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  1. Eukaryotic replication origins exhibit different initiation efficiencies and activation times within S-phase. Although local chromatin structure and function influences origin activity, the exact mechanisms re...

    Authors: Weihong Xu, Jennifer G Aparicio, Oscar M Aparicio and Simon Tavaré

    Citation: BMC Genomics 2006 7:276

    Content type: Research article

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  2. During the past decade, Sanger sequencing has been used to completely sequence hundreds of microbial and a few higher eukaryote genomes. In recent years, a number of alternative technologies became available, ...

    Authors: Thomas Wicker, Edith Schlagenhauf, Andreas Graner, Timothy J Close, Beat Keller and Nils Stein

    Citation: BMC Genomics 2006 7:275

    Content type: Research article

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  3. Body weight and length are economically important traits in foodfish species influenced by quantitative trait loci (QTL) and environmental factors. It is usually difficult to dissect the genetic and environmen...

    Authors: Chun Ming Wang, Loong Chueng Lo, Ze Yuan Zhu and Gen Hua Yue

    Citation: BMC Genomics 2006 7:274

    Content type: Research article

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  5. In this study, we addressed whether a single 454 Life Science GS20 sequencing run provides new gene discovery from a normalized cDNA library, and whether the short reads produced via this technology are of val...

    Authors: Foo Cheung, Brian J Haas, Susanne MD Goldberg, Gregory D May, Yongli Xiao and Christopher D Town

    Citation: BMC Genomics 2006 7:272

    Content type: Research article

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  6. Vertebrate genomes contain numerous duplicate genes, many of which are organised into paralagous regions indicating duplication of linked groups of genes. Comparison of genomic organisation in different lineag...

    Authors: Karl R Wotton and Sebastian M Shimeld

    Citation: BMC Genomics 2006 7:271

    Content type: Research article

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  7. Bacillus thuringiensis belongs to the Bacillus cereus sensu lato group of Gram-positive and spore-forming bacteria. Most isolates of B. thuringiensis can bear many endogenous plasmids, and the number and size of ...

    Authors: Junyan Huang, Suxia Guo, Jacques Mahillon, Géraldine A Van der Auwera, Li Wang, Dongmei Han, Ziniu Yu and Ming Sun

    Citation: BMC Genomics 2006 7:270

    Content type: Research article

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  8. The popularity of microsatellites has greatly increased in the last decade on account of their many applications. However, little is currently understood about the factors that influence their genesis and dist...

    Authors: Francesc López-Giráldez, Olga Andrés, Xavier Domingo-Roura and Montserrat Bosch

    Citation: BMC Genomics 2006 7:269

    Content type: Research article

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  9. A better understanding of the development of metastatic disease and the identification of molecular markers for cancer spread would be useful for the design of improved treatment strategies. This study was con...

    Authors: Heidi Lyng, Runar S Brøvig, Debbie H Svendsrud, Ruth Holm, Olav Kaalhus, Kjetil Knutstad, Halldis Oksefjell, Kolbein Sundfør, Gunnar B Kristensen and Trond Stokke

    Citation: BMC Genomics 2006 7:268

    Content type: Research article

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  10. Our understanding of the mechanisms that govern the cellular process of meiosis is limited in higher plants with polyploid genomes. Bread wheat is an allohexaploid that behaves as a diploid during meiosis. Chr...

    Authors: Wayne Crismani, Ute Baumann, Tim Sutton, Neil Shirley, Tracie Webster, German Spangenberg, Peter Langridge and Jason A Able

    Citation: BMC Genomics 2006 7:267

    Content type: Research article

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  11. Microarray normalizations typically apply methods that assume absence of global transcript shifts, or absence of changes in internal control features such as housekeeping genes. These normalization approaches ...

    Authors: Carole L Yauk, Andrew Williams, Sherri Boucher, Lynn M Berndt, Gu Zhou, Jenny L Zheng, Andrea Rowan-Carroll, Hongyan Dong, Iain B Lambert, George R Douglas and Craig L Parfett

    Citation: BMC Genomics 2006 7:266

    Content type: Methodology article

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  12. The identification of genes essential for survival is of theoretical importance in the understanding of the minimal requirements for cellular life, and of practical importance in the identification of potentia...

    Authors: Adam M Gustafson, Evan S Snitkin, Stephen CJ Parker, Charles DeLisi and Simon Kasif

    Citation: BMC Genomics 2006 7:265

    Content type: Research article

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  13. Little is known about the genome sequences of lepidopteran insects, although this group of insects has been studied extensively in the fields of endocrinology, development, immunity, and pathogen-host interact...

    Authors: Youping Deng, Yinghua Dong, Venkata Thodima, Rollie J Clem and A Lorena Passarelli

    Citation: BMC Genomics 2006 7:264

    Content type: Research article

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  14. Aplastic anemia (AA) is a bone marrow failure syndrome mostly characterized by an immune-mediated destruction of marrow hematopoietic progenitor/stem cells. The resulting hypocellularity limits a detailed anal...

    Authors: Anke Franzke, Robert Geffers, J Katrin Hunger, Susanne Pförtner, Wenji Piao, Philipp Ivanyi, Jens Grosse, Michael Probst-Kepper, Arnold Ganser and Jan Buer

    Citation: BMC Genomics 2006 7:263

    Content type: Research article

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  15. TILLING (T argeting I nduced L ocal L esions i n G enomes) is a reverse genetic technique based on the use of a mismatch-specific enzyme that identifies mutations in a target gene through heteroduplex analysis. W...

    Authors: Erin J Gilchrist, Nigel J O'Neil, Ann M Rose, Monique C Zetka and George W Haughn

    Citation: BMC Genomics 2006 7:262

    Content type: Methodology article

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  17. The multi-step process of carcinogenesis can be more fully understood by characterizing gene expression changes induced in cells by carcinogens. In this study, expression microarrays were used to monitor the a...

    Authors: Sarah L Hockley, Volker M Arlt, Daniel Brewer, Ian Giddings and David H Phillips

    Citation: BMC Genomics 2006 7:260

    Content type: Research article

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  18. Post-segregational killing systems are present in a large variety of microorganisms. When found on plasmids, they are described as addiction systems that act to maintain the plasmid during the partitioning of ...

    Authors: Sarah Fico and Jacques Mahillon

    Citation: BMC Genomics 2006 7:259

    Content type: Research article

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  19. Quantitative variation in gene expression has been proposed to underlie phenotypic variation among human individuals. A facilitating step towards understanding the basis for gene expression variability is asso...

    Authors: Vineet K Sharma, Anu Sharma, Naveen Kumar, Mamta Khandelwal, Kiran Kumar Mandapati, Shirley Horn-Saban, Liora Strichman-Almashanu, Doron Lancet, Samir K Brahmachari and Srinivasan Ramachandran

    Citation: BMC Genomics 2006 7:258

    Content type: Database

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  20. The ability to rapidly characterize an unknown microorganism is critical in both responding to infectious disease and biodefense. To do this, we need some way of anticipating an organism's phenotype based on t...

    Authors: Chern-Sing Goh, Tara A Gianoulis, Yang Liu, Jianrong Li, Alberto Paccanaro, Yves A Lussier and Mark Gerstein

    Citation: BMC Genomics 2006 7:257

    Content type: Methodology article

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  22. Dermatophytes are the primary causative agent of dermatophytoses, a disease that affects billions of individuals worldwide. Trichophyton rubrum is the most common of the superficial fungi. Although T. rubrum is a...

    Authors: Lingling Wang, Li Ma, Wenchuan Leng, Tao Liu, Lu Yu, Jian Yang, Li Yang, Wenliang Zhang, Qian Zhang, Jie Dong, Ying Xue, Yafang Zhu, Xingye Xu, Zhe Wan, Guohui Ding, Fudong Yu…

    Citation: BMC Genomics 2006 7:255

    Content type: Research article

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  24. Cross-species primers have been used with moderate success to address a variety of questions concerning genome structure, evolution, and gene function. However, the factors affecting their success have never b...

    Authors: Donna JE Housley, Zachary A Zalewski, Stephanie E Beckett and Patrick J Venta

    Citation: BMC Genomics 2006 7:253

    Content type: Research article

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  25. RNA amplification is necessary for profiling gene expression from small tissue samples. Previous studies have shown that the T7 based amplification techniques are reproducible but may distort the true abundanc...

    Authors: Ilhem Diboun, Lorenz Wernisch, Christine Anne Orengo and Martin Koltzenburg

    Citation: BMC Genomics 2006 7:252

    Content type: Research article

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  26. Allergy is a common debilitating and occasionally life threatening condition. The fungal kingdom contains a number of species that produce a wide range of well defined protein allergens although the vast major...

    Authors: Paul Bowyer, Marcin Fraczek and David W Denning

    Citation: BMC Genomics 2006 7:251

    Content type: Research article

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  27. Leishmania major is a protozoan parasite with a highly polarised cell shape that depends upon endocytosis and exocytosis from a single area of the plasma membrane, the flagellar pocket. SNAREs (soluble N-ethylmal...

    Authors: Sébastien Besteiro, Graham H Coombs and Jeremy C Mottram

    Citation: BMC Genomics 2006 7:250

    Content type: Research article

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  29. Pigment epithelium derived factor (PEDF), a member of the serpin family, regulates cell proliferation, promotes survival of neurons, and blocks growth of new blood vessels in mammals. Defining the molecular ph...

    Authors: Xuming Xu, Samuel Shao-Min Zhang, Colin J Barnstable and Joyce Tombran-Tink

    Citation: BMC Genomics 2006 7:248

    Content type: Research article

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  30. Chemostat cultures are commonly used in production of cellular material for systems-wide biological studies. We have used the novel TRAC (transcript analysis with aid of affinity capture) method to study expre...

    Authors: Jari J Rautio, Bart A Smit, Marilyn Wiebe, Merja Penttilä and Markku Saloheimo

    Citation: BMC Genomics 2006 7:247

    Content type: Research article

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  31. High throughput sequencing-by-synthesis is an emerging technology that allows the rapid production of millions of bases of data. Although the sequence reads are short, they can readily be used for re-sequencin...

    Authors: Matthew N Bainbridge, René L Warren, Martin Hirst, Tammy Romanuik, Thomas Zeng, Anne Go, Allen Delaney, Malachi Griffith, Matthew Hickenbotham, Vincent Magrini, Elaine R Mardis, Marianne D Sadar, Asim S Siddiqui, Marco A Marra and Steven JM Jones

    Citation: BMC Genomics 2006 7:246

    Content type: Methodology article

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  32. Members of the genus Phytophthora are notorious pathogens with world-wide distribution. The most devastating species include P. infestans, P. ramorum and P. sojae. In order to develop molecular methods for routin...

    Authors: Diana P Garnica, Andrés M Pinzón, Lina M Quesada-Ocampo, Adriana J Bernal, Emiliano Barreto, Niklaus J Grünwald and Silvia Restrepo

    Citation: BMC Genomics 2006 7:245

    Content type: Research article

    Published on:

  34. Abnormalities of pre-mRNA splicing are increasingly recognized as an important mechanism through which gene mutations cause disease. However, apart from the mutations in the donor and acceptor sites, the effec...

    Authors: Patrizia Lastella, Nicoletta Concetta Surdo, Nicoletta Resta, Ginevra Guanti and Alessandro Stella

    Citation: BMC Genomics 2006 7:243

    Content type: Research article

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  35. Mitochondrial DNA-derived sequences have become popular markers for evolutionary studies, as their comparison may yield significant insights into the evolution of both the organisms and their genomes. From the...

    Authors: Gen Hua Yue, Woei Chang Liew and Laszlo Orban

    Citation: BMC Genomics 2006 7:242

    Content type: Research article

    Published on:

  36. Sequence data and other characters from mitochondrial genomes (gene translocations, secondary structure of RNA molecules) are useful in phylogenetic studies among metazoan animals from population to phylum lev...

    Authors: Fabian Kilpert and Lars Podsiadlowski

    Citation: BMC Genomics 2006 7:241

    Content type: Research article

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  37. High throughput gene expression profiling (GEP) is becoming a routine technique in life science laboratories. With experimental designs that repeatedly span thousands of genes and hundreds of samples, relying ...

    Authors: Paul Honoré, Samuel Granjeaud, Rebecca Tagett, Stéphane Deraco, Emmanuel Beaudoing, Jacques Rougemont, Stéphane Debono and Pascal Hingamp

    Citation: BMC Genomics 2006 7:240

    Content type: Software

    Published on:

  38. Transcription factor proteins bind specific DNA sequences to control the expression of genes. They contain DNA binding domains which belong to several super-families, each with a specific mechanism of DNA bind...

    Authors: Shalev Itzkovitz, Tsvi Tlusty and Uri Alon

    Citation: BMC Genomics 2006 7:239

    Content type: Research article

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  39. The recent advancement in human genome sequencing and genotyping has revealed millions of single nucleotide polymorphisms (SNP) which determine the variation among human beings. One of the particular important...

    Authors: Erwin Tantoso, Yuchen Yang and Kuo-Bin Li

    Citation: BMC Genomics 2006 7:238

    Content type: Research article

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  40. Genome-wide profiling has allowed the regulatory interaction networks of many organisms to be visualised and the pattern of connections between genes to be studied. These networks are non-random, following a p...

    Authors: Tim F Cooper, Andrew P Morby, Annabel Gunn and Dominique Schneider

    Citation: BMC Genomics 2006 7:237

    Content type: Research article

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  41. Gene knockouts in a model organism such as mouse provide a valuable resource for the study of basic biology and human disease. Determining which gene has been inactivated by an untargeted gene trapping event p...

    Authors: Courtney A Harper, Conrad C Huang, Doug Stryke, Michiko Kawamoto, Thomas E Ferrin and Patricia C Babbitt

    Citation: BMC Genomics 2006 7:236

    Content type: Research article

    Published on:

  42. Changes in gene expression are known to be responsible for phenotypic variation and susceptibility to diseases. Identification and annotation of the genomic sequence variants that cause gene expression changes...

    Authors: Debraj GuhaThakurta, Tao Xie, Manish Anand, Stephen W Edwards, Guoya Li, Susanna S Wang and Eric E Schadt

    Citation: BMC Genomics 2006 7:235

    Content type: Research article

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  44. A semiparametric approach was used to identify groups of cDNAs and genes with distinct expression profiles across time and overcome the limitations of clustering to identify groups. The semiparametric approach...

    Authors: Sandra L Rodriguez-Zas, Bruce R Southey, Charles W Whitfield and Gene E Robinson

    Citation: BMC Genomics 2006 7:233

    Content type: Research article

    Published on:

  45. Factor analysis (FA) has been widely applied in microarray studies as a data-reduction-tool without any a-priori assumption regarding associations between observed data and latent structure (Exploratory Factor...

    Authors: Anne PG Crijns, Frans Gerbens, A Edo D Plantinga, Gert Jan Meersma, Steven de Jong, Robert MW Hofstra, Elisabeth GE de Vries, Ate GJ van der Zee, Geertruida H de Bock and Gerard J te Meerman

    Citation: BMC Genomics 2006 7:232

    Content type: Methodology article

    Published on:

  46. Previous studies demonstrated breast cancer tumor tissue samples could be classified into different subtypes based upon DNA microarray profiles. The most recent study presented evidence for the existence of fi...

    Authors: Amy V Kapp, Stefanie S Jeffrey, Anita Langerød, Anne-Lise Børresen-Dale, Wonshik Han, Dong-Young Noh, Ida RK Bukholm, Monica Nicolau, Patrick O Brown and Robert Tibshirani

    Citation: BMC Genomics 2006 7:231

    Content type: Research article

    Published on:

    The Erratum to this article has been published in BMC Genomics 2007 8:101

  47. The stringent response is the initial reaction of microorganisms to nutritional stress. During stringent response the small nucleotides (p)ppGpp act as global regulators and reprogram bacterial transcription. ...

    Authors: Olaf Brockmann-Gretza and Jörn Kalinowski

    Citation: BMC Genomics 2006 7:230

    Content type: Research article

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  48. Many agricultural species and their pathogens have sequenced genomes and more are in progress. Agricultural species provide food, fiber, xenotransplant tissues, biopharmaceuticals and biomedical models. Moreov...

    Authors: Fiona M McCarthy, Nan Wang, G Bryce Magee, Bindu Nanduri, Mark L Lawrence, Evelyn B Camon, Daniel G Barrell, David P Hill, Mary E Dolan, W Paul Williams, Dawn S Luthe, Susan M Bridges and Shane C Burgess

    Citation: BMC Genomics 2006 7:229

    Content type: Database

    Published on:

  49. More than 12,000 simple sequence repeats (SSRs) have been identified in the genome of Burkholderia mallei ATCC 23344. As a demonstrated mechanism of phase variation in other pathogenic bacteria, these may functio...

    Authors: Claudia M Romero, David DeShazer, Tamara Feldblyum, Jacques Ravel, Donald Woods, H Stanley Kim, Yan Yu, Catherine M Ronning and William C Nierman

    Citation: BMC Genomics 2006 7:228

    Content type: Research article

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  50. The cattle UL16-binding protein 1 (ULBP1) and ULBP2 genes encode members of the MHC Class I superfamily that have homology to the human ULBP genes. Human ULBP1 and ULBP2 interact with the NKG2D receptor to activa...

    Authors: Joshua H Larson, Brandy M Marron, Jonathan E Beever, Bruce A Roe and Harris A Lewin

    Citation: BMC Genomics 2006 7:227

    Content type: Research article

    Published on:

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