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  1. The Gram-negative bacterium Photorhabdus asymbiotica (Pa) has been recovered from human infections in both North America and Australia. Recently, Pa has been shown to have a nematode vector that can also infect i...

    Authors: Paul Wilkinson, Nicholas R Waterfield, Lisa Crossman, Craig Corton, Maria Sanchez-Contreras, Isabella Vlisidou, Andrew Barron, Alexandra Bignell, Louise Clark, Douglas Ormond, Matthew Mayho, Nathalie Bason, Frances Smith, Mark Simmonds, Carol Churcher, David Harris…
    Citation: BMC Genomics 2009 10:302
  2. GLV-1h68 is an attenuated recombinant vaccinia virus (VACV) that selectively colonizes established human xenografts inducing their complete regression.

    Authors: Andrea Worschech, Nanhai Chen, Yong A Yu, Qian Zhang, Zoltan Pos, Stephanie Weibel, Viktoria Raab, Marianna Sabatino, Alessandro Monaco, Hui Liu, Vladia Monsurró, R Mark Buller, David F Stroncek, Ena Wang, Aladar A Szalay and Francesco M Marincola
    Citation: BMC Genomics 2009 10:301
  3. Affymetrix GeneChip® high-density oligonucleotide arrays are widely used in biological and medical research because of production reproducibility, which facilitates the comparison of results between experiment ru...

    Authors: Zhongxue Chen, Monnie McGee, Qingzhong Liu, Megan Kong, Youping Deng and Richard H Scheuermann
    Citation: BMC Genomics 2009 10(Suppl 1):S19

    This article is part of a Supplement: Volume 10 Supplement 1

  4. DNA repair genes provide an important contribution towards the surveillance and repair of DNA damage. These genes produce a large network of interacting proteins whose mRNA expression is likely to be regulated...

    Authors: Jens Lichtenberg, Edwin Jacox, Joshua D Welch, Kyle Kurz, Xiaoyu Liang, Mary Qu Yang, Frank Drews, Klaus Ecker, Stephen S Lee, Laura Elnitski and Lonnie R Welch
    Citation: BMC Genomics 2009 10(Suppl 1):S18

    This article is part of a Supplement: Volume 10 Supplement 1

  5. In this study, we formulate a computational reaction model following a chemical kinetic theory approach to predict the binding rate constant for the siRNA-RISC complex formation reaction. The model allowed us ...

    Authors: Preetam Ghosh, Robert Dullea, James E Fischer, Tom G Turi, Ronald W Sarver, Chaoyang Zhang, Kalyan Basu, Sajal K Das and Bradley W Poland
    Citation: BMC Genomics 2009 10(Suppl 1):S17

    This article is part of a Supplement: Volume 10 Supplement 1

  6. Human protein-protein interaction (PPIs) data are the foundation for understanding molecular signalling networks and the functional roles of biomolecules. Several human PPI databases have become available; how...

    Authors: Jake Yue Chen, SudhaRani Mamidipalli and Tianxiao Huan
    Citation: BMC Genomics 2009 10(Suppl 1):S16

    This article is part of a Supplement: Volume 10 Supplement 1

  7. Intrinsically disordered proteins lack stable structure under physiological conditions, yet carry out many crucial biological functions, especially functions associated with regulation, recognition, signaling ...

    Authors: Uros Midic, Christopher J Oldfield, A Keith Dunker, Zoran Obradovic and Vladimir N Uversky
    Citation: BMC Genomics 2009 10(Suppl 1):S12

    This article is part of a Supplement: Volume 10 Supplement 1

  8. The steadily increasing number of prokaryotic genomes has accelerated the study of genome evolution; in particular, the availability of sets of genomes from closely related bacteria has facilitated the explora...

    Authors: Jianying Gu, Jennifer Neary, Hong Cai, Audrey Moshfeghian, Stephen A Rodriguez, Timothy G Lilburn and Yufeng Wang
    Citation: BMC Genomics 2009 10(Suppl 1):S11

    This article is part of a Supplement: Volume 10 Supplement 1

  9. Multiple Sequence Alignment (MSA) has always been an active area of research in Bioinformatics. MSA is mainly focused on discovering biologically meaningful relationships among different sequences or proteins ...

    Authors: Javid Taheri and Albert Y Zomaya
    Citation: BMC Genomics 2009 10(Suppl 1):S10

    This article is part of a Supplement: Volume 10 Supplement 1

  10. One of the most challenging tasks in the post-genomic era is to reconstruct the transcriptional regulatory networks. The goal is to reveal, for each gene that responds to a certain biological event, which tran...

    Authors: Jianhua Ruan, Youping Deng, Edward J Perkins and Weixiong Zhang
    Citation: BMC Genomics 2009 10(Suppl 1):S8

    This article is part of a Supplement: Volume 10 Supplement 1

  11. Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) lack stable tertiary and/or secondary structure yet fulfills key biological functions. The recent recognition of IDPs and ID...

    Authors: Vladimir N Uversky, Christopher J Oldfield, Uros Midic, Hongbo Xie, Bin Xue, Slobodan Vucetic, Lilia M Iakoucheva, Zoran Obradovic and A Keith Dunker
    Citation: BMC Genomics 2009 10(Suppl 1):S7

    This article is part of a Supplement: Volume 10 Supplement 1

  12. Alternative transcript diversity manifests itself as a prime cause of complexity in higher eukaryotes. Recently, transcript diversity studies have suggested that 60–80% of human genes are alternatively spliced...

    Authors: Elsa Chacko and Shoba Ranganathan
    Citation: BMC Genomics 2009 10(Suppl 1):S5

    This article is part of a Supplement: Volume 10 Supplement 1

  13. Human genes undergo various patterns of pre-mRNA splicing across different tissues. Such variation is primarily regulated by trans-acting factors that bind on exonic and intronic cis-acting RNA elements (CAEs). H...

    Authors: Xin Wang, Kejun Wang, Milan Radovich, Yue Wang, Guohua Wang, Weixing Feng, Jeremy R Sanford and Yunlong Liu
    Citation: BMC Genomics 2009 10(Suppl 1):S4

    This article is part of a Supplement: Volume 10 Supplement 1

  14. Male mosquitoes do not feed on blood and are not involved in delivery of pathogens to humans. Consequently, they are seldom the subjects of research, which results in a very poor understanding of their biology...

    Authors: Elzbieta Krzywinska and Jaroslaw Krzywinski
    Citation: BMC Genomics 2009 10:300
  15. In-depth sequencing analysis has not been able to determine the overall complexity of transcriptional activity of a plant organ or tissue sample. In some cases, deep parallel sequencing of Expressed Sequence T...

    Authors: Julio C Vega-Arreguín, Enrique Ibarra-Laclette, Beatriz Jiménez-Moraila, Octavio Martínez, Jean Philippe Vielle-Calzada, Luis Herrera-Estrella and Alfredo Herrera-Estrella
    Citation: BMC Genomics 2009 10:299
  16. An animal model commonly used to investigate pathways and potential therapeutic interventions relevant to abdominal aortic aneurysm (AAA) involves subcutaneous infusion of angiotensin II within the apolipoprot...

    Authors: Catherine Rush, Moses Nyara, Joseph V Moxon, Alexandra Trollope, Bradford Cullen and Jonathan Golledge
    Citation: BMC Genomics 2009 10:298
  17. Identification of disease susceptible genes requires access to DNA from numerous well-characterised subjects. Archived residual dried blood spot samples from national newborn screening programs may provide DNA...

    Authors: Mads V Hollegaard, Jonas Grauholm, Anders Børglum, Mette Nyegaard, Bent Nørgaard-Pedersen, Torben Ørntoft, Preben B Mortensen, Carsten Wiuf, Ole Mors, Michael Didriksen, Poul Thorsen and David M Hougaard
    Citation: BMC Genomics 2009 10:297
  18. Serial analysis of gene expression (LongSAGE) was applied for gene expression profiling in seeds of oilseed rape (Brassica napus ssp. napus). The usefulness of this technique for detailed expression profiling in ...

    Authors: Christian Obermeier, Bashir Hosseini, Wolfgang Friedt and Rod Snowdon
    Citation: BMC Genomics 2009 10:295
  19. Parasitic angiosperm Orobanche crenata infection represents a major constraint for the cultivation of legumes worldwide. The level of protection achieved to date is either incomplete or ephemeral. Hence, an effic...

    Authors: Ma Ángeles Castillejo, Ana M Maldonado, Eliane Dumas-Gaudot, Mónica Fernández-Aparicio, Rafael Susín, Rubiales Diego and Jesús V Jorrín
    Citation: BMC Genomics 2009 10:294
  20. The Hessian fly (Mayetiola destructor) is an important insect pest of wheat. It has tractable genetics, polytene chromosomes, and a small genome (158 Mb). Investigation of the Hessian fly presents excellent oppor...

    Authors: Rajat Aggarwal, Thiago R Benatti, Navdeep Gill, Chaoyang Zhao, Ming-Shun Chen, John P Fellers, Brandon J Schemerhorn and Jeff J Stuart
    Citation: BMC Genomics 2009 10:293
  21. Gender appears to be determined by independent programs controlled by the sex-chromosomes and by androgen-dependent programming during embryonic development. To enable experimental dissection of these componen...

    Authors: Paul-Martin Holterhus, Jan-Hendrik Bebermeier, Ralf Werner, Janos Demeter, Annette Richter-Unruh, Gunnar Cario, Mahesh Appari, Reiner Siebert, Felix Riepe, James D Brooks and Olaf Hiort
    Citation: BMC Genomics 2009 10:292
  22. In recent years there has been an increasing problem with Staphylococcus aureus strains that are resistant to treatment with existing antibiotics. An important starting point for the development of new antimicrob...

    Authors: Roy R Chaudhuri, Andrew G Allen, Paul J Owen, Gil Shalom, Karl Stone, Marcus Harrison, Timothy A Burgis, Michael Lockyer, Jorge Garcia-Lara, Simon J Foster, Stephen J Pleasance, Sarah E Peters, Duncan J Maskell and Ian G Charles
    Citation: BMC Genomics 2009 10:291
  23. The family Euscorpiidae, which covers Europe, Asia, Africa, and America, is one of the most widely distributed scorpion groups. However, no studies have been conducted on the venom of a Euscorpiidae species ye...

    Authors: Yibao Ma, Ruiming Zhao, Yawen He, Songryong Li, Jun Liu, Yingliang Wu, Zhijian Cao and Wenxin Li
    Citation: BMC Genomics 2009 10:290
  24. Puccinia striiformis f. sp. tritici is a fungal pathogen causing stripe rust, one of the most important wheat diseases worldwide. The fungus is strictly biotrophic and thus, completely dependent on living host ce...

    Authors: Xiaojie Wang, Chunlei Tang, Gang Zhang, Yingchun Li, Chenfang Wang, Bo Liu, Zhipeng Qu, Jie Zhao, Qingmei Han, Lili Huang, Xianming Chen and Zhensheng Kang
    Citation: BMC Genomics 2009 10:289

    The Erratum to this article has been published in BMC Genomics 2013 14:671

  25. Large-scale identification of the interrelationships between different components of the cell, such as the interactions between proteins, has recently gained great interest. However, unraveling large-scale pro...

    Authors: Stefanie De Bodt, Sebastian Proost, Klaas Vandepoele, Pierre Rouzé and Yves Van de Peer
    Citation: BMC Genomics 2009 10:288
  26. Many approaches have been used to study the evolution, population structure and genetic diversity of Escherichia coli O157:H7; however, observations made with different genotyping systems are not easily relatable...

    Authors: Chad R Laing, Cody Buchanan, Eduardo N Taboada, Yongxiang Zhang, Mohamed A Karmali, James E Thomas and Victor PJ Gannon
    Citation: BMC Genomics 2009 10:287
  27. Lepidoptera represents more than 160,000 insect species which include some of the most devastating pests of crops, forests, and stored products. However, the genomic information on lepidopteran insects is very...

    Authors: Chitvan Khajuria, Yu Cheng Zhu, Ming-Shun Chen, Lawrent L Buschman, Randall A Higgins, Jianxiu Yao, Andre LB Crespo, Blair D Siegfried, Subbaratnam Muthukrishnan and Kun Yan Zhu
    Citation: BMC Genomics 2009 10:286
  28. Barley and particularly wheat are two grass species of immense agricultural importance. In spite of polyploidization events within the latter, studies have shown that genotypically and phenotypically these spe...

    Authors: Andreas W Schreiber, Tim Sutton, Rico A Caldo, Elena Kalashyan, Ben Lovell, Gwenda Mayo, Gary J Muehlbauer, Arnis Druka, Robbie Waugh, Roger P Wise, Peter Langridge and Ute Baumann
    Citation: BMC Genomics 2009 10:285
  29. Manduca sexta, Heliothis virescens, and Heliconius erato represent three widely-used insect model species for genomic and fundamental studies in Lepidoptera. Large-insert BAC libraries of these insects are critic...

    Authors: Chengcang Wu, Dina Proestou, Dorothy Carter, Erica Nicholson, Filippe Santos, Shaying Zhao, Hong-Bin Zhang and Marian R Goldsmith
    Citation: BMC Genomics 2009 10:283
  30. Sand fly saliva plays an important role in blood feeding and Leishmania transmission as it was shown to increase parasite virulence. On the other hand, immunity to salivary components impedes the establishment of...

    Authors: Jitka Hostomská, Věra Volfová, Jianbing Mu, Mark Garfield, Iva Rohoušová, Petr Volf, Jesus G Valenzuela and Ryan C Jochim
    Citation: BMC Genomics 2009 10:282
  31. The expression levels of many genes show wide natural variation among strains or populations. This study investigated the potential for animal strain-related genotypic differences to confound gene expression p...

    Authors: Katherine J Deans, Peter C Minneci, Hao Chen, Steven J Kern, Carolea Logun, Sara Alsaaty, Kelly J Norsworthy, Stephanie M Theel, Joel D Sennesh, Jennifer J Barb, Peter J Munson, Robert L Danner and Michael A Solomon
    Citation: BMC Genomics 2009 10:280
  32. Water stress during grain filling has a marked effect on grain yield, leading to a reduced endosperm cell number and thus sink capacity to accumulate dry matter. The bread wheat cultivar Chinese Spring (CS), a...

    Authors: Alessio Aprile, Anna M Mastrangelo, Anna M De Leonardis, Gabor Galiba, Enrica Roncaglia, Francesco Ferrari, Luigi De Bellis, Luana Turchi, Giovanni Giuliano and Luigi Cattivelli
    Citation: BMC Genomics 2009 10:279
  33. Advances in the high-throughput omic technologies have made it possible to profile cells in a large number of ways at the DNA, RNA, protein, chromosomal, functional, and pharmacological levels. A persistent pr...

    Authors: Uma T Shankavaram, Sudhir Varma, David Kane, Margot Sunshine, Krishna K Chary, William C Reinhold, Yves Pommier and John N Weinstein
    Citation: BMC Genomics 2009 10:277
  34. Meta-analysis of QTLs combines the results of several QTL detection studies and provides narrow confidence intervals for meta-QTLs, permitting easier positional candidate gene identification. It is usually app...

    Authors: Farkhanda S Khowaja, Gareth J Norton, Brigitte Courtois and Adam H Price
    Citation: BMC Genomics 2009 10:276
  35. Seven-transmembrane region-containing receptors (7TMRs) play central roles in eukaryotic signal transduction. Due to their biomedical importance, thorough mining of 7TMRs from diverse genomes has been an activ...

    Authors: Guoqing Lu, Zhifang Wang, Alan M Jones and Etsuko N Moriyama
    Citation: BMC Genomics 2009 10:275
  36. Microarray technology helped to accumulate an immense pool of data on gene expression changes in response to different environmental factors. Yet, computer- generated gene profiling using expressed sequence ta...

    Authors: Alexander M Boutanaev, Olga A Postnikova and Lev G Nemchinov
    Citation: BMC Genomics 2009 10:273
  37. Wheat is an allopolyploid plant that harbors a huge, complex genome. Therefore, accumulation of expressed sequence tags (ESTs) for wheat is becoming particularly important for functional genomics and molecular...

    Authors: Kanako Kawaura, Keiichi Mochida, Akiko Enju, Yasushi Totoki, Atsushi Toyoda, Yoshiyuki Sakaki, Chikatoshi Kai, Jun Kawai, Yoshihide Hayashizaki, Motoaki Seki, Kazuo Shinozaki and Yasunari Ogihara
    Citation: BMC Genomics 2009 10:271
  38. Plasmodium sporozoites migrate to the liver where they traverse several hepatocytes before invading the one inside which they will develop and multiply into thousands of merozoites. Although this constitutes an e...

    Authors: Sónia S Albuquerque, Céline Carret, Ana Rita Grosso, Alice S Tarun, Xinxia Peng, Stefan HI Kappe, Miguel Prudêncio and Maria M Mota
    Citation: BMC Genomics 2009 10:270
  39. Housekeeping genes (HKG) are constitutively expressed in all tissues while tissue-enriched genes (TEG) are expressed at a much higher level in a single tissue type than in others. HKGs serve as valuable experi...

    Authors: Xinwei She, Carol A Rohl, John C Castle, Amit V Kulkarni, Jason M Johnson and Ronghua Chen
    Citation: BMC Genomics 2009 10:269
  40. Metagenomic sequence data are proving to be a vast resource for the discovery of biological components. Yet analysis of this data to identify functional RNAs lags behind efforts to characterize protein diversi...

    Authors: Michelle M Meyer, Tyler D Ames, Daniel P Smith, Zasha Weinberg, Michael S Schwalbach, Stephen J Giovannoni and Ronald R Breaker
    Citation: BMC Genomics 2009 10:268
  41. Filarial nematode parasites cause serious diseases such as elephantiasis and river blindness in humans, and heartworm infections in dogs. Third stage filarial larvae (L3) are a critical stage in the life cycle...

    Authors: Ben-Wen Li, Amy C Rush, Makedonka Mitreva, Yong Yin, David Spiro, Elodie Ghedin and Gary J Weil
    Citation: BMC Genomics 2009 10:267
  42. The deleterious effect of a mutation can be reverted by a second-site interacting residue. This is an epistatic compensatory process explaining why mutations that are deleterious in some species are tolerated ...

    Authors: Luísa Azevedo, João Carneiro, Barbara van Asch, Ana Moleirinho, Filipe Pereira and António Amorim
    Citation: BMC Genomics 2009 10:266
  43. Transcriptome sequencing using next-generation sequencing platforms will soon be competing with DNA microarray technologies for global gene expression analysis. As a preliminary evaluation of these promising t...

    Authors: Shrinivasrao P Mane, Clive Evans, Kristal L Cooper, Oswald R Crasta, Otto Folkerts, Stephen K Hutchison, Timothy T Harkins, Danielle Thierry-Mieg, Jean Thierry-Mieg and Roderick V Jensen
    Citation: BMC Genomics 2009 10:264

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