The GENCODE pseudogene resource. Abstract | Oculus: faster sequence alignment by streaming read compression. Population and sex differences in Drosophila melanogaster brain gene expression. Research article Ana Catalán, Stephan Hutter and John Parsch* * Corresponding author: John Parsch parsch@bio.lmu.de Author Affiliations Department of Biology II, University of Munich (LMU), Grosshaderner Str. 2, Planegg-Martinsried 82152, Germany For all author emails, please log on. BMC Genomics 2012, 13:654 doi:10.1186/1471-2164-13-654 Published: 21 November 2012 Abstract Background Changes in gene regulation are thought to be crucial for the adaptation of organisms to their environment.
Results Relatively few genes (<100) displayed sexually dimorphic expression in the brain, but there was an enrichment of sex-biased genes, especially male-biased genes, on the X chromosome. Conclusions Analysis of the brain transcriptome revealed many genes differing in expression between populations that were not detected in previous studies using whole flies. Keywords: Transcriptomics; Adaptation; Population genetics; Insecticide resistance; Sexual dimorphism close. Detection of genetic association and functional polymorphisms of UGDH affecting milk production trait in Chinese Holstein cattle.
Research article Qing Xu2†, Gui Mei13†, Dongxiao Sun1*, Qin Zhang1, Yuan Zhang1, Cengceng Yin1, Huiyong Chen1, Xiangdong Ding1 and Jianfeng Liu1 * Corresponding author: Dongxiao Sun sundx@cau.edu.cn † Equal contributors Author Affiliations 1 Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, China 2 Institute of Life Science and Biotechnology, Beijing Jiaotong University, Beijing 100044, China 3 Institute of Animal Science, Guangdong Academy of Agricultural Sciences; State Key Laboratory of Livestock and Poultry Breeding, Guangzhou 510640, China For all author emails, please log on.
BMC Genomics 2012, 13:590 doi:10.1186/1471-2164-13-590 Published: 2 November 2012 Abstract Background Results Conclusions Keywords: Dairy cattle; BTA6; Positional candidate; Milk traits; UGDH; Function validation. Transcriptional regulation of the operon encoding stress-responsive ECF sigma factor SigH and its anti-sigma factor RshA, and control of its regulatory network in Corynebacterium glutamicum. Decreased miR-192 expression in peripheral blood of asthmatic individuals undergoing an allergen inhalation challenge. BMC Microbiology | Abstract | The RNA processing enzyme polynucleotide phosphorylase negatively controls biofilm formation by repressing poly-N-acetylglucosamine (PNAG) production in Escherichia coli C.
Research article Thomas Carzaniga†, Davide Antoniani†, Gianni Dehò, Federica Briani* and Paolo Landini* BMC Microbiology 2012, 12:270 doi:10.1186/1471-2180-12-270 Published: 21 November 2012 Abstract Background Transition from planktonic cells to biofilm is mediated by production of adhesion factors, such as extracellular polysaccharides (EPS), and modulated by complex regulatory networks that, in addition to controlling production of adhesion factors, redirect bacterial cell metabolism to the biofilm mode. Results Deletion of the pnp gene, encoding polynucleotide phosphorylase, an RNA processing enzyme and a component of the RNA degradosome, results in increased biofilm formation in Escherichia coli. Conclusions Our results demonstrate that PNPase is necessary to maintain bacterial cells in the planktonic mode through down-regulation of pgaABCD expression and PNAG production. Keywords: Biofilm; RNA processing; Degradosome; EPS; Cell adhesion; PNPase close.
Human genes with CpG island promoters have a distinct transcription-associated chromatin organization. Research Tanya Vavouri1 and Ben Lehner2 Corresponding authors: Tanya Vavouri tvavouri@imppc.org - Ben Lehner ben.lehner@crg.eu Author Affiliations 1 Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona 08916, Spain 2 EMBL-CRG Systems Biology Unit and ICREA, Centre for Genomic Regulation and UPF, Barcelona 08003, Spain Genome Biology 2012, 13:R110 doi:10.1186/gb-2012-13-11-r110 Published: 27 November 2012 Abstract Background More than 50% of human genes initiate transcription from CpG dinucleotide-rich regions referred to as CpG islands. Results Here we report that genes with CpG island promoters have a characteristic transcription-associated chromatin organization. Conclusions These results suggest that active genes with CpG island promoters have a distinct step-like series of modified nucleosomes after the TSS.
Close Sign up to receive new article alerts from Genome Biology. Maternal 3'UTRs: from egg to onset of zygotic transcription in Atlantic cod. Research article Lene Kleppe1*, Rolf B Edvardsen1, Heiner Kuhl2, Ketil Malde1, Tomasz Furmanek1, Øyvind Drivenes1, Richard Reinhardt3, Geir L Taranger1 and Anna Wargelius1 * Corresponding author: Lene Kleppe lene.kleppe@imr.no Author Affiliations 1 Institute of Marine Research, P. 2 Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195, Berlin-Dahlem, Germany 3 Max-Planck Genome centre, MPI fuer Pflanzenzüchtungsforschung, Carl-von-Linné-Weg 10, D-80829, Koeln, Germany For all author emails, please log on.
BMC Genomics 2012, 13:443 doi:10.1186/1471-2164-13-443 Published: 1 September 2012 Abstract Background Zygotic transcription in fish embryos initiates around the time of gastrulation, and all prior development is initiated and controlled by maternally derived messenger RNAs. Results 22229 Sanger-sequences were obtained from 3’-end sequenced cDNA libraries prepared from oocyte, 1-2 cell, blastula and gastrula stages. Conclusions Keywords: close. Small RNA and transcriptome deep sequencing proffers insight into floral gene regulation in Rosa cultivars.
RNA-seq and microarray complement each other in transcriptome profiling. Research article Sunitha Kogenaru, Qing Yan, Yinping Guo and Nian Wang* * Corresponding author: Nian Wang nianwang@ufl.edu Author Affiliations Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred, 33850, USA For all author emails, please log on.
BMC Genomics 2012, 13:629 doi:10.1186/1471-2164-13-629 Published: 15 November 2012 Abstract Background RNA-seq and microarray are the two popular methods employed for genome-wide transcriptome profiling. Results We compared the performance of RNA-seq and microarray in their ability to detect known HrpX target genes by profiling the transcriptome from the wild-type and the hrpX mutant strains of γ-Proteobacterium Xanthomonas citri subsp. citri. Conclusions This study has significantly advanced our understanding of the regulome of the critical transcriptional factor HrpX. Keywords: close. Transcriptome profiling in conifers and the PiceaGenExpress database show patterns of diversification within gene families and interspecific conservation in vascular gene expression.
BMC Biology | Full text | Logic modeling and the ridiculome under the rug. Identification of proteins binding coding and non-coding human RNAs using protein microarrays. Regulatory elements of Caenorhabditis elegans ribosomal protein genes. BioMed Central | The Open Access Publisher. Transcriptome database resource and gene expression atlas for the rose. 1 Reproduction et Développement des Plantes UMR INRA-CNRS- Université Lyon 1-ENSL, Ecole Normale Supérieure, 46 allée d'Italie, Lyon Cedex 07, 69364, France 2 INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, F-31326, France 3 CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, F-31326, France 4 Laboratoire BVpam, EA2061, Université de Saint-Etienne, Université de Lyon, rue du Dr Michelon, Saint-Etienne, F-42023, France 5 INRA, Unité de Recherches Intégrées en Horticulture, 400 route des Chappes BP 167, Sophia Antipolis Cedex, 06903, France 6 Institut de Recherche en Horticulture et Semences (INRA, Agrocacmpus-Ouest, Université d’Angers), SFR 149 QUASAV, Beaucouzé cedex, BP 60057-49071, France 7 Université de Poitiers, UMR CNRS 7267 Écologie et Biologie des Interactions, 40 Av. du Recteur Pineau, Poitiers Cedex, 86022, France.
Hereditary Cancer in Clinical Practice | Abstract | DNA and RNA analyses in detection of genetic predisposition to cancer. Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features. Transcriptional profiling of lncRNAs and novel transcribed regions across a diverse panel of archived human cancers. Analysis of a comprehensive dataset of diversity generating retroelements generated by the program DiGReF. De Novo characterization of the banana root transcriptome and analysis of gene expression under Fusarium oxysporum f. sp. Cubense tropical race 4 infection. Asymmetric purine-pyrimidine distribution in cellular small RNA population of papaya. Abstract | Finding quasi-modules of human and viral miRNAs: a case study of human cytomegalovirus (HCMV) Research article Isana Veksler-Lublinsky1, Yonat Shemer-Avni2, Eti Meiri3, Zvi Bentwich2, Klara Kedem1 and Michal Ziv-Ukelson1* * Corresponding author: Michal Ziv-Ukelson michaluz@cs.bgu.ac.il Author Affiliations 1 Department of Computer Science, Ben-Gurion University, Beer-Sheva 84105, Israel 2 Virology and Developmental Genetics/Health Sciences, Ben-Gurion University 3 , Rosetta Genomics Ltd., 10 Plaut St., Rehovot, 76706, Israel For all author emails, please log on.
BMC Bioinformatics 2012, 13:322 doi:10.1186/1471-2105-13-322 Published: 3 December 2012 Abstract Background MicroRNAs (miRNAs) are important regulators of gene expression encoded by a variety of organisms, including viruses. Results In this paper we explore the compensating mode of mutual regulation upon Human Cytomegalovirus (HCMV) infection, when host miRNAs are down regulated and viral miRNAs compensate by mimicking their function.
Conclusions close Sign up to receive new article alerts from BMC Bioinformatics. Identification and analysis of pig chimeric mRNAs using RNA sequencing data. Research article Lei Ma12†, Shulin Yang1†, Weiming Zhao1†, Zhonglin Tang1, Tingting Zhang2 and Kui Li1* * Corresponding author: Kui Li kuili@iascaas.net.cn † Equal contributors Author Affiliations 1 The Key Laboratory for Domestic Animal Genetic Resources and Breeding of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, P. 2 College of Life Science, Shihezi University, Xinjiang, 832000, P. For all author emails, please log on. BMC Genomics 2012, 13:429 doi:10.1186/1471-2164-13-429 Published: 28 August 2012 Abstract Background Gene fusion is ubiquitous over the course of evolution.
Results The present study identified 669 putative chimeric mRNAs in pigs, of which 251 chimeric candidates were detected in a set of RNA-sequencing data. Conclusions The present study provided detailed information on some pig chimeric mRNAs. Keywords: Chimeric mRNA; Trans-splicing; RNA-sequencing; CTCF; Pig close. Small interfering RNA-producing loci in the ancient parasitic eukaryote Trypanosoma brucei. Genomic resources for a model in adaptation and speciation research: characterization of the Poecilia mexicana transcriptome. Cell & Bioscience | Abstract | Tombusvirus P19 RNA silencing suppressor (RSS) activity in mammalian cells correlates with charged amino acids that contribute to direct RNA-binding. Research Xiang Liu, Laurent Houzet and Kuan-Teh Jeang* * Corresponding author: Kuan-Teh Jeang kjeang@niaid.nih.gov Author Affiliations Molecular Virology Section, Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA For all author emails, please log on.
Cell & Bioscience 2012, 2:41 doi:10.1186/2045-3701-2-41 Published: 6 December 2012 Abstract Background Tombusvirus P19 is a protein encoded by tomato bushy stunt virus and related tombusviruses. Results We have studied the RSS effect of P19 in mammalian cells, HEK293T, HeLa, and mouse embryonic fibroblasts. Conclusions Our findings characterize a class of RNA-binding proteins that function as RSS moieties. Close Sign up to receive new article alerts from Cell & Bioscience. Complete sequence of heterogenous-composition mitochondrial genome (Brassica napus) and its exogenous source. Simultaneous RNA quantification of human and retroviral genomes reveals intact interferon signaling in HTLV-1-infected CD4+ T cell lines. BMC Evolutionary Biology | Abstract | Evolutionary genomics of host-use in bifurcating demes of RNA virus phi-6.
A gene expression profile of stem cell pluripotentiality and differentiation is conserved across diverse solid and hematopoietic cancers. Research Nathan P Palmer1†, Patrick R Schmid1†, Bonnie Berger12* and Isaac S Kohane3* * Corresponding authors: Bonnie Berger bab@mit.edu - Isaac S Kohane isaac_kohane@hms.harvard.edu † Equal contributors Author Affiliations 1 Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge MA 02139, USA 2 Department of Mathematics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge MA 02139, USA 3 Center for Biomedical Informatics, Harvard Medical School, 25 Shattuck Street, Boston MA 02115, USA For all author emails, please log on.
Genome Biology 2012, 13:R71 doi:10.1186/gb-2012-13-8-r71 Published: 21 August 2012 Abstract Background Understanding the fundamental mechanisms of tumorigenesis remains one of the most pressing problems in modern biology. Results We identify, in an unbiased fashion, mRNA transcription patterns associated with pluripotent stem cells. Conclusions close. Detecting transcription of ribosomal protein pseudogenes in diverse human tissues from RNA-seq data. Research article Peter Tonner1, Vinodh Srinivasasainagendra2, Shaojie Zhang1* and Degui Zhi2* * Corresponding authors: Shaojie Zhang shzhang@eecs.ucf.edu - Degui Zhi dzhi@soph.uab.edu Author Affiliations 1 Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL, 32816, USA 2 Department of Biostatistics, Section on Statistical Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA For all author emails, please log on. BMC Genomics 2012, 13:412 doi:10.1186/1471-2164-13-412 Published: 21 August 2012 Abstract Background Ribosomal proteins (RPs) have about 2000 pseudogenes in the human genome.
Results Here we developed a specialized pipeline for pseudogene transcription discovery. Conclusions Using a specialized bioinformatics method, we identified the transcription of ribosomal protein pseudogenes in human tissues using RNA-seq data. Keywords: Ribosomal protein; Pseudogene; Transcription; RNA-seq data close. Identification of common carp (Cyprinus carpio) microRNAs and microRNA-related SNPs. Genome-wide distribution of 5-formylcytosine in ES cells is associated with transcription and depends on thymine DNA glycosylase.
Proteo-Genomic characterization and mapping of nucleosomes decoded by Brd and HP1 proteins. Comparative transcript profiling of gene expression between seedless Ponkan mandarin and its seedy wild type during floral organ development by suppression subtractive hybridization and cDNA microarray. Research article Wen-Ming Qiu, An-Dan Zhu, Yao Wang, Li-Jun Chai, Xiao-Xia Ge, Xiu-Xin Deng and Wen-Wu Guo* * Corresponding author: Wen-Wu Guo guoww@mail.hzau.edu.cn Author Affiliations Key Laboratory of Horticultural Plant Biology (Ministry of Education); National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China For all author emails, please log on. BMC Genomics 2012, 13:397 doi:10.1186/1471-2164-13-397 Published: 16 August 2012 Abstract Background Seedlessness is an important agronomic trait for citrus, and male sterility (MS) is one main cause of seedless citrus fruit.
Results An integrative strategy combining suppression subtractive hybridization (SSH) library with cDNA microarray was employed to study the underlying mechanism of seedlessness of a Ponkan mandarin seedless mutant (Citrus reticulata Blanco). Conclusion Keywords: Citrus; cDNA microarray; Differential transcript; Male sterility-like protein; Seedlessness close.
RNA sequencing revealed novel actors of the acquisition of drug resistance in Candida albicans. Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data. Research article Jialei Duan12, Chuan Xia1, Guangyao Zhao1, Jizeng Jia1* and Xiuying Kong1* * Corresponding authors: Jizeng Jia jzjia@mail.caas.net.cn - Xiuying Kong xykong@mail.caas.net.cn Author Affiliations 1 Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 12 South Street, Zhongguancun, Beijing 100081, People's Republic of China 2 College of Biology Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100094, People's Republic of China For all author emails, please log on.
BMC Genomics 2012, 13:392 doi:10.1186/1471-2164-13-392 Published: 14 August 2012 Abstract Background Rapid advances in next-generation sequencing methods have provided new opportunities for transcriptome sequencing (RNA-Seq). Results Conclusions close. Computational prediction and validation of C/D, H/ACA and Eh_U3 snoRNAs of Entamoeba histolytica. Research article Devinder Kaur1, Abhishek Kumar Gupta1, Vandana Kumari1, Rahul Sharma1, Alok Bhattacharya2 and Sudha Bhattacharya1* * Corresponding author: Sudha Bhattacharya sb@mail.jnu.ac.in Author Affiliations 1 School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India 2 School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India For all author emails, please log on. BMC Genomics 2012, 13:390 doi:10.1186/1471-2164-13-390 Published: 14 August 2012 Abstract Background Small nucleolar RNAs are a highly conserved group of small RNAs found in eukaryotic cells.
Results We have searched snoRNAs of Entamoeba histolytica from the genome sequence using computational programmes (snoscan and snoSeeker) and we obtained 99 snoRNAs (C/D and H/ACA box snoRNAs) along with 5 copies of Eh_U3 snoRNAs. Conclusion Keywords: U3 snoRNA; Guide/ orphan snoRNAs; Entamoeba histolytica close Sign up to receive new article alerts from BMC Genomics. MicroRNAs in metamorphic and non-metamorphic transitions in hemimetabolan insect metamorphosis. sRNAdb: A small non-coding RNA database for gram-positive bacteria. Abstract | Modeling RNA polymerase interaction in mitochondria of chordates. Analysis of plant-derived miRNAs in animal small RNA datasets. BMC Infectious Diseases | Abstract | Short hairpin RNA targeting 2B gene of coxsackievirus B3 exhibits potential antiviral effects both in vitro and in vivo.
Transcriptome profiling of resistant and susceptible Cavendish banana roots following inoculation with Fusarium oxysporum f. sp. cubense tropical race 4. Development of a porcine (Sus scofa) embryo-specific microarray: array annotation and validation. High-throughput sequencing of small RNAs and analysis of differentially expressed microRNAs associated with pistil development in Japanese apricot.
Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions. Translational regulation of Anopheles gambiae mRNAs in the midgut during Plasmodium falciparum infection. Transcriptome sequencing of Eucalyptus camaldulensis seedlings subjected to water stress reveals functional single nucleotide polymorphisms and genes under selection.
Quantitative RNA-Seq analysis in non-model species: assessing transcriptome assemblies as a scaffold and the utility of evolutionary divergent genomic reference species. Characterization of microRNAs expression during maize seed development. The ribonuclease Dis3 is an essential regulator of the developmental transcriptome. Selective extracellular vesicle-mediated export of an overlapping set of microRNAs from multiple cell types. Cell & Bioscience | Abstract | Statistical methods for identifying differentially expressed genes in RNA-Seq experiments. Comprehensive microRNA profiling in B-cells of human centenarians by massively parallel sequencing. A complete mitochondrial genome sequence of Ogura-type male-sterile cytoplasm and its comparative analysis with that of normal cytoplasm in radish (Raphanus sativus L.) Bit. Microbial transformation from normal oral microbiota to acute endodontic infections.
Abstract | Opening of the TAR hairpin in the HIV-1 genome causes aberrant RNA dimerization and packaging. BMC Microbiology | Abstract | Role of the small RNA RyhB in the Fur regulon in mediating the capsular polysaccharide biosynthesis and iron acquisition systems in Klebsiella pneumoniae. A microRNA activity map of human mesenchymal tumors: connections to oncogenic pathways; an integrative transcriptomic study.
Characterization of the small RNA component of leaves and fruits from four different cucurbit species. Chips and tags suggest plant-environment interactions differ for two alpine Pachycladon species. Differential microRNA response to a high-cholesterol, high-fat diet in livers of low and high LDL-C baboons. RNA-seq liver transcriptome analysis reveals an activated MHC-I pathway and an inhibited MHC-II pathway at the early stage of vaccine immunization in zebrafish. Development and validation of genic-SSR markers in sesame by RNA-seq. An unbiased approach to identify genes involved in development in a turtle with temperature-dependent sex determination.
Let-7b regulates the expression of the growth hormone receptor gene in deletion-type dwarf chickens. De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): Genomic tools for an ecological model system. Abstract | Evaluating the Effect of Disturbed Ensemble Distributions on SCFG Based Statistical Sampling of RNA Secondary Structures.
PePPER: a webserver for prediction of prokaryote promoter elements and regulons. Transcriptional profile of Taxus chinensis cells in response to methyl jasmonate. Identification of genes specifically or preferentially expressed in maize silk reveals similarity and diversity in transcript abundance of different dry stigmas. Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. alpina): assembly, annotation and molecular marker discovery. Computational identification and analysis of novel sugarcane microRNAs. Abstract | Detecting sequence dependent transcriptional pauses from RNA and protein number time series. BMC Biotechnology | Abstract | Efficient recovery of whole blood RNA - a comparison of commercial RNA extraction protocols for high-throughput applications in wildlife species. Integrated analysis of microRNA expression and mRNA transcriptome in lungs of avian influenza virus infected broilers.
The complete mitochondrial genomes of two ghost moths, Thitarodes renzhiensis and Thitarodes yunnanensis: the ancestral gene arrangement in Lepidoptera. Identification of yeast genes that confer resistance to chitosan oligosaccharide (COS) using chemogenomics. Abstract | miREvo: an integrative microRNA evolutionary analysis platform for next-generation sequencing experiments. Abstract | Comparative study of classification algorithms for immunosignaturing data. Identification of novel MiRNAs and MiRNA expression profiling during grain development in indica rice.
The effects of contig length and depth on the estimation of SNP frequencies, and the relative abundance of SNPs in protein-coding and non-coding transcripts of tiger salamanders (Ambystoma tigrinum) Transcriptomic analysis of the stress response to weaning at housing in bovine leukocytes using RNA-seq technology.
Plant Methods | Abstract | Evaluation of alternative RNA labeling protocols for transcript profiling with Arabidopsis AGRONOMICS1 tiling arrays. Arthritis Research & Therapy | Abstract | Prevalence, correlates and clinical usefulness of antibodies to RNA Polymerase III in systemic sclerosis: a cross-sectional analysis of data from an Australian cohort. Journal of Biomedical Science | Abstract | Epigeneitc silencing of ribosomal RNA genes by Mybbp1a. BMC Genomics | Full text | Simultaneous prediction of RNA secondary structure and helix coaxial stacking.
Parasites & Vectors | Abstract | Spliced leader RNA silencing (SLS) - a programmed cell death pathway in Trypanosoma brucei that is induced upon ER stress. Transcripts with in silico predicted RNA structure are enriched everywhere in the mouse brain. Identification of chemosensory receptor genes in Manduca sexta and knockdown by RNA interference. RNA-seq analysis of differential gene expression in liver from lactating dairy cows divergent in negative energy balance. Estimating RNA-quality using GeneChip microarrays. Abstract | Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art. Abstract | HIV-1-encoded antisense RNA suppresses viral replication for a prolonged period. Abstract | Evolving stochastic context-free grammars for RNA secondary structure prediction. BMC Plant Biology | Abstract | Transcriptome analysis of stem development in the tumourous stem mustard Brassica juncea var. tumida Tsen et Lee by RNA sequencing.