BMC Genomics

A machine learning approach for genome-wide prediction of morbid and druggable human genes based on systems-level data

Author(s): Costa Pedro | Acencio Marcio | Lemke Ney
Volume: 11
Issue: Suppl 5
Year: 2010

SIGLa: an adaptable LIMS for multiple laboratories

Author(s): Melo Alexandre | Faria-Campos Alessandra | DeLaat Daiane | Keller Rodrigo | Abreu Vinícius | Campos Sérgio
Volume: 11
Issue: Suppl 5
Year: 2010

Unraveling the molecular mechanisms of nitrogenase conformational protection against oxygen in diazotrophic bacteria

Author(s): Lery Letícia | Bitar Mainá | Costa Mauricio | Rössle Shaila | Bisch Paulo
Volume: 11
Issue: Suppl 5
Year: 2010

Mining flexible-receptor docking experiments to select promising protein receptor snapshots

Author(s): Machado Karina | Winck Ana | Ruiz Duncan | Norberto de Souza Osmar
Volume: 11
Issue: Suppl 5
Year: 2010

How does heparin prevent the pH inactivation of cathepsin B? Allosteric mechanism elucidated by docking and molecular dynamics

Author(s): Costa Mauricio | Batista Paulo | Shida Cláudio | Robert Charles | Bisch Paulo | Pascutti Pedro
Volume: 11
Issue: Suppl 5
Year: 2010

Alternative splicing enriched cDNA libraries identify breast cancer-associated transcripts

Author(s): Ferreira Elisa | Rangel Maria | Galante Pedro | de Souza Jorge | Molina Gustavo | de Souza Sandro | Carraro Dirce
Volume: 11
Issue: Suppl 5
Year: 2010

Disclosing ambiguous gene aliases by automatic literature profiling

Author(s): Coimbra Roney | Vanderwall Dana | Oliveira Guilherme
Volume: 11
Issue: Suppl 5
Year: 2010

RNA interference-mediated knockdown of CD49e (α5 integrin chain) in human thymic epithelial cells modulates the expression of multiple genes and decreases thymocyte adhesion

Author(s): Linhares-Lacerda Leandra | Ribeiro-Alves Marcelo | Nogueira Ana Cristina | Mendes-da-Cruz Daniella | Magalhães Danielle | Dardenne Mireille | Passos Geraldo | Savino Wilson
Volume: 11
Issue: Suppl 5
Year: 2010

The role of exon shuffling in shaping protein-protein interaction networks

Author(s): Cancherini Douglas | França Gustavo | de Souza Sandro
Volume: 11
Issue: Suppl 5
Year: 2010

Decreasing the number of false positives in sequence classification

Author(s): Machado-Lima Ariane | Kashiwabara André | Durham Alan
Volume: 11
Issue: Suppl 5
Year: 2010

Tumor and reproductive traits are linked by RNA metabolism genes in the mouse ovary: a transcriptome-phenotype association analysis

Author(s): Urzúa Ulises | Owens Garrison | Zhang Gen-Mu | Cherry James | Sharp John | Munroe David
Volume: 11
Issue: Suppl 5
Year: 2010

Inhibition of the NEMO/IKKβ association complex formation, a novel mechanism associated with the NF-κB activation suppression by Withania somnifera’s key metabolite withaferin A

Author(s): Grover Abhinav | Shandilya Ashutosh | Punetha Ankita | Bisaria Virendra | Sundar Durai
Volume: 11
Issue: Suppl 4
Year: 2010

Algorithms and semantic infrastructure for mutation impact extraction and grounding

Author(s): Laurila Jonas | Naderi Nona | Witte René | Riazanov Alexandre | Kouznetsov Alexandre | Baker Christopher
Volume: 11
Issue: Suppl 4
Year: 2010

The interplay between evolution, regulation and tissue specificity in the Human Hereditary Diseasome

Author(s): Nagaraj Shivashankar | Ingham Aaron | Reverter Antonio
Volume: 11
Issue: Suppl 4
Year: 2010

Hierarchical kernel mixture models for the prediction of AIDS disease progression using HIV structural gp120 profiles

Author(s): Yoo Paul | Shwen Ho Yung | Ng Jason | Charleston Michael | Saksena Nitin | Yang Pengyi | Zomaya Albert
Volume: 11
Issue: Suppl 4
Year: 2010

SVM-based prediction of linear B-cell epitopes using Bayes Feature Extraction

Author(s): Wee Lawrence JK | Simarmata Diane | Kam Yiu-Wing | Ng Lisa FP | Tong Joo Chuan
Volume: 11
Issue: Suppl 4
Year: 2010

Predicting RNA-binding residues from evolutionary information and sequence conservation

Author(s): Huang Yu-Feng | Chiu Li-Yuan | Huang Chun-Chin | Huang Chien-Kang
Volume: 11
Issue: Suppl 4
Year: 2010

iCOD : an integrated clinical omics database based on the systems-pathology view of disease

Author(s): Shimokawa Kazuro | Mogushi Kaoru | Shoji Satoshi | Hiraishi Atsuko | Ido Keisuke | Mizushima Hiroshi | Tanaka Hiroshi
Volume: 11
Issue: Suppl 4
Year: 2010

Functional data analysis for identifying nonlinear models of gene regulatory networks

Author(s): Summer Georg | Perkins Theodore
Volume: 11
Issue: Suppl 4
Year: 2010

Exploring hierarchical and overlapping modular structure in the yeast protein interaction network

Author(s): Liu Changning | Li Jing | Zhao Yi
Volume: 11
Issue: Suppl 4
Year: 2010

Construction of a genetic AND gate under a new standard for assembly of genetic parts

Author(s): Ayukawa Shotaro | Kobayashi Akio | Nakashima Yusaku | Takagi Hidemasa | Hamada Shogo | Uchiyama Masahiko | Yugi Katsuyuki | Murata Satoshi | Sakakibara Yasubumi | Hagiya Masami | Yamamura Masayuki | Kiga Daisuke
Volume: 11
Issue: Suppl 4
Year: 2010

Probing the anticancer mechanism of prospective herbal drug Withaferin A on mammals: a case study on human and bovine proteasomes

Author(s): Grover Abhinav | Shandilya Ashutosh | Bisaria Virendra | Sundar Durai
Volume: 11
Issue: Suppl 4
Year: 2010

Qualitative reasoning of dynamic gene regulatory interactions from gene expression data

Author(s): Chen Yu | Park Byungkyu | Han Kyungsook
Volume: 11
Issue: Suppl 4
Year: 2010

PathLocdb: a comprehensive database for the subcellular localization of metabolic pathways and its application to multiple localization analysis

Author(s): Zhao Min | Qu Hong
Volume: 11
Issue: Suppl 4
Year: 2010

Refining orthologue groups at the transcript level

Author(s): Jia Yizhen | Wong Thomas | Song You-Qiang | Yiu Siu-Ming | Smith David
Volume: 11
Issue: Suppl 4
Year: 2010

Evolutionary patterns of amino acid substitutions in 12 Drosophila genomes

Author(s): Yampolsky Lev | Bouzinier Michael
Volume: 11
Issue: Suppl 4
Year: 2010

In vitro homology search array comprehensively reveals highly conserved genes and their functional characteristics in non-sequenced species

Author(s): Ogura Atsushi | Yoshida Masa-aki | Fukuzaki Mutsumi | Sese Jun
Volume: 11
Issue: Suppl 4
Year: 2010

Discovery and characterization of medaka miRNA genes by next generation sequencing platform

Author(s): Li Sung-Chou | Chan Wen-Ching | Ho Meng-Ru | Tsai Kuo-Wang | Hu Ling-Yueh | Lai Chun-Hung | Hsu Chun-Nan | Hwang Pung-Pung | Lin Wen-chang
Volume: 11
Issue: Suppl 4
Year: 2010

UPS 2.0: unique probe selector for probe design and oligonucleotide microarrays at the pangenomic/ genomic level

Author(s): Chen Shu-Hwa | Lo Chen-Zen | Su Sheng-Yao | Kuo Bao-Han | Hsiung Chao | Lin Chung-Yen
Volume: 11
Issue: Suppl 4
Year: 2010

dbDEMC: a database of differentially expressed miRNAs in human cancers

Author(s): Yang Zhen | Ren Fei | Liu Changning | He Shunmin | Sun Gang | Gao Qian | Yao Lei | Zhang Yangde | Miao Ruoyu | Cao Ying | Zhao Yi | Zhong Yang | Zhao Haitao
Volume: 11
Issue: Suppl 4
Year: 2010

Improving protein secondary structure prediction based on short subsequences with local structure similarity

Author(s): Lin Hsin-Nan | Sung Ting-Yi | Ho Shinn-Ying | Hsu Wen-Lian
Volume: 11
Issue: Suppl 4
Year: 2010

Advancing standards for bioinformatics activities: persistence, reproducibility, disambiguation and Minimum Information About a Bioinformatics investigation (MIABi)

Author(s): Tan Tin | Tong Joo | Khan Asif | de Silva Mark | Lim Kuan | Ranganathan Shoba
Volume: 11
Issue: Suppl 4
Year: 2010

TSCC: Two-Stage Combinatorial Clustering for virtual screening using protein-ligand interactions and physicochemical features

Author(s): Clinciu Daniel | Chen Yen-Fu | Ko Cheng-Neng | Lo Chi-Chun | Yang Jinn-Moon
Volume: 11
Issue: Suppl 4
Year: 2010

RNA editing of nuclear transcripts in Arabidopsis thaliana

Author(s): Meng Yijun | Chen Dijun | Jin YongFeng | Mao Chuanzao | Wu Ping | Chen Ming
Volume: 11
Issue: Suppl 4
Year: 2010

Challenges of the next decade for the Asia Pacific region: 2010 International Conference in Bioinformatics (InCoB 2010)

Author(s): Ranganathan Shoba | Schönbach Christian | Nakai Kenta | Tan Tin
Volume: 11
Issue: Suppl 4
Year: 2010

Sequence-dependent histone variant positioning signatures

Author(s): Le Ngoc | Ho Tu | Ho Bich
Volume: 11
Issue: Suppl 4
Year: 2010

Gerontome: a web-based database server for aging-related genes and analysis pipelines

Author(s): Kwon Jekeun | Lee Byungwook | Chung Haeyoung
Volume: 11
Issue: Suppl 4
Year: 2010

NGSQC: cross-platform quality analysis pipeline for deep sequencing data

Author(s): Dai Manhong | Thompson Robert | Maher Christopher | Contreras-Galindo Rafael | Kaplan Mark | Markovitz David | Omenn Gil | Meng Fan
Volume: 11
Issue: Suppl 4
Year: 2010

A Bayesian approach for identifying miRNA targets by combining sequence prediction and gene expression profiling

Author(s): Liu Hui | Yue Dong | Zhang Lin | Chen Yidong | Gao Shou-Jiang | Huang Yufei
Volume: 11
Issue: Suppl 3
Year: 2010

Robust inference of the context specific structure and temporal dynamics of gene regulatory network

Author(s): Meng Jia | Lu Mingzhu | Chen Yidong | Gao Shou-Jiang | Huang Yufei
Volume: 11
Issue: Suppl 3
Year: 2010

Effector prediction in host-pathogen interaction based on a Markov model of a ubiquitous EPIYA motif

Author(s): Xu Shunfu | Zhang Chao | Miao Yi | Gao Jianjiong | Xu Dong
Volume: 11
Issue: Suppl 3
Year: 2010

2K09 and thereafter : the coming era of integrative bioinformatics, systems biology and intelligent computing for functional genomics and personalized medicine research

Author(s): Yang Jack | Niemierko Andrzej | Bajcsy Ruzena | Xu Dong | Athey Brian | Zhang Aidong | Ersoy Okan | Li Guo-zheng | Borodovsky Mark | Zhang Joe | Arabnia Hamid | Deng Youping | Dunker A | Liu Yunlong | Ghafoor Arif
Volume: 11
Issue: Suppl 3
Year: 2010

Adipose segmentation in small animals at 7T: a preliminary study

Author(s): Tang Yang | Lee Susan | Nelson Marvin | Richard Simerly | Moats Rex
Volume: 11
Issue: Suppl 3
Year: 2010

ICPD-A New Peak Detection Algorithm for LC/MS

Author(s): Zhang Jianqiu | Haskins William
Volume: 11
Issue: Suppl 3
Year: 2010

3D-interologs: an evolution database of physical protein- protein interactions across multiple genomes

Author(s): Lo Yu-Shu | Chen Yung-Chiang | Yang Jinn-Moon
Volume: 11
Issue: Suppl 3
Year: 2010

Cross-domain neurobiology data integration and exploration

Author(s): Xuan Weijian | Dai Manhong | Buckner Josh | Mirel Barbara | Song Jean | Athey Brian | Watson Stanley | Meng Fan
Volume: 11
Issue: Suppl 3
Year: 2010

A comparative study of cancer proteins in the human protein-protein interaction network

Author(s): Sun Jingchun | Zhao Zhongming
Volume: 11
Issue: Suppl 3
Year: 2010

A new approach to construct pathway connected networks and its application in dose responsive gene expression profiles of rat liver regulated by 2,4DNT

Author(s): Chowbina Sudhir | Deng Youping | Ai Junmei | Wu Xiaogang | Guan Xin | Wilbanks Mitchell | Escalon Barbara | Meyer Sharon | Perkins Edward | Chen Jake
Volume: 11
Issue: Suppl 3
Year: 2010

Discrete diffusion models to study the effects of Mg2+ concentration on the PhoPQ signal transduction system

Author(s): Ghosh Preetam | Ghosh Samik | Basu Kalyan | Das Sajal | Zhang Chaoyang
Volume: 11
Issue: Suppl 3
Year: 2010

Predicting siRNA potency with random forests and support vector machines

Author(s): Wang Liangjiang | Huang Caiyan | Yang Jack
Volume: 11
Issue: Suppl 3
Year: 2010

Feature amplified voting algorithm for functional analysis of protein superfamily

Author(s): Hung Che-Lun | Lee Chihan | Lin Chun-Yuan | Chang Chih-Hung | Chung Yeh-Ching | Yi Tang Chuan
Volume: 11
Issue: Suppl 3
Year: 2010

Core genome components and lineage specific expansions in malaria parasites Plasmodium

Author(s): Cai Hong | Gu Jianying | Wang Yufeng
Volume: 11
Issue: Suppl 3
Year: 2010

TTS Mapping: integrative WEB tool for analysis of triplex formation target DNA Sequences, G-quadruplets and non-protein coding regulatory DNA elements in the human genome

Author(s): Jenjaroenpun Piroon | Kuznetsov Vladimir
Volume: 10
Issue: Suppl 3
Year: 2009

BioBarcode: a general DNA barcoding database and server platform for Asian biodiversity resources

Author(s): Lim Jeongheui | Kim Sang-Yoon | Kim Sungmin | Eo Hae-Seok | Kim Chang-Bae | Paek Woon | Kim Won | Bhak Jong
Volume: 10
Issue: Suppl 3
Year: 2009

Development of a database system for mapping insertional mutations onto the mouse genome with large-scale experimental data

Author(s): Yang Wenwei | Jin Ke | Xie Xing | Li Dongsheng | Yang Jigang | Wang Li | Gu Ning | Zhong Yang | Sun Ling
Volume: 10
Issue: Suppl 3
Year: 2009

A multi-factor model for caspase degradome prediction

Author(s): Wee Lawrence | Tong Joo Chuan | Tan Tin Wee | Ranganathan Shoba
Volume: 10
Issue: Suppl 3
Year: 2009

RExPrimer: an integrated primer designing tool increases PCR effectiveness by avoiding 3' SNP-in-primer and mis-priming from structural variation

Author(s): Piriyapongsa Jittima | Ngamphiw Chumpol | Assawamakin Anunchai | Wangkumhang Pongsakorn | Suwannasri Payiarat | Ruangrit Uttapong | Agavatpanitch Gallissara | Tongsima Sissades
Volume: 10
Issue: Suppl 3
Year: 2009

A proposed minimum skill set for university graduates to meet the informatics needs and challenges of the "-omics" era

Author(s): Tan Tin | Lim Shen | Khan Asif | Ranganathan Shoba
Volume: 10
Issue: Suppl 3
Year: 2009

COMUS: Clinician-Oriented locus-specific MUtation detection and deposition System

Author(s): Jho Sungwoong | Kim Byoung-Chul | Ghang Ho | Kim Ji-Han | Park Daeui | Kim Hak-Min | Jung Soo-young | Yoo Ki-young | Kim Hee-Jin | Lee Sunghoon | Bhak Jong
Volume: 10
Issue: Suppl 3
Year: 2009

A particle swarm based hybrid system for imbalanced medical data sampling

Author(s): Yang Pengyi | Xu Liang | Zhou Bing | Zhang Zili | Zomaya Albert
Volume: 10
Issue: Suppl 3
Year: 2009

A multi-species comparative structural bioinformatics analysis of inherited mutations in α-D-Mannosidase reveals strong genotype-phenotype correlation

Author(s): Khan Javed | Ranganathan Shoba
Volume: 10
Issue: Suppl 3
Year: 2009

PDbase: a database of Parkinson's Disease-related genes and genetic variation using substantia nigra ESTs

Author(s): Yang Jin Ok | Kim Woo-Yeon | Jeong So-Young | Oh Jung-Hwa | Jho Sungwoong | Bhak Jong | Kim Nam-Soon
Volume: 10
Issue: Suppl 3
Year: 2009

Alternative paths in HIV-1 targeted human signal transduction pathways

Author(s): Balakrishnan Sivaraman | Tastan Oznur | Carbonell Jaime | Klein-Seetharaman Judith
Volume: 10
Issue: Suppl 3
Year: 2009

An empirical study of choosing efficient discriminative seeds for oligonucleotide design

Author(s): Chung Won-Hyoung | Park Seong-Bae
Volume: 10
Issue: Suppl 3
Year: 2009

Identification of cell cycle-related regulatory motifs using a kernel canonical correlation analysis

Author(s): Rhee Je-Keun | Joung Je-Gun | Chang Jeong-Ho | Fei Zhangjun | Zhang Byoung-Tak
Volume: 10
Issue: Suppl 3
Year: 2009

Detecting robust time-delayed regulation in Mycobacterium tuberculosis

Author(s): Chaturvedi Iti | Rajapakse Jagath
Volume: 10
Issue: Suppl 3
Year: 2009

Characterizing nucleosome dynamics from genomic and epigenetic information using rule induction learning

Author(s): Le Ngoc | Ho Tu | Tran Dang
Volume: 10
Issue: Suppl 3
Year: 2009

Anomaly detection in gene expression via stochastic models of gene regulatory networks

Author(s): Kim Haseong | Gelenbe Erol
Volume: 10
Issue: Suppl 3
Year: 2009

Phylogenetic reconstruction using secondary structures and sequence motifs of ITS2 rDNA of Paragonimus westermani (Kerbert, 1878) Braun, 1899 (Digenea: Paragonimidae) and related species

Author(s): Prasad Pramod | Tandon Veena | Biswal Devendra | Goswami Lalit | Chatterjee Anupam
Volume: 10
Issue: Suppl 3
Year: 2009

Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin

Author(s): Jongkon Nipa | Mokmak Wanwimon | Chuakheaw Daungmanee | Shaw Philip | Tongsima Sissades | Sangma Chak
Volume: 10
Issue: Suppl 3
Year: 2009

DNA-binding residues and binding mode prediction with binding-mechanism concerned models

Author(s): Huang Yu-Feng | Huang Chun-Chin | Liu Yu-Cheng | Oyang Yen-Jen | Huang Chien-Kang
Volume: 10
Issue: Suppl 3
Year: 2009

A sequence-based hybrid predictor for identifying conformationally ambivalent regions in proteins

Author(s): Liu Yu-Cheng | Yang Meng-Han | Lin Win-Li | Huang Chien-Kang | Oyang Yen-Jen
Volume: 10
Issue: Suppl 3
Year: 2009

A modular kernel approach for integrative analysis of protein domain boundaries

Author(s): Yoo Paul | Zhou Bing | Zomaya Albert
Volume: 10
Issue: Suppl 3
Year: 2009

MitoInteractome: Mitochondrial protein interactome database, and its application in 'aging network' analysis

Author(s): Reja Rohit | Venkatakrishnan AJ | Lee Jungwoo | Kim Byoung-Chul | Ryu Jea-Woon | Gong Sungsam | Bhak Jong | Park Daeui
Volume: 10
Issue: Suppl 3
Year: 2009

BOAT: Basic Oligonucleotide Alignment Tool

Author(s): Zhao Shu-Qi | Wang Jun | Zhang Li | Li Jiong-Tang | Gu Xiaocheng | Gao Ge | Wei Liping
Volume: 10
Issue: Suppl 3
Year: 2009

Comparative study of protein-protein interaction observed in PolyGalacturonase-Inhibiting Proteins from Phaseolus vulgaris and Glycine max and PolyGalacturonase from Fusarium moniliforme

Author(s): Maulik Aditi | Ghosh Hiren | Basu Soumalee
Volume: 10
Issue: Suppl 3
Year: 2009

PutidaNET: Interactome database service and network analysis of Pseudomonas putida KT2440

Author(s): Park Seong-Jin | Choi Jong-Soon | Kim Byoung-Chul | Jho Seong-Woong | Ryu Jea-Woon | Park Daeui | Lee Kyung-A | Bhak Jong | Kim Seung Il
Volume: 10
Issue: Suppl 3
Year: 2009

MINER: exploratory analysis of gene interaction networks by machine learning from expression data

Author(s): Kadupitige Sidath | Leung Kin | Sellmeier Julia | Sivieng Jane | Catchpoole Daniel | Bain Michael | Gaëta Bruno
Volume: 10
Issue: Suppl 3
Year: 2009

A model selection approach to discover age-dependent gene expression patterns using quantile regression models

Author(s): Ho Joshua | Stefani Maurizio | dos Remedios Cristobal | Charleston Michael
Volume: 10
Issue: Suppl 3
Year: 2009

Improving gene expression similarity measurement using pathway-based analytic dimension

Author(s): Keum Changwon | Woo Jung | Oh Won | Park Sue-Nie | No Kyoung
Volume: 10
Issue: Suppl 3
Year: 2009

Measuring similarity between gene expression profiles: a Bayesian approach

Author(s): Nguyen Viet-Anh | Lió Pietro
Volume: 10
Issue: Suppl 3
Year: 2009

MapNext: a software tool for spliced and unspliced alignments and SNP detection of short sequence reads

Author(s): Bao Hua | Xiong Yuanyan | Guo Hui | Zhou Renchao | Lu Xuemei | Yang Zhen | Zhong Yang | Shi Suhua
Volume: 10
Issue: Suppl 3
Year: 2009

MitoVariome: a variome database of human mitochondrial DNA

Author(s): Lee Yong | Kim Woo-Yeon | Ji Mihyun | Kim Ji | Bhak Jong
Volume: 10
Issue: Suppl 3
Year: 2009

Genome-wide analysis of alternative splicing in cow: implications in bovine as a model for human diseases

Author(s): Chacko Elsa | Ranganathan Shoba
Volume: 10
Issue: Suppl 3
Year: 2009

The oligonucleotide frequency derived error gradient and its application to the binning of metagenome fragments

Author(s): Saeed Isaam | Halgamuge Saman
Volume: 10
Issue: Suppl 3
Year: 2009

Extending Asia Pacific bioinformatics into new realms in the "-omics" era

Author(s): Ranganathan Shoba | Eisenhaber Frank | Tong Joo | Tan Tin
Volume: 10
Issue: Suppl 3
Year: 2009

Recent advances in clustering methods for protein interaction networks

Author(s): Wang Jianxin | Li Min | Deng Youping | Pan Yi
Volume: 11
Issue: Suppl 3
Year: 2010

Computational identification and experimental validation of PPRE motifs in NHE1 and MnSOD genes of Human

Author(s): Venkatachalam Gireedhar | Kumar Alan | Yue Loo | Pervaiz Shazib | Clement Marie | Sakharkar Meena
Volume: 10
Issue: Suppl 3
Year: 2009

Human liver rate-limiting enzymes influence metabolic flux via branch points and inhibitors

Author(s): Zhao Min | Qu Hong
Volume: 10
Issue: Suppl 3
Year: 2009

Investigation gene and microRNA expression in glioblastoma

Author(s): Dong Hua | Siu Hoicheong | Luo Li | Fang Xiangzhong | Jin Li | Xiong Momiao
Volume: 11
Issue: Suppl 3
Year: 2010

Improving CT prediction of treatment response in patients with metastatic colorectal carcinoma using statistical learning theory

Author(s): Land Walker | Margolis Dan | Gottlieb Ronald | Krupinski Elizabeth | Yang Jack
Volume: 11
Issue: Suppl 3
Year: 2010

bNEAT: a Bayesian network method for detecting epistatic interactions in genome-wide association studies

Author(s): Han Bing | Chen Xue-wen
Volume: 12
Issue: Suppl 2
Year: 2011

Evaluation of short read metagenomic assembly

Author(s): Charuvaka Anveshi | Rangwala Huzefa
Volume: 12
Issue: Suppl 2
Year: 2011

Ψ-RA: a parallel sparse index for genomic read alignment

Author(s): Oğuzhan Külekci M | Hon Wing-Kai | Shah Rahul | Scott Vitter Jeffrey | Xu Bojian
Volume: 12
Issue: Suppl 2
Year: 2011

CAMBer: an approach to support comparative analysis of multiple bacterial strains

Author(s): Wozniak Michal | Wong Limsoon | Tiuryn Jerzy
Volume: 12
Issue: Suppl 2
Year: 2011

Building interpretable fuzzy models for high dimensional data analysis in cancer diagnosis

Author(s): Wang Zhenyu | Palade Vasile
Volume: 12
Issue: Suppl 2
Year: 2011

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

Author(s): Liu Bo | Gibbons Theodore | Ghodsi Mohammad | Treangen Todd | Pop Mihai
Volume: 12
Issue: Suppl 2
Year: 2011

FluReF, an automated flu virus reassortment finder based on phylogenetic trees

Author(s): Yurovsky Alisa | Moret Bernard
Volume: 12
Issue: Suppl 2
Year: 2011

Gene Cluster Profile Vectors: a method to infer functionally related gene sets by grouping proximity-based gene clusters

Author(s): Pejaver Vikas | Kim Sun
Volume: 12
Issue: Suppl 2
Year: 2011

Dynamic biclustering of microarray data by multi-objective immune optimization

Author(s): Liu Junwan | Li Zhoujun | Hu Xiaohua | Chen Yiming | Park EK
Volume: 12
Issue: Suppl 2
Year: 2011

Correlating CpG islands, motifs, and sequence variants in human chromosome 21

Author(s): Spontaneo Leah | Cercone Nick
Volume: 12
Issue: Suppl 2
Year: 2011

Sublineage structure analysis of Mycobacterium tuberculosis complex strains using multiple-biomarker tensors

Author(s): Ozcaglar Cagri | Shabbeer Amina | Vandenberg Scott | Yener Bülent | Bennett Kristin
Volume: 12
Issue: Suppl 2
Year: 2011

Analysis of long branch extraction and long branch shortening

Author(s): O’Connor Timothy | Sundberg Kenneth | Carroll Hyrum | Clement Mark | Snell Quinn
Volume: 11
Issue: Suppl 2
Year: 2010

An improved approach for the segmentation of starch granules in microscopic images

Author(s): Guo Shengwen | Tang Jinshan | Deng Youping | Xia Qun
Volume: 11
Issue: Suppl 2
Year: 2010

Discovery of pathway biomarkers from coupled proteomics and systems biology methods

Author(s): Zhang Fan | Chen Jake
Volume: 11
Issue: Suppl 2
Year: 2010

Predicting gene function using few positive examples and unlabeled ones

Author(s): Chen Yiming | Li Zhoujun | Wang Xiaofeng | Feng Jiali | Hu Xiaohua
Volume: 11
Issue: Suppl 2
Year: 2010

Speckle reducing bilateral filter for cattle follicle segmentation

Author(s): Tang Jinshan | Guo Shengwen | Sun Qingling | Deng Youping | Zhou Dongfeng
Volume: 11
Issue: Suppl 2
Year: 2010

Nucleosome structure incorporated histone acetylation site prediction in arabidopsis thaliana

Author(s): Zhao Chen | Liu Hui | Li Jiang | Deng Youping | Shi Tieliu
Volume: 11
Issue: Suppl 2
Year: 2010

Inferring gene regulatory networks from asynchronous microarray data with AIRnet

Author(s): Oviatt David | Clement Mark | Snell Quinn | Sundberg Kenneth | Lai Chun Wan | Allen Jared | Roper Randall
Volume: 11
Issue: Suppl 2
Year: 2010

Sequence feature-based prediction of protein stability changes upon amino acid substitutions

Author(s): Teng Shaolei | Srivastava Anand | Wang Liangjiang
Volume: 11
Issue: Suppl 2
Year: 2010

Generation, analysis and functional annotation of expressed sequence tags from the sheepshead minnow (Cyprinodon variegatus)

Author(s): Pirooznia Mehdi | Pozhitkov Alexander | Perkins Edward | Deng Youping | Brouwer Marius
Volume: 11
Issue: Suppl 2
Year: 2010

Density based pruning for identification of differentially expressed genes from microarray data

Author(s): Hu Jianjun | Xu Jia
Volume: 11
Issue: Suppl 2
Year: 2010

Global protein interactome exploration through mining genome-scale data in Arabidopsis thaliana

Author(s): Xu Feng | Li Guang | Zhao Chen | Li Yuhua | Li Peng | Cui Jian | Deng Youping | Shi Tieliu
Volume: 11
Issue: Suppl 2
Year: 2010

Microarray data integration for genome-wide analysis of human tissue-selective gene expression

Author(s): Wang Liangjiang | Srivastava Anand | Schwartz Charles
Volume: 11
Issue: Suppl 2
Year: 2010

A bacterial artificial chromosome library for the Australian saltwater crocodile (Crocodylus porosus) and its utilization in gene isolation and genome characterization

Author(s): Shan Xueyan | Ray David | Bunge John | Peterson Daniel
Volume: 10
Issue: Suppl 2
Year: 2009

Genome evolution in Reptilia: in silico chicken mapping of 12,000 BAC-end sequences from two reptiles and a basal bird

Author(s): Chapus Charles | Edwards Scott
Volume: 10
Issue: Suppl 2
Year: 2009

Integrative sequence and tissue expression profiling of chicken and mammalian aquaporins

Author(s): Isokpehi Raphael | Rajnarayanan Rajendram | Jeffries Cynthia | Oyeleye Tolulola | Cohly Hari
Volume: 10
Issue: Suppl 2
Year: 2009

BioNetBuilder2.0: bringing systems biology to chicken and other model organisms

Author(s): Konieczka Jay | Drew Kevin | Pine Alex | Belasco Kevin | Davey Sean | Yatskievych Tatiana | Bonneau Richard | Antin Parker
Volume: 10
Issue: Suppl 2
Year: 2009

The transcriptional response of Pasteurella multocida to three classes of antibiotics

Author(s): Nanduri Bindu | Shack Leslie | Burgess Shane | Lawrence Mark
Volume: 10
Issue: Suppl 2
Year: 2009

Extent and consistency of linkage disequilibrium and identification of DNA markers for production and egg quality traits in commercial layer chicken populations

Author(s): Abasht Behnam | Sandford Erin | Arango Jesus | Settar Petek | Fulton Janet | O'Sullivan Neil | Hassen Abebe | Habier David | Fernando Rohan | Dekkers Jack | Lamont Susan
Volume: 10
Issue: Suppl 2
Year: 2009

The value of avian genomics to the conservation of wildlife

Author(s): Romanov Michael | Tuttle Elaina | Houck Marlys | Modi William | Chemnick Leona | Korody Marisa | Mork Emily | Otten Christie | Renner Tanya | Jones Kenneth | Dandekar Sugandha | Papp Jeanette | Da Yang | Green Eric | Magrini Vincent | Hickenbotham Matthew | Glasscock Jarret | McGrath Sean | Mardis Elaine | Ryder Oliver
Volume: 10
Issue: Suppl 2
Year: 2009

Analyzing adjuvant radiotherapy suggests a non monotonic radio-sensitivity over tumor volumes

Author(s): Yang Jack | Niemierko Andrzej | Yang Mary | Deng Youping
Volume: 9
Issue: Suppl 2
Year: 2008

In silico comparison of transcript abundances during Arabidopsis thaliana and Glycine max resistance to Fusarium virguliforme

Author(s): Yuan Jiazheng | Zhu Mengxia | Lightfoot David | Iqbal M Javed | Yang Jack | Meksem Khalid
Volume: 9
Issue: Suppl 2
Year: 2008

Assessment of data processing to improve reliability of microarray experiments using genomic DNA reference

Author(s): Yang Yunfeng | Zhu Mengxia | Wu Liyou | Zhou Jizhong
Volume: 9
Issue: Suppl 2
Year: 2008

Selecting subsets of newly extracted features from PCA and PLS in microarray data analysis

Author(s): Li Guo-Zheng | Bu Hua-Long | Yang Mary | Zeng Xue-Qiang | Yang Jack
Volume: 9
Issue: Suppl 2
Year: 2008

A Poisson mixture model to identify changes in RNA polymerase II binding quantity using high-throughput sequencing technology

Author(s): Feng Weixing | Liu Yunlong | Wu Jiejun | Nephew Kenneth | Huang Tim | Li Lang
Volume: 9
Issue: Suppl 2
Year: 2008

Transcription factor and microRNA regulation in androgen-dependent and -independent prostate cancer cells

Author(s): Wang Guohua | Wang Yadong | Feng Weixing | Wang Xin | Yang Jack | Zhao Yuming | Wang Yue | Liu Yunlong
Volume: 9
Issue: Suppl 2
Year: 2008

Tumor classification ranking from microarray data

Author(s): Hewett Rattikorn | Kijsanayothin Phongphun
Volume: 9
Issue: Suppl 2
Year: 2008

Extending bicluster analysis to annotate unclassified ORFs and predict novel functional modules using expression data

Author(s): Bryan Kenneth | Cunningham Pádraig
Volume: 9
Issue: Suppl 2
Year: 2008

Array CGH data modeling and smoothing in Stationary Wavelet Packet Transform domain

Author(s): Huang Heng | Nguyen Nha | Oraintara Soontorn | Vo An
Volume: 9
Issue: Suppl 2
Year: 2008

Use artificial neural network to align biological ontologies

Author(s): Huang Jingshan | Dang Jiangbo | Huhns Michael | Zheng W Jim
Volume: 9
Issue: Suppl 2
Year: 2008

Phylogenetic reconstruction from transpositions

Author(s): Yue Feng | Zhang Meng | Tang Jijun
Volume: 9
Issue: Suppl 2
Year: 2008

Selecting informative genes for discriminant analysis using multigene expression profiles

Author(s): Yan Xin | Zheng Tian
Volume: 9
Issue: Suppl 2
Year: 2008

The unfoldomics decade: an update on intrinsically disordered proteins

Author(s): Dunker A Keith | Oldfield Christopher | Meng Jingwei | Romero Pedro | Yang Jack | Chen Jessica | Vacic Vladimir | Obradovic Zoran | Uversky Vladimir
Volume: 9
Issue: Suppl 2
Year: 2008

Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research

Author(s): Yang Jack | Yang Mary | Arabnia Hamid | Deng Youping
Volume: 9
Issue: Suppl 2
Year: 2008

Identifying functional relationships within sets of co-expressed genes by combining upstream regulatory motif analysis and gene expression information

Author(s): Martyanov Viktor | Gross Robert
Volume: 11
Issue: Suppl 2
Year: 2010

The chicken gene nomenclature committee report

Author(s): Burt David | Carrë Wilfrid | Fell Mark | Law Andy | Antin Parker | Maglott Donna | Weber Janet | Schmidt Carl | Burgess Shane | McCarthy Fiona
Volume: 10
Issue: Suppl 2
Year: 2009

Application of chicken microarrays for gene expression analysis in other avian species

Author(s): Crowley Tamsyn | Haring Volker | Burggraaf Simon | Moore Robert
Volume: 10
Issue: Suppl 2
Year: 2009

USDA animal genomics program: the view from the chicken coop

Author(s): Fulton Janet
Volume: 10
Issue: Suppl 2
Year: 2009

Introduction to the Proceedings of the Avian Genomics and Gene Ontology Annotation Workshop

Author(s): Bridges Susan | Burgess Shane | McCarthy Fiona
Volume: 10
Issue: Suppl 2
Year: 2009

Predicting protein disorder by analyzing amino acid sequence

Author(s): Yang Jack | Yang Mary
Volume: 9
Issue: Suppl 2
Year: 2008

Biomarker discovery across annotated and unannotated microarray datasets using semi-supervised learning

Author(s): Harris Cole | Ghaffari Noushin
Volume: 9
Issue: Suppl 2
Year: 2008

Protein intrinsic disorder toolbox for comparative analysis of viral proteins

Author(s): Goh Gerard | Dunker A Keith | Uversky Vladimir
Volume: 9
Issue: Suppl 2
Year: 2008

Diversity of core promoter elements comprising human bidirectional promoters

Author(s): Yang Mary | Elnitski Laura
Volume: 9
Issue: Suppl 2
Year: 2008

Gene selection algorithm by combining reliefF and mRMR

Author(s): Zhang Yi | Ding Chris | Li Tao
Volume: 9
Issue: Suppl 2
Year: 2008

Short Linear Motifs recognized by SH2, SH3 and Ser/Thr Kinase domains are conserved in disordered protein regions

Author(s): Ren Siyuan | Uversky Vladimir | Chen Zhengjun | Dunker A Keith | Obradovic Zoran
Volume: 9
Issue: Suppl 2
Year: 2008

MeDor: a metaserver for predicting protein disorder

Author(s): Lieutaud Philippe | Canard Bruno | Longhi Sonia
Volume: 9
Issue: Suppl 2
Year: 2008

The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending to novel applications

Author(s): Halperin Inbal | Glazer Dariya | Wu Shirley | Altman Russ
Volume: 9
Issue: Suppl 2
Year: 2008

Inferring gene regulatory networks by thermodynamic modeling

Author(s): Chen Chieh-Chun | Zhong Sheng
Volume: 9
Issue: Suppl 2
Year: 2008

A stable iterative method for refining discriminative gene clusters

Author(s): Xu Min | Zhu Mengxia | Zhang Louxin
Volume: 9
Issue: Suppl 2
Year: 2008

Approaches to reduce false positives and false negatives in the analysis of microarray data: applications in type 1 diabetes research

Author(s): Wu Jian | Lenchik Nataliya | Gerling Ivan
Volume: 9
Issue: Suppl 2
Year: 2008

ILOOP – a web application for two-channel microarray interwoven loop design

Author(s): Pirooznia Mehdi | Gong Ping | Yang Jack | Yang Mary | Perkins Edward | Deng Youping
Volume: 9
Issue: Suppl 2
Year: 2008

Batch Blast Extractor: an automated blastx parser application

Author(s): Pirooznia Mehdi | Perkins Edward | Deng Youping
Volume: 9
Issue: Suppl 2
Year: 2008

Identifying protein complexes from interaction networks based on clique percolation and distance restriction

Author(s): Wang Jianxin | Liu Binbin | Li Min | Pan Yi
Volume: 11
Issue: Suppl 2
Year: 2010

Classification of genomic islands using decision trees and their ensemble algorithms

Author(s): Che Dongsheng | Hockenbury Cory | Marmelstein Robert | Rasheed Khaled
Volume: 11
Issue: Suppl 2
Year: 2010

Improving the specificity of exon prediction using comparative genomics

Author(s): Wu Jing
Volume: 9
Issue: Suppl 2
Year: 2008

Environment sensing and response mediated by ABC transporters

Author(s): Giuliani Sarah | Frank Ashley | Corgliano Danielle | Seifert Catherine | Hauser Loren | Collart Frank
Volume: 12
Issue: Suppl 1
Year: 2011

A nuclear magnetic resonance based approach to accurate functional annotation of putative enzymes in the methanogen Methanosarcina acetivorans

Author(s): Chen Yihong | Apolinario Ethel | Brachova Libuse | Kelman Zvi | Li Zhuo | Nikolau Basil | Showman Lucas | Sowers Kevin | Orban John
Volume: 12
Issue: Suppl 1
Year: 2011

Improved genome annotation through untargeted detection of pathway-specific metabolites

Author(s): Bowen Benjamin | Fischer Curt | Baran Richard | Banfield Jillian | Northen Trent
Volume: 12
Issue: Suppl 1
Year: 2011

Filtering "genic" open reading frames from genomic DNA samples for advanced annotation

Author(s): D'Angelo Sara | Velappan Nileena | Mignone Flavio | Santoro Claudio | Sblattero Daniele | Kiss Csaba | Bradbury Andrew
Volume: 12
Issue: Suppl 1
Year: 2011

Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii

Author(s): Ghamsari Lila | Balaji Santhanam | Shen Yun | Yang Xinping | Balcha Dawit | Fan Changyu | Hao Tong | Yu Haiyuan | Papin Jason | Salehi-Ashtiani Kourosh
Volume: 12
Issue: Suppl 1
Year: 2011

Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus

Author(s): Rodionov Dmitry | Novichkov Pavel | Stavrovskaya Elena | Rodionova Irina | Li Xiaoqing | Kazanov Marat | Ravcheev Dmitry | Gerasimova Anna | Kazakov Alexey | Kovaleva Galina | Permina Elizabeth | Laikova Olga | Overbeek Ross | Romine Margaret | Fredrickson James | Arkin Adam | Dubchak Inna | Osterman Andrei | Gelfand Mikhail
Volume: 12
Issue: Suppl 1
Year: 2011

Synergistic use of plant-prokaryote comparative genomics for functional annotations

Author(s): Gerdes Svetlana | El Yacoubi Basma | Bailly Marc | Blaby Ian | Blaby-Haas Crysten | Jeanguenin Linda | Lara-Núñez Aurora | Pribat Anne | Waller Jeffrey | Wilke Andreas | Overbeek Ross | Hanson Andrew | de Crécy-Lagard Valérie
Volume: 12
Issue: Suppl 1
Year: 2011

Genome-wide protein localization prediction strategies for gram negative bacteria

Author(s): Romine Margaret
Volume: 12
Issue: Suppl 1
Year: 2011

Introduction: Validation methods for function genome annotation

Author(s): Stodolsky Marvin
Volume: 12
Issue: Suppl 1
Year: 2011

Protein disorder prediction at multiple levels of sensitivity and specificity

Author(s): Hecker Joshua | Yang Jack | Cheng Jianlin
Volume: 9
Issue: Suppl 1
Year: 2008

Investigation of transmembrane proteins using a computational approach

Author(s): Yang Jack | Yang Mary | Dunker A Keith | Deng Youping | Huang Xudong
Volume: 9
Issue: Suppl 1
Year: 2008

Supervised learning-based tagSNP selection for genome-wide disease classifications

Author(s): Liu Qingzhong | Yang Jack | Chen Zhongxue | Yang Mary Qu | Sung Andrew | Huang Xudong
Volume: 9
Issue: Suppl 1
Year: 2008

Transcription network construction for large-scale microarray datasets using a high-performance computing approach

Author(s): Zhu Mengxia (Michelle) | Wu Qishi
Volume: 9
Issue: Suppl 1
Year: 2008

Bayesian biclustering of gene expression data

Author(s): Gu Jiajun | Liu Jun
Volume: 9
Issue: Suppl 1
Year: 2008

Improving prediction accuracy of tumor classification by reusing genes discarded during gene selection

Author(s): Yang Jack | Li Guo-Zheng | Meng Hao-Hua | Yang Mary | Deng Youping
Volume: 9
Issue: Suppl 1
Year: 2008

Gene rearrangement analysis and ancestral order inference from chloroplast genomes with inverted repeat

Author(s): Yue Feng | Cui Liying | dePamphilis Claude | Moret Bernard | Tang Jijun
Volume: 9
Issue: Suppl 1
Year: 2008

Algorithms to estimate the lower bounds of recombination with or without recurrent mutations

Author(s): Liu Xiaoming | Fu Yun-Xin
Volume: 9
Issue: Suppl 1
Year: 2008

A hybrid machine learning-based method for classifying the Cushing's Syndrome with comorbid adrenocortical lesions

Author(s): Yang Jack | Yang Mary Qu | Luo Zuojie | Ma Yan | Li Jianling | Deng Youping | Huang Xudong
Volume: 9
Issue: Suppl 1
Year: 2008

Efficient non-unique probes selection algorithms for DNA microarray

Author(s): Deng Ping | Thai My | Ma Qingkai | Wu Weili
Volume: 9
Issue: Suppl 1
Year: 2008

Stability analysis of genetic regulatory network with additive noises

Author(s): Jin Yufang | Lindsey Merry
Volume: 9
Issue: Suppl 1
Year: 2008

xMAN: extreme MApping of OligoNucleotides

Author(s): Li Wei | Carroll Jason | Brown Myles | Liu X Shirley
Volume: 9
Issue: Suppl 1
Year: 2008

Prediction-based approaches to characterize bidirectional promoters in the mammalian genome

Author(s): Yang Mary Qu | Elnitski Laura
Volume: 9
Issue: Suppl 1
Year: 2008

Supervised learning method for the prediction of subcellular localization of proteins using amino acid and amino acid pair composition

Author(s): Habib Tanwir | Zhang Chaoyang | Yang Jack | Yang Mary Qu | Deng Youping
Volume: 9
Issue: Suppl 1
Year: 2008

Transcriptomic analysis of RDX and TNT interactive sublethal effects in the earthworm Eisenia fetida

Author(s): Gong Ping | Guan Xin | Inouye Laura | Deng Youping | Pirooznia Mehdi | Perkins Edward
Volume: 9
Issue: Suppl 1
Year: 2008

Transcriptome profiling of Saccharomyces cerevisiae mutants lacking C2H2 zinc finger proteins

Author(s): Mao Jinghe | Habib Tanwir | Shenwu Ming | Kang Baobin | Allen Wilbur | Robertson LaShonda | Yang Jack | Deng Youping
Volume: 9
Issue: Suppl 1
Year: 2008

A comparative study of different machine learning methods on microarray gene expression data

Author(s): Pirooznia Mehdi | Yang Jack | Yang Mary Qu | Deng Youping
Volume: 9
Issue: Suppl 1
Year: 2008

An integrative approach to characterize disease-specific pathways and their coordination: a case study in cancer

Author(s): Xu Min | Kao Ming-Chih | Nunez-Iglesias Juan | Nevins Joseph | West Mike | Zhou Xianghong Jasmine
Volume: 9
Issue: Suppl 1
Year: 2008

Characterization of the Shewanella oneidensis Fur gene: roles in iron and acid tolerance response

Author(s): Yang Yunfeng | Harris Daniel | Luo Feng | Wu Liyou | Parsons Andrea | Palumbo Anthony | Zhou Jizhong
Volume: 9
Issue: Suppl 1
Year: 2008

Promoting synergistic research and education in genomics and bioinformatics

Author(s): Yang Jack | Yang Mary Qu | Zhu Mengxia (Michelle) | Arabnia Hamid | Deng Youping
Volume: 9
Issue: Suppl 1
Year: 2008

Projection of gene-protein networks to the functional space of the proteome and its application to analysis of organism complexity

Author(s): Kanapin Alexander | Mulder Nicola | Kuznetsov Vladimir
Volume: 11
Issue: Suppl 1
Year: 2010

Computational approaches for detecting protein complexes from protein interaction networks: a survey

Author(s): Li Xiaoli | Wu Min | Kwoh Chee-Keong | Ng See-Kiong
Volume: 11
Issue: Suppl 1
Year: 2010

Collective motions and specific effectors: a statistical mechanics perspective on biological regulation

Author(s): Giuliani Alessandro
Volume: 11
Issue: Suppl 1
Year: 2010

Parameterization of disorder predictors for large-scale applications requiring high specificity by using an extended benchmark dataset

Author(s): Sirota Fernanda | Ooi Hong-Sain | Gattermayer Tobias | Schneider Georg | Eisenhaber Frank | Maurer-Stroh Sebastian
Volume: 11
Issue: Suppl 1
Year: 2010

Reducing the haystack to find the needle: improved protein identification after fast elimination of non-interpretable peptide MS/MS spectra and noise reduction

Author(s): Mujezinovic Nedim | Schneider Georg | Wildpaner Michael | Mechtler Karl | Eisenhaber Frank
Volume: 11
Issue: Suppl 1
Year: 2010

Statistics of protein-DNA binding and the total number of binding sites for a transcription factor in the mammalian genome

Author(s): Kuznetsov Vladimir | Singh Onkar | Jenjaroenpun Piroon
Volume: 11
Issue: Suppl 1
Year: 2010

Transposon identification using profile HMMs

Author(s): Edlefsen Paul | Liu Jun
Volume: 11
Issue: Suppl 1
Year: 2010

Mechanisms of chromosomal rearrangement in the human genome

Author(s): Tsai Albert | Lieber Michael
Volume: 11
Issue: Suppl 1
Year: 2010

Complex sense-antisense architecture of TNFAIP1/POLDIP2 on 17q11.2 represents a novel transcriptional structural-functional gene module involved in breast cancer progression

Author(s): Grinchuk Oleg | Motakis Efthimios | Kuznetsov Vladimir
Volume: 11
Issue: Suppl 1
Year: 2010

Analysis of deep sequencing microRNA expression profile from human embryonic stem cells derived mesenchymal stem cells reveals possible role of let-7 microRNA family in downstream targeting of Hepatic Nuclear Factor 4 Alpha

Author(s): Koh Winston | Sheng Chen | Tan Betty | Lee Qian | Kuznetsov Vladimir | Kiang Lim | Tanavde Vivek
Volume: 11
Issue: Suppl 1
Year: 2010

Energy profile and secondary structure impact shRNA efficacy

Author(s): Zhou Hong | Zeng Xiao
Volume: 10
Issue: Suppl 1
Year: 2009

An ensemble learning approach to reverse-engineering transcriptional regulatory networks from time-series gene expression data

Author(s): Ruan Jianhua | Deng Youping | Perkins Edward | Zhang Weixiong
Volume: 10
Issue: Suppl 1
Year: 2009

Unfoldomics of human diseases: linking protein intrinsic disorder with diseases

Author(s): Uversky Vladimir | Oldfield Christopher | Midic Uros | Xie Hongbo | Xue Bin | Vucetic Slobodan | Iakoucheva Lilia | Obradovic Zoran | Dunker A Keith
Volume: 10
Issue: Suppl 1
Year: 2009

Annotating the human genome with Disease Ontology

Author(s): Osborne John | Flatow Jared | Holko Michelle | Lin Simon | Kibbe Warren | Zhu Lihua | Danila Maria | Feng Gang | Chisholm Rex
Volume: 10
Issue: Suppl 1
Year: 2009

Comprehensive splicing graph analysis of alternative splicing patterns in chicken, compared to human and mouse

Author(s): Chacko Elsa | Ranganathan Shoba
Volume: 10
Issue: Suppl 1
Year: 2009

Genome-wide prediction of cis-acting RNA elements regulating tissue-specific pre-mRNA alternative splicing

Author(s): Wang Xin | Wang Kejun | Radovich Milan | Wang Yue | Wang Guohua | Feng Weixing | Sanford Jeremy | Liu Yunlong
Volume: 10
Issue: Suppl 1
Year: 2009

Comparison of feature selection and classification for MALDI-MS data

Author(s): Liu Qingzhong | Sung Andrew | Qiao Mengyu | Chen Zhongxue | Yang Jack | Yang Mary | Huang Xudong | Deng Youping
Volume: 10
Issue: Suppl 1
Year: 2009

Reconstruct gene regulatory network using slice pattern model

Author(s): Wang Yadong | Wang Guohua | Yang Bo | Tao Haijun | Yang Jack | Deng Youping | Liu Yunlong
Volume: 10
Issue: Suppl 1
Year: 2009

A distribution-free convolution model for background correction of oligonucleotide microarray data

Author(s): Chen Zhongxue | McGee Monnie | Liu Qingzhong | Kong Megan | Deng Youping | Scheuermann Richard
Volume: 10
Issue: Suppl 1
Year: 2009

Word-based characterization of promoters involved in human DNA repair pathways

Author(s): Lichtenberg Jens | Jacox Edwin | Welch Joshua | Kurz Kyle | Liang Xiaoyu | Yang Mary | Drews Frank | Ecker Klaus | Lee Stephen | Elnitski Laura | Welch Lonnie
Volume: 10
Issue: Suppl 1
Year: 2009

Comparing 2-nt 3' overhangs against blunt-ended siRNAs: a systems biology based study

Author(s): Ghosh Preetam | Dullea Robert | Fischer James | Turi Tom | Sarver Ronald | Zhang Chaoyang | Basu Kalyan | Das Sajal | Poland Bradley
Volume: 10
Issue: Suppl 1
Year: 2009

HAPPI: an online database of comprehensive human annotated and predicted protein interactions

Author(s): Chen Jake | Mamidipalli SudhaRani | Huan Tianxiao
Volume: 10
Issue: Suppl 1
Year: 2009

Reverse engineering module networks by PSO-RNN hybrid modeling

Author(s): Zhang Yuji | Xuan Jianhua | de los Reyes Benildo | Clarke Robert | Ressom Habtom
Volume: 10
Issue: Suppl 1
Year: 2009

Differences in duplication age distributions between human GPCRs and their downstream genes from a network prospective

Author(s): Huang Yong | Zheng Ying | Su Zhixi | Gu Xun
Volume: 10
Issue: Suppl 1
Year: 2009

PDA: an automatic and comprehensive analysis program for protein-DNA complex structures

Author(s): Kim RyangGuk | Guo Jun-tao
Volume: 10
Issue: Suppl 1
Year: 2009

Protein disorder in the human diseasome: unfoldomics of human genetic diseases

Author(s): Midic Uros | Oldfield Christopher | Dunker A Keith | Obradovic Zoran | Uversky Vladimir
Volume: 10
Issue: Suppl 1
Year: 2009

Genomic and systems evolution in Vibrionaceae species

Author(s): Gu Jianying | Neary Jennifer | Cai Hong | Moshfeghian Audrey | Rodriguez Stephen | Lilburn Timothy | Wang Yufeng
Volume: 10
Issue: Suppl 1
Year: 2009

RBT-GA: a novel metaheuristic for solving the multiple sequence alignment problem

Author(s): Taheri Javid | Zomaya Albert
Volume: 10
Issue: Suppl 1
Year: 2009

Prediction of DNA-binding residues from protein sequence information using random forests

Author(s): Wang Liangjiang | Yang Mary | Yang Jack
Volume: 10
Issue: Suppl 1
Year: 2009

High-throughput next-generation sequencing technologies foster new cutting-edge computing techniques in bioinformatics

Author(s): Yang Mary | Athey Brian | Arabnia Hamid | Sung Andrew | Liu Qingzhong | Yang Jack | Mao Jinghe | Deng Youping
Volume: 10
Issue: Suppl 1
Year: 2009

Bioinformatic search of plant microtubule-and cell cycle related serine-threonine protein kinases

Author(s): Karpov Pavel | Nadezhdina Elena | Yemets Alla | Matusov Vadym | Nyporko Alexey | Shashina Nadezhda | Blume Yaroslav
Volume: 11
Issue: Suppl 1
Year: 2010

Modeling neutral evolution of Alu elements using a branching process

Author(s): Kimmel Marek | Mathaes Matthias
Volume: 11
Issue: Suppl 1
Year: 2010

Bimodal gene expression patterns in breast cancer

Author(s): Bessarabova Marina | Kirillov Eugene | Shi Weiwei | Bugrim Andrej | Nikolsky Yuri | Nikolskaya Tatiana
Volume: 11
Issue: Suppl 1
Year: 2010

Data integration and exploration for the identification of molecular mechanisms in tumor-immune cells interaction

Author(s): Mlecnik Bernhard | Sanchez-Cabo Fatima | Charoentong Pornpimol | Bindea Gabriela | Pagès Franck | Berger Anne | Galon Jerome | Trajanoski Zlatko
Volume: 11
Issue: Suppl 1
Year: 2010

Differences in the transactivation domains of p53 family members: a computational study

Author(s): Mavinahalli Jagadeesh | Madhumalar Arumugam | Beuerman Roger | Lane David | Verma Chandra
Volume: 11
Issue: Suppl 1
Year: 2010

HMMEditor: a visual editing tool for profile hidden Markov model

Author(s): Dai Jianyong | Cheng Jianlin
Volume: 9
Issue: Suppl 1
Year: 2008

Using RNase sequence specificity to refine the identification of RNA-protein binding regions

Author(s): Wang Xin | Wang Guohua | Shen Changyu | Li Lang | Wang Xinguo | Mooney Sean | Edenberg Howard | Sanford Jeremy | Liu Yunlong
Volume: 9
Issue: Suppl 1
Year: 2008

Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners

Author(s): Oldfield Christopher | Meng Jingwei | Yang Jack | Yang Mary Qu | Uversky Vladimir | Dunker A Keith
Volume: 9
Issue: Suppl 1
Year: 2008

Identification of transcription factor and microRNA binding sites in responsible to fetal alcohol syndrome

Author(s): Wang Guohua | Wang Xin | Wang Yadong | Yang Jack | Li Lang | Nephew Kenneth | Edenberg Howard | Zhou Feng | Liu Yunlong
Volume: 9
Issue: Suppl 1
Year: 2008

Selection of thermodynamic models for combinatorial control of multiple transcription factors in early differentiation of embryonic stem cells

Author(s): Chen Chieh-Chun | Zhu Xin-Guang | Zhong Sheng
Volume: 9
Issue: Suppl 1
Year: 2008

Semantically linking and browsing PubMed abstracts with gene ontology

Author(s): Vanteru Bhanu | Shaik Jahangheer | Yeasin Mohammed
Volume: 9
Issue: Suppl 1
Year: 2008

Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli

Author(s): Shinhara Atsuko | Matsui Motomu | Hiraoka Kiriko | Nomura Wataru | Hirano Reiko | Nakahigashi Kenji | Tomita Masaru | Mori Hirotada | Kanai Akio
Volume: 12
Issue: 1
Year: 2011

Evidence for post-transcriptional regulation of clustered microRNAs in Drosophila

Author(s): Ryazansky Sergei | Gvozdev Vladimir | Berezikov Eugene
Volume: 12
Issue: 1
Year: 2011

Transcriptome characterization and polymorphism detection between subspecies of big sagebrush (Artemisia tridentata)

Author(s): Bajgain Prabin | Richardson Bryce | Price Jared | Cronn Richard | Udall Joshua
Volume: 12
Issue: 1
Year: 2011

Complete genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus

Author(s): Tang Kuo-Hsiang | Barry Kerrie | Chertkov Olga | Dalin Eileen | Han Cliff | Hauser Loren | Honchak Barbara | Karbach Lauren | Land Miriam | Lapidus Alla | Larimer Frank | Mikhailova Natalia | Pitluck Samuel | Pierson Beverly | Blankenship Robert
Volume: 12
Issue: 1
Year: 2011

Large scale genome-wide association and LDLA mapping study identifies QTLs for boar taint and related sex steroids

Author(s): Grindflek Eli | Lien Sigbjørn | Hamland Hanne | Hansen Marianne | Kent Matthew | van Son Maren | Meuwissen Theo
Volume: 12
Issue: 1
Year: 2011

Transcriptomic response of the red tide dinoflagellate, Karenia brevis, to nitrogen and phosphorus depletion and addition

Author(s): Morey Jeanine | Monroe Emily | Kinney Amanda | Beal Marion | Johnson Jillian | Hitchcock Gary | Van Dolah Frances
Volume: 12
Issue: 1
Year: 2011

RsaI repetitive DNA in Buffalo Bubalus bubalis representing retrotransposons, conserved in bovids, are part of the functional genes

Author(s): Pathak Deepali | Ali Sher
Volume: 12
Issue: 1
Year: 2011

Immunogenicity of autoantigens

Author(s): Backes Christina | Ludwig Nicole | Leidinger Petra | Harz Christian | Hoffmann Jana | Keller Andreas | Meese Eckart | Lenhof Hans-Peter
Volume: 12
Issue: 1
Year: 2011

EST mining identifies proteins putatively secreted by the anthracnose pathogen Colletotrichum truncatum

Author(s): Bhadauria Vijai | Banniza Sabine | Vandenberg Albert | Selvaraj Gopalan | Wei Yangdou
Volume: 12
Issue: 1
Year: 2011

Implication of next-generation sequencing on association studies

Author(s): Siu Hoicheong | Zhu Yun | Jin Li | Xiong Momiao
Volume: 12
Issue: 1
Year: 2011

Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle

Author(s): Qanbari Saber | Gianola Daniel | Hayes Ben | Schenkel Flavio | Miller Steve | Moore Stephen | Thaller Georg | Simianer Henner
Volume: 12
Issue: 1
Year: 2011

Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine

Author(s): Chancerel Emilie | Lepoittevin Camille | Le Provost Grégoire | Lin Yao-Cheng | Jaramillo-Correa Juan | Eckert Andrew | Wegrzyn Jill | Zelenika Diana | Boland Anne | Frigerio Jean-Marc | Chaumeil Philippe | Garnier-Géré Pauline | Boury Christophe | Grivet Delphine | González-Martínez Santiago | Rouzé Pierre | Van de Peer Yves | Neale David | Cervera Maria | Kremer Antoine | Plomion Christophe
Volume: 12
Issue: 1
Year: 2011

Single-nucleotide polymorphism discovery by high-throughput sequencing in sorghum

Author(s): Nelson James | Wang Shichen | Wu Yuye | Li Xianran | Antony Ginny | White Frank | Yu Jianming
Volume: 12
Issue: 1
Year: 2011

Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna

Author(s): Orsini Luisa | Jansen Mieke | Souche Erika | Geldof Sarah | De Meester Luc
Volume: 12
Issue: 1
Year: 2011

Transcriptomic analysis of grain amaranth (Amaranthus hypochondriacus) using 454 pyrosequencing: comparison with A. tuberculatus, expression profiling in stems and in response to biotic and abiotic stress

Author(s): Délano-Frier John | Avilés-Arnaut Hamlet | Casarrubias-Castillo Kena | Casique-Arroyo Gabriela | Castrillón-Arbeláez Paula | Herrera-Estrella Luis | Massange-Sánchez Julio | Martínez-Gallardo Norma | Parra-Cota Fannie | Vargas-Ortiz Erandi | Estrada-Hernández María
Volume: 12
Issue: 1
Year: 2011

Gene discovery using next-generation pyrosequencing to develop ESTs for Phalaenopsis orchids

Author(s): Hsiao Yu-Yun | Chen Yun-Wen | Huang Shi-Ching | Pan Zhao-Jun | Fu Chih-Hsiung | Chen Wen-Huei | Tsai Wen-Chieh | Chen Hong-Hwa
Volume: 12
Issue: 1
Year: 2011

Identification of alternative splice variants in Aspergillus flavus through comparison of multiple tandem MS search algorithms

Author(s): Chang Kung-Yen | Muddiman David
Volume: 12
Issue: 1
Year: 2011

Generating libraries of iTol2-end insertions at BAC ends using loxP and lox511 Tn10 transposons

Author(s): Shakes Leighcraft | Abe Gembu | Eltayeb Mugtaba | Wolf Hope | Kawakami Koichi | Chatterjee Pradeep
Volume: 12
Issue: 1
Year: 2011

Investigating the global genomic diversity of Escherichia coli using a multi-genome DNA microarray platform with novel gene prediction strategies

Author(s): Jackson Scott | Patel Isha | Barnaba Tammy | LeClerc Joseph | Cebula Thomas
Volume: 12
Issue: 1
Year: 2011

Exome-wide DNA capture and next generation sequencing in domestic and wild species

Author(s): Cosart Ted | Beja-Pereira Albano | Chen Shanyuan | Ng Sarah | Shendure Jay | Luikart Gordon
Volume: 12
Issue: 1
Year: 2011

MicroRNA genes preferentially expressed in dendritic cells contain sites for conserved transcription factor binding motifs in their promoters

Author(s): Jansen Bastiaan | Sama Iziah | Eleveld-Trancikova Dagmar | van Hout-Kuijer Maaike | Jansen Joop | Huynen Martijn | Adema Gosse
Volume: 12
Issue: 1
Year: 2011

Site-Specific Mobilization of Vinyl Chloride Respiration Islands by a Mechanism Common in Dehalococcoides

Author(s): McMurdie Paul | Hug Laura | Edwards Elizabeth | Holmes Susan | Spormann Alfred
Volume: 12
Issue: 1
Year: 2011

Influence of cell cycle on responses of MCF-7 cells to benzo[a]pyrene

Author(s): Hamouchene Hamza | Arlt Volker | Giddings Ian | Phillips David
Volume: 12
Issue: 1
Year: 2011

Characterization of the small RNA component of the transcriptome from grain and sweet sorghum stems

Author(s): Calviño Martín | Bruggmann Rémy | Messing Joachim
Volume: 12
Issue: 1
Year: 2011

Construction of an American mink Bacterial Artificial Chromosome (BAC) library and sequencing candidate genes important for the fur industry

Author(s): Anistoroaei Razvan | ten Hallers Boudewijn | Nefedov Michael | Christensen Knud | de Jong Pieter
Volume: 12
Issue: 1
Year: 2011

The characterisation of piRNA-related 19mers in the mouse

Author(s): Oey Harald | Youngson Neil | Whitelaw Emma
Volume: 12
Issue: 1
Year: 2011

Identification of ejaculated proteins in the house mouse (Mus domesticus) via isotopic labeling

Author(s): Dean Matthew | Findlay Geoffrey | Hoopmann Michael | Wu Christine | MacCoss Michael | Swanson Willie | Nachman Michael
Volume: 12
Issue: 1
Year: 2011

InterMitoBase: An annotated database and analysis platform of protein-protein interactions for human mitochondria

Author(s): Gu Zuguang | Li Jie | Gao Song | Gong Ming | Wang Junling | Xu Hua | Zhang Chenyu | Wang Jin
Volume: 12
Issue: 1
Year: 2011

Gene discovery by genome-wide CDS re-prediction and microarray-based transcriptional analysis in phytopathogen Xanthomonas campestris

Author(s): Zhou Lian | Vorhölter Frank-Jörg | He Yong-Qiang | Jiang Bo-Le | Tang Ji-Liang | Xu Yuquan | Pühler Alfred | He Ya-Wen
Volume: 12
Issue: 1
Year: 2011

Identification and characterization of microRNAs from Phaeodactylum tricornutum by high-throughput sequencing and bioinformatics analysis

Author(s): Huang Aiyou | He Linwen | Wang Guangce
Volume: 12
Issue: 1
Year: 2011

Evolutionary conserved microRNAs are ubiquitously expressed compared to tick-specific miRNAs in the cattle tick Rhipicephalus (Boophilus) microplus

Author(s): Barrero Roberto | Keeble-Gagnère Gabriel | Zhang Bing | Moolhuijzen Paula | Ikeo Kazuho | Tateno Yoshio | Gojobori Takashi | Guerrero Felix | Lew-Tabor Ala | Bellgard Matthew
Volume: 12
Issue: 1
Year: 2011

Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis

Author(s): Llorens Franc | Hummel Manuela | Pastor Xavier | Ferrer Anna | Pluvinet Raquel | Vivancos Ana | Castillo Ester | Iraola Susana | Mosquera Ana | González Eva | Lozano Juanjo | Ingham Matthew | Dohm Juliane | Noguera Marc | Kofler Robert | del Río Jose | Bayés Mònica | Himmelbauer Heinz | Sumoy Lauro
Volume: 12
Issue: 1
Year: 2011

A comprehensive characterization of the caspase gene family in insects from the order Lepidoptera

Author(s): Courtiade Juliette | Pauchet Yannick | Vogel Heiko | Heckel David
Volume: 12
Issue: 1
Year: 2011

RASOnD - A comprehensive resource and search tool for RAS superfamily oncogenes from various species

Author(s): Kulsum Umay | Singh Vishwadeep | Sharma Sujata | Srinivasan A | Singh Tej | Kaur Punit
Volume: 12
Issue: 1
Year: 2011

Unresolved orthology and peculiar coding sequence properties of lamprey genes: the KCNA gene family as test case

Author(s): Qiu Huan | Hildebrand Falk | Kuraku Shigehiro | Meyer Axel
Volume: 12
Issue: 1
Year: 2011

Comparative genome analysis and genome-guided physiological analysis of Roseobacter litoralis

Author(s): Kalhoefer Daniela | Thole Sebastian | Voget Sonja | Lehmann Rüdiger | Liesegang Heiko | Wollher Antje | Daniel Rolf | Simon Meinhard | Brinkhoff Thorsten
Volume: 12
Issue: 1
Year: 2011

RNA-seq: technical variability and sampling

Author(s): McIntyre Lauren | Lopiano Kenneth | Morse Alison | Amin Victor | Oberg Ann | Young Linda | Nuzhdin Sergey
Volume: 12
Issue: 1
Year: 2011

Directional RNA deep sequencing sheds new light on the transcriptional response of Anabaena sp. strain PCC 7120 to combined-nitrogen deprivation

Author(s): Flaherty Britt | Van Nieuwerburgh F | Head Steven | Golden James
Volume: 12
Issue: 1
Year: 2011

Genome-wide expression quantitative trait loci (eQTL) analysis in maize

Author(s): Holloway Beth | Luck Stanley | Beatty Mary | Rafalski J-Antoni | Li Bailin
Volume: 12
Issue: 1
Year: 2011

Transcriptomic, proteomic and metabolomic analysis of UV-B signaling in maize

Author(s): Casati Paula | Campi Mabel | Morrow Darren | Fernandes John | Walbot Virginia
Volume: 12
Issue: 1
Year: 2011

Global analysis of gene expression in mineralizing fish vertebra-derived cell lines: new insights into anti-mineralogenic effect of vanadate

Author(s): Tiago Daniel | Laizé Vincent | Bargelloni Luca | Ferraresso Serena | Romualdi Chiara | Cancela M
Volume: 12
Issue: 1
Year: 2011

Genome-wide gene expression analysis supports a developmental model of low temperature tolerance gene regulation in wheat (Triticum aestivum L.)

Author(s): Laudencia-Chingcuanco Debbie | Ganeshan Seedhabadee | You Frank | Fowler Brian | Chibbar Ravindra | Anderson Olin
Volume: 12
Issue: 1
Year: 2011

Characterization of single-nucleotide variation in Indian-origin rhesus macaques (Macaca mulatta)

Author(s): Fawcett Gloria | Raveendran Muthuswamy | Deiros David | Chen David | Yu Fuli | Harris Ronald | Ren Yanru | Muzny Donna | Reid Jeffrey | Wheeler David | Worley Kimberly | Shelton Steven | Kalin Ned | Milosavljevic Aleksandar | Gibbs Richard | Rogers Jeffrey
Volume: 12
Issue: 1
Year: 2011

Identification of novel soybean microRNAs involved in abiotic and biotic stresses

Author(s): Kulcheski Franceli | de Oliveira Luiz | Molina Lorrayne | Almerão Maurício | Rodrigues Fabiana | Marcolino Juliana | Barbosa Joice | Stolf-Moreira Renata | Nepomuceno Alexandre | Marcelino-Guimarães Francismar | Abdelnoor Ricardo | Nascimento Leandro | Carazzolle Marcelo | Pereira Gonçalo | Margis Rogério
Volume: 12
Issue: 1
Year: 2011

An untargeted multi-technique metabolomics approach to studying intracellular metabolites of HepG2 cells exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin

Author(s): Ruiz-Aracama Ainhoa | Peijnenburg Ad | Kleinjans Jos | Jennen Danyel | van Delft Joost | Hellfrisch Caroline | Lommen Arjen
Volume: 12
Issue: 1
Year: 2011

Chromatin structure characteristics of pre-miRNA genomic sequences

Author(s): Zhu Shijia | Jiang Qinghua | Wang Guohua | Liu Bo | Teng Mingxiang | Wang Yadong
Volume: 12
Issue: 1
Year: 2011

Turbot reovirus (SMReV) genome encoding a FAST protein with a non-AUG start site

Author(s): Ke Fei | He Li-Bo | Pei Chao | Zhang Qi-Ya
Volume: 12
Issue: 1
Year: 2011

Evolutionarily conserved bias of amino-acid usage refines the definition of PDZ-binding motif

Author(s): Chimura Takahiko | Launey Thomas | Ito Masao
Volume: 12
Issue: 1
Year: 2011

Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome

Author(s): Faivre Rampant Patricia | Lesur Isabelle | Boussardon Clément | Bitton Frédérique | Martin-Magniette Marie-Laure | Bodénès Catherine | Le Provost Grégoire | Bergès Hélène | Fluch Sylvia | Kremer Antoine | Plomion Christophe
Volume: 12
Issue: 1
Year: 2011

Diverse and tissue-enriched small RNAs in the plant pathogenic fungus, Magnaporthe oryzae

Author(s): Nunes Cristiano | Gowda Malali | Sailsbery Joshua | Xue Minfeng | Chen Feng | Brown Douglas | Oh YeonYee | Mitchell Thomas | Dean Ralph
Volume: 12
Issue: 1
Year: 2011

Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny

Author(s): Véron Amélie | Lemaitre Claire | Gautier Christian | Lacroix Vincent | Sagot Marie-France
Volume: 12
Issue: 1
Year: 2011

Comprehensive genetic dissection of wood properties in a widely-grown tropical tree: Eucalyptus

Author(s): Gion Jean-Marc | Carouché Audrey | Deweer Sylvie | Bedon Franck | Pichavant Frédérique | Charpentier Jean-Paul | Baillères Henri | Rozenberg Philippe | Carocha Victor | Ognouabi Nina | Verhaegen Daniel | Grima-Pettenati Jacqueline | Vigneron Philippe | Plomion Christophe
Volume: 12
Issue: 1
Year: 2011

Comparative genomic analysis of Vibrio parahaemolyticus: serotype conversion and virulence

Author(s): Chen Yuansha | Stine O Colin | Badger Jonathan | Gil Ana | Nair G Balakrish | Nishibuchi Mitsuaki | Fouts Derrick
Volume: 12
Issue: 1
Year: 2011

Polyomic profiling reveals significant hepatic metabolic alterations in glucagon-receptor (GCGR) knockout mice: implications on anti-glucagon therapies for diabetes

Author(s): Yang Jianxin | MacDougall Margit | McDowell Michael | Xi Li | Wei Ru | Zavadoski William | Molloy Mark | Baker John | Kuhn Max | Cabrera Over | Treadway Judith
Volume: 12
Issue: 1
Year: 2011

A comprehensive gene expression atlas of sex- and tissue-specificity in the malaria vector, Anopheles gambiae

Author(s): Baker Dean | Nolan Tony | Fischer Bettina | Pinder Alex | Crisanti Andrea | Russell Steven
Volume: 12
Issue: 1
Year: 2011

A comprehensive transcriptome and immune-gene repertoire of the lepidopteran model host Galleria mellonella

Author(s): Vogel Heiko | Altincicek Boran | Glöckner Gernot | Vilcinskas Andreas
Volume: 12
Issue: 1
Year: 2011

MicroRNA expression profiling during the life cycle of the silkworm (Bombyx mori)

Author(s): Liu Shiping | Zhang Liang | Li Qibin | Zhao Ping | Duan Jun | Cheng Daojun | Xiang Zhonghuai | Xia Qingyou
Volume: 12
Issue: 1
Year: 2011

BMP signaling components in embryonic transcriptomes of the hover fly Episyrphus balteatus (Syrphidae)

Author(s): Lemke Steffen | Antonopoulos Dionysios | Meyer Folker | Domanus Marc | Schmidt-Ott Urs
Volume: 12
Issue: 1
Year: 2011

Global analysis of gene expression in response to L-Cysteine deprivation in the anaerobic protozoan parasite Entamoeba histolytica

Author(s): Husain Afzal | Jeelani Ghulam | Sato Dan | Nozaki Tomoyoshi
Volume: 12
Issue: 1
Year: 2011

De novo sequence assembly and characterization of the floral transcriptome in cross- and self-fertilizing plants

Author(s): Ness Rob | Siol Mathieu | Barrett Spencer
Volume: 12
Issue: 1
Year: 2011

Minimal regulatory spaces in yeast genomes

Author(s): Chen Wei-Hua | Wei Wu | Lercher Martin
Volume: 12
Issue: 1
Year: 2011

A simple Bayesian estimate of direct RNAi gene regulation events from differential gene expression profiles

Author(s): Wilson Paul | Plucinski Mathew
Volume: 12
Issue: 1
Year: 2011

Single nucleotide polymorphism discovery in elite north american potato germplasm

Author(s): Hamilton John | Hansey Candice | Whitty Brett | Stoffel Kevin | Massa Alicia | Van Deynze Allen | De Jong Walter | Douches David | Buell C Robin
Volume: 12
Issue: 1
Year: 2011

Seeds for effective oligonucleotide design

Author(s): Ilie Lucian | Ilie Silvana | Khoshraftar Shima | Bigvand Anahita
Volume: 12
Issue: 1
Year: 2011

Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance

Author(s): Feldmeyer Barbara | Wheat Christopher | Krezdorn Nicolas | Rotter Björn | Pfenninger Markus
Volume: 12
Issue: 1
Year: 2011

Identification of SNP and SSR markers in eggplant using RAD tag sequencing

Author(s): Barchi Lorenzo | Lanteri Sergio | Portis Ezio | Acquadro Alberto | Valè Giampiero | Toppino Laura | Rotino Giuseppe
Volume: 12
Issue: 1
Year: 2011

Profiling the venom gland transcriptomes of Costa Rican snakes by 454 pyrosequencing

Author(s): Durban Jordi | Juárez Paula | Angulo Yamileth | Lomonte Bruno | Flores-Diaz Marietta | Alape-Girón Alberto | Sasa Mahmood | Sanz Libia | Gutiérrez José | Dopazo Joaquín | Conesa Ana | Calvete Juan
Volume: 12
Issue: 1
Year: 2011

A canine model of Cohen syndrome: Trapped Neutrophil Syndrome

Author(s): Shearman Jeremy | Wilton Alan
Volume: 12
Issue: 1
Year: 2011

A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa)

Author(s): Wang Lu | Yu Xiang | Wang Han | Lu Yi-Zhen | de Ruiter Marjo | Prins Marcel | He Yu-Ke
Volume: 12
Issue: 1
Year: 2011

Gene coexpression clusters and putative regulatory elements underlying seed storage reserve accumulation in Arabidopsis

Author(s): Peng Fred | Weselake Randall
Volume: 12
Issue: 1
Year: 2011

Transcriptome profiling of chemosensory appendages in the malaria vector Anopheles gambiae reveals tissue- and sex-specific signatures of odor coding

Author(s): Pitts R | Rinker David | Jones Patrick | Rokas Antonis | Zwiebel Laurence
Volume: 12
Issue: 1
Year: 2011

Genomic comparison of multi-drug resistant invasive and colonizing Acinetobacter baumannii isolated from diverse human body sites reveals genomic plasticity

Author(s): Sahl Jason | Johnson J Kristie | Harris Anthony | Phillippy Adam | Hsiao William | Thom Kerri | Rasko David
Volume: 12
Issue: 1
Year: 2011

Transcriptional profiling of fetal hypothalamic TRH neurons

Author(s): Guerra-Crespo Magdalena | Pérez-Monter Carlos | Janga Sarath | Castillo-Ramírez Santiago | Gutiérrez-Rios Rosa | Joseph-Bravo Patricia | Pérez-Martínez Leonor | Charli Jean-Louis
Volume: 12
Issue: 1
Year: 2011

Analysis of BAC-end sequences in rainbow trout: Content characterization and assessment of synteny between trout and other fish genomes

Author(s): Genet Carine | Dehais Patrice | Palti Yniv | Gao Guangtu | Gavory Frederick | Wincker Patrick | Quillet Edwige | Boussaha Mekki
Volume: 12
Issue: 1
Year: 2011