Volume 15, issue 1, December 2014
1186 articles in this issue
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A hyper-dynamic nature of bivalent promoter states underlies coordinated developmental gene expression modules
Authors
- Akshay Shah
- Anja Oldenburg
- Philippe Collas
- Content type: Research article
- Open Access
- Published: 30 December 2014
- Article: 1186
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Transcriptomic and proteomic dynamics in the metabolism of a diazotrophic cyanobacterium, Cyanothece sp. PCC 7822 during a diurnal light–dark cycle
Authors (first, second and last of 12)
- David Welkie
- Xiaohui Zhang
- Louis A Sherman
- Content type: Research article
- Open Access
- Published: 29 December 2014
- Article: 1185
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Erratum to: genomic comparison of 93 Bacillus phages reveals 12 clusters, 14 singletons and remarkable diversity
Authors (first, second and last of 4)
- Julianne H Grose
- Garrett L Jensen
- Donald P Breakwell
- Content type: Erratum
- Open Access
- Published: 29 December 2014
- Article: 1184
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Analysis of the basal chordate Botryllus schlosseri reveals a set of genes associated with fertility
Authors (first, second and last of 9)
- Delany Rodriguez
- Erin N Sanders
- Anthony W De Tomaso
- Content type: Research article
- Open Access
- Published: 26 December 2014
- Article: 1183
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Functional mechanisms of drought tolerance in subtropical maize (Zea mays L.) identified using genome-wide association mapping
Authors (first, second and last of 15)
- Nepolean Thirunavukkarasu
- Firoz Hossain
- Hari Shankar Gupta
- Content type: Research article
- Open Access
- Published: 24 December 2014
- Article: 1182
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Reproducibility enhancement and differential expression of non predefined functional gene sets in human genome
Authors (first, second and last of 4)
- Samoel RM da Silva
- Gabriel C Perrone
- Rita MC de Almeida
- Content type: Research article
- Open Access
- Published: 24 December 2014
- Article: 1181
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TREC-IN: gene knock-in genetic tool for genomes cloned in yeast
Authors (first, second and last of 9)
- Suchismita Chandran
- Vladimir N Noskov
- Ray-Yuan Chuang
- Content type: Methodology article
- Open Access
- Published: 24 December 2014
- Article: 1180
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The use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuis
Authors (first, second and last of 18)
- Kate J Howell
- Lucy A Weinert
- Duncan J Maskell
- Content type: Research article
- Open Access
- Published: 24 December 2014
- Article: 1179
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Systematic exploration of autonomous modules in noisy microRNA-target networks for testing the generality of the ceRNA hypothesis
Authors
- Danny Kit-Sang Yip
- Iris K Pang
- Kevin Y Yip
- Content type: Methodology article
- Open Access
- Published: 24 December 2014
- Article: 1178
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CAGE-defined promoter regions of the genes implicated in Rett Syndrome
Authors (first, second and last of 17)
- Morana Vitezic
- Nicolas Bertin
- The FANTOM Consortium
- Content type: Research article
- Open Access
- Published: 24 December 2014
- Article: 1177
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Distinct gene signatures in aortic tissue from ApoE-/-mice exposed to pathogens or Western diet
Authors (first, second and last of 13)
- Carolyn D Kramer
- Ellen O Weinberg
- Caroline A Genco
- Content type: Research article
- Open Access
- Published: 24 December 2014
- Article: 1176
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The translation initiation complex eIF3 in trypanosomatids and other pathogenic excavates – identification of conserved and divergent features based on orthologue analysis
Authors (first, second and last of 8)
- Antonio M Rezende
- Ludmila A Assis
- Osvaldo P de Melo Neto
- Content type: Research article
- Open Access
- Published: 23 December 2014
- Article: 1175
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Quantification of epigenetic biomarkers: an evaluation of established and emerging methods for DNA methylation analysis
Authors (first, second and last of 5)
- Nicholas Redshaw
- Jim F Huggett
- Alison S Devonshire
- Content type: Research article
- Open Access
- Published: 23 December 2014
- Article: 1174
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Changes in activity of metabolic and regulatory pathways during germination of S. coelicolor
Authors (first, second and last of 4)
- Jan Bobek
- Eva Strakova
- Jiri Vohradsky
- Content type: Research article
- Open Access
- Published: 23 December 2014
- Article: 1173
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Are special read alignment strategies necessary and cost-effective when handling sequencing reads from patient-derived tumor xenografts?
Authors (first, second and last of 4)
- Kai-Yuen Tso
- Sau Dan Lee
- Kevin Y Yip
- Content type: Methodology article
- Open Access
- Published: 23 December 2014
- Article: 1172
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Genomic prediction of genetic merit using LD-based haplotypes in the Nordic Holstein population
Authors
- Beatriz CD Cuyabano
- Guosheng Su
- Mogens S Lund
- Content type: Research article
- Open Access
- Published: 23 December 2014
- Article: 1171
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Sub-genomic selection patterns as a signature of breeding in the allopolyploid Brassica napus genome
Authors
- Lunwen Qian
- Wei Qian
- Rod J Snowdon
- Content type: Research article
- Open Access
- Published: 23 December 2014
- Article: 1170
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Integrative analysis of high-throughput RNAi screen data identifies the FER and CRKL tyrosine kinases as new regulators of the mitogenic ERK-dependent pathways in transformed cells
Authors (first, second and last of 8)
- Philippe Nizard
- Frédéric Ezan
- Nathalie Théret
- Content type: Research article
- Open Access
- Published: 23 December 2014
- Article: 1169
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NextGen sequencing reveals short double crossovers contribute disproportionately to genetic diversity in Toxoplasma gondii
Authors (first, second and last of 9)
- Asis Khan
- Jahangheer S Shaik
- L David Sibley
- Content type: Research article
- Open Access
- Published: 23 December 2014
- Article: 1168
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Proteome changes underpin improved meat quality and yield of chickens (Gallus gallus) fed the probiotic Enterococcus faecium
Authors (first, second and last of 10)
- Aijuan Zheng
- Jianjie Luo
- Bin Yao
- Content type: Research article
- Open Access
- Published: 23 December 2014
- Article: 1167
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Fine mapping of Rcr1 and analyses of its effect on transcriptome patterns during infection by Plasmodiophora brassicae
Authors (first, second and last of 11)
- Mingguang Chu
- Tao Song
- Gary Peng
- Content type: Research article
- Open Access
- Published: 23 December 2014
- Article: 1166
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Proteomics of muscle chronological ageing in post-menopausal women
Authors (first, second and last of 12)
- Marine Gueugneau
- Cécile Coudy-Gandilhon
- Daniel Béchet
- Content type: Research article
- Open Access
- Published: 23 December 2014
- Article: 1165
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Susceptibility loci revealed for bovine respiratory disease complex in pre-weaned holstein calves
Authors (first, second and last of 15)
- Holly L Neibergs
- Christopher M Seabury
- The Bovine Respiratory Disease Complex Coordinated Agricultural Project Research Team
- Content type: Research article
- Open Access
- Published: 22 December 2014
- Article: 1164
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Comparative genomic analysis of Acinetobacter baumannii clinical isolates reveals extensive genomic variation and diverse antibiotic resistance determinants
Authors (first, second and last of 6)
- Fei Liu
- Yuying Zhu
- Yongfei Hu
- Content type: Research article
- Open Access
- Published: 22 December 2014
- Article: 1163
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Simultaneous analysis of large-scale RNAi screens for pathogen entry
Authors (first, second and last of 42)
- Pauli Rämö
- Anna Drewek
- Christoph Dehio
- Content type: Research article
- Open Access
- Published: 22 December 2014
- Article: 1162
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Cytokine systems approach demonstrates differences in innate and pro-inflammatory host responses between genetically distinct MERS-CoV isolates
Authors (first, second and last of 10)
- Christian Selinger
- Jennifer Tisoncik-Go
- Michael G Katze
- Content type: Research article
- Open Access
- Published: 22 December 2014
- Article: 1161
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The ecological genomic basis of salinity adaptation in Tunisian Medicago truncatula
Authors (first, second and last of 18)
- Maren L Friesen
- Eric JB von Wettberg
- Sergey V Nuzhdin
- Content type: Research article
- Open Access
- Published: 22 December 2014
- Article: 1160
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Sequence search and analysis of gene products containing RNA recognition motifs in the human genome
Authors
- Sony Malhotra
- Ramanathan Sowdhamini
- Content type: Research article
- Open Access
- Published: 22 December 2014
- Article: 1159
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An SNP-based saturated genetic map and QTL analysis of fruit-related traits in cucumber using specific-length amplified fragment (SLAF) sequencing
Authors (first, second and last of 9)
- Qingzhen Wei
- Yunzhu Wang
- Jinfeng Chen
- Content type: Research article
- Open Access
- Published: 22 December 2014
- Article: 1158
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Complex coding of endogenous siRNA, transcriptional silencing and H3K9 methylation on native targets of germline nuclear RNAi in C. elegans
Authors
- Julie Zhouli Ni
- Esteban Chen
- Sam Guoping Gu
- Content type: Research article
- Open Access
- Published: 22 December 2014
- Article: 1157
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The compact mitochondrial genome of Zorotypus medoensis provides insights into phylogenetic position of Zoraptera
Authors (first, second and last of 5)
- Chuan Ma
- Yeying Wang
- Chunxiang Liu
- Content type: Research article
- Open Access
- Published: 21 December 2014
- Article: 1156
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Exome sequencing and genome-wide copy number variant mapping reveal novel associations with sensorineural hereditary hearing loss
Authors (first, second and last of 8)
- Rajini R Haraksingh
- Fereshteh Jahanbani
- Michael P Snyder
- Content type: Research article
- Open Access
- Published: 20 December 2014
- Article: 1155
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Systems genomics evaluation of the SH-SY5Y neuroblastoma cell line as a model for Parkinson’s disease
Authors (first, second and last of 20)
- Abhimanyu Krishna
- Maria Biryukov
- Patrick May
- Content type: Research article
- Open Access
- Published: 20 December 2014
- Article: 1154
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The draft genome of the pest tephritid fruit fly Bactrocera tryoni: resources for the genomic analysis of hybridising species
Authors (first, second and last of 8)
- Anthony Stuart Gilchrist
- Deborah CA Shearman
- John A Sved
- Content type: Research article
- Open Access
- Published: 20 December 2014
- Article: 1153
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Mapping in the era of sequencing: high density genotyping and its application for mapping TYLCV resistance in Solanum pimpinellifolium
Authors (first, second and last of 8)
- Marcela VÃquez-Zamora
- Myluska Caro
- Sjaak van Heusden
- Content type: Research article
- Open Access
- Published: 20 December 2014
- Article: 1152
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Discovery of a novel small secreted protein family with conserved N-terminal IGY motif in Dikarya fungi
Authors (first, second and last of 6)
- Qiang Cheng
- Haoran Wang
- Minren Huang
- Content type: Research article
- Open Access
- Published: 20 December 2014
- Article: 1151
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Sequencing methods and datasets to improve functional interpretation of sleeping beauty mutagenesis screens
Authors (first, second and last of 7)
- Jesse D Riordan
- Luke J Drury
- Adam J Dupuy
- Content type: Methodology article
- Open Access
- Published: 19 December 2014
- Article: 1150
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RNA-seq analysis reveals significant transcriptome changes in turbot (Scophthalmus maximus) suffering severe enteromyxosis
Authors (first, second and last of 10)
- Diego Robledo
- Paolo Ronza
- Paulino MartÃnez
- Content type: Research article
- Open Access
- Published: 19 December 2014
- Article: 1149
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Histone modifications involved in cassette exon inclusions: a quantitative and interpretable analysis
Authors (first, second and last of 4)
- Hui Liu
- Ting Jin
- Shuigeng Zhou
- Content type: Research article
- Open Access
- Published: 19 December 2014
- Article: 1148
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An RNA sequencing transcriptome analysis of the high-temperature stressed tall fescue reveals novel insights into plant thermotolerance
Authors (first, second and last of 5)
- Tao Hu
- Xiaoyan Sun
- Jinmin Fu
- Content type: Research article
- Open Access
- Published: 19 December 2014
- Article: 1147
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Core and accessory genome architecture in a group of Pseudomonas aeruginosa Mu-like phages
Authors
- Adrián Cazares
- Guillermo Mendoza-Hernández
- Gabriel Guarneros
- Content type: Research article
- Open Access
- Published: 19 December 2014
- Article: 1146
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Genomic and transcriptomic differences in community acquired methicillin resistant Staphylococcus aureus USA300 and USA400 strains
Authors (first, second and last of 8)
- Marcus B Jones
- Christopher P Montgomery
- Robert S Daum
- Content type: Research article
- Open Access
- Published: 19 December 2014
- Article: 1145
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Co-acting gene networks predict TRAIL responsiveness of tumour cells with high accuracy
Authors (first, second and last of 8)
- Paul O’Reilly
- Csaba Ortutay
- Eva Szegezdi
- Content type: Research article
- Open Access
- Published: 19 December 2014
- Article: 1144
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Evolutionarily emerged G tracts between the polypyrimidine tract and 3′ AG are splicing silencers enriched in genes involved in cancer
Authors (first, second and last of 6)
- Muhammad Sohail
- Wenguang Cao
- Jiuyong Xie
- Content type: Research article
- Open Access
- Published: 19 December 2014
- Article: 1143
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Automated genomic context analysis and experimental validation platform for discovery of prokaryote transcriptional regulator functions
Authors (first, second and last of 6)
- Ricardo MartÃ-Arbona
- Fangping Mu
- Pat J Unkefer
- Content type: Research article
- Open Access
- Published: 18 December 2014
- Article: 1142
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Tissue-specific transcriptomics, chromosomal localization, and phylogeny of chemosensory and odorant binding proteins from the red flour beetle Tribolium castaneum reveal subgroup specificities for olfaction or more general functions
Authors (first, second and last of 10)
- Stefan Dippel
- Georg Oberhofer
- Sergio Angeli
- Content type: Research article
- Open Access
- Published: 18 December 2014
- Article: 1141
This is part of 1 collection: -
A new scoring function for top-down spectral deconvolution
Authors
- Qiang Kou
- Si Wu
- Xiaowen Liu
- Content type: Research article
- Open Access
- Published: 18 December 2014
- Article: 1140
This is part of 1 collection: -
A genome-guided analysis of energy conservation in the thermophilic, cytochrome-free acetogenic bacterium Thermoanaerobacter kivui
Authors (first, second and last of 5)
- Verena Hess
- Anja Poehlein
- Volker Müller
- Content type: Research article
- Open Access
- Published: 18 December 2014
- Article: 1139
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A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes
Authors (first, second and last of 5)
- Holly B Bratcher
- Craig Corton
- Martin CJ Maiden
- Content type: Methodology article
- Open Access
- Published: 18 December 2014
- Article: 1138
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