Nucleotide diversity analysis highlights functionally important genomic regions

The mysterious orphans of Mycoplasmataceae

(2016) Tatiana V. Tatarinova et al.   Biology Direct

Cis regulatory motifs and antisense transcriptional control in the apicomplexan Theileria parva

(2016) Kyle Tretina et al.   BMC GENOMICS

Open access resources for genome-wide association mapping in rice

(2016) Susan R. McCouch et al.   Nature Communications

Population Genomics for Understanding Adaptation in Wild Plant Species

(2015) Detlef Weigel et al.   Annual Review of Genetics

The Evolution of Bony Vertebrate Enhancers at Odds with Their Coding Sequence Landscape

(2015) Aisha Yousaf et al.   Genome Biology and Evolution

GC skew defines distinct RNA polymerase pause sites in CpG island promoters

(2015) Wendy A. Kellner et al.   GENOME RESEARCH

A GCC-box motif in the promoter of nudix hydrolase 7 ( AtNUDT7 ) gene plays a role in ozone response of Arabidopsis ecotypes

(2015) Meenakumari Muthuramalingam et al.   GENOMICS

Cell-of-origin chromatin organization shapes the mutational landscape of cancer

(2015) Paz Polak et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

The effects of chromatin organization on variation in mutation rates in the genome

(2015) Kateryna D. Makova et al.   NATURE REVIEWS GENETICS

Transcription termination and the control of the transcriptome: why, where and how to stop

(2015) Odil Porrua et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The nucleosome landscape ofPlasmodium falciparumreveals chromatin architecture and dynamics of regulatory sequences

(2015) Philip Reiner Kensche et al.   NUCLEIC ACIDS RESEARCH

Whole Genome Sequencing of Elite Rice Cultivars as a Comprehensive Information Resource for Marker Assisted Selection

(2015) Jorge Duitama et al.   PLoS One

Discerning mechanistically rewired biological pathways by cumulative interaction heterogeneity statistics

(2015) Travis B. Cotton et al.   Scientific Reports

Naturally occurring diversity helps to reveal genes of adaptive importance in legumes

(2015) Laurent Gentzbittel et al.   Frontiers in Plant Science

Gene expression and nucleotide composition are associated with genic methylation level in Oryza sativa

(2014) Eran Elhaik et al.   BMC BIOINFORMATICS

Genomic Signature of Adaptation to Climate inMedicago truncatula

(2014) Jeremy B. Yoder et al.   GENETICS

SNP-Seek database of SNPs derived from 3000 rice genomes

(2014) Nickolai Alexandrov et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide DNA Polymorphisms in Seven Rice Cultivars of Temperate and Tropical Japonica Groups

(2014) Yuko Arai-Kichise et al.   PLoS One

Rapid diversification of fiveOryzaAA genomes associated with rice adaptation

(2014) Qun-Jie Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Case for Junk DNA

(2014) Alexander F. Palazzo et al.   PLoS Genetics

A Genome-Wide Analysis of Genetic Diversity in Trypanosoma cruzi Intergenic Regions

(2014) Leonardo G. Panunzi et al.   PLoS Neglected Tropical Diseases

The 3,000 rice genomes project

(2014)   GigaScience

cisExpress: motif detection in DNA sequences

(2013) Martin Triska et al.   BIOINFORMATICS

Cross-Species Analysis of Genic GC3 Content and DNA Methylation Patterns

(2013) Tatiana Tatarinova et al.   Genome Biology and Evolution

The influence of genomic context on mutation patterns in the human genome inferred from rare variants

(2013) V. M. Schaibley et al.   GENOME RESEARCH

Genomewide discovery of DNA polymorphisms in rice cultivars with contrasting drought and salinity stress response and their functional relevance

(2013) Mukesh Jain et al.   PLANT BIOTECHNOLOGY JOURNAL

Yield Trends Are Insufficient to Double Global Crop Production by 2050

(2013) Deepak K. Ray et al.   PLoS One

Translational control by 3'-UTR-binding proteins

(2012) E. Szostak et al.   Briefings in Functional Genomics

Fine-Scale Population Recombination Rates, Hotspots, and Correlates of Recombination in the Medicago truncatula Genome

(2012) Timothy Paape et al.   Genome Biology and Evolution

Natural diversity in the model legumeMedicago truncatulaallows identifying distinct genetic mechanisms conferring partial resistance toVerticilliumwilt

(2012) Cécile Ben et al.   JOURNAL OF EXPERIMENTAL BOTANY

Evidence of non-random mutation rates suggests an evolutionary risk management strategy

(2012) Iñigo Martincorena et al.   NATURE

A map of rice genome variation reveals the origin of cultivated rice

(2012) Xuehui Huang et al.   NATURE

Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel

(2012) Matthew W Horton et al.   NATURE GENETICS

Analysis of variation at transcription factor binding sites in Drosophila and humans

(2012) Mikhail Spivakov et al.   GENOME BIOLOGY

Tandem termination signal in plant mRNAs

(2011) Alex V. Kochetov et al.   GENE

Biological pathways to adaptability - interactions between genome, epigenome, nervous system and environment for adaptive behavior

(2011) C. Wolf et al.   GENES BRAIN AND BEHAVIOR

Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons

(2011) S. Gelfman et al.   GENOME RESEARCH

The large-scale distribution of somatic mutations in cancer genomes

(2011) Alan Hodgkinson et al.   HUMAN MUTATION

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

SNPs Occur in Regions with Less Genomic Sequence Conservation

(2011) John C. Castle   PLoS One

Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula

(2011) A. Branca et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pack-Mutator-like transposable elements (Pack-MULEs) induce directional modification of genes through biased insertion and DNA acquisition

(2011) N. Jiang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GC3 biology in corn, rice, sorghum and other grasses

(2010) Tatiana V Tatarinova et al.   BMC GENOMICS

Identification of TATA and TATA-less promoters in plant genomes by integrating diversity measure, GC-Skew and DNA geometric flexibility

(2010) Yong-Chun Zuo et al.   GENOMICS

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

(2010) Susanna Atwell et al.   NATURE

Extensive sequence-influenced DNA methylation polymorphism in the human genome

(2010) Asaf Hellman et al.   Epigenetics & Chromatin

Transcription termination by nuclear RNA polymerases

(2009) P. Richard et al.   GENES & DEVELOPMENT

Genome-Wide Discovery of cis-Elements in Promoter Sequences Using Gene Expression

(2009) Maxim Troukhan et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Evolutionarily Conserved Regulatory Motifs in the Promoter of the Arabidopsis Clock Gene LATE ELONGATED HYPOCOTYL

(2009) M. Spensley et al.   PLANT CELL

Analysis of Context Sequence Surrounding Translation Initiation Site from Complete Genome of Model Plants

(2008) L. Rangan et al.   MOLECULAR BIOTECHNOLOGY

Genome level analysis of rice mRNA 3′-end processing signals and alternative polyadenylation

(2008) Yingjia Shen et al.   NUCLEIC ACIDS RESEARCH

Insights into corn genes derived from large-scale cDNA sequencing

(2008) Nickolai N. Alexandrov et al.   PLANT MOLECULAR BIOLOGY

Hypermutable Non-Synonymous Sites Are under Stronger Negative Selection

(2008) Steffen Schmidt et al.   PLoS Genetics

Human-macaque comparisons illuminate variation in neutral substitution rates

(2008) Svitlana Tyekucheva et al.   GENOME BIOLOGY