Research article  

RNA-Seq quantification of the human small airway epithelium transcriptome

Neil R Hackett, Marcus W Butler, Renat Shaykhiev, Jacqueline Salit, Larsson Omberg, Juan L Rodriguez-Flores, Jason G Mezey, Yael Strulovici-Barel, Guoqing Wang, Lukas Didon, Ronald G Crystal BMC Genomics 2012, 13:82 (29 February 2012)

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Research article  

Altered gene expression profiles in the hippocampus and prefrontal cortex of type 2 diabetic rats

Omar Abdul-Rahman, Maria Sasvari-Szekely, Agota Ver, Klara Rosta, Bernadett K Szasz, Eva Kereszturi, Gergely Keszler BMC Genomics 2012, 13:81 (27 February 2012)

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Research article  

High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping

Cristina Esteras, Pedro Gómez, Antonio J Monforte, José Blanca, Nelly Vicente-Dólera, Cristina Roig, Fernando Nuez, Belén Picó BMC Genomics 2012, 13:80 (22 February 2012)

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Research article  

A minimal model of peptide binding predicts ensemble properties of serum antibodies

Victor Greiff, Henning Redestig, Juliane Lück, Nicole Bruni, Atijeh Valai, Susanne Hartmann, Sebastian Rausch, Johannes Schuchhardt, Michal Or-Guil BMC Genomics 2012, 13:79 (21 February 2012)

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Research article  

Whole-Genome sequencing and genetic variant analysis of a quarter Horse mare

Ryan Doan, Noah D Cohen, Jason Sawyer, Noushin Ghaffari, Charles D Johnson, Scott V Dindot BMC Genomics 2012, 13:78 (17 February 2012)

Abstract | Full text | PDF | PubMed |  Editor’s summary

Research article  

Comprehensive evaluation of SNP identification with the Restriction Enzyme-based Reduced Representation Library (RRL) method

Ye Du, Hui Jiang, Ying Chen, Cong Li, Meiru Zhao, Jinghua Wu, Yong Qiu, Qibin Li, Xiuqing Zhang BMC Genomics 2012, 13:77 (16 February 2012)

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Research article  

Sexual and asexual oogenesis require the expression of unique and shared sets of genes in the insect Acyrthosiphon pisum

Aurore Gallot, Shuji Shigenobu, Tomomi Hashiyama, Stéphanie Jaubert-Possamai, Denis Tagu BMC Genomics 2012, 13:76 (15 February 2012)

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Research article  

Identification and localisation of the NB-LRR gene family within the potato genome

Florian Jupe, Leighton Pritchard, Graham J Etherington, Katrin MacKenzie, Peter JA Cock, Frank Wright, Sanjeev Kumar Sharma, Dan Bolser, Glenn J Bryan, Jonathan DG Jones, Ingo Hein BMC Genomics 2012, 13:75 (15 February 2012)

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Software  

GemSIM: general, error-model based simulator of next-generation sequencing data

Kerensa E McElroy, Fabio Luciani, Torsten Thomas BMC Genomics 2012, 13:74 (15 February 2012)

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Research article  

High-throughput proteogenomics of Ruegeria pomeroyi: seeding a better genomic annotation for the whole marine Roseobacter clade

Joseph A Christie-Oleza, Guylaine Miotello, Jean Armengaud BMC Genomics 2012, 13:73 (15 February 2012)

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Methodology article  

Reference genome-independent assessment of mutation density using restriction enzyme-phased sequencing

Jennifer Monson-Miller, Diana C Sanchez-Mendez, Joseph Fass, Isabelle M Henry, Thomas H Tai, Luca Comai BMC Genomics 2012, 13:72 (14 February 2012)

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Research article  

Identification of common genetic modifiers of neurodegenerative diseases from an integrative analysis of diverse genetic screens in model organisms

Xi Chen, Robert D Burgoyne BMC Genomics 2012, 13:71 (14 February 2012)

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Research article  

Orthologous genes identified by transcriptome sequencing in the spider genus Stegodyphus

Tiina M Mattila, Jesper S Bechsgaard, Troels T Hansen, Mikkel H Schierup, Trine Bilde BMC Genomics 2012, 13:70 (14 February 2012)

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Research article  

Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC

Stefan Engelen, David Vallenet, Claudine Médigue, Antoine Danchin BMC Genomics 2012, 13:69 (14 February 2012)

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Research article  

Transcription analysis on response of porcine alveolar macrophages to Haemophilus parasuis

Yang Wang, Chong Liu, Ying Fang, Xiaoli Liu, Wentao Li, Shuqing Liu, Yingyu Liu, Yuxi Liu, Catherine Charreyre, Jean-Christophe Audonnet, Pin Chen, Qigai He BMC Genomics 2012, 13:68 (13 February 2012)

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Research article  

Aluminum tolerance association mapping in triticale

Agnieszka Niedziela, Piotr T Bednarek, Henryk Cichy, Grzegorz Budzianowski, Andrzej Kilian, Andrzej Anioł BMC Genomics 2012, 13:67 (13 February 2012)

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Research article  

Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands

Jon Bohlin, Mark WJ van Passel, Lars Snipen, Anja B Kristoffersen, David Ussery, Simon P Hardy BMC Genomics 2012, 13:66 (10 February 2012)

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Methodology article  

Peptide markers of aminoacyl tRNA synthetases facilitate taxa counting in metagenomic data

Erez Persi, Uri Weingart, Shiri Freilich, David Horn BMC Genomics 2012, 13:65 (10 February 2012)

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Research article  

Transcriptome profiling of low temperature-treated cassava apical shoots showed dynamic responses of tropical plant to cold stress

Dong An, Jun Yang, Peng Zhang BMC Genomics 2012, 13:64 (10 February 2012)

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Research article  

Global changes in gene expression by the opportunistic pathogen Burkholderia cenocepacia in response to internalization by murine macrophages

Jennifer S Tolman, Miguel A Valvano BMC Genomics 2012, 13:63 (9 February 2012)

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Research article  

Transcriptomic and proteomic analyses of the Aspergillus fumigatus hypoxia response using an oxygen-controlled fermenter

Bridget M Barker, Kristin Kroll, Martin Vödisch, Aurélien Mazurie, Olaf Kniemeyer, Robert A Cramer BMC Genomics 2012, 13:62 (6 February 2012)

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Research article  

Ac/Ds-transposon activation tagging in poplar: a powerful tool for gene discovery

Matthias Fladung, Olaf Polak BMC Genomics 2012, 13:61 (6 February 2012)

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Database  

Medicago truncatula transporter database: a comprehensive database resource for M. truncatula transporters

Zhenyan Miao, Daofeng Li, Zhenhai Zhang, Jiangli Dong, Zhen Su, Tao Wang BMC Genomics 2012, 13:60 (6 February 2012)

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Research article  

Heritable genome-wide variation of gene expression and promoter methylation between wild and domesticated chickens

Daniel Nätt, Carl-Johan Rubin, Dominic Wright, Martin Johnsson, Johan Beltéky, Leif Andersson, Per Jensen BMC Genomics 2012, 13:59 (4 February 2012)

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Research article  

Analysis of the SOS response of Vibrio and other bacteria with multiple chromosomes

Neus Sanchez-Alberola, Susana Campoy, Jordi Barbé, Ivan Erill BMC Genomics 2012, 13:58 (3 February 2012)

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Research article  

Post-genomic analyses of fungal lignocellulosic biomass degradation reveal the unexpected potential of the plant pathogen Ustilago maydis

Marie Couturier, David Navarro, Caroline Olivé, Didier Chevret, Mireille Haon, Anne Favel, Laurence Lesage-Meessen, Bernard Henrissat, Pedro M Coutinho, Jean-Guy Berrin BMC Genomics 2012, 13:57 (2 February 2012)

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Research article  

The diversity of cyanobacterial metabolism: genome analysis of multiple phototrophic microorganisms

Christian Beck, Henning Knoop, Ilka M Axmann, Ralf Steuer BMC Genomics 2012, 13:56 (2 February 2012)

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Research article  

Conservation and divergence of chemical defense system in the tunicate Oikopleura dioica revealed by genome wide response to two xenobiotics

Fekadu Yadetie, Stephen Butcher, Hilde E Førde, Coen Campsteijn, Jean-Marie Bouquet, Odd A Karlsen, France Denoeud, Raghu Metpally, Eric M Thompson, J Robert Manak, Anders Goksøyr, Daniel Chourrout BMC Genomics 2012, 13:55 (2 February 2012)

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Research article  

Zonation related function and ubiquitination regulation in human hepatocellular carcinoma cells in dynamic vs. static culture conditions

Shu Cheng, Jean-Matthieu Prot, Eric Leclerc, Frédéric Y Bois BMC Genomics 2012, 13:54 (1 February 2012)

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Research article  

Gene alterations at Drosophila inversion breakpoints provide prima facie evidence for natural selection as an explanation for rapid chromosomal evolution

Yolanda Guillén, Alfredo Ruiz BMC Genomics 2012, 13:53 (1 February 2012)

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Research article  

Microgravity simulation by diamagnetic levitation: effects of a strong gradient magnetic field on the transcriptional profile of Drosophila melanogaster

Raul Herranz, Oliver J Larkin, Camelia E Dijkstra, Richard JA Hill, Paul Anthony, Michael R Davey, Laurence Eaves, Jack JWA van Loon, F Javier Medina, Roberto Marco BMC Genomics 2012, 13:52 (1 February 2012)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Research article  

Genome-wide analysis of hepatic LRH-1 reveals a promoter binding preference and suggests a role in regulating genes of lipid metabolism in concert with FXR

Hansook Chong, Jacob Biesinger, Young-Kyo Seo, Xiaohui Xie, Timothy F Osborne BMC Genomics 2012, 13:51 (1 February 2012)

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