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* Corresponding author: Robert C Gentleman rgentlem@jimmy.harvard.edu
Genome Biology 2004, 5:R80 doi:10.1186/gb-2004-5-10-r80
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BioMed Central: 435 citations
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Research article
Genome-wide landscape of liver X receptor chromatin binding and gene regulation in human macrophages Petri Pehkonen, Lynn Welter-Stahl, Janine Diwo, Jussi Ryynanen, Anke Wienecke-Baldacchino, Sami Heikkinen, Eckardt Treuter, Knut R Steffensen, Carsten Carlberg BMC Genomics 2012, 13:50 (31 January 2012) |
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Research article
Rex S Chiu, Hardeep Nahal, Nicholas J Provart, Sonia Gazzarrini BMC Plant Biology 2012, 12:15 (27 January 2012) |
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Research article
An evaluation of two-channel ChIP-on-chip and DNA methylation microarray normalization strategies. Michiel E Adriaens, Magali Jaillard, Lars MT Eijssen, Claus-Dieter Mayer, Chris TA Evelo BMC Genomics 2012, 13:42 (25 January 2012) |
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Research article
Lars L Eftang, Ying Esbensen, Tone M Tannaes, Ida RK Bukholm, Geir Bukholm BMC Microbiology 2012, 12:9 (17 January 2012) |
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Research article
The genetic control of growth rate: a systems biology study in yeast. Pinar Pir, Alex Gutteridge, Jian Wu, Bharat Rash, Douglas B Kell, Nianshu Zhang, Stephen G Oliver BMC Systems Biology 2012, 6:4 (13 January 2012) |
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Research
Amanda B Hummon, Jason J Pitt, Jordi Camps, Georg Emons, Susan B Skube, Konrad Huppi, Tamara L Jones, Tim Beissbarth, Frank Kramer, Marian Grade, Michael J Difilippantonio, Thomas Ried, Natasha J Caplen Molecular Cancer 2012, 11:1 (4 January 2012) |
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Methodology article
Partition decoupling for multi-gene analysis of gene expression profiling data Rosemary Braun, Gregory Leibon, Scott Pauls, Daniel Rockmore BMC Bioinformatics 2011, 12:497 (30 December 2011) |
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Research article
Correlation of gene expression and protein production rate - a system wide study Mikko Arvas, Tiina Pakula, Bart Smit, Jari Rautio, Heini Koivistoinen, Paula Jouhten, Erno Lindfors, Marilyn Wiebe, Merja Penttilä, Markku Saloheimo BMC Genomics 2011, 12:616 (20 December 2011) |
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Research article
Kate E Killick, John A Browne, Stephen DE Park, David A Magee, Irene Martin, Kieran G Meade, Stephen V Gordon, Eamonn Gormley, Cliona O'Farrelly, Karsten Hokamp, David E MacHugh BMC Genomics 2011, 12:611 (19 December 2011) |
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Research article
Rudi Alberts, Hairong Chen, Claudia Pommerenke, August B Smit, Sabine Spijker, Robert W Williams, Robert Geffers, Dunja Bruder, Klaus Schughart BMC Genomics 2011, 12:610 (19 December 2011) |
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Research article
Genetic architecture of gene expression in ovine skeletal muscle Lisette JA Kogelman, Keren Byrne, Tony Vuocolo, Nathan S Watson-Haigh, Haja N Kadarmideen, James W Kijas, Hutton V Oddy, Graham E Gardner, Cedric Gondro, Ross L Tellam BMC Genomics 2011, 12:607 (15 December 2011) |
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Methodology article
Jetset: selecting the optimal microarray probe set to represent a gene Qiyuan Li, Nicolai J Birkbak, Balazs Gyorffy, Zoltan Szallasi, Aron C Eklund BMC Bioinformatics 2011, 12:474 (15 December 2011) |
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Research article
Genome-wide transcriptome analysis of gametophyte development in Physcomitrella patens Lihong Xiao, Hui Wang, Ping Wan, Tingyun Kuang, Yikun He BMC Plant Biology 2011, 11:177 (15 December 2011) |
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Research article
Variants on the promoter region of PTEN affect breast cancer progression and patient survival Tuomas Heikkinen, Dario Greco, Liisa M Pelttari, Johanna Tommiska, Pia Vahteristo, Päivi Heikkilä, Carl Blomqvist, Kristiina Aittomäki, Heli Nevanlinna Breast Cancer Research 2011, 13:R130 (15 December 2011) |
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Research article
Anna-Katharina Göhler, Öznur Kökpinar, Wolfgang Schmidt-Heck, Robert Geffers, Reinhard Guthke, Ursula Rinas, Stefan Schuster, Knut Jahreis, Christoph Kaleta BMC Systems Biology 2011, 5:197 (14 December 2011) |
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Research article
Danning He, Zhi-Ping Liu, Luonan Chen BMC Genomics 2011, 12:592 (2 December 2011) |
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Research
Caroline Pont, Florent Murat, Carole Confolent, Sandrine Balzergue, Jérôme Salse Genome Biology 2011, 12:R119 (2 December 2011) Transcriptomics reveals the evolutionary trajectory of polyploidization, with insights into gene networks and genome organization
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Research article
Vivek A Bhadri, Mark J Cowley, Warren Kaplan, Toby N Trahair, Richard B Lock BMC Genomics 2011, 12:565 (17 November 2011) |
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Research article
Janet M Young, Ralf M Luche, Barbara J Trask BMC Genomics 2011, 12:561 (15 November 2011) |
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Research article
Genome-wide analysis of gene expression during Xenopus tropicalis tadpole tail regeneration Nick R Love, Yaoyao Chen, Boyan Bonev, Michael J Gilchrist, Lynne Fairclough, Robert Lea, Timothy J Mohun, Roberto Paredes, Leo AH Zeef, Enrique Amaya BMC Developmental Biology 2011, 11:70 (15 November 2011) |
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Methodology article
Lam C Tsoi, Tingting Qin, Elizabeth H Slate, W Jim Zheng BMC Bioinformatics 2011, 12:438 (11 November 2011) |
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Research article
Isabelle Boutet, Raymond Ripp, Odile Lecompte, Carole Dossat, Erwan Corre, Arnaud Tanguy, François H Lallier BMC Genomics 2011, 12:530 (28 October 2011) |
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Research article
Gene network analyses point to the importance of human tissue kallikreins in melanoma progression Waleska K Martins, Gustavo H Esteves, Otávio M Almeida, Gisele G Rezze, Gilles Landman, Sarah M Marques, Alex F Carvalho, Luiz F L Reis, João P Duprat, Beatriz S Stolf BMC Medical Genomics 2011, 4:76 (27 October 2011) |
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Research article
Jérôme Ambroise, Bertrand Bearzatto, Annie Robert, Bernadette Govaerts, Benoît Macq, Jean-Luc Gala BMC Bioinformatics 2011, 12:413 (25 October 2011) |
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Method
David Sims, Ana M Mendes-Pereira, Jessica Frankum, Darren Burgess, Maria-Antonietta Cerone, Cristina Lombardelli, Costas Mitsopoulos, Jarle Hakas, Nirupa Murugaesu, Clare M Isacke, Kerry Fenwick, Ioannis Assiotis, Iwanka Kozarewa, Marketa Zvelebil, Alan Ashworth, Christopher J Lord Genome Biology 2011, 12:R104 (21 October 2011) The incorporation of next generation sequencing into RNAi screening makes for a rapid, user-friendly and high-throughput method
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Methodology
Konstantina Dimitrakopoulou, Charalampos Tsimpouris, George Papadopoulos, Claudia Pommerenke, Esther Wilk, Kyriakos N Sgarbas, Klaus Schughart, Anastasios Bezerianos Journal of Clinical Bioinformatics 2011, 1:27 (21 October 2011) |
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Research article
Jesper Dahlgaard, Wiktor Mazin, Thomas Jensen, Mette Pøhl, Wiam Bshara, Anker Hansen, Eric Kanisto, Stephen Hamilton-Dutoit, Olfred Hansen, Henrik Hager, Henrik J Ditzel, Sai Yendamuri, Steen Knudsen BMC Research Notes 2011, 4:424 (19 October 2011) |
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Methodology article
A computable cellular stress network model for non-diseased pulmonary and cardiovascular tissue Walter K Schlage, Jurjen W Westra, Stephan Gebel, Natalie L Catlett, Carole Mathis, Brian P Frushour, Arnd Hengstermann, Aaron Van Hooser, Carine Poussin, Ben Wong, Michael Lietz, Jennifer Park, David Drubin, Emilija Veljkovic, Manuel C Peitsch, Julia Hoeng, Renee Deehan BMC Systems Biology 2011, 5:168 (19 October 2011) |
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Method
SpeCond: a method to detect condition-specific gene expression Florence MG Cavalli, Richard Bourgon, Wolfgang Huber, Juan M Vaquerizas, Nicholas M Luscombe Genome Biology 2011, 12:R101 (18 October 2011) A method to detect condition-specific gene expression from microarray data
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Research article
Hong Zhu, Chris D Dardick, Eric P Beers, Ann M Callanhan, Rui Xia, Rongcai Yuan BMC Plant Biology 2011, 11:138 (17 October 2011) |
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Software
Chipster: user-friendly analysis software for microarray and other high-throughput data M Aleksi Kallio, Jarno T Tuimala, Taavi Hupponen, Petri Klemelä, Massimiliano Gentile, Ilari Scheinin, Mikko Koski, Janne Käki, Eija I Korpelainen BMC Genomics 2011, 12:507 (14 October 2011) |
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Research article
Deciphering c-MYC-regulated genes in two distinct tissues Samuel C Robson, Lesley Ward, Helen Brown, Heather Turner, Ewan Hunter, Stella Pelengaris, Michael Khan BMC Genomics 2011, 12:476 (30 September 2011) |
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Software
Mulcom: a multiple comparison statistical test for microarray data in Bioconductor Claudio Isella, Tommaso Renzulli, Davide Corà, Enzo Medico BMC Bioinformatics 2011, 12:382 (28 September 2011) |
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Research article
Marieke L Kuijjer, Heidi M Namløs, Esther I Hauben, Isidro Machado, Stine H Kresse, Massimo Serra, Antonio Llombart-Bosch, Pancras CW Hogendoorn, Leonardo A Meza-Zepeda, Ola Myklebost, Anne-Marie Cleton-Jansen BMC Medical Genomics 2011, 4:66 (20 September 2011) |
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Software
Thawing Frozen Robust Multi-array Analysis (fRMA) Matthew N McCall, Rafael A Irizarry BMC Bioinformatics 2011, 12:369 (16 September 2011) |
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Research article
Genome-wide expression assay comparison across frozen and fixed postmortem brain tissue samples Maggie L Chow, Hai-Ri Li, Mary E Winn, Craig April, Cynthia C Barnes, Anthony Wynshaw-Boris, Jian-Bing Fan, Xiang-Dong Fu, Eric Courchesne, Nicholas J Schork BMC Genomics 2011, 12:449 (10 September 2011) |
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Research article
Pei-Ing Hwang, Huan-Bin Wu, Chin-Di Wang, Bai-Ling Lin, Cheng-Tao Chen, Shinsheng Yuan, Guani Wu, Ker-Chau Li BMC Genomics 2011, 12:439 (1 September 2011) Gene Expression Templates (GET) can be used to identify the normal physiological state of various human tissues, with variation from this template allowing the identification of cancerous tissues and cell lines.
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Research article
Jana Goldová, Aleš Ulrych, Kamil Hercík, Pavel Branny BMC Genomics 2011, 12:437 (31 August 2011) |
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Software
Cistrome: an integrative platform for transcriptional regulation studies Tao Liu, Jorge A Ortiz, Len Taing, Clifford A Meyer, Bernett Lee, Yong Zhang, Hyunjin Shin, Swee S Wong, Jian Ma, Ying Lei, Utz J Pape, Michael Poidinger, Yiwen Chen, Kevin Yeung, Myles Brown, Yaron Turpaz, X Shirley Liu Genome Biology 2011, 12:R83 (22 August 2011) A Galaxy-based web application for integrative analysis of ChIP data
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Methodology article
Extracting quantitative genetic interaction phenotypes from matrix combinatorial RNAi Elin Axelsson, Thomas Sandmann, Thomas Horn, Michael Boutros, Wolfgang Huber , Bernd Fischer BMC Bioinformatics 2011, 12:342 (17 August 2011) |
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Research article
Gene expression profiling of human whole blood samples with the Illumina WG-DASL assay Mary E Winn, Marian Shaw, Craig April, Brandy Klotzle, Jian-Bing Fan, Sarah S Murray, Nicholas J Schork BMC Genomics 2011, 12:412 (15 August 2011) |
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Methodology article
NETGEM: Network Embedded Temporal GEnerative Model for gene expression data Vinay Jethava, Chiranjib Bhattacharyya, Devdatt Dubhashi, Goutham N Vemuri BMC Bioinformatics 2011, 12:327 (8 August 2011) |
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Research article
Nik Kovinich, Ammar Saleem, John T Arnason, Brian Miki BMC Genomics 2011, 12:381 (29 July 2011) |
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Research
Miklós Sárvári, Erik Hrabovszky, Imre Kalló, Norbert Solymosi, Kinga Tóth, István Likó, János Széles, Sándor Mahó, Béla Molnár, Zsolt Liposits Journal of Neuroinflammation 2011, 8:82 (20 July 2011) |
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Research article
Fabian Grammes, Harald Takle BMC Immunology 2011, 12:41 (20 July 2011) |
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Methodology article
Construction of a computable cell proliferation network focused on non-diseased lung cells Jurjen W Westra, Walter K Schlage, Brian P Frushour, Stephan Gebel, Natalie L Catlett, Wanjiang Han, Sean F Eddy, Arnd Hengstermann, Andrea L Matthews, Carole Mathis, Rosemarie B Lichtner, Carine Poussin, Marja Talikka, Emilija Veljkovic, Aaron A Van Hooser, Benjamin Wong, Michael J Maria, Manuel C Peitsch, Renee Deehan, Julia Hoeng BMC Systems Biology 2011, 5:105 (2 July 2011) |
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Research article
The functional cancer map: A systems-level synopsis of genetic deregulation in cancer Markus Krupp, Thorsten Maass, Jens U Marquardt, Frank Staib, Tobias Bauer, Rainer König, Stefan Biesterfeld, Peter R Galle, Achim Tresch, Andreas Teufel BMC Medical Genomics 2011, 4:53 (30 June 2011) |
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Research article
Bastiaan JH Jansen, Iziah E Sama, Dagmar Eleveld-Trancikova, Maaike A van Hout-Kuijer, Joop H Jansen, Martijn A Huynen, Gosse J Adema BMC Genomics 2011, 12:330 (27 June 2011) |
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Methodology article
Cell subset prediction for blood genomic studies Christopher R Bolen, Mohamed Uduman, Steven H Kleinstein BMC Bioinformatics 2011, 12:258 (24 June 2011) |
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Research article
Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data Ewa Szczurek, Florian Markowetz, Irit Gat-Viks, Przemysław Biecek, Jerzy Tiuryn, Martin Vingron BMC Bioinformatics 2011, 12:249 (21 June 2011) |
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Report
Shao Li, Bo Zhang, Ningbo Zhang BMC Systems Biology 2011, 5(Suppl 1):S10 (20 June 2011) |
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Research article
Comparative genomics of Escherichia coli isolated from patients with inflammatory bowel disease Rebecca Vejborg, Viktoria Hancock, Andreas M Petersen, Karen A Krogfelt, Per Klemm BMC Genomics 2011, 12:316 (15 June 2011) |
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Research article
Srinivasan Yegnasubramanian, Zhijin Wu, Michael C Haffner, David Esopi, Martin J Aryee, Raghav Badrinath, Tony L He, James D Morgan, Benilton Carvalho, Qizhi Zheng, Angelo M De Marzo, Rafael A Irizarry, William G Nelson BMC Genomics 2011, 12:313 (13 June 2011) |
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Research article
Koji Kadota, Kentaro Shimizu BMC Bioinformatics 2011, 12:227 (6 June 2011) |
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Research article
Fred Y Peng, Randall J Weselake BMC Genomics 2011, 12:286 (2 June 2011) |
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Software
OntoCAT -- simple ontology search and integration in Java, R and REST/JavaScript Tomasz Adamusiak, Tony Burdett, Natalja Kurbatova, K Joeri van der Velde, Niran Abeygunawardena, Despoina Antonakaki, Misha Kapushesky, Helen Parkinson, Morris A Swertz BMC Bioinformatics 2011, 12:218 (29 May 2011) |
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Methodology article
Multiple testing for gene sets from microarray experiments Insuk Sohn, Kouros Owzar, Johan Lim, Stephen L George, Stephanie Mackey Cushman, Sin-Ho Jung BMC Bioinformatics 2011, 12:209 (26 May 2011) |
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Proceedings
Managing and querying gene expression data using Curray Hasan Jamil, Aminul Islam BMC Proceedings 2011, 5(Suppl 2):S10 (28 April 2011) |
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Data Note
Josef Spidlen, Parisa Shooshtari, Tobias R Kollmann, Ryan R Brinkman BMC Research Notes 2011, 4:50 (7 March 2011) This article is part of a collection on Data standardization... Novel open file formats can be used to describe flow cytometry data analysis in a standardized and computationally exchangeable format allowing for enhanced scientific collaboration and highlights the need for a public data repository.
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Proceedings
Laurent Gautier BMC Bioinformatics 2010, 11(Suppl 12):S11 (21 December 2010) |
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Proceedings
An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics Ronald C Taylor BMC Bioinformatics 2010, 11(Suppl 12):S1 (21 December 2010) |
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Methodology article
Optimizing transformations for automated, high throughput analysis of flow cytometry data Greg Finak, Juan-Manuel Perez, Andrew Weng, Raphael Gottardo BMC Bioinformatics 2010, 11:546 (4 November 2010) |
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Technical Note
EMA - A R package for Easy Microarray data analysis Nicolas Servant, Eleonore Gravier, Pierre Gestraud, Cecile Laurent, Caroline Paccard, Anne Biton, Isabel Brito, Jonas Mandel, Bernard Asselain, Emmanuel Barillot, Philippe Hupé BMC Research Notes 2010, 3:277 (3 November 2010) This article is part of a collection on Microarray normalization... |
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Research
Meng-Ju Wu, Chia-Ing Jan, Yeou-Guang Tsay, Yau-Hua Yu, Chih-Yang Huang, Shu-Chun Lin, Chung-Ji Liu, Yu-Syuan Chen, Jeng-Fan Lo, Cheng-Chia Yu Molecular Cancer 2010, 9:283 (27 October 2010) |
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Proceedings
Shrunken methodology to genome-wide SNPs selection and construction of SNPs networks Yang Liu, Michael Ng BMC Systems Biology 2010, 4(Suppl 2):S5 (13 September 2010) |
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Research highlight
The missing graphical user interface for genomics Michael C Schatz Genome Biology 2010, 11:128 (25 August 2010) The Galaxy package for genomic analysis empowers regular users through a much-needed and user-friendly graphical web interface.
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Software
Jeremy Goecks, Anton Nekrutenko, James Taylor, Genome Biology 2010, 11:R86 (25 August 2010) This article is part of a collection on Cloud computing tools and... The Galaxy computing platform allows researchers to share data and data analysis workflows, facilitating easily reproducible analyses.
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Review
Ole Mortensen, Hanne Olsen, Lis Frandsen, Peter Nielsen, Finn Nielsen, Niels Grunnet, Bjørn Quistorff Journal of Biomedical Science 2010, 17(Suppl 1):S38 (24 August 2010) |
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Introduction
Proceedings of the ninth annual UT-ORNL-KBRIN Bioinformatics Summit 2010 Eric C Rouchka, Robert M Flight, Claire Rinehart BMC Bioinformatics 2010, 11(Suppl 4):I1 (23 July 2010) |
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Research article
Dennis Janz, Katja Behnke, Jörg-Peter Schnitzler, Basem Kanawati, Philippe Schmitt-Kopplin, Andrea Polle BMC Plant Biology 2010, 10:150 (17 July 2010) |
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Research
Maria H Traka, Caroline A Spinks, Joanne F Doleman, Antonietta Melchini, Richard Y Ball, Robert D Mills, Richard F Mithen Molecular Cancer 2010, 9:189 (13 July 2010) The isothiocyanate sulforaphane found at high levels in broccoli modulates PTEN tumor suppressor gene activity and provides further evidence that dietary components could be of benefit in preventing prostate cancer.
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Methodology article
ChIP on Chip: surprising results are often artifacts Torsten Waldminghaus, Kirsten Skarstad BMC Genomics 2010, 11:414 (5 July 2010) |
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Software
A flexible R package for nonnegative matrix factorization Renaud Gaujoux, Cathal Seoighe BMC Bioinformatics 2010, 11:367 (2 July 2010) |
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Research article
Karen J Taylor, Andrew H Sims, Liang Liang, Dana Faratian, Morwenna Muir, Graeme Walker, Barbara Kuske, J Michael Dixon, David A Cameron, David J Harrison, Simon P Langdon Breast Cancer Research 2010, 12:R39 (22 June 2010) |
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Research article
Tatyana Kalinina, Cenap Güngör, Sabrina Thieltges, Maren Möller-Krull, Eva Murga Penas, Daniel Wicklein, Thomas Streichert, Udo Schumacher, Viacheslav Kalinin, Ronald Simon, Benjamin Otto, Judith Dierlamm, Heidi Schwarzenbach, Katharina E Effenberger, Maximilian Bockhorn, Jakob R Izbicki, Emre F Yekebas BMC Cancer 2010, 10:295 (16 June 2010) |
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Research article
Muscle transcriptomic profiles in pigs with divergent phenotypes for fatness traits Angela Cánovas, Raquel Quintanilla, Marcel Amills, Ramona N Pena BMC Genomics 2010, 11:372 (11 June 2010) |
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Research
Patti C Zeidler-Erdely, Michael L Kashon, Shengqiao Li, James M Antonini Respiratory Research 2010, 11:70 (3 June 2010) |
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Research article
Nutrient control of eukaryote cell growth: a systems biology study in yeast Alex Gutteridge, Pınar Pir, Juan I Castrillo, Philip D Charles, Kathryn S Lilley, Stephen G Oliver BMC Biology 2010, 8:68 (24 May 2010) In a study on the –omics of yeast cell growth, Stephen Oliver and colleagues measure the response to nutrient deprivation and the global perturbation of the genetic circuitry that accompanies carbon deprivation.
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Research article
Youko Horiuchi, Yoshiaki Harushima, Hironori Fujisawa, Takako Mochizuki, Masanori Kawakita, Takayuki Sakaguchi, Nori Kurata BMC Genomics 2010, 11:315 (20 May 2010) |
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Research article
Plasmodium infection alters Anopheles gambiae detoxification gene expression Rute C Félix, Pie Müller, Vera Ribeiro, Hilary Ranson, Henrique Silveira BMC Genomics 2010, 11:312 (19 May 2010) |
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Methodology article
Arnald Alonso, Antonio Julià, Raül Tortosa, Cristina Canaleta, Juan D Cañete, Javier Ballina, Alejandro Balsa, Jesús Tornero, Sara Marsal BMC Bioinformatics 2010, 11:264 (19 May 2010) |
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Research article
Min-Han Tan, Chin Wong, Hwei Tan, Ximing J Yang, Jonathon Ditlev, Daisuke Matsuda, Sok Khoo, Jun Sugimura, Tomoaki Fujioka, Kyle A Furge, Eric Kort, Sophie Giraud, Sophie Ferlicot, Philippe Vielh, Delphine Amsellem-Ouazana, Bernard Debré, Thierry Flam, Nicolas Thiounn, Marc Zerbib, Gérard Benoît, Stéphane Droupy, Vincent Molinié, Annick Vieillefond, Puay Tan, Stéphane Richard, Bin Teh BMC Cancer 2010, 10:196 (12 May 2010) |
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Methodology article
Consistent annotation of gene expression arrays Benoît Ballester, Nathan Johnson, Glenn Proctor, Paul Flicek BMC Genomics 2010, 11:294 (11 May 2010) This article is part of a collection on Ensembl update 2010 |
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Software
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data Lihua J Zhu, Claude Gazin, Nathan D Lawson, Hervé Pagès, Simon M Lin, David S Lapointe, Michael R Green BMC Bioinformatics 2010, 11:237 (11 May 2010) |
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Research article
James R Bradford, Yvonne Hey, Tim Yates, Yaoyong Li, Stuart D Pepper, Crispin J Miller BMC Genomics 2010, 11:282 (5 May 2010) |
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Research
The dissection of transcriptional modules regulated by various drugs of abuse in the mouse striatum Marcin Piechota, Michal Korostynski, Wojciech Solecki, Agnieszka Gieryk, Michal Slezak, Wiktor Bilecki, Barbara Ziolkowska, Elzbieta Kostrzewa, Iwona Cymerman, Lukasz Swiech, Jacek Jaworski, Ryszard Przewlocki Genome Biology 2010, 11:R48 (4 May 2010) The transcriptional response to six commonly-abused drugs was assessed in the mouse brain revealing common modules of drug-induced genes. |
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Research article
Michael Pierre, Benoît DeHertogh, Anthoula Gaigneaux, Bertrand DeMeulder, Fabrice Berger, Eric Bareke, Carine Michiels, Eric Depiereux BMC Cancer 2010, 10:176 (30 April 2010) |
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Research article
Ivy D Moffat, Paul C Boutros, Hanbo Chen, Allan B Okey, Raimo Pohjanvirta BMC Genomics 2010, 11:263 (26 April 2010) |
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Research article
Tove Båge, Johan Lindberg, Joakim Lundeberg, Thomas Modéer, Tülay Yucel-Lindberg BMC Genomics 2010, 11:241 (15 April 2010) |
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Software
web cellHTS2: A web-application for the analysis of high-throughput screening data Oliver Pelz, Moritz Gilsdorf, Michael Boutros BMC Bioinformatics 2010, 11:185 (12 April 2010) |
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Software
CNAReporter: a GenePattern pipeline for the generation of clinical reports of genomic alterations Yuri Kotliarov, Serdar Bozdag, Hangjiong Cheng, Stefan Wuchty, Jean-Claude Zenklusen, Howard A Fine BMC Medical Genomics 2010, 3:11 (9 April 2010) |
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Software
Saurin D Jani, Gary L Argraves, Jeremy L Barth, W Scott Argraves BMC Bioinformatics 2010, 11:166 (1 April 2010) |
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Research article
Bacterial diversity at different stages of the composting process Pasi Partanen, Jenni Hultman, Lars Paulin, Petri Auvinen, Martin Romantschuk BMC Microbiology 2010, 10:94 (29 March 2010) |
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Research article
Elgene Lim, Di Wu, Bhupinder Pal, Toula Bouras, Marie-Liesse Asselin-Labat, François Vaillant, Hideo Yagita, Geoffrey J Lindeman, Gordon K Smyth, Jane E Visvader Breast Cancer Research 2010, 12:R21 (26 March 2010) |
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Short Report
Colin S Gillespie, Guiyuan Lei, Richard J Boys, Amanda Greenall, Darren J Wilkinson BMC Research Notes 2010, 3:81 (19 March 2010) This article is part of a collection on Microarray normalization... |
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Research article
Janneke de Wilde, Martijn FM Hulshof, Mark V Boekschoten, Philip de Groot, Egbert Smit, Edwin CM Mariman BMC Genomics 2010, 11:176 (15 March 2010) |
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Software
Morris A Swertz, K Joeri Velde, Bruno M Tesson, Richard A Scheltema, Danny Arends, Gonzalo Vera, Rudi Alberts, Martijn Dijkstra, Paul Schofield, Klaus Schughart, John M Hancock, Damian Smedley, Katy Wolstencroft, Carole Goble, Engbert O de Brock, Andrew R Jones, Helen E Parkinson, Ritsert C Jansen Genome Biology 2010, 11:R27 (9 March 2010) XGAP, a software platform for the integration and analysis of genotype and phenotype data. |
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Research article
Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved elements Danilo Licastro, Vincenzo A Gennarino, Francesca Petrera, Remo Sanges, Sandro Banfi, Elia Stupka BMC Genomics 2010, 11:151 (4 March 2010) |
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Method
A scaling normalization method for differential expression analysis of RNA-seq data Mark D Robinson, Alicia Oshlack Genome Biology 2010, 11:R25 (2 March 2010) A novel and empirical method for normalization of RNA-seq data is presented |
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Research article
Modeling expression quantitative trait loci in data combining ethnic populations Ching-Lin Hsiao, Ie-Bin Lian, Ai-Ru Hsieh, Cathy SJ Fann BMC Bioinformatics 2010, 11:111 (27 February 2010) |
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Research article
Simone Mitterhuemer, Wolfram Petzl, Stefan Krebs, Daniel Mehne, Andrea Klanner, Eckhard Wolf, Holm Zerbe, Helmut Blum BMC Genomics 2010, 11:138 (25 February 2010) |
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Methodology article
Jakub Mieczkowski, Magdalena E Tyburczy, Michal Dabrowski, Piotr Pokarowski BMC Bioinformatics 2010, 11:104 (24 February 2010) |
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Research article
Variability of gene expression profiles in human blood and lymphoblastoid cell lines Josine L Min, Amy Barrett, Tim Watts, Fredrik H Pettersson, Helen E Lockstone, Cecilia M Lindgren, Jennifer M Taylor, Maxine Allen, Krina T Zondervan, Mark I McCarthy BMC Genomics 2010, 11:96 (8 February 2010) |
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Software
Mark J Alston, John Seers, Jay CD Hinton, Sacha Lucchini BMC Bioinformatics 2010, 11:73 (3 February 2010) |
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Research
Tiebing Liang, Mark W Kimpel, Jeanette N McClintick, Ashley R Skillman, Kevin McCall, Howard J Edenberg, Lucinda G Carr Genome Biology 2010, 11:R11 (3 February 2010) Transcriptional profiling of specific regions of inbred rat brains reveals genes associated with alcohol preference in a known QTL locus on chromosome 4 |
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Research article
Maaria Kankare, Tiina Salminen, Asta Laiho, Laura Vesala, Anneli Hoikkala BMC Ecology 2010, 10:3 (1 February 2010) |
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Methodology article
Mayer Alvo, Zhongzhu Liu, Andrew Williams, Carole Yauk BMC Bioinformatics 2010, 11:60 (28 January 2010) |
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Research article
Ashraf Abdeen, Jaimie Schnell, Brian Miki BMC Genomics 2010, 11:69 (28 January 2010) |
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Methodology article
Corey M Yanofsky, David R Bickel BMC Bioinformatics 2010, 11:63 (28 January 2010) |
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Short Report
Processing of Agilent microRNA array data Pedro López-Romero, Manuel A González, Sergio Callejas, Ana Dopazo, Rafael A Irizarry BMC Research Notes 2010, 3:18 (22 January 2010) This article is part of a collection on Microarray normalization... |
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Research article
Quantitative model for inferring dynamic regulation of the tumour suppressor gene p53 Junbai Wang, Tianhai Tian BMC Bioinformatics 2010, 11:36 (19 January 2010) |
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Research article
Gene expression profiling of peripheral blood cells for early detection of breast cancer Jørgen Aarøe, Torbjørn Lindahl, Vanessa Dumeaux, Solve Sæbø, Derek Tobin, Nina Hagen, Per Skaane, Anders Lönneborg, Praveen Sharma, Anne-Lise Børresen-Dale Breast Cancer Research 2010, 12:R7 (15 January 2010) |
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Research article
Beatrice A McGivney, Suzanne S Eivers, David E MacHugh, James N MacLeod, Grace M O'Gorman, Stephen DE Park, Lisa M Katz, Emmeline W Hill BMC Genomics 2009, 10:638 (30 December 2009) |
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Method
Mariano Alvarez, Pavel Sumazin, Presha Rajbhandari, Andrea Califano Genome Biology 2009, 10:R143 (30 December 2009) Cleaner is a method for removing uninformative and flawed probes from microarray experiment data, thus improving reproducibility between replicate experiments. |
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Software
Álvaro Cuadros-Inostroza, Camila Caldana, Henning Redestig, Miyako Kusano, Jan Lisec, Hugo Peña-Cortés, Lothar Willmitzer, Matthew A Hannah BMC Bioinformatics 2009, 10:428 (16 December 2009) |
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Research article
Hans-Ulrich Klein, Christian Ruckert, Alexander Kohlmann, Lars Bullinger, Christian Thiede, Torsten Haferlach, Martin Dugas BMC Bioinformatics 2009, 10:422 (15 December 2009) |
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Proceedings
PutidaNET: Interactome database service and network analysis of Pseudomonas putida KT2440 Seong-Jin Park, Jong-Soon Choi, Byoung-Chul Kim, Seong-Woong Jho, Jea-Woon Ryu, Daeui Park, Kyung-A Lee, Jong Bhak, Seung Il Kim BMC Genomics 2009, 10(Suppl 3):S18 (3 December 2009) |
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Research article
Herman MJ Sontrop, Perry D Moerland, René van den Ham, Marcel JT Reinders, Wim FJ Verhaegh BMC Bioinformatics 2009, 10:389 (26 November 2009) |
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Research article
Characterisation of microRNA expression in post-natal mouse mammary gland development Stefanie Avril-Sassen, Leonard D Goldstein, John Stingl, Cherie Blenkiron, John Le Quesne, Inmaculada Spiteri, Konstantina Karagavriilidou, Christine J Watson, Simon Tavaré, Eric A Miska, Carlos Caldas BMC Genomics 2009, 10:548 (20 November 2009) |
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Research article
Imke E Mulder, Bettina Schmidt, Christopher R Stokes, Marie Lewis, Mick Bailey, Rustam I Aminov, James I Prosser, Bhupinder P Gill, John R Pluske, Claus-Dieter Mayer, Corran C Musk, Denise Kelly BMC Biology 2009, 7:79 (20 November 2009) Pigs reared indoors or in isolation have a less healthy gut microbiota than outdoor-reared pigs, and signs of immune activation in gut tissues, reinforcing human data associating childhood hygiene with inflammatory bowel disease.
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Research article
Differentially expressed genes for aggressive pecking behaviour in laying hens Bart Buitenhuis, Jakob Hedegaard, Luc Janss, Peter Sørensen BMC Genomics 2009, 10:544 (19 November 2009) |
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Research article
The choroid plexus response to a repeated peripheral inflammatory stimulus Fernanda Marques, João C Sousa, Giovanni Coppola, Daniel H Geschwind, Nuno Sousa, Joana A Palha, Margarida Correia-Neves BMC Neuroscience 2009, 10:135 (18 November 2009) |
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Research article
Endogenous control genes in complex vascular tissue samples Lasse Folkersen, Sanela Kurtovic, Anton Razuvaev, Hanna E Agardh, Anders Gabrielsen, Gabrielle Paulsson-Berne BMC Genomics 2009, 10:516 (10 November 2009) |
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Software
Enrico Glaab, Jonathan M Garibaldi, Natalio Krasnogor BMC Bioinformatics 2009, 10:358 (28 October 2009) |
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Research article
Genetical genomic determinants of alcohol consumption in rats and humans Boris Tabakoff, Laura Saba, Morton Printz, Pam Flodman, Colin Hodgkinson, David Goldman, George Koob, Heather N Richardson, Katerina Kechris, Richard L Bell, Norbert Hübner, Matthias Heinig, Michal Pravenec, Jonathan Mangion, Lucie Legault, Maurice Dongier, Katherine M Conigrave, John B Whitfield, John Saunders, Bridget Grant, Paula L Hoffman, BMC Biology 2009, 7:70 (27 October 2009) Genetic pathways involving appetite, satiety and reward affect alcohol consumption in rats and humans, specifically GABAergic and dopaminergic signaling, but genes in these pathways are not linked to alcohol dependence or abuse in people.
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Research article
Riccardo D'Elia, Matthew L deSchoolmeester, Leo AH Zeef, Steven H Wright, Alan D Pemberton, Kathryn J Else BMC Genomics 2009, 10:492 (24 October 2009) |
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Research article
Javier Agustí, Paz Merelo, Manuel Cercós, Francisco R Tadeo, Manuel Talón BMC Plant Biology 2009, 9:127 (23 October 2009) |
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Research
Audra A Winder, Christine Wohlford-Lenane, Todd E Scheetz, Brie N Nardy, Lori J Manzel, Dwight C Look, Paul B McCray Respiratory Research 2009, 10:96 (16 October 2009) |
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Research
Luca Corradi, Valentina Mirisola, Ivan Porro, Livia Torterolo, Marco Fato, Paolo Romano, Ulrich Pfeffer BMC Bioinformatics 2009, 10(Suppl 12):S10 (15 October 2009) |
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Research article
Albert Mascarell-Creus, Joaquin Cañizares, Josep Vilarrasa-Blasi, Santiago Mora-García, José Blanca, Daniel Gonzalez-Ibeas, Montserrat Saladié, Cristina Roig, Wim Deleu, Belén Picó-Silvent, Nuria López-Bigas, Miguel A Aranda, Jordi Garcia-Mas, Fernando Nuez, Pere Puigdomènech, Ana I Caño-Delgado BMC Genomics 2009, 10:467 (12 October 2009) An oligo-based microarray derived from over 30,000 melon (Cucumis melo) ESTs provides a platform for the functional genomic study of experimental conditions such as fruit quality and response to viral and fungal infections.
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Research article
Sung-Chur Sim, Matthew D Robbins, Charles Chilcott, Tong Zhu, David M Francis BMC Genomics 2009, 10:466 (9 October 2009) |
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Proceedings
Threshold selection in gene co-expression networks using spectral graph theory techniques Andy D Perkins, Michael A Langston BMC Bioinformatics 2009, 10(Suppl 11):S4 (8 October 2009) |
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Research article
Petri Törönen, Pauli J Ojala, Pekka Marttinen, Liisa Holm BMC Bioinformatics 2009, 10:307 (23 September 2009) |
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Research article
Mapping of HNF4α target genes in intestinal epithelial cells Mette Boyd, Simon Bressendorff, Jette Møller, Jørgen Olsen, Jesper T Troelsen BMC Gastroenterology 2009, 9:68 (17 September 2009) |
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Proceedings
Xinan Yang, Yong Huang, James L Chen, Jianming Xie, Xiao Sun, Yves A Lussier BMC Bioinformatics 2009, 10(Suppl 9):S6 (17 September 2009) |
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Research article
Reciprocal regulation of microRNA and mRNA profiles in neuronal development and synapse formation Sergei A Manakov, Seth GN Grant, Anton J Enright BMC Genomics 2009, 10:419 (8 September 2009) |
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Debate
A cross-study gene set enrichment analysis identifies critical pathways in endometriosis Hongbo Zhao, Qishan Wang, Chunyan Bai, Kan He, Yuchun Pan Reproductive Biology and Endocrinology 2009, 7:94 (8 September 2009) |
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Research
Jonathan M Dreyfuss, Mark D Johnson, Peter J Park Molecular Cancer 2009, 8:71 (4 September 2009) |
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Research article
Molecular mechanisms of tungstate-induced pancreatic plasticity: a transcriptomics approach Jordi Altirriba, Albert Barbera, Héctor Del Zotto, Belen Nadal, Sandra Piquer, Alex Sánchez-Pla, Juan J Gagliardino, Ramon Gomis BMC Genomics 2009, 10:406 (28 August 2009) Sodium tungstate acts via several glycemia-independent pathways to induce pancreatic beta cell proliferation in a rat model of diabetes, with the MAPK pathway playing a key role.
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Software
Gregor Rot, Anup Parikh, Tomaz Curk, Adam Kuspa, Gad Shaulsky, Blaz Zupan BMC Bioinformatics 2009, 10:265 (25 August 2009) |
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Research article
Blanca M Herrera, Helen E Lockstone, Jennifer M Taylor, Quin F Wills, Pamela J Kaisaki, Amy Barrett, Carme Camps, Christina Fernandez, Jiannis Ragoussis, Dominique Gauguier, Mark I McCarthy, Cecilia M Lindgren BMC Medical Genomics 2009, 2:54 (18 August 2009) Combining global microRNA and mRNA expression data indicates MiR-125a is over-expressed in the liver of hyperglycaemic rats and is a putative modulator of glucose and lipid metabolism in a rat model of type 2 diabetes.
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Research article
Xinxia Peng, Yu Li, Kathie-Anne Walters, Elizabeth R Rosenzweig, Sharon L Lederer, Lauri D Aicher, Sean Proll, Michael G Katze BMC Genomics 2009, 10:373 (11 August 2009) |
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Research article
Grapevine cell early activation of specific responses to DIMEB, a resveratrol elicitor Anita Zamboni, Pamela Gatto, Alessandro Cestaro, Stefania Pilati, Roberto Viola, Fulvio Mattivi, Claudio Moser, Riccardo Velasco BMC Genomics 2009, 10:363 (6 August 2009) |
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Methodology article
Tao Xu, JianLei Gu, Yan Zhou, LinFang Du BMC Bioinformatics 2009, 10:240 (5 August 2009) |
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Research article
Gene copy number variation throughout the Plasmodium falciparum genome Ian H Cheeseman, Natalia Gomez-Escobar, Celine K Carret, Alasdair Ivens, Lindsay B Stewart, Kevin KA Tetteh, David J Conway BMC Genomics 2009, 10:353 (4 August 2009) |
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Research article
Erik Kristiansson, Noomi Asker, Lars Förlin, DG Joakim Larsson BMC Genomics 2009, 10:345 (31 July 2009) |
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Research article
Betti Giusti, Marina Marini, Luciana Rossi, Ilaria Lapini, Alberto Magi, Andrea Capalbo, Rosa Lapalombella, Simona di Tullio, Michele Samaja, Fabio Esposito, Vittoria Margonato, Maria Boddi, Rosanna Abbate, Arsenio Veicsteinas BMC Genomics 2009, 10:342 (30 July 2009) |
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Software
Christian Schwager, Ute Wirkner, Amir Abdollahi, Peter E Huber BMC Bioinformatics 2009, 10:235 (29 July 2009) |
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Methodology article
CLEAN: CLustering Enrichment ANalysis Johannes M Freudenberg, Vineet K Joshi, Zhen Hu, Mario Medvedovic BMC Bioinformatics 2009, 10:234 (29 July 2009) |
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Method
Essi Laajala, Tero Aittokallio, Riitta Lahesmaa, Laura L Elo Genome Biology 2009, 10:R77 (16 July 2009) A novel statistical procedure is presented that uses probe-level information on Affymetrix exon arrays to detect differential splicing. |
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Research
Microarray data mining using Bioconductor packages Haisheng Nie, Pieter BT Neerincx, Jan Poel, Francesco Ferrari, Silvio Bicciato, Jack AM Leunissen, Martien AM Groenen BMC Proceedings 2009, 3(Suppl 4):S9 (16 July 2009) |
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Research
Gene set analysis methods applied to chicken microarray expression data Axel Skarman, Li Jiang, Henrik Hornshøj, Bart Buitenhuis, Jakob Hedegaard, Lene N Conley, Peter Sørensen BMC Proceedings 2009, 3(Suppl 4):S8 (16 July 2009) |
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Research
Pieter BT Neerincx, Pierrot Casel, Dennis Prickett, Haisheng Nie, Michael Watson, Jack AM Leunissen, Martien AM Groenen, Christophe Klopp BMC Proceedings 2009, 3(Suppl 4):S1 (16 July 2009) |
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Research article
Howard Thomas, Lin Huang, Mike Young, Helen Ougham BMC Evolutionary Biology 2009, 9:163 (14 July 2009) |
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Research article
Philippe Broët, Patrick Tan, Marco Alifano, Sophie Camilleri-Broët, Sylvia Richardson BMC Medical Genomics 2009, 2:43 (14 July 2009) |
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Research article
Genomic profiling of breast tumours in relation to BRCA abnormalities and phenotypes Olafur Stefansson, Jon Jonasson, Oskar Johannsson, Kristrun Olafsdottir, Margret Steinarsdottir, Sigridur Valgeirsdottir, Jorunn Eyfjord Breast Cancer Research 2009, 11:R47 (9 July 2009) |
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Research
A distribution-free convolution model for background correction of oligonucleotide microarray data Zhongxue Chen, Monnie McGee, Qingzhong Liu, Megan Kong, Youping Deng, Richard H Scheuermann BMC Genomics 2009, 10(Suppl 1):S19 (7 July 2009) |
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Research article
Sequence diversity in three tomato species: SNPs, markers, and molecular evolution José M Jiménez-Gómez, Julin N Maloof BMC Plant Biology 2009, 9:85 (3 July 2009) Analysis of the available expressed sequence tags (ESTs) for one cultivated and two wild tomato species highlights sets of genes and polymorphisms with potential significance for the evolution and domestication of this important crop.
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Research article
Unsupervised assessment of microarray data quality using a Gaussian mixture model Brian E Howard, Beate Sick, Steffen Heber BMC Bioinformatics 2009, 10:191 (22 June 2009) |
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Research article
Daniela Eggle, Svenja Debey-Pascher, Marc Beyer, Joachim L Schultze BMC Bioinformatics 2009, 10:186 (18 June 2009) |
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Research article
Sónia S Albuquerque, Céline Carret, Ana Grosso, Alice S Tarun, Xinxia Peng, Stefan HI Kappe, Miguel Prudêncio, Maria M Mota BMC Genomics 2009, 10:270 (17 June 2009) |
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Proceedings
Expression pattern divergence of duplicated genes in rice Zhe Li, He Zhang, Song Ge, Xiaocheng Gu, Ge Gao, Jingchu Luo BMC Bioinformatics 2009, 10(Suppl 6):S8 (16 June 2009) |
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Research article
Meng Li, Curt Balch, John S Montgomery, Mikyoung Jeong, Jae Chung, Pearlly Yan, Tim HM Huang, Sun Kim, Kenneth P Nephew BMC Medical Genomics 2009, 2:34 (8 June 2009) |
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Research article
Tristan E Coram, Matthew L Settles, Xianming Chen BMC Genomics 2009, 10:253 (29 May 2009) |
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Research article
Charles G Danko, Arkady M Pertsov BMC Medical Genomics 2009, 2:31 (28 May 2009) |
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Research article
Dean A Baker, Steven Russell BMC Genomics 2009, 10:242 (24 May 2009) |
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Methodology article
Differential splicing using whole-transcript microarrays Mark D Robinson, Terence P Speed BMC Bioinformatics 2009, 10:156 (22 May 2009) The Affymetrix GeneChip microarray platform, widely used to assay gene expression, can also detect differential splicing events with the help of a new statistical method called FIRMAGene that analyses information from poorly fitting adjacent probes.
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Research article
Laura W Harris, Helen E Lockstone, Phillipp Khaitovich, Cynthia Weickert, Maree J Webster, Sabine Bahn BMC Medical Genomics 2009, 2:28 (20 May 2009) |
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Database
MIMAS 3.0 is a Multiomics Information Management and Annotation System Alexandre Gattiker, Leandro Hermida, Robin Liechti, Ioannis Xenarios, Olivier Collin, Jacques Rougemont, Michael Primig BMC Bioinformatics 2009, 10:151 (18 May 2009) An international collaboration of software developers, computer scientists, life scientists and research technicians has extended a database tool that manages microarray data from various sources to include data from the latest ultra-high throughput DNA sequencing technologies.
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Software
flowClust: a Bioconductor package for automated gating of flow cytometry data Kenneth Lo, Florian Hahne, Ryan R Brinkman, Raphael Gottardo BMC Bioinformatics 2009, 10:145 (14 May 2009) |
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Research
Wouter Wegdam, Perry D Moerland, Marrije R Buist, Emiel van Themaat, Boris Bleijlevens, Huub CJ Hoefsloot, Chris G de Koster, Johannes MFG Aerts Proteome Science 2009, 7:19 (14 May 2009) |
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Research article
Erik F Hensen, Jelle J Goeman, Jan Oosting, Andel GL Van der Mey, Pancras CW Hogendoorn, Cor WRJ Cremers, Peter Devilee, Cees J Cornelisse BMC Medical Genomics 2009, 2:25 (11 May 2009) |
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Research
Yvonne JK Edwards, Anna E Lobley, Melissa M Pentony, David T Jones Genome Biology 2009, 10:R50 (11 May 2009) Signals for microRNA targeting and ubiquitination are enriched in intrinsically disordered proteins, but some highly disordered proteins can escape rapid degradation. |
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Short Report
José F Rodríguez-Quiñones, José R Rodríguez-Medina BMC Research Notes 2009, 2:87 (9 May 2009) |
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Research
Systemic analysis of the response of Aspergillus niger to ambient pH Mikael R Andersen, Linda Lehmann, Jens Nielsen Genome Biology 2009, 10:R47 (1 May 2009) Systems modeling of |
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Research
Koji Kadota, Yuji Nakai, Kentaro Shimizu Algorithms for Molecular Biology 2009, 4:7 (22 April 2009) |
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Software
flowCore: a Bioconductor package for high throughput flow cytometry Florian Hahne, Nolwenn LeMeur, Ryan R Brinkman, Byron Ellis, Perry Haaland, Deepayan Sarkar, Josef Spidlen, Errol Strain, Robert Gentleman BMC Bioinformatics 2009, 10:106 (9 April 2009) |
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Research article
Christine Steinhoff, Martina Paulsen, Szymon Kielbasa, Jörn Walter, Martin Vingron BMC Genomics 2009, 10:144 (31 March 2009) |
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Research article
Nora Hinsch, Matthias Frank, Claudia Döring, Christian Vorländer, Martin-Leo Hansmann BMC Cancer 2009, 9:93 (26 March 2009) |
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Methodology article
Detection of genomic deletions in rice using oligonucleotide microarrays Myron Bruce, Ann Hess, Jianfa Bai, Ramil Mauleon, M Genaleen Diaz, Nobuko Sugiyama, Alicia Bordeos, Guo-Liang Wang, Hei Leung, Jan E Leach BMC Genomics 2009, 10:129 (25 March 2009) |
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Research
MicroRNA and gene expression patterns in the differentiation of human embryonic stem cells Jiaqiang Ren, Ping Jin, Ena Wang, Francesco M Marincola, David F Stroncek Journal of Translational Medicine 2009, 7:20 (23 March 2009) |
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Research article
Fedora Sutton, Ding-Geng Chen, Xijin Ge, Don Kenefick BMC Plant Biology 2009, 9:34 (23 March 2009) |
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Research article
Debra J Skinner, Charles S Gasser BMC Plant Biology 2009, 9:29 (16 March 2009) Comparison of Arabidopsis mutants 'inner no outer' and 'aintegumenta' with wild-type using microarray analysis identified candidate genes expressed specifically in the integuments of ovules providing a useful resource for functional analysis.
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Research article
Jesse J Smith, Renée Kenney, David J Gagne, Brian P Frushour, William Ladd, Heidi L Galonek, Kristine Israelian, Jeffrey Song, Giedre Razvadauskaite, Amy V Lynch, David P Carney, Robin J Johnson, Siva Lavu, Andre Iffland, Peter J Elliott, Philip D Lambert, Keith O Elliston, Michael R Jirousek, Jill C Milne, Olivier Boss BMC Systems Biology 2009, 3:31 (10 March 2009) |
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Technical Note
Recent developments in StemBase: a tool to study gene expression in human and murine stem cells Reatha Sandie, Gareth A Palidwor, Matthew R Huska, Christopher J Porter, Paul M Krzyzanowski, Enrique M Muro, Carolina Perez-Iratxeta, Miguel A Andrade-Navarro BMC Research Notes 2009, 2:39 (10 March 2009) This article is part of a collection on Databases StemBase, the comprehensive online repository developed by the Canadian Stem Cell Network, now supports the analysis of gene coexpression patterns in human and mouse stem cells, and the visualization of expression data by genomic regions.
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Research article
Achim Rody, Uwe Holtrich, Laos Pusztai, Cornelia Liedtke, Regine Gaetje, Eugen Ruckhaeberle, Christine Solbach, Lars Hanker, Andre Ahr, Dirk Metzler, Knut Engels, Thomas Karn, Manfred Kaufmann Breast Cancer Research 2009, 11:R15 (9 March 2009) The T-cell metagene LCK identifies ER negative breast cancers, commonly associated with poor disease free survival, and may also identify differences in prognosis within this tumor subtype.
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Methodology article
Donna M Toleno, Gabriel Renaud, Tyra G Wolfsberg, Munirul Islam, Derek E Wildman, Kimberly D Siegmund, Joseph G Hacia BMC Bioinformatics 2009, 10:77 (5 March 2009) |
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Software
RGG: A general GUI Framework for R scripts Ilhami Visne, Erkan Dilaveroglu, Klemens Vierlinger, Martin Lauss, Ahmet Yildiz, Andreas Weinhaeusel, Christa Noehammer, Friedrich Leisch, Albert Kriegner BMC Bioinformatics 2009, 10:74 (2 March 2009) |
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Research article
Five QTL hotspots for yield in short rotation coppice bioenergy poplar: The Poplar Biomass Loci Anne M Rae, Nathaniel Street, Kathryn Robinson, Nicole Harris, Gail Taylor BMC Plant Biology 2009, 9:23 (26 February 2009) |
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Research article
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