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  1. Differential gene expression specifies the highly diverse cell types that constitute the nervous system. With its sequenced genome and simple, well-defined neuroanatomy, the nematode C. elegans is a useful model ...

    Authors: Rebecca M Fox, Stephen E Von Stetina, Susan J Barlow, Christian Shaffer, Kellen L Olszewski, Jason H Moore, Denis Dupuy, Marc Vidal and David M Miller III

    Citation: BMC Genomics 2005 6:42

    Content type: Methodology article

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  2. A chicken egg contains several biotin-binding proteins (BBPs), whose complete DNA and amino acid sequences are not known. In order to identify and characterise these genes and proteins we studied chicken cDNAs...

    Authors: Einari A Niskanen, Vesa P Hytönen, Alessandro Grapputo, Henri R Nordlund, Markku S Kulomaa and Olli H Laitinen

    Citation: BMC Genomics 2005 6:41

    Content type: Research article

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  3. The retina is a well-defined portion of the central nervous system (CNS) that has been used as a model for CNS development and function studies. The full specification of transcripts in an individual tissue or...

    Authors: Samuel Shao-Min Zhang, Xuming Xu, Jinming Li, Mu-Gen Liu, Hongyu Zhao, M Bento Soares, Colin J Barnstable and Xin-Yuan Fu

    Citation: BMC Genomics 2005 6:40

    Content type: Research article

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  4. In Micrococcus luteus growth and resuscitation from starvation-induced dormancy is controlled by the production of a secreted growth factor. This autocrine r esuscitation-p romoting f actor (Rpf) is the founder m...

    Authors: Adriana Ravagnani, Christopher L Finan and Michael Young

    Citation: BMC Genomics 2005 6:39

    Content type: Research article

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  5. Germline mutations or large-scale deletions in the coding region and splice sites of STK11/LKB1 do not account for all cases of Peutz-Jeghers syndrome (PJS). It is conceivable that, on the basis of data from othe...

    Authors: Nicholas CM Hearle, Ian Tomlinson, Wendy Lim, Victoria Murday, Edwin Swarbrick, Guan Lim, Robin Phillips, Peter Lee, John O'Donohue, Richard C Trembath, Patrick J Morrison, Andrew Norman, Rohan Taylor, Shirley Hodgson, Anneke Lucassen and Richard S Houlston

    Citation: BMC Genomics 2005 6:38

    Content type: Research article

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  6. Estrogens are known to regulate the proliferation of breast cancer cells and to modify their phenotypic properties. Identification of estrogen-regulated genes in human breast tumors is an essential step toward...

    Authors: Martín C Abba, Yuhui Hu, Hongxia Sun, Jeffrey A Drake, Sally Gaddis, Keith Baggerly, Aysegul Sahin and C Marcelo Aldaz

    Citation: BMC Genomics 2005 6:37

    Content type: Research article

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  7. High-throughput genotyping of single nucleotide polymorphisms (SNPs) generates large amounts of data. In many SNP genotyping assays, the genotype assignment is based on scatter plots of signals corresponding t...

    Authors: Lovisa Lovmar, Annika Ahlford, Mats Jonsson and Ann-Christine Syvänen

    Citation: BMC Genomics 2005 6:35

    Content type: Methodology article

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  8. The Marine Genomics project is a functional genomics initiative developed to provide a pipeline for the curation of Expressed Sequence Tags (ESTs) and gene expression microarray data for marine organisms. It p...

    Authors: David J McKillen, Yian A Chen, Chuming Chen, Matthew J Jenny, Harold F Trent III, Javier Robalino, David C McLean Jr, Paul S Gross, Robert W Chapman, Gregory W Warr and Jonas S Almeida

    Citation: BMC Genomics 2005 6:34

    Content type: Database

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  9. Malaria caused by protozoan parasites of the genus Plasmodium spp. is a major health burden in tropical countries. The development of new control tools, including vaccines and drugs, is urgently needed. The avail...

    Authors: Achim G Schneider and Odile Mercereau-Puijalon

    Citation: BMC Genomics 2005 6:30

    Content type: Research article

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  10. We generated the gene expression profile of the total testis from the adult C57BL/6J male mice using serial analysis of gene expression (SAGE). Two high-quality SAGE libraries containing a total of 76 854 tags...

    Authors: Petr Divina, Čestmír Vlček, Petr Strnad, Václav Pačes and Jiří Forejt

    Citation: BMC Genomics 2005 6:29

    Content type: Research article

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  11. Formins are multidomain proteins defined by a conserved FH2 (formin homology 2) domain with actin nucleation activity preceded by a proline-rich FH1 (formin homology 1) domain. Formins act as profilin-modulate...

    Authors: Francisco Rivero, Tetsuya Muramoto, Ann-Kathrin Meyer, Hideko Urushihara, Taro QP Uyeda and Chikako Kitayama

    Citation: BMC Genomics 2005 6:28

    Content type: Research article

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  12. Small quantities of RNA (1–4 μg total RNA) available from biological samples frequently require a single round of amplification prior to analysis, but current amplification strategies have limitations that may...

    Authors: Nicholas F Marko, Bryan Frank, John Quackenbush and Norman H Lee

    Citation: BMC Genomics 2005 6:27

    Content type: Methodology article

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  13. Core promoters are the gene regulatory regions most proximal to the transcription start site (TSS), central to the formation of pre-initiation complexes and for combinatorial gene regulation. The DNA elements ...

    Authors: Carlos Molina and Erich Grotewold

    Citation: BMC Genomics 2005 6:25

    Content type: Research article

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  14. Promoters are key players in gene regulation. They receive signals from various sources (e.g. cell surface receptors) and control the level of transcription initiation, which largely determines gene expression...

    Authors: Christoph Dieterich, Steffen Grossmann, Andrea Tanzer, Stefan Röpcke, Peter F Arndt, Peter F Stadler and Martin Vingron

    Citation: BMC Genomics 2005 6:24

    Content type: Database

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  15. Earlier comparative maps between the genomes of rice (Oryza sativa L.), barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.) were linkage maps based on cDNA-RFLP markers. The low number of polymorphic RFL...

    Authors: Mauricio La Rota, Ramesh V Kantety, Ju-Kyung Yu and Mark E Sorrells

    Citation: BMC Genomics 2005 6:23

    Content type: Research article

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  16. Clusters or runs of purines on the mRNA synonymous strand have been found in many different organisms including orthopoxviruses. The purine bias that is exhibited by these clusters can be observed using a puri...

    Authors: Melissa Da Silva and Chris Upton

    Citation: BMC Genomics 2005 6:22

    Content type: Research article

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  17. Prediction of structure and function for uncharacterized protein families by identification of evolutionary links to characterized families and known structures is one of the cornerstones of genomics. Theoreti...

    Authors: Marcin Feder and Janusz M Bujnicki

    Citation: BMC Genomics 2005 6:21

    Content type: Research article

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  18. Small G proteins, which are essential regulators of multiple cellular functions, are activated by guanine nucleotide exchange factors (GEFs) that stimulate the exchange of the tightly bound GDP nucleotide by G...

    Authors: Barbara Mouratou, Valerie Biou, Alexandra Joubert, Jean Cohen, David J Shields, Niko Geldner, Gerd Jürgens, Paul Melançon and Jacqueline Cherfils

    Citation: BMC Genomics 2005 6:20

    Content type: Research article

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  19. The metabolism of bacterial peptidoglycan is a dynamic process, synthases and cleavage enzymes are functionally coordinated. Lytic Transglycosylase enzymes (LT) are part of multienzyme complexes which regulate...

    Authors: Estelle Pagliero, Otto Dideberg, Thierry Vernet and Anne Marie Di Guilmi

    Citation: BMC Genomics 2005 6:19

    Content type: Research article

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  20. Over 4 million single nucleotide polymorphisms (SNPs) are currently reported to exist within the human genome. Only a small fraction of these SNPs alter gene function or expression, and therefore might be asso...

    Authors: Salim Mottagui-Tabar, Mohammad A Faghihi, Yosuke Mizuno, Pär G Engström, Boris Lenhard, Wyeth W Wasserman and Claes Wahlestedt

    Citation: BMC Genomics 2005 6:18

    Content type: Research article

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  21. Various analytical methods exist that first quantify gene expression and then analyze differentially expressed genes from Affymetrix GeneChip® gene expression analysis array data. These methods differ in the choi...

    Authors: Wenhong Fan, Joel I Pritchard, James M Olson, Najma Khalid and Lue Ping Zhao

    Citation: BMC Genomics 2005 6:16

    Content type: Research article

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  22. In human carcinomas, overexpression of cortactin correlates with poor prognosis. Cortactin is an F-actin-binding protein involved in cytoskeletal rearrangements and cell migration by promoting actin-related pr...

    Authors: Agnes GSH van Rossum, Ellen Schuuring-Scholtes, Vera van Buuren-van Seggelen, Philip M Kluin and Ed Schuuring

    Citation: BMC Genomics 2005 6:15

    Content type: Research article

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  23. The enormous amount of genome sequence data asks for user-oriented databases to manage sequences and annotations. Queries must include search tools permitting function identification through exploration of rel...

    Authors: Gang Fang, Christine Ho, Yaowu Qiu, Virginie Cubas, Zhou Yu, Cédric Cabau, Frankie Cheung, Ivan Moszer and Antoine Danchin

    Citation: BMC Genomics 2005 6:14

    Content type: Database

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  24. The application of microarray technology to functional genomic analysis in the chicken has been limited by the lack of arrays containing large numbers of genes.

    Authors: Joan Burnside, Paul Neiman, Jianshan Tang, Ryan Basom, Richard Talbot, Mark Aronszajn, David Burt and Jeff Delrow

    Citation: BMC Genomics 2005 6:13

    Content type: Methodology article

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  25. The ChickRH6 whole chicken genome radiation hybrid (RH) panel recently produced has already been used to build radiation hybrid maps for several chromosomes, generating comparative maps with the human and mous...

    Authors: Sophie Leroux, Mélanie Dottax, Suzanne Bardes, Florence Vignoles, Katia Fève, Frédérique Pitel, Mireille Morisson and Alain Vignal

    Citation: BMC Genomics 2005 6:12

    Content type: Research article

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  26. Hematopoiesis is a complex developmental process controlled by a large number of factors that regulate stem cell renewal, lineage commitment and differentiation. Secreted proteins, including the hematopoietic ...

    Authors: Demet Nalbant, Hyewon Youn, S Isil Nalbant, Savitha Sharma, Everardo Cobos, Elmus G Beale, Yang Du and Simon C Williams

    Citation: BMC Genomics 2005 6:11

    Content type: Research article

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  27. Horizontal gene transfer is central to evolution in most bacterial species. The detection of exchanged regions is often based upon analysis of compositional characteristics and their comparison to the organism...

    Authors: Nigel J Saunders, Prawit Boonmee, John F Peden and Stephen A Jarvis

    Citation: BMC Genomics 2005 6:9

    Content type: Research article

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  28. In Aedes and Anopheles mosquitoes, ribosomal protein RPS6 has an unusual C-terminal extension that resembles histone H1 proteins. To explore homology between a mosquito H1 histone and the RPS6 tail, we took advan...

    Authors: Yongjiao Zhai and Ann M Fallon

    Citation: BMC Genomics 2005 6:8

    Content type: Research article

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  29. During excessive pressure or volume overload, cardiac cells are subjected to increased mechanical stress (MS). We set out to investigate how the stress response of cardiac cells to MS can be compared to genoto...

    Authors: Marjan Boerma, Caroline GC van der Wees, Harry Vrieling, J Peter Svensson, Jan Wondergem, Arnoud van der Laarse, Leon HF Mullenders and Albert A van Zeeland

    Citation: BMC Genomics 2005 6:6

    Content type: Research article

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  30. Blood feeding, or hematophagy, is a behavior exhibited by female mosquitoes required both for reproduction and for transmission of pathogens. We determined the expression patterns of 3,068 ESTs, representing ~...

    Authors: Ali N Dana, Young S Hong, Marcia K Kern, Maureen E Hillenmeyer, Brent W Harker, Neil F Lobo, James R Hogan, Patricia Romans and Frank H Collins

    Citation: BMC Genomics 2005 6:5

    Content type: Research article

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  31. The pregnancy-specific glycoprotein (Psg) genes encode proteins of unknown function, and are members of the carcinoembryonic antigen (Cea) gene family, which is a member of the immunoglobulin gene (Ig) superfamil...

    Authors: Andrew S McLellan, Beate Fischer, Gabriela Dveksler, Tomomi Hori, Freda Wynne, Melanie Ball, Katsuzumi Okumura, Tom Moore and Wolfgang Zimmermann

    Citation: BMC Genomics 2005 6:4

    Content type: Research article

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  32. Microarray technologies are rapidly becoming available for new species including teleost fishes. We constructed a rainbow trout cDNA microarray targeted at the identification of genes which are differentially ...

    Authors: Aleksei Krasnov, Heikki Koskinen, Petri Pehkonen, Caird E Rexroad III, Sergey Afanasyev and Hannu Mölsä

    Citation: BMC Genomics 2005 6:3

    Content type: Research article

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  33. Basic manufacturing principles are becoming increasingly important in high-throughput sequencing facilities where there is a constant drive to increase quality, increase efficiency, and decrease operating cost...

    Authors: George S Yang, Jeffery M Stott, Duane Smailus, Sarah A Barber, Miruna Balasundaram, Marco A Marra and Robert A Holt

    Citation: BMC Genomics 2005 6:2

    Content type: Research article

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  34. AlkB-like proteins are members of the 2-oxoglutarate- and Fe(II)-dependent oxygenase superfamily. In Escherichia coli the protein protects RNA and DNA against damage from methylating agents. 1-methyladenine and 3...

    Authors: Marit S Bratlie and Finn Drabløs

    Citation: BMC Genomics 2005 6:1

    Content type: Research article

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  35. Evolutionarily conserved sequences within or adjoining orthologous genes often serve as critical cis-regulatory regions. Recent studies have identified long, non-coding genomic regions that are perfectly conserve...

    Authors: Albin Sandelin, Peter Bailey, Sara Bruce, Pär G Engström, Joanna M Klos, Wyeth W Wasserman, Johan Ericson and Boris Lenhard

    Citation: BMC Genomics 2004 5:99

    Content type: Research article

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  36. The understanding of whole genome sequences in higher eukaryotes depends to a large degree on the reliable definition of transcription units including exon/intron structures, translated open reading frames (OR...

    Authors: 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 and Jean-Marie Buerstedde

    Citation: BMC Genomics 2004 5:98

    Content type: Research article

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  37. A significant portion (about 8% in the human genome) of mammalian mRNA sequences contains AU (Adenine and Uracil) rich elements or AREs at their 3' untranslated regions (UTR). These mRNA sequences are usually ...

    Authors: Hyeong Jun An, Doheon Lee, Kwang Hyung Lee and Jonghwa Bhak

    Citation: BMC Genomics 2004 5:97

    Content type: Research article

    Published on:

  38. While studies of non-model organisms are critical for many research areas, such as evolution, development, and environmental biology, they present particular challenges for both experimental and computational ...

    Authors: Justin E Paschall, Marjorie F Oleksiak, Jeffrey D VanWye, Jennifer L Roach, J Andrew Whitehead, Gerald J Wyckoff, Kevin J Kolell and Douglas L Crawford

    Citation: BMC Genomics 2004 5:96

    Content type: Research article

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  39. DNA homopolymer tracts, poly(dA).poly(dT) and poly(dG).poly(dC), are the simplest of simple sequence repeats. Homopolymer tracts have been systematically examined in the coding, intron and flanking regions of ...

    Authors: Yue Zhou, Jeffrey W Bizzaro and Kenneth A Marx

    Citation: BMC Genomics 2004 5:95

    Content type: Research article

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  40. The GOLD.db (Genomics of Lipid-Associated Disorders Database) was developed to address the need for integrating disparate information on the function and properties of genes and their products that are particu...

    Authors: Hubert Hackl, Michael Maurer, Bernhard Mlecnik, Jürgen Hartler, Gernot Stocker, Diego Miranda-Saavedra and Zlatko Trajanoski

    Citation: BMC Genomics 2004 5:93

    Content type: Database

    Published on:

  41. Defensins are important components of innate immunity to combat bacterial and viral infections, and can even elicit antitumor responses. Clusters of defensin (DEF) genes are located in a 2 Mb range of the huma...

    Authors: 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 and Matthias Platzer

    Citation: BMC Genomics 2004 5:92

    Content type: Research article

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