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Editor-in-Chief
Melissa Norton, MD Biology Editor
Penelope Webb, PhD In-house Editor
Erik Alexandersson
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Research article
  
Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes
Albin Sandelin, Peter Bailey, Sara Bruce, P r G Engstr m, Joanna M Klos, Wyeth W Wasserman, Johan Ericson, Boris Lenhard
BMC Genomics 2004, 5:99 (21December2004)
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Research article
Evaluation of the chicken transcriptome by SAGE of B cells and the DT40 cell line
Matthias B Wahl, Randolph B Caldwell, Andrzej M Kierzek, Hiroshi Arakawa, Eduardo Eyras, Nina Hubner, Christian Jung, Manuel Soeldenwagner, Manuela Cervelli, Yan-Dong Wang, Volkmar Liebscher, Jean-Marie Buerstedde
BMC Genomics 2004, 5:98 (21December2004)
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Research article
The association of Alu repeats with the generation of potential AU-rich elements (ARE) at 3' untranslated regions.
Hyeong Jun An, Doheon Lee, Kwang Hyung Lee, Jonghwa Bhak
BMC Genomics 2004, 5:97 (21December2004)
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Research article
FunnyBase: a systems level functional annotation of Fundulus ESTs for the analysis of gene expression
Justin E Paschall, Marjorie F Oleksiak, Jeffrey D VanWye, Jennifer L Roach, J Andrew Whitehead, Gerald J Wyckoff, Kevin J Kolell, Douglas L Crawford
BMC Genomics 2004, 5:96 (20December2004)
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Research article
Homopolymer tract length dependent enrichments in functional regions of 27 eukaryotes and their novel dependence on the organism DNA (G+C)% composition
Yue Zhou, Jeffrey W Bizzaro, Kenneth A Marx
BMC Genomics 2004, 5:95 (14December2004)
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Research article
Prognostic meta-signature of breast cancer developed by two-stage mixture modeling of microarray data
Ronglai Shen, Debashis Ghosh, Arul M Chinnaiyan
BMC Genomics 2004, 5:94 (14December2004)
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Database
GOLD.db: genomics of lipid-associated disorders database
Hubert Hackl, Michael Maurer, Bernhard Mlecnik, J rgen Hartler, Gernot Stocker, Diego Miranda-Saavedra, Zlatko Trajanoski
BMC Genomics 2004, 5:93 (10December2004)
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Research article
Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence
Stefan Taudien, Petra Galgoczy, Klaus Huse, Kathrin Reichwald, Markus Schilhabel, Karol Szafranski, Atsushi Shimizu, Shuichi Asakawa, Adam Frankish, Ivan F Loncarevic, Nobuyoshi Shimizu, Roman Siddiqui, Matthias Platzer
BMC Genomics 2004, 5:92 (10December2004)
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Research article
Lower rate of genomic variation identified in the trans-membrane domain of monoamine sub-class of Human G-Protein Coupled Receptors: The Human GPCR-DB Database
Claes Wahlestedt, Anthony J Brookes, Salim Mottagui-Tabar
BMC Genomics 2004, 5:91 (4December2004)
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Research article
Characterization of the chicken inward rectifier K+ channel IRK1/Kir2.1 gene
Hideki Mutai, Lawrence C Kenyon, Emily Locke, Nami Kikuchi, John Carl Oberholtzer
BMC Genomics 2004, 5:90 (29November2004)
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Research article
The rehydration transcriptome of the desiccation-tolerant bryophyte Tortula ruralis: transcript classification and analysis
Melvin J Oliver, Scot E Dowd, Joaquin Zaragoza, Steven A Mauget, Paxton R Payton
BMC Genomics 2004, 5:89 (16November2004)
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Research article
Comparison of frozen and RNALater solid tissue storage methods for use in RNA expression microarrays
George L Mutter, David Zahrieh, Chunmei Liu, Donna Neuberg, David Finkelstein, Heather E Baker, Janet A Warrington
BMC Genomics 2004, 5:88 (10November2004)
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Research article
Sample size for detecting differentially expressed genes in microarray experiments
Caimiao Wei, Jiangning Li, Roger E Bumgarner
BMC Genomics 2004, 5:87 (8November2004)
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Research article
Genomic structure and cloning of two transcript isoforms of human Sp8
Maria-athina Milona, Julie E Gough, Alasdair J Edgar
BMC Genomics 2004, 5:86 (8November2004)
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Research article
Functional characterization in Caenorhabditis elegans of transmembrane worm-human orthologs
Anna Henricson, Erik LL Sonnhammer, David L Baillie, Ana Vaz Gomes
BMC Genomics 2004, 5:85 (8November2004)
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Research article
The use of Open Reading frame ESTs (ORESTES) for analysis of the honey bee transcriptome
Francis MF Nunes, Valeria Valente, Josane F Sousa, Marco AV Cunha, Daniel G Pinheiro, Rafaela M Maia, Daniela D Araujo, Maria CR Costa, Waleska K Martins, Alex F Carvalho, Nadia Monesi, Adriana M Nascimento, Pablo MV Peixoto, Maria FR Silva, Ricardo GP Ramos, Luis FL Reis, Emmanuel Dias-Neto, Sandro J Souza, Andrew JG Simpson, Marco A Zago, Ademilson EE Soares, Marcia MG Bitondi, Enilza M Espreafico, Foued S Espindola, Maria L Paco-Larson, Zila LP Simoes, Klaus Hartfelder, Wilson A Silva Jr
BMC Genomics 2004, 5:84 (3November2004)
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Research article
Cross-species hybridisation of human and bovine orthologous genes on high density cDNA microarrays
James Adjaye, Ralf Herwig, Doris Herrmann, Wasco Wruck, Alia BenKahla, Thore C Brink, Monika Nowak, Joseph W Carnwath, Claus Hultschig, Heiner Niemann, Hans Lehrach
BMC Genomics 2004, 5:83 (28October2004)
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Research article
Microarray and comparative genomics-based identification of genes and gene regulatory regions of the mouse immune system
John J Hutton, Anil G Jegga, Sue Kong, Ashima Gupta, Catherine Ebert, Sarah Williams, Jonathan D Katz, Bruce J Aronow
BMC Genomics 2004, 5:82 (25October2004)
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Software
GeneLink: a database to facilitate genetic studies of complex traits
Elizabeth M Gillanders, Anthony Masiello, Derek Gildea, Lowell Umayam, Priya Duggal, Mary Pat Jones, Alison P Klein, Diana Freas-Lutz, Grace Ibay, Ken Trout, Tyra G Wolfsberg, Jeffrey M Trent, Joan E Bailey-Wilson, Andreas D Baxevanis
BMC Genomics 2004, 5:81 (18October2004)
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Research article
Reconstruction of putative DNA virus from endogenous rice tungro bacilliform virus-like sequences in the rice genome: implications for integration and evolution
Motoyuki Kunii, Masanori Kanda, Hironori Nagano, Ichiro Uyeda, Yuji Kishima, Yoshio Sano
BMC Genomics 2004, 5:80 (18October2004)
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Research article
Protein kinases of the human malaria parasite Plasmodium falciparum: the kinome of a divergent eukaryote
Pauline Ward, Leila Equinet, Jeremy Packer, Christian Doerig
BMC Genomics 2004, 5:79 (12October2004)
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Database
i-Genome: A database to summarize oligonucleotide data in genomes
Feng-Mao Lin, Hsien-Da Huang, Yu-Chung Chang, Jorng-Tzong Horng
BMC Genomics 2004, 5:78 (9October2004)
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Research article
Integrating linkage and radiation hybrid mapping data for bovine chromosome 15
Warren M Snelling, Mathieu Gautier, John W Keele, Timothy PL Smith, Roger T Stone, Gregory P Harhay, Gary L Bennett, Naoya Ihara, Akiko Takasuga, Haruko Takeda, Yoshikazu Sugimoto, Andr Eggen
BMC Genomics 2004, 5:77 (8October2004)
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Methodology article
Evaluation of sense-strand mRNA amplification by comparative quantitative PCR
Loyal A Goff, Jessica Bowers, Jaime Schwalm, Kevin Howerton, Robert C Getts, Ronald P Hart
BMC Genomics 2004, 5:76 (6October2004)
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Research article
Extreme conservation of noncoding DNA near HoxD complex of vertebrates
Chilaka Sabarinadh, Subbaya Subramanian, Anshuman Tripathi, Rakesh K Mishra
BMC Genomics 2004, 5:75 (6October2004)
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Research article
Genome wide analysis of common and specific stress responses in adult drosophila melanogaster
Fabrice Girardot, Vronique Monnier, Herv Tricoire
BMC Genomics 2004, 5:74 (30September2004)
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Research article
Microarrays for global expression constructed with a low redundancy set of 27,500 sequenced cDNAs representing an array of developmental stages and physiological conditions of the soybean plant
Lila O Vodkin, Anupama Khanna, Robin Shealy, Steven J Clough, Delkin Orlando Gonzalez, Reena Philip, Gracia Zabala, Fran oise Thibaud-Nissen, Mark Sidarous, Martina V Strmvik, Elizabeth Shoop, Christina Schmidt, Ernest Retzel, John Erpelding, Randy C Shoemaker, Alicia M Rodriguez-Huete, Joseph C Polacco, Virginia Coryell, Paul Keim, George Gong, Lei Liu, Jose Pardinas, Peter Schweitzer
BMC Genomics 2004, 5:73 (29September2004)
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Methodology article
Strengths and weaknesses of EST-based prediction of tissue-specific alternative splicing
Shobhit Gupta, Dorothea Zink, Bernhard Korn, Martin Vingron, Stefan A Haas
BMC Genomics 2004, 5:72 (28September2004)
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Research article
Inter-Platform comparability of microarrays in acute lymphoblastic leukemia
Stephanie A Mitchell, Kevin M Brown, Michael M Henry, Michelle Mintz, Daniel Catchpoole, Bonnie LaFleur, Dietrich A Stephan
BMC Genomics 2004, 5:71 (23September2004)
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Research article
cDNA array-CGH profiling identifies genomic alterations specific to stage and MYCN-amplification in neuroblastoma
Qing-Rong Chen, Sven Bilke, Jun S Wei, Craig C Whiteford, Nicola Cenacchi, Alexei L Krasnoselsky, Braden T Greer, Chang-Gue Son, Frank Westermann, Frank Berthold, Manfred Schwab, Daniel Catchpoole, Javed Khan
BMC Genomics 2004, 5:70 (20September2004)
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Research article
Comparative genomics of cyclin-dependent kinases suggest co-evolution of the RNAP II C-terminal domain and CTD-directed CDKs
Zhenhua Guo, John W Stiller
BMC Genomics 2004, 5:69 (20September2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Database
PEDRo: A database for storing, searching and disseminating experimental proteomics data
Kevin Garwood, Thomas McLaughlin, Chris Garwood, Scott Joens, Norman Morrison, Christopher F Taylor, Kathleen Carroll, Caroline Evans, Anthony D Whetton, Sarah Hart, David Stead, Zhikang Yin, Alistair JP Brown, Andrew Hesketh, Keith Chater, Lena Hansson, Muriel Mewissen, Peter Ghazal, Julie Howard, Kathryn S Lilley, Simon J Gaskell, Andy Brass, Simon J Hubbard, Stephen G Oliver, Norman W Paton
BMC Genomics 2004, 5:68 (17September2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Complete mitochondrial genome sequence of Urechis caupo, a representative of the phylum Echiura
Jeffrey L Boore
BMC Genomics 2004, 5:67 (15September2004)
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Research article
A high-resolution radiation hybrid map of chicken chromosome 5 and comparison with human chromosomes
Frdrique Pitel, Behnam Abasht, Mireille Morisson, Richard PMA Crooijmans, Florence Vignoles, Sophie Leroux, Katia Feve, Suzanne Bardes, Denis Milan, Sandrine Lagarrigue, Martien AM Groenen, Madeleine Douaire, Alain Vignal
BMC Genomics 2004, 5:66 (15September2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
An integrated 4249 marker FISH/RH map of the canine genome
Matthew Breen, Christophe Hitte, Travis D Lorentzen, Rachael Thomas, Edouard Cadieu, Leah Sabacan, Allyson Scott, Gwenaelle Evanno, Heidi G Parker, Ewen F Kirkness, Ruth Hudson, Richard Guyon, Gregory G Mahairas, Boris Gelfenbeyn, Claire M Fraser, Catherine Andr, Francis Galibert, Elaine A Ostrander
BMC Genomics 2004, 5:65 (13September2004)
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Software
A method for detecting and correcting feature misidentification on expression microarrays
I-Ping Tu, Marci Schaner, Maximilian Diehn, Branimir I Sikic, Patrick O Brown, David Botstein, Michael J Fero
BMC Genomics 2004, 5:64 (9September2004)
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Research article
Integrated analysis of metabolic phenotypes in Saccharomyces cerevisiae
Natalie C Duarte, Bernhard  Palsson, Pengcheng Fu
BMC Genomics 2004, 5:63 (8September2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Enhancer trapping in zebrafish using the Sleeping Beauty transposon
Darius Balciunas, Ann E Davidson, Sridhar Sivasubbu, Spencer B Hermanson, Zachary Welle, Stephen C Ekker
BMC Genomics 2004, 5:62 (3September2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Performance evaluation of commercial short-oligonucleotide microarrays and the impact of noise in making cross-platform correlations
Richard Shippy, Timothy J Sendera, Randall Lockner, Chockalingam Palaniappan, Tamma Kaysser-Kranich, George Watts, John Alsobrook
BMC Genomics 2004, 5:61 (2September2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
POSA: Perl Objects for DNA Sequencing Data Analysis
Jan A Aerts, Bart J Jungerius, Martien AM Groenen
BMC Genomics 2004, 5:60 (27August2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Combined analysis of expression data and transcription factor binding sites in the yeast genome
Vijayalakshmi H Nagaraj, Ruadhan A O'Flanagan, Adrian R Bruning, Jonathan R Mathias, Andrew K Vershon, Anirvan M Sengupta
BMC Genomics 2004, 5:59 (26August2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Cross-species global and subset gene expression profiling identifies genes involved in prostate cancer response to selenium
Michael Schlicht, Brian Matysiak, Tracy Brodzeller, Xinyu Wen, Hang Liu, Guohui Zhou, Rajiv Dhir, Martin J Hessner, Peter Tonellato, Mark Suckow, Morris Pollard, Milton W Datta
BMC Genomics 2004, 5:58 (20August2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Gene expression variation between mouse inbred strains
Rolf Turk, Peter AC 't Hoen, Ellen Sterrenburg, Rene X de Menezes, Emile J de Meijer, Judith M Boer, Gert-Jan B van Ommen, Johan T den Dunnen
BMC Genomics 2004, 5:57 (18August2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
A genome-wide screen identifies a single  -defensin gene cluster in the chicken: implications for the origin and evolution of mammalian defensins
Yanjing Xiao, Austin L Hughes, Junko Ando, Yoichi Matsuda, Jan-Fang Cheng, Donald Skinner-Noble, Guolong Zhang
BMC Genomics 2004, 5:56 (13August2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [F1000 Biology] [Cited on BioMed Central]
Research article
Selection and validation of endogenous reference genes using a high throughput approach
Ping Jin, Yingdong Zhao, Yvonne Ngalame, Monica C Panelli, Dirk Nagorsen, Vladia Monsurr , Kina Smith, Nan Hu, Hua Su, Phil R Taylor, Francesco M Marincola, Ena Wang
BMC Genomics 2004, 5:55 (13August2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
From biomedicine to natural history research: EST resources for ambystomatid salamanders
Srikrishna Putta, Jeramiah J Smith, John A Walker, Mathieu Rondet, David W Weisrock, James Monaghan, Amy K Samuels, Kevin Kump, David C King, Nicholas J Maness, Bianca Habermann, Elly Tanaka, Susan V Bryant, David M Gardiner, David M Parichy, S Randal Voss
BMC Genomics 2004, 5:54 (13August2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Immobilized probe and glass surface chemistry as variables in microarray fabrication
Martin J Hessner, Lisa Meyer, Jennifer Tackes, Sanaa Muheisen, Xujing Wang
BMC Genomics 2004, 5:53 (4August2004)
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Research article
Retrieving sequences of enzymes experimentally characterized but erroneously annotated : the case of the putrescine carbamoyltransferase
Daniil G Naumoff, Ying Xu, Nicolas Glansdorff, Bernard Labedan
BMC Genomics 2004, 5:52 (2August2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
C-type lectin-like domains in Fugu rubripes
Alex N Zelensky, Jill E Gready
BMC Genomics 2004, 5:51 (1August2004)
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Research article
The Retinome  Defining a reference transcriptome of the adult mammalian retina/retinal pigment epithelium
Heidi L Schulz, Thomas Goetz, Juergen Kaschkoetoe, Bernhard HF Weber
BMC Genomics 2004, 5:50 (29July2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [F1000 Biology] [Cited on BioMed Central]
Research article
The FU gene and its possible protein isoforms
Torben sterlund, David B Everman, Regina C Betz, Monica Mosca, Markus M Nthen, Charles E Schwartz, Peter G Zaphiropoulos, Rune Toftg rd
BMC Genomics 2004, 5:49 (22July2004)
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Research article
Characterization of the GATC regulatory network in E. coli
Alessandra Riva, Marie-Odile Delorme, Tony Chevalier, Nicolas Guilhot, Corinne Hnaut, Alain Hnaut
BMC Genomics 2004, 5:48 (20July2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
A molecular 'signature' of primary breast cancer cultures; patterns resembling tumor tissue
Shanaz H Dairkee, Youngran Ji, Yong Ben, Dan H Moore, Zhenhang Meng, Stefanie S Jeffrey
BMC Genomics 2004, 5:47 (19July2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Expression profile of genes regulated by activity of the Na-H exchanger NHE1
Luanna K Putney, Diane L Barber
BMC Genomics 2004, 5:46 (16July2004)
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Research article
Novel conserved domains in proteins with predicted roles in eukaryotic cell-cycle regulation, decapping and RNA stability
Vivek Anantharaman, L Aravind
BMC Genomics 2004, 5:45 (16July2004)
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Research article
Formin homology 2 domains occur in multiple contexts in angiosperms
Fatima Cvr kov , Marian Novotn , Denisa P ckov, Viktor  rsk
BMC Genomics 2004, 5:44 (15July2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Synaptotagmin gene content of the sequenced genomes
Molly Craxton
BMC Genomics 2004, 5:43 (6July2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Biologically meaningful expression profiling across species using heterologous hybridization to a cDNA microarray
Susan CP Renn, Nadia Aubin-Horth, Hans A Hofmann
BMC Genomics 2004, 5:42 (6July2004)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
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