liu Feifan | Vishnyakova Dina | Ruch Patrick | Romacker Martin | Rinaldi Fabio | Bhattacharya Sanmitra | Srinivasan Padmini | Liu Hongfang | Torii Manabu | Matos Sergio | Campos David | Verspoor Karin | Livingston Kevin | Wilbur W
Volume: 12
Issue: Suppl 8
Year: 2011
Detection of interaction articles and experimental methods in biomedical literature

Author(s): Schneider Gerold | Clematide Simon | Rinaldi Fabio
Volume: 12
Issue: Suppl 8
Year: 2011
A linear classifier based on entity recognition tools and a statistical approach to method extraction in the protein-protein interaction literature

Author(s): Lourenço Anália | Conover Michael | Wong Andrew | Nematzadeh Azadeh | Pan Fengxia | Shatkay Hagit | Rocha Luis
Volume: 12
Issue: Suppl 8
Year: 2011
Detecting experimental techniques and selecting relevant documents for protein-protein interactions from biomedical literature

Author(s): Wang Xinglong | Rak Rafal | Restificar Angelo | Nobata Chikashi | Rupp CJ | Batista-Navarro Riza Theresa | Nawaz Raheel | Ananiadou Sophia
Volume: 12
Issue: Suppl 8
Year: 2011
Overview of the BioCreative III Workshop

Author(s): Arighi Cecilia | Lu Zhiyong | Krallinger Martin | Cohen Kevin | Wilbur W | Valencia Alfonso | Hirschman Lynette | Wu Cathy
Volume: 12
Issue: Suppl 8
Year: 2011
Infinite mixture-of-experts model for sparse survival regression with application to breast cancer

Author(s): Raman Sudhir | Fuchs Thomas | Wild Peter | Dahl Edgar | Buhmann Joachim | Roth Volker
Volume: 11
Issue: Suppl 8
Year: 2010
Exploiting physico-chemical properties in string kernels

Author(s): Toussaint Nora | Widmer Christian | Kohlbacher Oliver | Rätsch Gunnar
Volume: 11
Issue: Suppl 8
Year: 2010
Inferring latent task structure for Multitask Learning by Multiple Kernel Learning

Author(s): Widmer Christian | Toussaint Nora | Altun Yasemin | Rätsch Gunnar
Volume: 11
Issue: Suppl 8
Year: 2010
Classifying and scoring of molecules with the NGN: new datasets, significance tests, and generalization

Author(s): Ma Eddie | Cameron Christopher | Kremer Stefan
Volume: 11
Issue: Suppl 8
Year: 2010
A machine learning pipeline for quantitative phenotype prediction from genotype data

Author(s): Guzzetta Giorgio | Jurman Giuseppe | Furlanello Cesare
Volume: 11
Issue: Suppl 8
Year: 2010
MtSNPscore: a combined evidence approach for assessing cumulative impact of mitochondrial variations in disease PDF available

Author(s): Bhardwaj Anshu | Mukerji Mitali | Sharma Shipra | Paul Jinny | Gokhale Chaitanya | Srivastava Achal | Tiwari Shrish
Volume: 10
Issue: Suppl 8
Year: 2009
From SNPs to pathways: integration of functional effect of sequence variations on models of cell signalling pathways PDF available

Author(s): Bauer-Mehren Anna | Furlong Laura | Rautschka Michael | Sanz Ferran
Volume: 10
Issue: Suppl 8
Year: 2009
An integrated approach to the interpretation of Single Amino Acid Polymorphisms within the framework of CATH and Gene3D PDF available

Author(s): Izarzugaza Jose | Baresic Anja | McMillan Lisa | Yeats Corin | Clegg Andrew | Orengo Christine | Martin Andrew | Valencia Alfonso
Volume: 10
Issue: Suppl 8
Year: 2009
Annotation of protein residues based on a literature analysis: cross-validation against UniProtKb PDF available

Author(s): Nagel Kevin | Jimeno-Yepes Antonio | Rebholz-Schuhmann Dietrich
Volume: 10
Issue: Suppl 8
Year: 2009
Improved mutation tagging with gene identifiers applied to membrane protein stability prediction PDF available

Author(s): Winnenburg Rainer | Plake Conrad | Schroeder Michael
Volume: 10
Issue: Suppl 8
Year: 2009
EnzyMiner: automatic identification of protein level mutations and their impact on target enzymes from PubMed abstracts PDF available

Author(s): Yeniterzi Süveyda | Sezerman Uğur
Volume: 10
Issue: Suppl 8
Year: 2009
Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease PDF available

Author(s): Haq Omar | Levy Ronald | Morozov Alexandre | Andrec Michael
Volume: 10
Issue: Suppl 8
Year: 2009
Extraction of human kinase mutations from literature, databases and genotyping studies PDF available

Author(s): Krallinger Martin | Izarzugaza Jose | Rodriguez-Penagos Carlos | Valencia Alfonso
Volume: 10
Issue: Suppl 8
Year: 2009
Graphical models for inferring single molecule dynamics

Author(s): Bronson Jonathan | Hofman Jake | Fei Jingyi | Gonzalez Ruben | Wiggins Chris
Volume: 11
Issue: Suppl 8
Year: 2010
Efficient motif finding algorithms for large-alphabet inputs

Author(s): Kuksa Pavel | Pavlovic Vladimir
Volume: 11
Issue: Suppl 8
Year: 2010
Correlating protein function and stability through the analysis of single amino acid substitutions PDF available

Author(s): Bromberg Yana | Rost Burkhard
Volume: 10
Issue: Suppl 8
Year: 2009
Semi-supervised class discovery using quantitative phenotypes – CVD as a case study PDF available

Author(s): Steinfeld Israel | Navon Roy | Ardigò Diego | Zavaroni Ivana | Yakhini Zohar
Volume: 8
Issue: Suppl 8
Year: 2007
Integrating biological data – the Distributed Annotation System PDF available

Author(s): Jenkinson Andrew | Albrecht Mario | Birney Ewan | Blankenburg Hagen | Down Thomas | Finn Robert | Hermjakob Henning | Hubbard Tim | Jimenez Rafael | Jones Philip | Kähäri Andreas | Kulesha Eugene | Macías José | Reeves Gabrielle | Prlić Andreas
Volume: 9
Issue: Suppl 8
Year: 2008
Integrating protein-protein interactions and text mining for protein function prediction PDF available

Author(s): Jaeger Samira | Gaudan Sylvain | Leser Ulf | Rebholz-Schuhmann Dietrich
Volume: 9
Issue: Suppl 8
Year: 2008
Semi-supervised prediction of protein subcellular localization using abstraction augmented Markov models

Author(s): Caragea Cornelia | Caragea Doina | Silvescu Adrian | Honavar Vasant
Volume: 11
Issue: Suppl 8
Year: 2010
Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations PDF available

Author(s): Reumers Joke | Schymkowitz Joost | Rousseau Fréderic
Volume: 10
Issue: Suppl 8
Year: 2009
Between proteins and phenotypes: annotation and interpretation of mutations PDF available

Author(s): Baker Christopher | Rebholz-Schuhmann Dietrich
Volume: 10
Issue: Suppl 8
Year: 2009
Review of the selected proceedings of the Fifth International Workshop on Data Integration in the Life Sciences 2008 PDF available

Author(s): Bairoch Amos | Cohen-Boulakia Sarah | Froidevaux Christine
Volume: 9
Issue: Suppl 8
Year: 2008
Mining expression-dependent modules in the human interaction network PDF available

Author(s): Georgii Elisabeth | Dietmann Sabine | Uno Takeaki | Pagel Philipp | Tsuda Koji
Volume: 8
Issue: Suppl 8
Year: 2007
Combining dissimilarity based classifiers for cancer prediction using gene expression profiles PDF available

Author(s): Blanco Ángela | Martín-Merino Manuel | De Las Rivas Javier
Volume: 8
Issue: Suppl 8
Year: 2007
ChIP-on-chip significance analysis reveals ubiquitous transcription factor binding PDF available

Author(s): Margolin Adam | Palomero Teresa | Ferrando Adolfo | Califano Andrea | Stolovitzky Gustavo
Volume: 8
Issue: Suppl 8
Year: 2007
Variation of geometrical and physicochemical properties in protein binding pockets and their ligands PDF available

Author(s): Kahraman Abdullah | Morris Richard | Laskowski Roman | Thornton Janet
Volume: 8
Issue: Suppl 8
Year: 2007
Multiple alignment and structure prediction of non-coding RNA sequences PDF available

Author(s): Lindgreen Stinus | Gardner Paul | Krogh Anders
Volume: 8
Issue: Suppl 8
Year: 2007
A systematic strategy for the discovery of candidate genes responsible for phenotypic variation PDF available

Author(s): Fisher Paul | Hedeler Cornelia | Wolstencroft Katherine | Hulme Helen | Noyes Harry | Kemp Stephen | Stevens Robert | Brass Andrew
Volume: 8
Issue: Suppl 8
Year: 2007
A procedure to decompose high resolution mass spectra PDF available

Author(s): Barbarini Nicola | Magni Paolo | Bellazzi Riccardo
Volume: 8
Issue: Suppl 8
Year: 2007
Shared transcriptional correlations in seed formation and in plants response to drought PDF available

Author(s): Ashkenazi Maital | Moshelion Menachem
Volume: 8
Issue: Suppl 8
Year: 2007
Optimising oligonucleotide array design for ChIP-on-chip PDF available

Author(s): Nielsen Fiona | Graef Stefan | Zhang Xinmin | Kurtz Stefan | Denissov Sergei | Green Roland | Birney Ewan | Flicek Paul | Huynen Martijn | Stunnenberg Henk
Volume: 8
Issue: Suppl 8
Year: 2007
T2DM-GeneMiner a web resource for meta-analysis and marker identification for type 2 diabetes mellitus PDF available

Author(s): Rasche Axel | Herwig Ralf
Volume: 8
Issue: Suppl 8
Year: 2007
Homology modeling of a voltage-gated potassium channel (human Kv7.1) PDF available

Author(s): Goncearenco Alexandr | Karimi-Nejad Yasmin | Koehler Konrad
Volume: 8
Issue: Suppl 8
Year: 2007
Logical modelling and analysis of the budding yeast cell cycle PDF available

Author(s): Fauré Adrien | Chaouiya Claudine | Ciliberto Andrea | Thieffry Denis
Volume: 8
Issue: Suppl 8
Year: 2007
Phage Eco-Locator: a web tool for visualization and analysis of phage genomes in metagenomic data sets PDF available

Author(s): Aziz Ramy | Dwivedi Bhakti | Breitbart Mya | Edwards Robert
Volume: 12
Issue: Suppl 7
Year: 2011
Protected Research Information Management Environment (PRIME) provides a secure open source data management option for clinical and scientific research PDF available

Author(s): Viangteeravat Teeradache | Nagisetty Venkateswara | Anyanwu Matthew | Kuscu Emin | Brooks Ian | McDonald Chanchai
Volume: 12
Issue: Suppl 7
Year: 2011
mDAG: a web-based tool for analyzing microarray data with multiple treatments PDF available

Author(s): Phan Vinhthuy | Vo Nam | Sutter Thomas
Volume: 12
Issue: Suppl 7
Year: 2011
Determining anion-quadrupole interactions among protein, DNA, and ligand molecules PDF available

Author(s): Harris Jason | Jenkins David | Reyles Jonathan | Rickett Stephanie | Utley Jordan | Howell Elizabeth | Baudry Jerome | Hinde Robert
Volume: 12
Issue: Suppl 7
Year: 2011
A novel noise handling method to improve clustering of gene expression patterns PDF available

Author(s): Bhattacharya Anindya | De Rajat
Volume: 12
Issue: Suppl 7
Year: 2011
Meta-analysis of gene expression changes in response to radiation exposure PDF available

Author(s): Kirtley John | Rouchka Eric | Flight Robert | Sethu Palaniappan | Eaton John | Keynton Robert
Volume: 12
Issue: Suppl 7
Year: 2011
Identification of alcohol preference relevant genes in QTL on mouse chromosome 2 PDF available

Author(s): Wang Lishi | Jiao Yan | Gibson Griffin | Liu Xiaoyun | Huang Yue | Bennett Beth | Hamre Kristin | Williams Robert | Gu Weikuan
Volume: 12
Issue: Suppl 7
Year: 2011
Statistical analysis of microarray gene expression data from a mouse model of toxoplasmosis PDF available

Author(s): Pawar Shrikant | Davis Cheryl | Rinehart Claire
Volume: 12
Issue: Suppl 7
Year: 2011
Integration of bioinformatics tools in candidate gene prioritization of co-regulated gene sets in Saccharomyces cerevisiae PDF available

Author(s): Abedi Vida | Yeasin Mohammed | Sutter Thomas
Volume: 12
Issue: Suppl 7
Year: 2011
Bioinformatic challenges for proteomic biomarkers of cancer PDF available

Author(s): Tabb David | Liebler Daniel
Volume: 12
Issue: Suppl 7
Year: 2011
categoryCompare: high-throughput data meta-analysis using gene annotations PDF available

Author(s): Flight Robert | Petruska Jeffrey | Harrison Benjamin | Rouchka Eric
Volume: 12
Issue: Suppl 7
Year: 2011
Gene expression based prototype for automatic tumor prediction PDF available

Author(s): Islam Atiq | Iftekharuddin Khan | George Olusegun
Volume: 12
Issue: Suppl 7
Year: 2011
Next-gen sequencing of multi-drug resistant Acinetobacter baumanii at Nashville General Hospital at Meharry PDF available

Author(s): Dent Leon | Ismail Nahed | Robinson Steven | Rogers Gary | Pratap Siddharth | Marshall Dana
Volume: 12
Issue: Suppl 7
Year: 2011
MSCTrees: a mean-shift based toolkit for cluster analysis of phylogenetic trees PDF available

Author(s): Li Weixi | Jaromczyk Jerzy
Volume: 12
Issue: Suppl 7
Year: 2011
Comparative studies of high-throughput biological graphs PDF available

Author(s): Reyles Jonathan | Phillips Charles
Volume: 12
Issue: Suppl 7
Year: 2011
ColonyTrak: a web tool and database system for managing experimental animal models PDF available

Author(s): Vadlamudi Laasya | Jones Lynn | Homayouni Ramin
Volume: 12
Issue: Suppl 7
Year: 2011
PharmacoMicrobiomics or how bugs modulate drugs: an educational initiative to explore the effects of human microbiome on drugs PDF available

Author(s): Aziz Ramy | Saad Rama | Rizkallah Mariam
Volume: 12
Issue: Suppl 7
Year: 2011
Proceedings of the Tenth Annual UT-ORNL-KBRIN Bioinformatics Summit 2011 PDF available

Author(s): Rouchka Eric | Flight Robert | Homayouni Ramin
Volume: 12
Issue: Suppl 7
Year: 2011
Cloning, analysis and functional annotation of expressed sequence tags from the Earthworm Eisenia fetida

Author(s): Pirooznia Mehdi | Gong Ping | Guan Xin | Inouye Laura | Yang Kuan | Perkins Edward | Deng Youping
Volume: 8
Issue: Suppl 7
Year: 2007
Statistical tools for transgene copy number estimation based on real-time PCR

Author(s): Yuan Joshua | Burris Jason | Stewart Nathan | Mentewab Ayalew | Stewart C Neal
Volume: 8
Issue: Suppl 7
Year: 2007
Structure and function predictions of the Msa protein in Staphylococcus aureus

Author(s): Nagarajan Vijayaraj | Elasri Mohamed
Volume: 8
Issue: Suppl 7
Year: 2007
Gene expression changes induced by the tumorigenic pyrrolizidine alkaloid riddelliine in liver of Big Blue rats

Author(s): Mei Nan | Guo Lei | Liu Ruqing | Fuscoe James | Chen Tao
Volume: 8
Issue: Suppl 7
Year: 2007
Metabonomics evaluations of age-related changes in the urinary compositions of male Sprague Dawley rats and effects of data normalization methods on statistical and quantitative analysis

Author(s): Schnackenberg Laura | Sun Jinchun | Espandiari Parvaneh | Holland Ricky | Hanig Joseph | Beger Richard
Volume: 8
Issue: Suppl 7
Year: 2007
ProtQuant: a tool for the label-free quantification of MudPIT proteomics data

Author(s): Bridges Susan | Magee G Bryce | Wang Nan | Williams W Paul | Burgess Shane | Nanduri Bindu
Volume: 8
Issue: Suppl 7
Year: 2007
Prediction of peptides observable by mass spectrometry applied at the experimental set level

Author(s): Sanders William | Bridges Susan | McCarthy Fiona | Nanduri Bindu | Burgess Shane
Volume: 8
Issue: Suppl 7
Year: 2007
Comparison of gene expression profiles altered by comfrey and riddelliine in rat liver

Author(s): Guo Lei | Mei Nan | Dial Stacey | Fuscoe James | Chen Tao
Volume: 8
Issue: Suppl 7
Year: 2007
A survey of DNA motif finding algorithms

Author(s): Das Modan | Dai Ho-Kwok
Volume: 8
Issue: Suppl 7
Year: 2007
Systems biology approach for mapping the response of human urothelial cells to infection by Enterococcus faecalis

Author(s): Dozmorov Mikhail | Kyker Kimberly | Saban Ricardo | Shankar Nathan | Baghdayan Arto | Centola Michael | Hurst Robert
Volume: 8
Issue: Suppl 7
Year: 2007
A novel, fast, HMM-with-Duration implementation – for application with a new, pattern recognition informed, nanopore detector

Author(s): Winters-Hilt Stephen | Baribault Carl
Volume: 8
Issue: Suppl 7
Year: 2007
SVM clustering

Author(s): Winters-Hilt Stephen | Merat Sam
Volume: 8
Issue: Suppl 7
Year: 2007
Automatic delineation of malignancy in histopathological head and neck slides

Author(s): Mete Mutlu | Xu Xiaowei | Fan Chun-Yang | Shafirstein Gal
Volume: 8
Issue: Suppl 7
Year: 2007
Computational analysis of biological functions and pathways collectively targeted by co-expressed microRNAs in cancer

Author(s): Gusev Yuriy | Schmittgen Thomas | Lerner Megan | Postier Russell | Brackett Daniel
Volume: 8
Issue: Suppl 7
Year: 2007
Analysis of circadian pattern reveals tissue-specific alternative transcription in leptin signaling pathway

Author(s): Ptitsyn Andrey | Gimble Jeffrey
Volume: 8
Issue: Suppl 7
Year: 2007
Duration learning for analysis of nanopore ionic current blockades

Author(s): Churbanov Alexander | Baribault Carl | Winters-Hilt Stephen
Volume: 8
Issue: Suppl 7
Year: 2007
Comparison of probabilistic Boolean network and dynamic Bayesian network approaches for inferring gene regulatory networks

Author(s): Li Peng | Zhang Chaoyang | Perkins Edward | Gong Ping | Deng Youping
Volume: 8
Issue: Suppl 7
Year: 2007
Analysis of nanopore detector measurements using Machine-Learning methods, with application to single-molecule kinetic analysis

Author(s): Landry Matthew | Winters-Hilt Stephen
Volume: 8
Issue: Suppl 7
Year: 2007
Preliminary nanopore cheminformatics analysis of aptamer-target binding strength

Author(s): Thomson Karen | Amin Iftekhar | Morales Eric | Winters-Hilt Stephen
Volume: 8
Issue: Suppl 7
Year: 2007
Network analysis of human protein location PDF available

Author(s): Kumar Gaurav | Ranganathan Shoba
Volume: 11
Issue: Suppl 7
Year: 2010
Integrating diverse biological and computational sources for reliable protein-protein interactions PDF available

Author(s): Wu Min | Li Xiaoli | Chua Hon | Kwoh Chee-Keong | Ng See-Kiong
Volume: 11
Issue: Suppl 7
Year: 2010
Intrinsically disordered domains deviate significantly from random sequences in mammalian proteins PDF available

Author(s): Teraguchi Shunsuke | Patil Ashwini | Standley Daron
Volume: 11
Issue: Suppl 7
Year: 2010
DODO: an efficient orthologous genes assignment tool based on domain architectures. Domain based ortholog detection PDF available

Author(s): Chen Ting-wen | Wu Timothy | Ng Wailap | Lin Wen-chang
Volume: 11
Issue: Suppl 7
Year: 2010
A quantitatively-modeled homozygosity mapping algorithm, qHomozygosityMapping, utilizing whole genome single nucleotide polymorphism genotyping data PDF available

Author(s): Huqun* | Fukuyama Shun-ichiro | Morino Hiroyuki | Miyazawa Hiroshi | Tanaka Tomoaki | Suzuki Tomoko | Kohda Masakazu | Kawakami Hideshi | Okazaki Yasushi | Seyama Kuniaki | Hagiwara Koichi
Volume: 11
Issue: Suppl 7
Year: 2010
T3SEdb: data warehousing of virulence effectors secreted by the bacterial Type III Secretion System PDF available

Author(s): Tay Daniel | Govindarajan Kunde | Khan Asif | Ong Terenze | Samad Hanif | Soh Wei | Tong Minyan | Zhang Fan | Tan Tin
Volume: 11
Issue: Suppl 7
Year: 2010
Robust and accurate prediction of noncoding RNAs from aligned sequences PDF available

Author(s): Saito Yutaka | Sato Kengo | Sakakibara Yasubumi
Volume: 11
Issue: Suppl 7
Year: 2010
Gradual transition from mosaic to global DNA methylation patterns during deuterostome evolution PDF available

Author(s): Okamura Kohji | Matsumoto Kazuaki | Nakai Kenta
Volume: 11
Issue: Suppl 7
Year: 2010
IKKβ inhibitor identification: a multi-filter driven novel scaffold PDF available

Author(s): Nagarajan Shanthi | Choo Hyunah | Cho Yong | Shin Kye Jung | Oh Kwang-Seok | Lee Byung | Pae Ae
Volume: 11
Issue: Suppl 7
Year: 2010
DiScRIBinATE: a rapid method for accurate taxonomic classification of metagenomic sequences PDF available

Author(s): Ghosh Tarini | Haque M Monzoorul | Mande Sharmila
Volume: 11
Issue: Suppl 7
Year: 2010
Modeling the competition between lung metastases and the immune system using agents PDF available

Author(s): Pennisi Marzio | Pappalardo Francesco | Palladini Ariannna | Nicoletti Giordano | Nanni Patrizia | Lollini Pier-Luigi | Motta Santo
Volume: 11
Issue: Suppl 7
Year: 2010
Sensitivity analysis of dynamic biological systems with time-delays PDF available

Author(s): Wu Wu | Wang Feng | Chang Maw
Volume: 11
Issue: Suppl 7
Year: 2010
Modularity of Escherichia coli sRNA regulation revealed by sRNA-target and protein network analysis PDF available

Author(s): Wu Timothy | Chang Ian | Chu Li-chieh | Huang Hsuan-Cheng | Ng Wailap
Volume: 11
Issue: Suppl 7
Year: 2010
Analysis and verification of the HMGB1 signaling pathway PDF available

Author(s): Gong Haijun | Zuliani Paolo | Komuravelli Anvesh | Faeder James | Clarke Edmund
Volume: 11
Issue: Suppl 7
Year: 2010
InCoB2010 - 9th International Conference on Bioinformatics at Tokyo, Japan, September 26-28, 2010 PDF available

Author(s): Schönbach Christian | Nakai Kenta | Tan Tin | Ranganathan Shoba
Volume: 11
Issue: Suppl 7
Year: 2010
Genomic analysis of gene regulation complexity

Author(s): Barker Brandon | Lund Jim
Volume: 9
Issue: Suppl 7
Year: 2008
MedSurv: a software application for creating, conducting and managing medical surveys and questionnaires

Author(s): Ware Zachary | Selby Lisbeth | Jaromczyk Jerzy
Volume: 9
Issue: Suppl 7
Year: 2008
Techniques for the analysis of trichome Pelagonium xhortorum expressed sequence tags

Author(s): Morris Joseph | Rouchka Eric | Schultz David
Volume: 9
Issue: Suppl 7
Year: 2008
De novo identification of in vivo binding sites from ChIP-chip data

Author(s): Jin Victor | Rabinovich Alina | O'Geen Henny | Iyengar Sushma | Farnham Peggy
Volume: 9
Issue: Suppl 7
Year: 2008
Modeling mis-folded lysozyme aggregates

Author(s): Chotikasemsri Pongsathorn | Rinehart Claire
Volume: 9
Issue: Suppl 7
Year: 2008
A computational and analysis tool for proteomics research

Author(s): Niu Xinnan | McAfee K Jill | Duncan Dexter | Assink Michael | Link Andrew
Volume: 9
Issue: Suppl 7
Year: 2008
Proteome discovery pipeline for mass spectrometry-based proteomics

Author(s): Gough Erik | Oh Cheolhwan | He Jing | Riley Catherine | Buck Charles | Zhang Xiang
Volume: 9
Issue: Suppl 7
Year: 2008
i-SEGOPubmed: a web interface for semantic enabled browsing of PubMed using Gene Ontology

Author(s): Yeasin Mohammed | Vanteru Bhanu | Shaik Jahangheer | Ahmed Faruk
Volume: 9
Issue: Suppl 7
Year: 2008
Candidate genes within known QTL of type 1 diabetes from mouse models

Author(s): Gu Weikuan | Gerling Ivan | Jiao Yan | Gao Peng | Xiong Qing
Volume: 9
Issue: Suppl 7
Year: 2008
Robust detection method for differential expression studies

Author(s): Rai Shesh | Pounds Stanley
Volume: 9
Issue: Suppl 7
Year: 2008
Gene classification for microarray data with multiple time measurements

Author(s): Quiton Jonathan | Rinehart Claire | Chavarria-Smith Joseph | Rice Nancy
Volume: 9
Issue: Suppl 7
Year: 2008
Analysis of the transcriptome of CD4 T-Lymphocytes from young Non-Obese Diabetic (NOD) mice suggests a key role for cytokines and apoptosis

Author(s): Kakoola Dorothy | Lenchik Nataliya | Curcio-Brint Anita | Gerling Ivan
Volume: 9
Issue: Suppl 7
Year: 2008
Microarray analysis of gene expression during auditory hair cell regeneration in zebrafish (Danio rerio)

Author(s): Schuck Julie | Smith Michael | Li Xiaohong | Cooper Nigel
Volume: 9
Issue: Suppl 7
Year: 2008
Random number generation for DNA-based security circuitry

Author(s): Bogard Christy | Rouchka Eric | Arazi Benjamin
Volume: 9
Issue: Suppl 7
Year: 2008
A permutation-based method to identify loss-of-heterozygosity using paired genotype microarray data

Author(s): Pounds Stan | Cheng Cheng | Yang Wenjian | Onar Arzu | Hartford Christine | Raimondi Susana | Relling Mary
Volume: 9
Issue: Suppl 7
Year: 2008
Evaluation of pooled allelotyping versus individual genotyping for genome-wide association analysis of complex disease

Author(s): Pratap Siddharth | Williams Scott | Levy Shawn
Volume: 9
Issue: Suppl 7
Year: 2008
Robust clustering in high dimensional data using statistical depths

Author(s): Ding Yuanyuan | Dang Xin | Peng Hanxiang | Wilkins Dawn
Volume: 8
Issue: Suppl 7
Year: 2007
Towards validating the hypothesis of phylogenetic profiling

Author(s): Loganantharaj Raja | Atwi Mazen
Volume: 8
Issue: Suppl 7
Year: 2007
Nanopore-based kinetics analysis of individual antibody-channel and antibody-antigen interactions

Author(s): Winters-Hilt Stephen | Morales Eric | Amin Iftekhar | Stoyanov Alexander
Volume: 8
Issue: Suppl 7
Year: 2007
Model of visual attention for video sequences

Author(s): Milanova Mariofanna
Volume: 9
Issue: Suppl 7
Year: 2008
QTL mapping arthritis traits in CXB mice

Author(s): Marshall Dana | Peirce Jeremy | Zhou Fang | Lu Lu | Williams Rob | Manly Ken | Stuart John
Volume: 9
Issue: Suppl 7
Year: 2008
Using a literature-based NMF model for discovering gene functional relationships

Author(s): Tjioe Elina | Berry Michael | Homayouni Ramin | Heinrich Kevin
Volume: 9
Issue: Suppl 7
Year: 2008
Proceedings of the Seventh Annual UT-ORNL-KBRIN Bioinformatics Summit 2008

Author(s): Rouchka Eric | Krushkal Julia | Goldowitz Daniel
Volume: 9
Issue: Suppl 7
Year: 2008
Haplotypes of the imprinted insulin gene are associated with size for gestational age and umbilical cord IGF-II levels

Author(s): Adkins Ronald | Krushkal Julia | Klauser Chad | Magann Everett | Somes Grant | Fain John | Morrison John
Volume: 9
Issue: Suppl 7
Year: 2008
Buffered codons in human transcriptional units

Author(s): Mahdi Rami | Rouchka Eric
Volume: 9
Issue: Suppl 7
Year: 2008
Global profile of genes regulated by securin

Author(s): Kakar Sham | Panguluri Siva | Waigel Sabine
Volume: 9
Issue: Suppl 7
Year: 2008
Bioinformatics analysis of immune response to group A streptococcal sepsis integrating quantitative trait loci mapping with genome-wide expression studies

Author(s): Abdeltawab Nourtan | Kansal Rita | Rowe Sarah | Gardner Lidia | Brannen Charity | Nooh Mohammed | Mukundan Santhosh | Abdelsamed Hossam | Attia Ramy | Taylor William | Lu Lu | Williams Robert | Kotb Malak
Volume: 9
Issue: Suppl 7
Year: 2008
Scientific Laboratory Information Management System: Tissue Bank

Author(s): McDonald Chanchai | Kulkarni Anand | Viangteeravat Teeradache
Volume: 9
Issue: Suppl 7
Year: 2008
Proceedings of the Fourth Annual Conference of the MidSouth Computational Biology and Bioinformatics Society

Author(s): Wilkins Dawn | Gusev Yuriy | Loganantharaj Raja | Bridges Susan | Winters-Hilt Stephen | Wren Jonathan
Volume: 8
Issue: Suppl 7
Year: 2007
A Hidden Markov Model for Copy Number Variant prediction from whole genome resequencing data PDF available

Author(s): Shen Yufeng | Gu Yiwei | Pe’er Itsik
Volume: 12
Issue: Suppl 6
Year: 2011
Assembly of non-unique insertion content using next-generation sequencing PDF available

Author(s): Parrish Nathaniel | Hormozdiari Farhad | Eskin Eleazar
Volume: 12
Issue: Suppl 6
Year: 2011
Genotyping common and rare variation using overlapping pool sequencing PDF available

Author(s): He Dan | Zaitlen Noah | Pasaniuc Bogdan | Eskin Eleazar | Halperin Eran
Volume: 12
Issue: Suppl 6
Year: 2011
Inferring viral quasispecies spectra from 454 pyrosequencing reads

Author(s): Astrovskaya Irina | Tork Bassam | Mangul Serghei | Westbrooks Kelly | Măndoiu Ion | Balfe Peter | Zelikovsky Alex
Volume: 12
Issue: Suppl 6
Year: 2011
Dimension reduction with redundant gene elimination for tumor classification

Author(s): Zeng Xue-Qiang | Li Guo-Zheng | Yang Jack | Yang Mary | Wu Geng-Feng
Volume: 9
Issue: Suppl 6
Year: 2008
Asymmetric bagging and feature selection for activities prediction of drug molecules

Author(s): Li Guo-Zheng | Meng Hao-Hua | Lu Wen-Cong | Yang Jack | Yang Mary
Volume: 9
Issue: Suppl 6
Year: 2008
BioGraphE: high-performance bionetwork analysis using the Biological Graph Environment

Author(s): Chin George | Chavarria Daniel | Nakamura Grant | Sofia Heidi
Volume: 9
Issue: Suppl 6
Year: 2008
Protein structural class prediction based on an improved statistical strategy

Author(s): Gu Fei | Chen Hang | Ni Jun
Volume: 9
Issue: Suppl 6
Year: 2008
MLIP: using multiple processors to compute the posterior probability of linkage

Author(s): Govil Manika | Segre Alberto | Vieland Veronica
Volume: 9
Issue: Suppl 6
Year: 2008
ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses

Author(s): Stokes Todd | Torrance JT | Li Henry | Wang May
Volume: 9
Issue: Suppl 6
Year: 2008
Quantitative analysis of numerical solvers for oscillatory biomolecular system models

Author(s): Quo Chang | Wang May
Volume: 9
Issue: Suppl 6
Year: 2008
An improved string composition method for sequence comparison

Author(s): Lu Guoqing | Zhang Shunpu | Fang Xiang
Volume: 9
Issue: Suppl 6
Year: 2008
Improving the power for detecting overlapping genes from multiple DNA microarray-derived gene lists

Author(s): Deng Xutao | Xu Jun | Wang Charles
Volume: 9
Issue: Suppl 6
Year: 2008
Quality assessment of peptide tandem mass spectra

Author(s): Wu Fang-Xiang | Gagné Pierre | Droit Arnaud | Poirier Guy
Volume: 9
Issue: Suppl 6
Year: 2008
Drug interaction prediction using ontology-driven hypothetical assertion framework for pathway generation followed by numerical simulation

Author(s): Arikuma Takeshi | Yoshikawa Sumi | Azuma Ryuzo | Watanabe Kentaro | Matsumura Kazumi | Konagaya Akihiko
Volume: 9
Issue: Suppl 6
Year: 2008
Application of the Linux cluster for exhaustive window haplotype analysis using the FBAT and Unphased programs

Author(s): Mishima Hiroyuki | Lidral Andrew | Ni Jun
Volume: 9
Issue: Suppl 6
Year: 2008
Dissecting complex transcriptional responses using pathway-level scores based on prior information

Author(s): Bussemaker Harmen | Ward Lucas | Boorsma Andre
Volume: 8
Issue: Suppl 6
Year: 2007
Finding regulatory elements and regulatory motifs: a general probabilistic framework

Author(s): van Nimwegen Erik
Volume: 8
Issue: Suppl 6
Year: 2007
Time lagged information theoretic approaches to the reverse engineering of gene regulatory networks

Author(s): Chaitankar Vijender | Ghosh Preetam | Perkins Edward | Gong Ping | Zhang Chaoyang
Volume: 11
Issue: Suppl 6
Year: 2010
Phylometrics: a pipeline for inferring phylogenetic trees from a sequence relationship network perspective

Author(s): Smits Samuel | Ouverney Cleber
Volume: 11
Issue: Suppl 6
Year: 2010
HPIDB - a unified resource for host-pathogen interactions

Author(s): Kumar Ranjit | Nanduri Bindu
Volume: 11
Issue: Suppl 6
Year: 2010
Next generation models for storage and representation of microbial biological annotation

Author(s): Quest Daniel | Land Miriam | Brettin Thomas | Cottingham Robert
Volume: 11
Issue: Suppl 6
Year: 2010
Quail Genomics: a knowledgebase for Northern bobwhite

Author(s): Rawat Arun | Gust Kurt | Elasri Mohamed | Perkins Edward
Volume: 11
Issue: Suppl 6
Year: 2010
Mixed reality simulation of rasping procedure in artificial cervical disc replacement (ACDR) surgery

Author(s): Halic Tansel | Kockara Sinan | Bayrak Coskun | Rowe Richard
Volume: 11
Issue: Suppl 6
Year: 2010
Evaluation of gene expression data generated from expired Affymetrix GeneChip® microarrays using MAQC reference RNA samples

Author(s): Wen Zhining | Wang Charles | Shi Quan | Huang Ying | Su Zhenqiang | Hong Huixiao | Tong Weida | Shi Leming
Volume: 11
Issue: Suppl 6
Year: 2010
Analysis of Bovine Viral Diarrhea Viruses-infected monocytes: identification of cytopathic and non-cytopathic biotype differences

Author(s): Ammari Mais | McCarthy Fiona | Nanduri Bindu | Pinchuk Lesya
Volume: 11
Issue: Suppl 6
Year: 2010
Identification of diagnostic subnetwork markers for cancer in human protein-protein interaction network

Author(s): Su Junjie | Yoon Byung-Jun | Dougherty Edward
Volume: 11
Issue: Suppl 6
Year: 2010
PEPPI: a peptidomic database of human protein isoforms for proteomics experiments

Author(s): Zhou Ao | Zhang Fan | Chen Jake
Volume: 11
Issue: Suppl 6
Year: 2010
Two new ArrayTrack libraries for personalized biomedical research

Author(s): Xu Joshua | Wise Carolyn | Varma Vijayalakshmi | Fang Hong | Ning Baitang | Hong Huixiao | Tong Weida | Kaput Jim
Volume: 11
Issue: Suppl 6
Year: 2010
The EDKB: an established knowledge base for endocrine disrupting chemicals

Author(s): Ding Don | Xu Lei | Fang Hong | Hong Huixiao | Perkins Roger | Harris Steve | Bearden Edward | Shi Leming | Tong Weida
Volume: 11
Issue: Suppl 6
Year: 2010
An FDA bioinformatics tool for microbial genomics research on molecular characterization of bacterial foodborne pathogens using microarrays

Author(s): Fang Hong | Xu Joshua | Ding Don | Jackson Scott | Patel Isha | Frye Jonathan | Zou Wen | Nayak Rajesh | Foley Steven | Chen James | Su Zhenqiang | Ye Yanbin | Turner Steve | Harris Steve | Zhou Guangxu | Cerniglia Carl | Tong Weida
Volume: 11
Issue: Suppl 6
Year: 2010
GOModeler- A tool for hypothesis-testing of functional genomics datasets

Author(s): Manda Prashanti | Freeman McKinley | Bridges Susan | Jankun-Kelly TJ | Nanduri Bindu | McCarthy Fiona | Burgess Shane
Volume: 11
Issue: Suppl 6
Year: 2010
Analysis of density based and fuzzy c-means clustering methods on lesion border extraction in dermoscopy images

Author(s): Kockara Sinan | Mete Mutlu | Chen Bernard | Aydin Kemal
Volume: 11
Issue: Suppl 6
Year: 2010
Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize

Author(s): Kelley Rowena | Gresham Cathy | Harper Jonathan | Bridges Susan | Warburton Marilyn | Hawkins Leigh | Pechanova Olga | Peethambaran Bela | Pechan Tibor | Luthe Dawn | Mylroie J | Ankala Arunkanth | Ozkan Seval | Henry W | Williams W
Volume: 11
Issue: Suppl 6
Year: 2010
Dynamics of protofibril elongation and association involved in Aβ42 peptide aggregation in Alzheimer’s disease

Author(s): Ghosh Preetam | Kumar Amit | Datta Bhaswati | Rangachari Vijayaraghavan
Volume: 11
Issue: Suppl 6
Year: 2010
Lesion detection in demoscopy images with novel density-based and active contour approaches

Author(s): Mete Mutlu | Sirakov Nikolay
Volume: 11
Issue: Suppl 6
Year: 2010
Comparative genome analysis of PHB gene family reveals deep evolutionary origins and diverse gene function

Author(s): Di Chao | Xu Wenying | Su Zhen | Yuan Joshua
Volume: 11
Issue: Suppl 6
Year: 2010
A predictive model for secondary RNA structure using graph theory and a neural network

Author(s): Koessler Denise | Knisley Debra | Knisley Jeff | Haynes Teresa
Volume: 11
Issue: Suppl 6
Year: 2010
A framework for automated enrichment of functionally significant inverted repeats in whole genomes

Author(s): Kandoth Cyriac | Ercal Fikret | Frank Ronald
Volume: 11
Issue: Suppl 6
Year: 2010
Applying internal coordinate mechanics to model the interactions between 8R-lipoxygenase and its substrate

Author(s): Bai Shuju | Du Tianchuan | Khosravi Ebrahim
Volume: 11
Issue: Suppl 6
Year: 2010
Functional assessment of time course microarray data PDF available

Author(s): Nueda María | Sebastián Patricia | Tarazona Sonia | García-García Francisco | Dopazo Joaquín | Ferrer Alberto | Conesa Ana
Volume: 10
Issue: Suppl 6
Year: 2009
Expression pattern divergence of duplicated genes in rice PDF available

Author(s): Li Zhe | Zhang He | Ge Song | Gu Xiaocheng | Gao Ge | Luo Jingchu
Volume: 10
Issue: Suppl 6
Year: 2009
The Mycoplasma conjunctivae genome sequencing, annotation and analysis PDF available

Author(s): Calderon-Copete Sandra | Wigger George | Wunderlin Christof | Schmidheini Tobias | Frey Joachim | Quail Michael | Falquet Laurent
Volume: 10
Issue: Suppl 6
Year: 2009
DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes PDF available

Author(s): Sebestyén Endre | Nagy Tibor | Suhai Sándor | Barta Endre
Volume: 10
Issue: Suppl 6
Year: 2009
RegExpBlasting (REB), a Regular Expression Blasting algorithm based on multiply aligned sequences PDF available

Author(s): Rubino Francesco | Attimonelli Marcella
Volume: 10
Issue: Suppl 6
Year: 2009
RetroTector online, a rational tool for analysis of retroviral elements in small and medium size vertebrate genomic sequences PDF available

Author(s): Sperber Göran | Lövgren Anders | Eriksson Nils-Einar | Benachenhou Farid | Blomberg Jonas
Volume: 10
Issue: Suppl 6
Year: 2009
Databases of homologous gene families for comparative genomics PDF available

Author(s): Penel Simon | Arigon Anne-Muriel | Dufayard Jean-François | Sertier Anne-Sophie | Daubin Vincent | Duret Laurent | Gouy Manolo | Perrière Guy
Volume: 10
Issue: Suppl 6
Year: 2009
Computational annotation of UTR cis-regulatory modules through Frequent Pattern Mining PDF available

Author(s): Turi Antonio | Loglisci Corrado | Salvemini Eliana | Grillo Giorgio | Malerba Donato | D'Elia Domenica
Volume: 10
Issue: Suppl 6
Year: 2009
A novel similarity-measure for the analysis of genetic data in complex phenotypes PDF available

Author(s): Lagani Vincenzo | Montesanto Alberto | Di Cianni Fausta | Moreno Victor | Landi Stefano | Conforti Domenico | Rose Giuseppina | Passarino Giuseppe
Volume: 10
Issue: Suppl 6
Year: 2009
A bioinformatics knowledge discovery in text application for grid computing PDF available

Author(s): Castellano Marcello | Mastronardi Giuseppe | Bellotti Roberto | Tarricone Gianfranco
Volume: 10
Issue: Suppl 6
Year: 2009
Massive non-natural proteins structure prediction using grid technologies PDF available

Author(s): Minervini Giovanni | Evangelista Giuseppe | Villanova Laura | Slanzi Debora | De Lucrezia Davide | Poli Irene | Luisi Pier Luigi | Polticelli Fabio
Volume: 10
Issue: Suppl 6
Year: 2009
The GENIUS Grid Portal and robot certificates: a new tool for e-Science PDF available

Author(s): Barbera Roberto | Donvito Giacinto | Falzone Alberto | La Rocca Giuseppe | Milanesi Luciano | Maggi Giorgio | Vicario Saverio
Volume: 10
Issue: Suppl 6
Year: 2009
Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application PDF available

Author(s): Roubelakis Maria | Zotos Pantelis | Papachristoudis Georgios | Michalopoulos Ioannis | Pappa Kalliopi | Anagnou Nicholas | Kossida Sophia
Volume: 10
Issue: Suppl 6
Year: 2009
Statistical assessment of discriminative features for protein-coding and non coding cross-species conserved sequence elements PDF available

Author(s): Creanza Teresa | Horner David | D'Addabbo Annarita | Maglietta Rosalia | Mignone Flavio | Ancona Nicola | Pesole Graziano
Volume: 10
Issue: Suppl 6
Year: 2009
Visualising biological data: a semantic approach to tool and database integration PDF available

Author(s): Pettifer Steve | Thorne David | McDermott Philip | Marsh James | Villéger Alice | Kell Douglas | Attwood Teresa
Volume: 10
Issue: Suppl 6
Year: 2009
Annotation and visualization of endogenous retroviral sequences using the Distributed Annotation System (DAS) and eBioX PDF available

Author(s): Martínez Barrio Álvaro | Lagercrantz Erik | Sperber Göran | Blomberg Jonas | Bongcam-Rudloff Erik
Volume: 10
Issue: Suppl 6
Year: 2009
Deciphering the connectivity structure of biological networks using MixNet PDF available

Author(s): Picard Franck | Miele Vincent | Daudin Jean-Jacques | Cottret Ludovic | Robin Stéphane
Volume: 10
Issue: Suppl 6
Year: 2009
Modeling heterocyst pattern formation in cyanobacteria PDF available

Author(s): Gerdtzen Ziomara | Salgado J Cristian | Osses Axel | Asenjo Juan | Rapaport Ivan | Andrews Barbara
Volume: 10
Issue: Suppl 6
Year: 2009
Towards barcode markers in Fungi: an intron map of Ascomycota mitochondria PDF available

Author(s): Santamaria Monica | Vicario Saverio | Pappadà Graziano | Scioscia Gaetano | Scazzocchio Claudio | Saccone Cecilia
Volume: 10
Issue: Suppl 6
Year: 2009
iBarcode.org: web-based molecular biodiversity analysis PDF available

Author(s): Singer Gregory | Hajibabaei Mehrdad
Volume: 10
Issue: Suppl 6
Year: 2009
A chemogenomics view on protein-ligand spaces PDF available

Author(s): Strömbergsson Helena | Kleywegt Gerard
Volume: 10
Issue: Suppl 6
Year: 2009
'Brukin2D': a 2D visualization and comparison tool for LC-MS data PDF available

Author(s): Tsagkrasoulis Dimosthenis | Zerefos Panagiotis | Loudos George | Vlahou Antonia | Baumann Marc | Kossida Sophia
Volume: 10
Issue: Suppl 6
Year: 2009
GIBA: a clustering tool for detecting protein complexes PDF available

Author(s): Moschopoulos Charalampos | Pavlopoulos Georgios | Schneider Reinhard | Likothanassis Spiridon | Kossida Sophia
Volume: 10
Issue: Suppl 6
Year: 2009
EasyCluster: a fast and efficient gene-oriented clustering tool for large-scale transcriptome data PDF available

Author(s): Picardi Ernesto | Mignone Flavio | Pesole Graziano
Volume: 10
Issue: Suppl 6
Year: 2009
Promoter prediction in E. coli based on SIDD profiles and Artificial Neural Networks

Author(s): Bland Charles | Newsome Abigail | Markovets Aleksandra
Volume: 11
Issue: Suppl 6
Year: 2010
Discovering gene functional relationships using FAUN (Feature Annotation Using Nonnegative matrix factorization)

Author(s): Tjioe Elina | Berry Michael | Homayouni Ramin
Volume: 11
Issue: Suppl 6
Year: 2010
IView: introgression library visualization and query tool

Author(s): Bottoms Christopher | Flint-Garcia Sherry | McMullen Michael
Volume: 11
Issue: Suppl 6
Year: 2010
The 20th anniversary of EMBnet: 20 years of bioinformatics for the Life Sciences community PDF available

Author(s): D'Elia Domenica | Gisel Andreas | Eriksson Nils-Einar | Kossida Sophia | Mattila Kimmo | Klucar Lubos | Bongcam-Rudloff Erik
Volume: 10
Issue: Suppl 6
Year: 2009
MCM-test: a fuzzy-set-theory-based approach to differential analysis of gene pathways

Author(s): Liang Lily | Mandal Vinay | Lu Yi | Kumar Deepak
Volume: 9
Issue: Suppl 6
Year: 2008
Genetic weighted k-means algorithm for clustering large-scale gene expression data

Author(s): Wu Fang-Xiang
Volume: 9
Issue: Suppl 6
Year: 2008
Current approaches to gene regulatory network modelling

Author(s): Schlitt Thomas | Brazma Alvis
Volume: 8
Issue: Suppl 6
Year: 2007
From biophysics to evolutionary genetics: statistical aspects of gene regulation

Author(s): Lässig Michael
Volume: 8
Issue: Suppl 6
Year: 2007
Comparative analyses of bidirectional promoters in vertebrates

Author(s): Yang Mary | Taylor James | Elnitski Laura
Volume: 9
Issue: Suppl 6
Year: 2008
Evolutionary conservation of DNA-contact residues in DNA-binding domains

Author(s): Chang Yao-Lin | Tsai Huai-Kuang | Kao Cheng-Yan | Chen Yung-Chian | Hu Yuh-Jyh | Yang Jinn-Moon
Volume: 9
Issue: Suppl 6
Year: 2008
A practical comparison of two K-Means clustering algorithms

Author(s): Wilkin Gregory | Huang Xiuzhen
Volume: 9
Issue: Suppl 6
Year: 2008
Enzyme structure dynamics of xylanase I from Trichoderma longibrachiatum

Author(s): Uzuner Ugur | Shi Weibing | Liu Lantao | Liu Sanmin | Dai Susie | Yuan Joshua
Volume: 11
Issue: Suppl 6
Year: 2010
Assessing constancy of substitution rates in viruses over evolutionary time

Author(s): Melcher Ulrich
Volume: 11
Issue: Suppl 6
Year: 2010
Constructing non-stationary Dynamic Bayesian Networks with a flexible lag choosing mechanism

Author(s): Jia Yi | Huan Jun
Volume: 11
Issue: Suppl 6
Year: 2010
Proceedings of the 2010 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference

Author(s): Wren Jonathan | Kupfer Doris | Perkins Edward | Bridges Susan | Berleant Daniel
Volume: 11
Issue: Suppl 6
Year: 2010
Graphs in molecular biology

Author(s): Huber Wolfgang | Carey Vincent | Long Li | Falcon Seth | Gentleman Robert
Volume: 8
Issue: Suppl 6
Year: 2007
Inferring cellular networks – a review

Author(s): Markowetz Florian | Spang Rainer
Volume: 8
Issue: Suppl 6
Year: 2007
Computational analyses of eukaryotic promoters

Author(s): Zhang Michael
Volume: 8
Issue: Suppl 6
Year: 2007
Transcriptional regulation at a glance

Author(s): Sperling Silke
Volume: 8
Issue: Suppl 6
Year: 2007
The Otto Warburg International Summer School and Workshop on Networks and Regulation

Author(s): Arndt Peter | Vingron Martin
Volume: 8
Issue: Suppl 6
Year: 2007
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