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Prokaryote microbial genomics

This section covers the structure and function of the genomes of prokaryotic and archaea microorganisms.

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  1. Despite being one of the most intensely studied model organisms, many questions still remain about the evolutionary biology and ecology of Escherichia coli. An important step toward achieving a more complete unde...

    Authors: Eric J de Muinck, Karin Lagesen, Jan Egil Afset, Xavier Didelot, Kjersti S Rønningen, Knut Rudi, Nils Chr Stenseth and Pål Trosvik

    Citation: BMC Genomics 2013 14:81

    Content type: Research article

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  2. Buchnera aphidicola is an obligate symbiotic bacterium, associated with most of the aphididae, whose genome has drastically shrunk during intracellular evolution. Gene regulation in Buchnera has been a matter of ...

    Authors: Lilia Brinza, Federica Calevro and Hubert Charles

    Citation: BMC Genomics 2013 14:73

    Content type: Research article

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  3. Pseudomonas fluorescens F113 is a plant growth-promoting rhizobacterium (PGPR) isolated from the sugar-beet rhizosphere. This bacterium has been extensively studied as a model strain for genetic regulation of sec...

    Authors: Miguel Redondo-Nieto, Matthieu Barret, John Morrissey, Kieran Germaine, Francisco Martínez-Granero, Emma Barahona, Ana Navazo, María Sánchez-Contreras, Jennifer A Moynihan, Candela Muriel, David Dowling, Fergal O’Gara, Marta Martín and Rafael Rivilla

    Citation: BMC Genomics 2013 14:54

    Content type: Research article

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  4. Both large deletions in genome and heat shock stress would lead to alterations in the gene expression profile; however, whether there is any potential linkage between these disturbances to the transcriptome ha...

    Authors: Bei-Wen Ying, Shigeto Seno, Fuyuro Kaneko, Hideo Matsuda and Tetsuya Yomo

    Citation: BMC Genomics 2013 14:25

    Content type: Research article

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  5. The endosymbiont Wolbachia pipientis causes diverse and sometimes dramatic phenotypes in its invertebrate hosts. Four Wolbachia strains sequenced to date indicate that the constitution of the genome is dynamic, b...

    Authors: Anne Duplouy, Iñaki Iturbe-Ormaetxe, Scott A Beatson, Jan M Szubert, Jeremy C Brownlie, Conor J McMeniman, Elizabeth A McGraw, Gregory D D Hurst, Sylvain Charlat, Scott L O’Neill and Megan Woolfit

    Citation: BMC Genomics 2013 14:20

    Content type: Research article

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  6. Actinobacteria form a major bacterial phylum that includes numerous human pathogens. Actinobacteria are primary contributors to carbon cycling and also represent a primary source of industrial high value produ...

    Authors: Esteban Marcellin, Tim R Mercer, Cuauhtemoc Licona-Cassani, Robin W Palfreyman, Marcel E Dinger, Jennifer A Steen, John S Mattick and Lars K Nielsen

    Citation: BMC Genomics 2013 14:15

    Content type: Research article

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  7. Sequencing technologies have different biases, in single-genome sequencing and metagenomic sequencing; these can significantly affect ORFs recovery and the population distribution of a metagenome. In this pape...

    Authors: Fabio Gori, Susannah G Tringe, Gianluigi Folino, Sacha AFT van Hijum, Huub JM Op den Camp, Mike SM Jetten and Elena Marchiori

    Citation: BMC Genomics 2013 14:7

    Content type: Research article

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  8. Rhizobium tropici CIAT 899 and Rhizobium sp. PRF 81 are α-Proteobacteria that establish nitrogen-fixing symbioses with a range of legume hosts. These strains are broadly used in commercial inoculants for applicat...

    Authors: Ernesto Ormeño-Orrillo, Pâmela Menna, Luiz Gonzaga P Almeida, Francisco Javier Ollero, Marisa Fabiana Nicolás, Elisete Pains Rodrigues, Andre Shigueyoshi Nakatani, Jesiane Stefânia Silva Batista, Ligia Maria Oliveira Chueire, Rangel Celso Souza, Ana Tereza Ribeiro Vasconcelos, Manuel Megías, Mariangela Hungria and Esperanza Martínez-Romero

    Citation: BMC Genomics 2012 13:735

    Content type: Research article

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  9. Thermacetogenium phaeum is a thermophilic strictly anaerobic bacterium oxidizing acetate to CO2 in syntrophic association with a methanogenic partner. It can also grow in pure culture, e.g., by fermentation of me...

    Authors: Dirk Oehler, Anja Poehlein, Andreas Leimbach, Nicolai Müller, Rolf Daniel, Gerhard Gottschalk and Bernhard Schink

    Citation: BMC Genomics 2012 13:723

    Content type: Research article

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  10. One of the main goals of genomic analysis is to elucidate the comprehensive functions (functionome) in individual organisms or a whole community in various environments. However, a standard evaluation method f...

    Authors: Hideto Takami, Takeaki Taniguchi, Yuki Moriya, Tomomi Kuwahara, Minoru Kanehisa and Susumu Goto

    Citation: BMC Genomics 2012 13:699

    Content type: Methodology article

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  11. Broad-spectrum fluoroquinolone antibiotics are central in modern health care and are used to treat and prevent a wide range of bacterial infections. The recently discovered qnr genes provide a mechanism of resist...

    Authors: Fredrik Boulund, Anna Johnning, Mariana Buongermino Pereira, DG Joakim Larsson and Erik Kristiansson

    Citation: BMC Genomics 2012 13:695

    Content type: Methodology article

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  12. The bacterium Pelobacter carbinolicus is able to grow by fermentation, syntrophic hydrogen/formate transfer, or electron transfer to sulfur from short-chain alcohols, hydrogen or formate; it does not oxidize acet...

    Authors: Muktak Aklujkar, Shelley A Haveman, Raymond DiDonato Jr, Olga Chertkov, Cliff S Han, Miriam L Land, Peter Brown and Derek R Lovley

    Citation: BMC Genomics 2012 13:690

    Content type: Research article

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  13. The increasing number of infections caused by strains of Klebsiella pneumoniae that are resistant to multiple antibiotics has developed into a major medical problem worldwide. The development of next-generation s...

    Authors: Joo-Hyun Seo, Jay Sung-Joong Hong, Donghyuk Kim, Byung-Kwan Cho, Tzu-Wen Huang, Shih-Feng Tsai, Bernhard O Palsson and Pep Charusanti

    Citation: BMC Genomics 2012 13:679

    Content type: Research article

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  14. Evolution equipped Bdellovibrio bacteriovorus predatory bacteria to invade other bacteria, digesting and replicating, sealed within them thus preventing nutrient-sharing with organisms in the surrounding environm...

    Authors: Laura Hobley, Thomas R Lerner, Laura E Williams, Carey Lambert, Rob Till, David S Milner, Sarah M Basford, Michael J Capeness, Andrew K Fenton, Robert J Atterbury, Maximilian ATS Harris and R Elizabeth Sockett

    Citation: BMC Genomics 2012 13:670

    Content type: Research article

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  15. The Gram-negative bacterium Chlamydia pneumoniae (Cpn) is the leading intracellular human pathogen responsible for respiratory infections such as pneumonia and bronchitis. Basic and applied research in pathogen b...

    Authors: Christina J Maier, Richard H Maier, Dezso Peter Virok, Matthias Maass, Helmut Hintner, Johann W Bauer and Kamil Önder

    Citation: BMC Genomics 2012 13:632

    Content type: Research article

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  16. Pantoea spp. are frequently isolated from a wide range of ecological niches and have various biological roles, as plant epi- or endophytes, biocontrol agents, plant-growth promoters or as pathogens of both plant ...

    Authors: Pieter De Maayer, Wai-Yin Chan, Jochen Blom, Stephanus N Venter, Brion Duffy, Theo H M Smits and Teresa A Coutinho

    Citation: BMC Genomics 2012 13:625

    Content type: Research article

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  17. Cyanobacteria can form massive toxic blooms in fresh and brackish bodies of water and are frequently responsible for the poisoning of animals and pose a health risk for humans. Anabaena is a genus of filamentous ...

    Authors: Hao Wang, Kaarina Sivonen, Leo Rouhiainen, David P Fewer, Christina Lyra, Anne Rantala-Ylinen, Johanna Vestola, Jouni Jokela, Kaisa Rantasärkkä, Zhijie Li and Bin Liu

    Citation: BMC Genomics 2012 13:613

    Content type: Research article

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  18. Francisella is a genus of gram-negative bacterium highly virulent in fishes and human where F. tularensis is causing the serious disease tularaemia in human. Recently Francisella species have been reported to cau...

    Authors: Settu Sridhar, Animesh Sharma, Heidi Kongshaug, Frank Nilsen and Inge Jonassen

    Citation: BMC Genomics 2012 13:598

    Content type: Research article

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  19. Porphyromonas gingivalis is a Gram-negative anaerobic bacterium associated with periodontal disease onset and progression. Genetic tools for the manipulation of bacterial genomes allow for in-depth mechanistic st...

    Authors: Brian A Klein, Elizabeth L Tenorio, David W Lazinski, Andrew Camilli, Margaret J Duncan and Linden T Hu

    Citation: BMC Genomics 2012 13:578

    Content type: Research article

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  20. Synthetic biology allows the development of new biochemical pathways for the production of chemicals from renewable sources. One major challenge is the identification of suitable microorganisms to hold these p...

    Authors: Lucas P Parizzi, Maria Carolina B Grassi, Luige A Llerena, Marcelo F Carazzolle, Verônica L Queiroz, Inês Lunardi, Ane F Zeidler, Paulo JPL Teixeira, Piotr Mieczkowski, Johana Rincones and Gonçalo AG Pereira

    Citation: BMC Genomics 2012 13:562

    Content type: Research article

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  21. Small non-coding RNAs (sRNAs) have attracted attention as a new class of gene regulators in both eukaryotes and bacteria. Genome-wide screening methods have been successfully applied in Gram-negative bacteria ...

    Authors: Nadja Patenge, André Billion, Peter Raasch, Jana Normann, Aleksandra Wisniewska-Kucper, Julia Retey, Valesca Boisguérin, Thomas Hartsch, Torsten Hain and Bernd Kreikemeyer

    Citation: BMC Genomics 2012 13:550

    Content type: Research article

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  22. The classical Bordetella subspecies are phylogenetically closely related, yet differ in some of the most interesting and important characteristics of pathogens, such as host range, virulence and persistence. The ...

    Authors: Jihye Park, Ying Zhang, Anne M Buboltz, Xuqing Zhang, Stephan C Schuster, Umesh Ahuja, Minghsun Liu, Jeff F Miller, Mohammed Sebaihia, Stephen D Bentley, Julian Parkhill and Eric T Harvill

    Citation: BMC Genomics 2012 13:545

    Content type: Research article

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  23. The bacterium Caulobacter crescentus is a popular model for the study of cell cycle regulation and senescence. The large prolate siphophage phiCbK has been an important tool in C. crescentus biology, and has been...

    Authors: Jason J Gill, Joel D Berry, William K Russell, Lauren Lessor, Diego A Escobar-Garcia, Daniel Hernandez, Ashley Kane, Jennifer Keene, Matthew Maddox, Rebecca Martin, Sheba Mohan, Ashlyn M Thorn, David H Russell and Ry Young

    Citation: BMC Genomics 2012 13:542

    Content type: Research article

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  24. Bacteria of the genus Arthrobacter are ubiquitous in soil environments and can be considered as true survivalists. Arthrobacter sp. strain Rue61a is an isolate from sewage sludge able to utilize quinaldine (2-met...

    Authors: Heiko Niewerth, Jörg Schuldes, Katja Parschat, Patrick Kiefer, Julia A Vorholt, Rolf Daniel and Susanne Fetzner

    Citation: BMC Genomics 2012 13:534

    Content type: Research article

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  25. The broad ecological distribution of L. casei makes it an insightful subject for research on genome evolution and lifestyle adaptation. To explore evolutionary mechanisms that determine genomic diversity of L. ca...

    Authors: Jeff R Broadbent, Eric C Neeno-Eckwall, Buffy Stahl, Kanokwan Tandee, Hui Cai, Wesley Morovic, Philippe Horvath, Jessie Heidenreich, Nicole T Perna, Rodolphe Barrangou and James L Steele

    Citation: BMC Genomics 2012 13:533

    Content type: Research article

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  26. Staphylococcus aureus Repeat (STAR) elements are a type of interspersed intergenic direct repeat. In this study the conservation and variation in these elements was explored by bioinformatic analyses of published...

    Authors: Joanne Purves, Matthew Blades, Yasrab Arafat, Salman A Malik, Christopher D Bayliss and Julie A Morrissey

    Citation: BMC Genomics 2012 13:515

    Content type: Research article

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  27. In Gram-negative bacteria, the outer membrane is composed of an asymmetric lipid bilayer of phopspholipids and lipopolysaccharides, and the transmembrane proteins that reside in this membrane are almost exclus...

    Authors: Nagarajan Paramasivam, Michael Habeck and Dirk Linke

    Citation: BMC Genomics 2012 13:510

    Content type: Research article

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  28. Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is a significant bacterial pathogen that poses considerable clinical and public health challenges. The majority of the CA-MRSA disease...

    Authors: Ryan Tewhey, Christopher R Cannavino, John AD Leake, Vikas Bansal, Eric J Topol, Ali Torkamani, John S Bradley and Nicholas J Schork

    Citation: BMC Genomics 2012 13:508

    Content type: Research article

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  29. Silicon plays important biological roles, but the mechanisms of cellular responses to silicon are poorly understood. We report the first analysis of cell cycle arrest and recovery from silicon starvation in th...

    Authors: Roshan Prakash Shrestha, Benoit Tesson, Trina Norden-Krichmar, Stephen Federowicz, Mark Hildebrand and Andrew E Allen

    Citation: BMC Genomics 2012 13:499

    Content type: Research article

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  30. Extensive genetic diversity in viral populations within infected hosts and the divergence of variants from existing reference genomes impede the analysis of deep viral sequencing data. A de novo population consen...

    Authors: Xiao Yang, Patrick Charlebois, Sante Gnerre, Matthew G Coole, Niall J Lennon, Joshua Z Levin, James Qu, Elizabeth M Ryan, Michael C Zody and Matthew R Henn

    Citation: BMC Genomics 2012 13:475

    Content type: Methodology article

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  31. A new strain of Geobacter sulfurreducens, strain KN400, produces more electrical current in microbial fuel cells and reduces insoluble Fe(III) oxides much faster than the wildtype strain, PCA. The genome of KN400...

    Authors: Jessica E Butler, Nelson D Young, Muktak Aklujkar and Derek R Lovley

    Citation: BMC Genomics 2012 13:471

    Content type: Research article

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  32. Yersinia enterocolitica is a gastrointestinal foodborne pathogen found worldwide and which especially affects infants and young children. While different bioserotypes have been associated with varying pathogenici...

    Authors: Debora Garzetti, Hicham Bouabe, Juergen Heesemann and Alexander Rakin

    Citation: BMC Genomics 2012 13:467

    Content type: Research article

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  33. Animals co-evolve with their gut microbiota; the latter can perform complex metabolic reactions that cannot be done independently by the host. Although the importance of gut microbiota has been well demonstrat...

    Authors: Hsiao-Pei Lu, Yu-bin Wang, Shiao-Wei Huang, Chung-Yen Lin, Martin Wu, Chih-hao Hsieh and Hon-Tsen Yu

    Citation: BMC Genomics 2012 13:466

    Content type: Research article

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  34. The genus Saccharothrix is a representative of the family Pseudonocardiaceae, known to include producer strains of a wide variety of potent antibiotics. Saccharothrix espanaensis produces both saccharomicins A an...

    Authors: Tina Strobel, Arwa Al-Dilaimi, Jochen Blom, Arne Gessner, Jörn Kalinowski, Marta Luzhetska, Alfred Pühler, Rafael Szczepanowski, Andreas Bechthold and Christian Rückert

    Citation: BMC Genomics 2012 13:465

    Content type: Research article

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  35. The anaerobic spirochaete Brachyspira pilosicoli causes enteric disease in avian, porcine and human hosts, amongst others. To date, the only available genome sequence of B. pilosicoli is that of strain 95/1000, a...

    Authors: Luke J Mappley, Michael L Black, Manal AbuOun, Alistair C Darby, Martin J Woodward, Julian Parkhill, A Keith Turner, Matthew I Bellgard, Tom La, Nyree D Phillips, Roberto M La Ragione and David J Hampson

    Citation: BMC Genomics 2012 13:454

    Content type: Research article

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  36. A large number of genome-scale metabolic networks is now available for many organisms, mostly bacteria. Previous works on minimal gene sets, when analysing host-dependent bacteria, found small common sets of m...

    Authors: Cecilia Coimbra Klein, Ludovic Cottret, Janice Kielbassa, Hubert Charles, Christian Gautier, Ana Tereza Ribeiro de Vasconcelos, Vincent Lacroix and Marie-France Sagot

    Citation: BMC Genomics 2012 13:438

    Content type: Research article

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  37. Francisella tularensis is an intracellular pathogen that causes tularemia in humans and the public health importance of this bacterium has been well documented in recent history. Francisella philomiragia, a dista...

    Authors: Shivakumara Siddaramappa, Jean F Challacombe, Jeannine M Petersen, Segaran Pillai and Cheryl R Kuske

    Citation: BMC Genomics 2012 13:422

    Content type: Research article

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  38. In recent years an increasing number of yeast infections in humans have been related to certain clinical isolates of Saccharomyces cerevisiae. Some clinical strains showed in vivo and in vitro virulence traits an...

    Authors: Silvia Llopis, Amparo Querol, Antje Heyken, Bernhard Hube, Lene Jespersen, M Teresa Fernández-Espinar and Roberto Pérez-Torrado

    Citation: BMC Genomics 2012 13:419

    Content type: Research article

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  39. In Bacillus subtilis and its relatives carbon catabolite control, a mechanism enabling to reach maximal efficiency of carbon and energy sources metabolism, is achieved by the global regulator CcpA (carbon catabol...

    Authors: Bogumiła C Marciniak, Monika Pabijaniak, Anne de Jong, Robert Dűhring, Gerald Seidel, Wolfgang Hillen and Oscar P Kuipers

    Citation: BMC Genomics 2012 13:401

    Content type: Research article

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  40. The class of small non-coding RNA molecules (sRNA) regulates gene expression by different mechanisms and enables bacteria to mount a physiological response due to adaptation to the environment or infection. Ov...

    Authors: Jordan Pischimarov, Carsten Kuenne, André Billion, Jüergen Hemberger, Franz Cemič, Trinad Chakraborty and Torsten Hain

    Citation: BMC Genomics 2012 13:384

    Content type: Database

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  41. Oenococcus oeni, a member of the lactic acid bacteria, is one of a limited number of microorganisms that not only survive, but actively proliferate in wine. It is also unusual as, unlike the majority of bacteria ...

    Authors: Anthony R Borneman, Jane M McCarthy, Paul J Chambers and Eveline J Bartowsky

    Citation: BMC Genomics 2012 13:373

    Content type: Research article

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  42. Previous work has shown that the hypersaline-adapted archaeon, Halobacterium salinarum NRC-1, is highly resistant to oxidative stress caused by exposure to hydrogen peroxide, UV, and gamma radiation. Dynamic alte...

    Authors: Kriti Sharma, Nicholas Gillum, J Lomax Boyd and Amy Schmid

    Citation: BMC Genomics 2012 13:351

    Content type: Research article

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  43. Genomic Islands (GIs) have key roles since they modulate the structure and size of bacterial genomes displaying a diverse set of laterally transferred genes. Despite their importance, GIs in marine bacterial g...

    Authors: Beatriz Fernández-Gómez, Antonio Fernàndez-Guerra, Emilio O Casamayor, José M González, Carlos Pedrós-Alió and Silvia G Acinas

    Citation: BMC Genomics 2012 13:347

    Content type: Research article

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  44. Endodontic infections are a leading cause of oro-facial pain and tooth loss in western countries, and may lead to severe life-threatening infections. These infections are polymicrobial with high bacterial dive...

    Authors: William W L Hsiao, Kevin L Li, Zhenqiu Liu, Cheron Jones, Claire M Fraser-Liggett and Ashraf F Fouad

    Citation: BMC Genomics 2012 13:345

    Content type: Research article

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  45. Prior to this study, relatively few strains of Francisella had been genome-sequenced. Previously published Francisella genome sequences were largely restricted to the zoonotic agent F. tularensis. Only limited da...

    Authors: Andreas Sjödin, Kerstin Svensson, Caroline Öhrman, Jon Ahlinder, Petter Lindgren, Samuel Duodu, Anders Johansson, Duncan J Colquhoun, Pär Larsson and Mats Forsman

    Citation: BMC Genomics 2012 13:268

    Content type: Research article

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