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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
  
Comparison of gene expression signatures of diamide, H2O2 and menadione exposed Aspergillus nidulans cultures  linking genome-wide transcriptional changes to cellular physiology
Istv n P csi, Mrton Miskei, Zsolt Karnyi, Tams Emri, Patricia Ayoubi, T nde Pusztahelyi, Gy rgy Balla, Rolf A Prade
BMC Genomics 2005, 6:182 (20December2005)
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Commentary
Sal-Site: Integrating new and existing ambystomatid salamander research and informational resources
Jeramiah J Smith, Srikrishna Putta, John A Walker, D Kevin Kump, Amy K Samuels, James R Monaghan, David W Weisrock, Chuck Staben, S Randal Voss
BMC Genomics 2005, 6:181 (16December2005)
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Research article
A method for accurate detection of genomic microdeletions using real-time quantitative PCR
Rosanna Weksberg, Simon Hughes, Laura Moldovan, Anne S Bassett, Eva WC Chow, Jeremy A Squire
BMC Genomics 2005, 6:180 (13December2005)
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Research article
Comparative genome analysis reveals a conserved family of actin-like proteins in apicomplexan parasites
Jennifer L Gordon, L David Sibley
BMC Genomics 2005, 6:179 (12December2005)
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Database
GPX-Macrophage Expression Atlas: A database for expression profiles of macrophages challenged with a variety of pro-inflammatory, anti-inflammatory, benign and pathogen insults
Graeme R Grimes, Stuart Moodie, John S Beattie, Marie Craigon, Paul Dickinson, Thorsten Forster, Andrew D Livingston, Muriel Mewissen, Kevin A Robertson, Alan J Ross, Garwin Sing, Peter Ghazal
BMC Genomics 2005, 6:178 (12December2005)
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Research article
Comparative analysis of programmed cell death pathways in filamentous fungi
Natalie D Fedorova, Jonathan H Badger, Geoff D Robson, Jennifer R Wortman, William C Nierman
BMC Genomics 2005, 6:177 (8December2005)
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Methodology article
ASAP: Amplification, sequencing & annotation of plastomes
Amit Dhingra, Kevin M Folta
BMC Genomics 2005, 6:176 (7December2005)
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Research article
Sequence comparisons of plasmids pBJS-O of Spiroplasma citri and pSKU146 of S. kunkelii: implications for plasmid evolution
Bharat D Joshi, Michael Berg, Janet Rogers, Jacqueline Fletcher, Ulrich Melcher
BMC Genomics 2005, 6:175 (7December2005)
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Research article
Bacterial genome adaptation to niches: Divergence of the potential virulence genes in three Burkholderia species of different survival strategies
H Stanley Kim, Mark A Schell, Yan Yu, Ricky L Ulrich, Saul H Sarria, William C Nierman, David DeShazer
BMC Genomics 2005, 6:174 (7December2005)
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Research article
The odorant receptor repertoire of teleost fish
Tyler S Alioto, John Ngai
BMC Genomics 2005, 6:173 (6December2005)
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Research article
The angiotensin-converting enzyme (ACE) gene family of Anopheles gambiae
Susan Burnham, Judith A Smith, Alison J Lee, R Elwyn Isaac, Alan D Shirras
BMC Genomics 2005, 6:172 (5December2005)
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Research article
An EST-based approach for identifying genes expressed in the intestine and gills of pre-smolt Atlantic salmon (Salmo salar)
Heidi Hagen-Larsen, Jon K Laerdahl, Frank Panitz, Alexei Adzhubei, Bj rn Hyheim
BMC Genomics 2005, 6:171 (1December2005)
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Research article
Efficient single nucleotide polymorphism discovery in laboratory rat strains using wild rat-derived SNP candidates
Bart MG Smits, Victor Guryev, Dimphy Zeegers, Dirk Wedekind, Hans J Hedrich, Edwin Cuppen
BMC Genomics 2005, 6:170 (29November2005)
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Research article
The EH1 motif in metazoan transcription factors
Richard R Copley
BMC Genomics 2005, 6:169 (27November2005)
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Research article
Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes
Soohyun Lee, Isaac Kohane, Simon Kasif
BMC Genomics 2005, 6:168 (27November2005)
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Research article
Analysis of vertebrate genomes suggests a new model for clade B serpin evolution
Dion Kaiserman, Phillip I Bird
BMC Genomics 2005, 6:167 (23November2005)
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Methodology article
Characterization of 954 bovine full-CDS cDNA sequences
Gregory P Harhay, Tad S Sonstegard, John W Keele, Michael P Heaton, Michael L Clawson, Warren M Snelling, Ralph T Wiedmann, Curt P Van Tassell, Timothy PL Smith
BMC Genomics 2005, 6:166 (23November2005)
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Research article
Expression and genomic organization of zonadhesin-like genes in three species of fish give insight into the evolutionary history of a mosaic protein
Peter ND Hunt, Michael D Wilson, Kristian R von Schalburg, William S Davidson, Ben F Koop
BMC Genomics 2005, 6:165 (22November2005)
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Research article
Efficient gene-driven germ-line point mutagenesis of C57BL/6J mice
Edward J Michaud, Cymbeline T Culiat, Mitchell L Klebig, Paul E Barker, KT Cain, Debra J Carpenter, Lori L Easter, Carmen M Foster, Alysyn W Gardner, ZY Guo, Kay J Houser, Lori A Hughes, Marilyn K Kerley, Zhaowei Liu, Robert E Olszewski, Irina Pinn, Ginger D Shaw, Sarah G Shinpock, Ann M Wymore, Eugene M Rinchik, Dabney K Johnson
BMC Genomics 2005, 6:164 (21November2005)
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Research article
An acquisition account of genomic islands based on genome signature comparisons
MWJ van Passel, A Bart, HH Thygesen, ACM Luyf, AHC van Kampen, A van der Ende
BMC Genomics 2005, 6:163 (18November2005)
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Research article
Assessing the precision of high-throughput computational and laboratory approaches for the genome-wide identification of protein subcellular localization in bacteria
S bastien Rey, Jennifer L Gardy, Fiona SL Brinkman
BMC Genomics 2005, 6:162 (17November2005)
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Research article
Construction and characterization of a genomic BAC library for the Mus m. musculus mouse subspecies (PWD/Ph inbred strain)
Petr Jansa, Petr Divina, Ji  Forejt
BMC Genomics 2005, 6:161 (16November2005)
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Research article
Leveraging human genomic information to identify nonhuman primate sequences for expression array development
Eliot R Spindel, Mark A Pauley, Yibing Jia, Courtney Gravett, Shaun L Thompson, Nicholas F Boyle, Sergio R Ojeda, Robert B Norgren Jr
BMC Genomics 2005, 6:160 (15November2005)
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Research article
Preferential attachment in the evolution of metabolic networks
Sara Light, Per Kraulis, Arne Elofsson
BMC Genomics 2005, 6:159 (10November2005)
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Research article
Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains
Elisa Giuntini, Alessio Mengoni, Carlotta De Filippo, Duccio Cavalieri, Nadia Aubin-Horth, Christian R Landry, Anke Becker, Marco Bazzicalupo
BMC Genomics 2005, 6:158 (10November2005)
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Research article
Genetic mapping of putative Chrna7 and Luzp2 neuronal transcriptional enhancers due to impact of a transgene-insertion and 6.8 Mb deletion in a mouse model of Prader-Willi and Angelman syndromes
Mihaela Stefan, Kathryn C Claiborn, Edyta Stasiek, Jing-Hua Chai, Tohru Ohta, Richard Longnecker, John M Greally, Robert D Nicholls
BMC Genomics 2005, 6:157 (9November2005)
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Research article
The zebrafish progranulin gene family and antisense transcripts
Beno t Cadieux, Babykumari P Chitramuthu, David Baranowski, Hugh PJ Bennett
BMC Genomics 2005, 6:156 (8November2005)
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Methodology article
SSH adequacy to preimplantation mammalian development: Scarce specific transcripts cloning despite irregular normalisation
LC Bui, RD Landri, JP Renard, V Duranthon
BMC Genomics 2005, 6:155 (8November2005)
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Research article
Characterization of SR3 reveals abundance of non-LTR retrotransposons of the RTE clade in the genome of the human blood fluke, Schistosoma mansoni
Thewarach Laha, Nonglack Kewgrai, Alex Loukas, Paul J Brindley
BMC Genomics 2005, 6:154 (4November2005)
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Methodology article
A rigorous method for multigenic families' functional annotation: the peptidyl arginine deiminase (PADs) proteins family example
N Balandraud, P Gouret, EGJ Danchin, M Blanc, D Zinn, J Roudier, P Pontarotti
BMC Genomics 2005, 6:153 (4November2005)
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Research article
A genome-wide survey of Major Histocompatibility Complex (MHC) genes and their paralogues in zebrafish
Jennifer G Sambrook, Felipe Figueroa, Stephan Beck
BMC Genomics 2005, 6:152 (4November2005)
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Research article
cGMP-independent nitric oxide signaling and regulation of the cell cycle
Xiaolin Cui, Jianhua Zhang, Penglin Ma, Daniela E Myers, Ilana G Goldberg, Kelly J Sittler, Jennifer J Barb, Peter J Munson, Ana del Pilar Cintron, J Philip McCoy, Shuibang Wang, Robert L Danner
BMC Genomics 2005, 6:151 (3November2005)
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Methodology article
Proposed methods for testing and selecting the ERCC external RNA controls
External RNA Controls Consortium
BMC Genomics 2005, 6:150 (2November2005)
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Research article
SNiPer: Improved SNP genotype calling for Affymetrix 10K GeneChip microarray data
Matthew J Huentelman, David W Craig, Albert D Shieh, Jason J Corneveaux, Diane Hu-Lince, John V Pearson, Dietrich A Stephan
BMC Genomics 2005, 6:149 (31October2005)
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Research article
Specificity and overlap in gene segment-defined antibody repertoires
Ramy A Arnaout
BMC Genomics 2005, 6:148 (28October2005)
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Research article
Limitations of mRNA amplification from small-size cell samples
Vigdis Nygaard, Marit Holden, Anders Lland, Mette Langaas, Ola Myklebost, Eivind Hovig
BMC Genomics 2005, 6:147 (27October2005)
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Research article
Identification of genes involved in Ca2+ ionophore A23187-mediated apoptosis and demonstration of a high susceptibility for transcriptional repression of cell cycle genes in B lymphoblasts from a patient with Scott syndrome
Detlef Kozian, Valrie Proulle, Almut Nitsche, Marie Galitzine, Marie-Carmen Martinez, Beatrice Schumann, Dominique Meyer, Matthias Herrmann, Jean-Marie Freyssinet, Dani le Kerbiriou-Nabias
BMC Genomics 2005, 6:146 (21October2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
i-Tracker: For quantitative proteomics using iTRAQ
Ian P Shadforth, Tom PJ Dunkley, Kathryn S Lilley, Conrad Bessant
BMC Genomics 2005, 6:145 (20October2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters
Nathalie Pavy, Charles Paule, Lee Parsons, John A Crow, Marie-Josee Morency, Janice Cooke, James E Johnson, Etienne Noumen, Carine Guillet-Claude, Yaron Butterfield, Sarah Barber, George Yang, Jerry Liu, Jeff Stott, Robert Kirkpatrick, Asim Siddiqui, Robert Holt, Marco Marra, Armand Seguin, Ernest Retzel, Jean Bousquet, John MacKay
BMC Genomics 2005, 6:144 (19October2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
EST analysis in Ginkgo biloba: an assessment of conserved developmental regulators and gymnosperm specific genes
Eric D Brenner, Manpreet S Katari, Dennis W Stevenson, Stephen A Rudd, Andrew W Douglas, Walter N Moss, Richard W Twigg, Suzan J Runko, Giulia M Stellari, WR McCombie, Gloria M Coruzzi
BMC Genomics 2005, 6:143 (15October2005)
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Research article
Macrodissection versus microdissection of rectal carcinoma: minor influence of stroma cells to tumor cell gene expression profiles
Elza C de Bruin, Simone van de Pas, Esther H Lips, Ronald van Eijk, Minke MC van der Zee, Marcel Lombaerts, Tom van Wezel, Corrie AM Marijnen, J Han JM van Krieken, Jan Paul Medema, Cornelis JH van de Velde, Paul HC Eilers, Lucy TC Peltenburg
BMC Genomics 2005, 6:142 (14October2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
The stress response against denatured proteins in the deletion of cytosolic chaperones SSA1/2 is different from heat-shock response in Saccharomyces cerevisiae
Rena Matsumoto, Kuniko Akama, Randeep Rakwal, Hitoshi Iwahashi
BMC Genomics 2005, 6:141 (7October2005)
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Research article
The distribution of SNPs in human gene regulatory regions
Yongjian Guo, D Curtis Jamison
BMC Genomics 2005, 6:140 (6October2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
In silico characterization of the family of PARP-like poly(ADP-ribosyl)transferases (pARTs)
Helge Otto, Pedro A Reche, Fernando Bazan, Katharina Dittmar, Friedrich Haag, Friedrich Koch-Nolte
BMC Genomics 2005, 6:139 (4October2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Methodology article
Identification of disease causing loci using an array-based genotyping approach on pooled DNA
David W Craig, Matthew J Huentelman, Diane Hu-Lince, Victoria L Zismann, Michael C Kruer, Anne M Lee, Erik G Puffenberger, John M Pearson, Dietrich A Stephan
BMC Genomics 2005, 6:138 (30September2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
A TNF-induced gene expression program under oscillatory NF- B control
Bing Tian, David E Nowak, Allan R Brasier
BMC Genomics 2005, 6:137 (28September2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Mitochondrial-encoded membrane protein transcripts are pyrimidine-rich while soluble protein transcripts and ribosomal RNA are purine-rich
Patrick C Bradshaw, Anand Rathi, David C Samuels
BMC Genomics 2005, 6:136 (26September2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Construction and validation of a Bovine Innate Immune Microarray
Laurelea Donaldson, Tony Vuocolo, Christian Gray, Ylva Strandberg, Antonio Reverter, Sean McWilliam, YongHong Wang, Keren Byrne, Ross Tellam
BMC Genomics 2005, 6:135 (22September2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software
GeneSeer: A sage for gene names and genomic resources
Andrew J Olson, Tim Tully, Ravi Sachidanandam
BMC Genomics 2005, 6:134 (21September2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Comparative analysis of a BAC contig of porcine chromosome 13q31-q32 and human chromosome 3q21-q22
Mario Van Poucke, David Bourry, Fran ois Piumi, Marc Mattheeuws, Alex Van Zeveren, Patrick Chardon, Luc J Peelman
BMC Genomics 2005, 6:133 (21September2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Molecular signature of clinical severity in recovering patients with severe acute respiratory syndrome coronavirus (SARS-CoV)
Yun-Shien Lee, Chun-Houh Chen, Angel Chao, En-Shih Chen, Min-Li Wei, Lung-Kun Chen, Kuender D Yang, Meng-Chih Lin, Yi-Hsi Wang, Jien-Wei Liu, Hock-Liew Eng, Ping-Cherng Chiang, Ting-Shu Wu, Kuo-Chein Tsao, Chung-Guei Huang, Yin-Jing Tien, Tzu-Hao Wang, Hsing-Shih Wang, Ying-Shiung Lee
BMC Genomics 2005, 6:132 (21September2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Effect of dataset selection on the topological interpretation of protein interaction networks
Luke Hakes, David L Robertson, Stephen G Oliver
BMC Genomics 2005, 6:131 (20September2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Characterization of the global profile of genes expressed in cervical epithelium by Serial Analysis of Gene Expression (SAGE)
Carlos Prez-Plasencia, Gregory Riggins, Guelaguetza Vzquez-Ortiz, Jos Moreno, Hugo Arreola, Alfredo Hidalgo, Patricia Pi a-Sanchez, Mauricio Salcedo
BMC Genomics 2005, 6:130 (19September2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Diversity in domain architectures of Ser/Thr kinases and their homologues in prokaryotes
A Krupa, N Srinivasan
BMC Genomics 2005, 6:129 (19September2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Genome annotation of Anopheles gambiae using mass spectrometry-derived data
Drio E Kalume, Suraj Peri, Raghunath Reddy, Jun Zhong, Mobolaji Okulate, Nirbhay Kumar, Akhilesh Pandey
BMC Genomics 2005, 6:128 (19September2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Comparative analysis of the kinomes of three pathogenic trypanosomatids: Leishmania major, Trypanosoma brucei and Trypanosoma cruzi
Marilyn Parsons, Elizabeth A Worthey, Pauline N Ward, Jeremy C Mottram
BMC Genomics 2005, 6:127 (15September2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [F1000 Biology] [Cited on BioMed Central]
Methodology article
Fish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray
Kristian R von Schalburg, Matthew L Rise, Glenn A Cooper, Gordon D Brown, A Ross Gibbs, Colleen C Nelson, William S Davidson, Ben F Koop
BMC Genomics 2005, 6:126 (15September2005)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
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