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Editor-in-Chief
Melissa Norton, MD Biology Editor
Penelope Webb, PhD In-house Editor
Erik Alexandersson
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Volume 9 Suppl 1
Research
Las Vegas, NV, USA. 25-28 June 2007
more supplements 
Research article
 
Deciphering downstream gene targets of PI3K/mTOR/p70S6K pathway in breast cancer
Henna Heinonen, Anni Nieminen, Matti Saarela, Anne Kallioniemi, Juha Klefstrom, Sampsa Hautaniemi, Outi Monni
BMC Genomics 2008, 9:348 (24July2008)
[Abstract] [Provisional PDF]
Research article
Large-scale Gene Ontology analysis of plant transcriptome-derived sequences retrieved by AFLP technology
Alessandro Botton, Giulio Galla, Ana Conesa, Christian Bachem, Angelo Ramina, Gianni Barcaccia
BMC Genomics 2008, 9:347 (24July2008)
[Abstract] [Provisional PDF]
Research article
Structural conservation versus functional divergence of maternally expressed microRNAs in the Dlk1/Gtl2 imprinting region
Martin Kircher, Christoph Bock, Martina Paulsen
BMC Genomics 2008, 9:346 (23July2008)
[Abstract] [Provisional PDF]
Research article
Highly conserved gene order and numerous novel repetitive elements in genomic regions linked to wing pattern variation in Heliconius butterflies
Riccardo Papa, Clayton M Morrison, James R Walters, Brian A Counterman, Rui Chen, Georg Halder, Laura Ferguson, Nicola Chamberlain, Richard ffrench-Constant, Durrell D Kapan, Chris D Jiggins, Robert D Reed, William O McMillan
BMC Genomics 2008, 9:345 (22July2008)
[Abstract] [Provisional PDF]
Research article
Gene expression patterns of sulfur starvation
in Synechocystis sp. PCC 6803
Zhigang Zhang, Ninad D Pendse, Katherine N Phillips, James B Cotner, Arkady Khodursky
BMC Genomics 2008, 9:344 (21July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Growth rate regulated genes and their wide involvement in the Lactococcus lactis stress responses
Clementine Dressaire, Emma Redon, Helene Milhem, Philippe Besse, Pascal Loubiere, Muriel Cocaign-Bousquet
BMC Genomics 2008, 9:343 (21July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Parasitization by the wasp Eretmocerus mundus induces transcription of genes related to immune response and symbiotic bacteria proliferation in the whitefly Bemisia tabaci
Assaf Mahadav, Dan Gerling, Yuval Gottlieb, Henryk Czosnek, Murad Ghanim
BMC Genomics 2008, 9:342 (18July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: a three factor design
Alessandro Fazio, Michael C Jewett, Pascale Daran-Lapujade, Roberta Mustacchi, Renata Usaite, Jack T Pronk, Christopher T Workman, Jens Nielsen
BMC Genomics 2008, 9:341 (18July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Comparative transcriptomics of human multipotent stem cells during adipogenesis and osteoblastogenesis
Marcel Scheideler, Christian Elabd, Laure-Emmanuelle Zaragosi, Chiara Chiellini, Hubert Hackl, Fatima Sanchez-Cabo, Sunaina Yadav, Kalina Duszka, Gerald Friedl, Christine Papak, Andreas Prokesch, Reinhard Windhager, Gerard Ailhaud, Christian Dani, Ez-Zoubir Amri, Zlatko Trajanoski
BMC Genomics 2008, 9:340 (17July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Database
PRFdb: A database of computationally predicted eukaryotic programmed -1 ribosomal frameshift signals
Ashton T Belew, Nicholas L Hepler, Jonathan L Jacobs, Jonathan D Dinman
BMC Genomics 2008, 9:339 (17July2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Database
WildSilkbase: An EST database of wild silkmoths
KP Arunkumar, Archana Tomar, Takaaki Daimon, Toru Shimada, J Nagaraju
BMC Genomics 2008, 9:338 (17July2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Evolutionary conservation of zinc finger transcription factor binding sites in promoters of genes co-expressed with WT1 in prostate cancer
Kurtis Eisermann, Sunpreet Tandon, Anton Bazarov, Adina Brett, Gail Fraizer, Helen Piontkivska
BMC Genomics 2008, 9:337 (16July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Genetic interaction network of the Saccharomyces cerevisiae type 1 phosphatase Glc7
Michael R Logan, Thao Nguyen, Nicolas Szapiel, James Knockleby, Hanting Por, Megan Zadworny, Michael Neszt, Paul Harrison, Howard Bussey, Craig A Mandato, Jackie Vogel, Guillaume Lesage
BMC Genomics 2008, 9:336 (15July2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions?
Albert Pallej , Eoghan D Harrington, Peer Bork
BMC Genomics 2008, 9:335 (15July2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Transcriptional profiling in C. elegans suggests DNA damage dependent apoptosis as an ancient function of the p53 family
Sebastian Greiss, Bjorn Schumacher, Kaj Grandien, Jonathan Rothblatt, Anton Gartner
BMC Genomics 2008, 9:334 (15July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Structure and properties of transcriptional networks driving selenite stress response in yeasts.
Helene Salin, Vivienne Fardeau, Eugenia Piccini, Gaelle Lelandais, Veronique Tanty, Sophie Lemoine, Claude Jacq, Frederic Devaux
BMC Genomics 2008, 9:333 (15July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Low nucleosome occupancy is encoded around functional human transcription factor binding sites
Floris Daenen, Frans van Roy, Pieter J De Bleser
BMC Genomics 2008, 9:332 (15July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
The complete mitochondrial genome of the bag-shelter moth
Ochrogaster lunifer (Lepidoptera, Notodontidae)
Paola Salvato, Mauro Simonato, Andrea Battisti, Enrico Negrisolo
BMC Genomics 2008, 9:331 (15July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
An in silico analysis of T-box regulated genes and T-box evolution in prokaryotes, with emphasis on prediction of substrate specificity of transporters
Michiel Wels, Tom Groot Kormelink, Michiel Kleerebezem, Roland J Siezen, Christof Francke
BMC Genomics 2008, 9:330 (14July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Polymorphisms in the selenoprotein S gene: lack of association with autoimmune inflammatory diseases
Alfonso Martinez, Jose Luis Santiago, Jezabel Varade, Ana Marquez, Jose Ramon Lamas, Juan Luis Mendoza, Hermenegildo de la Calle, Manuel Diaz-Rubio, Emilio G de la Concha, Benjamin Fernandez-Gutierrez, Elena Urcelay
BMC Genomics 2008, 9:329 (14July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Cross-platform comparison of SYBR Green real-time PCR with TaqMan PCR, microarrays and other gene expression measurement technologies evaluated in the MicroArray Quality Control (MAQC) study
Emi Arikawa, Yanyang Sun, Jie Wang, Qiong Zhou, Baitang Ning, Stacey L Dial, Lei Guo, Jingping Yang
BMC Genomics 2008, 9:328 (11July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
The Hypocrea jecorina (Trichoderma reesei) hypercellulolytic mutant RUT C30 lacks a 85 kb (29 gene-encoding) region of the wild-type genome
Verena Seidl, Christian Gamauf, Irina S Druzhinina, Bernhard Seiboth, Lukas Hartl, Christian P Kubicek
BMC Genomics 2008, 9:327 (11July2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Immunity related genes in dipterans share common enrichment of AT-rich motifs in their 5 prime regulatory regions that are potentially involved in nucleosome formation.
Jesus Hernandez-Romano, Francisco J Carlos-Rivera, Heladia Salgado, Hector Lamadrid-Figueroa, Veronica Valverde-Garduno, Mario H Rodriguez, Jesus Martinez-Barnetche
BMC Genomics 2008, 9:326 (9July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Altered gene expression changes in Arabidopsis leaf tissues and protoplasts in response to Plum pox virus infection
Mohan Babu, Jonathan S Griffiths, Tyng-Shyan Huang, Aiming Wang
BMC Genomics 2008, 9:325 (9July2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Topoisomerase II inhibition involves characteristic
chromosomal expression patterns
Susanne Reymann, Juergen Borlak
BMC Genomics 2008, 9:324 (8July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Re-annotation of the physical map of Glycine max for polyploid-like regions by BAC end sequence driven whole genome shotgun read assembly
Navinder Saini, Jeffry Shultz, David A Lightfoot
BMC Genomics 2008, 9:323 (7July2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Meta-analysis of nasopharyngeal carcinoma microarray data explores mechanism of EBV-regulated neoplastic transformation
Xia Chen, Shuang Liang, Wenling Zheng, Zhijun Liao, Tao Shan, Wenli Ma
BMC Genomics 2008, 9:322 (7July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
The ORFeome of Staphylococcus aureus v 1.1
Christina J Brandner, Richard H Maier, Daryl S Henderson, Helmut Hintner, Johann W Bauer, Kamil  nder
BMC Genomics 2008, 9:321 (7July2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Software
T2D-Db: An integrated platform to study the molecular basis of Type 2 diabetes
Shipra Agrawal, Nevenka Dimitrova, Prasanthi Nathan, Udayakumar K., Sailakshmi S., Sriram S., Manjusha N, Urmi Sengupta
BMC Genomics 2008, 9:320 (7July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles] [1 comment]
Methodology article
Between-groups within-gene heterogeneity of residual variances in microarray gene expression data
Joaquim Casellas, Luis Varona
BMC Genomics 2008, 9:319 (4July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Methodology article
A genome-wide 20K citrus microarray for gene expression analysis
M. ANGELES Martinez-Godoy, Nuria Mauri, Jose Juarez, M. CARMEN Marques, Julia Santiago, Javier Forment, Jose Gadea
BMC Genomics 2008, 9:318 (3July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Strong position-dependent effects of sequence mismatches on signal ratios measured using long oligonucleotide microarrays
Catriona Rennie, Harry A Noyes, Stephen J Kemp, Helen Hulme, Andy Brass, David C Hoyle
BMC Genomics 2008, 9:317 (3July2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example
Gustavo A de Souza, Hiwa Malen, Tina Softeland, Gisle Salensminde, Swati Prasad, Inge Jonassen, Harald G Wiker
BMC Genomics 2008, 9:316 (2July2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
The complete mitochondrial genome of the Antarctic springtail Cryptopygus antarcticus (Hexapoda: Collembola)
Antonio Carapelli, Sara Comandi, Peter Convey, Francesco Nardi, Francesco Frati
BMC Genomics 2008, 9:315 (1July2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
A preliminary analysis of genome structure and composition in Gossypium hirsutum
Wangzhen Guo, Caiping Cai, Changbiao Wang, Liang Zhao, Lei Wang, Tianzhen Zhang
BMC Genomics 2008, 9:314 (1July2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
The topology of the bacterial co-conserved protein network and its implications for predicting protein function
Anis Karimpour-Fard, Sonia M Leach, Lawrence E Hunter, Ryan T Gill
BMC Genomics 2008, 9:313 (30June2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome
Evandro Novaes, Derek R Drost, William G Farmerie, Georgios J Pappas Jr, Dario Grattapaglia, Ronald R Sederoff, Matias Kirst
BMC Genomics 2008, 9:312 (30June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Comparative genomic profiling of Dutch clinical Bordetella pertussis isolates using DNA microarrays: Identification of genes absent from epidemic strains
Audrey J King, Tamara van Gorkom, Jeroen LA Pennings, Han GJ van der Heide, Qiushui He, Dimitri Diavatopoulos, Kees Heuvelman, Marjolein van Gent, Karin van Leeuwen, Frits R Mooi
BMC Genomics 2008, 9:311 (30June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Meta-Analysis Approach identifies Candidate Genes and associated Molecular Networks for Type-2 Diabetes Mellitus
Axel Rasche, Hadi Al-Hasani, Ralf Herwig
BMC Genomics 2008, 9:310 (30June2008)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Research article
Microarray analysis identifies a common set of cellular genes modulated by different HCV replicon clones
Anna Rita Ciccaglione, Cinzia Marcantonio, Elena Tritarelli, Paola Tataseo, Alessandro Ferraris, Roberto Bruni, Bruno Dallapiccola, Germano Gerosolimo, Angela Costantino, Maria Rapicetta
BMC Genomics 2008, 9:309 (30June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
RAWUL: A new ubiquitin-like domain in PRC1 Ring finger proteins that unveils putative plant and worm PRC1 orthologs
Luis Sanchez-Pulido, Damien Devos, Zinmay R Sung, Myriam Calonje
BMC Genomics 2008, 9:308 (27June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Expression profiling of a high-fertility mouse line by microarray analysis and qPCR
Jens Vanselow, Gerd N rnberg, Dirk Koczan, Martina Langhammer, Hans-Jrgen Thiesen, Norbert Reinsch
BMC Genomics 2008, 9:307 (27June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
The linear chromosome of the plant-pathogenic mycoplasma 'Candidatus Phytoplasma mali'
Michael Kube, Bernd Schneider, Heiner Kuhl, Thomas Dandekar, Katja Heitmann, Alexander M Migdoll, Richard Reinhardt, Erich Seemller
BMC Genomics 2008, 9:306 (26June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
A physical map of human Alu repeats cleavage by restriction endonucleases
Murat A Abdurashitov, Victor N Tomilov, Valery A Chernukhin, Sergey Kh Degtyarev
BMC Genomics 2008, 9:305 (26June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Database
SjTPdb: integrated transcriptome and proteome database and analysis platform for Schistosoma japonicum
Feng Liu, Ping Chen, Shu-Jian Cui, Zhi-Qin Wang, Ze-Guang Han
BMC Genomics 2008, 9:304 (26June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Proteomic profile of dormant Trichophyton Rubrum conidia
Wenchuan Leng, Tao Liu, Rui Li, Jian Yang, Candong Wei, Wenliang Zhang, Qi Jin
BMC Genomics 2008, 9:303 (25June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells
Seraya Maouche, Odette Poirier, Tiphaine Godefroy, Robert Olaso, Ivo Gut, Jean-Phillipe Collet, Gilles Montalescot, Fran ois Cambien
BMC Genomics 2008, 9:302 (25June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Differential gene expression of the honey bee Apis mellifera associated with Varroa destructor infection
M Navajas, A Migeon, C Alaux, ML Martin-Magniette, GE Robinson, JD Evans, S Cros-Arteil, D Crauser, Y Le Conte
BMC Genomics 2008, 9:301 (25June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Expressed sequence tags from Peromyscus testis and placenta tissue: Analysis, annotation, and utility for mapping
Julie L Weston Glenn, Chin-Fu Chen, Adrienne Lewandowski, Chun-Huai Cheng, Clifton M Ramsdell, Rebecca Bullard-Dillard, Jianguo Chen, Michael J Dewey, Travis C Glenn
BMC Genomics 2008, 9:300 (24June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Functional genomics reveals increases in cholesterol biosynthetic genes and highly unsaturated fatty acid biosynthesis after dietary substitution of fish oil with vegetable oils in Atlantic salmon (Salmo salar)
Michael J Leaver, Laure AN Villeneuve, Alex Obach, Linda Jensen, James E Bron, Douglas R Tocher, John B Taggart
BMC Genomics 2008, 9:299 (24June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
The trypanosome transcriptome is remodelled during differentiation but displays limited responsiveness within life stages
V Lila Koumandou, Senthil Kumar A Natesan, Tatiana Sergeenko, Mark C Field
BMC Genomics 2008, 9:298 (23June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Basal DNA repair machinery is subject to positive selection in ionizing-radiation-resistant bacteria
Ha tham Sghaier, Kas Ghedira, Alia Benkahla, Insaf Barkallah
BMC Genomics 2008, 9:297 (21June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
ESTs from the microsporidian Edhazardia aedis
Erin E Gill, James J Becnel, Naomi M Fast
BMC Genomics 2008, 9:296 (20June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Double feature selection and cluster analyses in mining of microarray data from cotton
Magdy S Alabady, Eunseog Youn, Thea A Wilkins
BMC Genomics 2008, 9:295 (20June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Methodology article
Coupling amplified DNA from flow-sorted chromosomes to high-density SNP mapping in barley
Hana  imkov , Jan T Svensson, Pascal Condamine, Eva H ibov, Pavla Suchnkov, Prasanna R Bhat, Jan Barto , Jan af, Timothy J Close, Jaroslav Dole el
BMC Genomics 2008, 9:294 (19June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins
Phillip Hahn, Jens B se, Stefanie Edler, Andreas Lengeling
BMC Genomics 2008, 9:293 (18June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Relative effects of mutability and selection on single nucleotide polymorphisms in transcribed regions of the human genome
Ivan P Gorlov, Olga Y Gorlova, Christopher I Amos
BMC Genomics 2008, 9:292 (17June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Genome-wide transcriptional changes induced by phagocytosis or growth on bacteria in Dictyostelium
Alessio Sillo, Gareth Bloomfield, Alessandra Balest, Alessandra Balbo, Barbara Pergolizzi, Barbara Peracino, Jason Skelton, Alasdair Ivens, Salvatore Bozzaro
BMC Genomics 2008, 9:291 (17June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Chloroplast DNA sequence of the green alga Oedogonium cardiacum (Chlorophyceae): Unique genome architecture, derived characters shared with the Chaetophorales and novel genes acquired through horizontal transfer
Jean-Simon Brouard, Christian Otis, Claude Lemieux, Monique Turmel
BMC Genomics 2008, 9:290 (16June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Venezuelan equine encephalitis virus infection causes modulation of inflammatory and immune response genes in mouse brain
Anuj Sharma, Bhaskar Bhattacharya, Raj K Puri, Radha K Maheshwari
BMC Genomics 2008, 9:289 (16June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Genes related to apoptosis predict necrosis of the liver as a phenotype observed in rats exposed to a compendium of hepatotoxicants
Lingkang Huang, Alexandra N Heinloth, Zhao-Bang Zeng, Richard S Paules, Pierre R Bushel
BMC Genomics 2008, 9:288 (16June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping
Franois L Luro, Gilles Costantino, Javier Terol, Xavier Argout, Thierry Allario, Patrick Wincker, Manuel Talon, Patrick Ollitrault, Raphael Morillon
BMC Genomics 2008, 9:287 (16June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition
Wei Zhu, Shu Ouyang, Marina Iovene, Kimberly O'Brien, Hue Vuong, Jiming Jiang, C Robin Buell
BMC Genomics 2008, 9:286 (13June2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles]
Research article
Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories
Michael J Boedigheimer, Russell D Wolfinger, Michael B Bass, Pierre R Bushel, Jeff W Chou, Matthew Cooper, J Christopher Corton, Jennifer Fostel, Susan Hester, Janice S Lee, Fenglong Liu, Jie Liu, Hui-Rong Qian, John Quackenbush, Syril Pettit, Karol L Thompson
BMC Genomics 2008, 9:285 (12June2008)
[Abstract] [Full text] [PDF] [PubMed] [ |
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