VTBuilder: a tool for the assembly of multi isoform transcriptomes

Medically important differences in snake venom composition are dictated by distinct postgenomic mechanisms

(2014) N. R. Casewell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genesis of an exceptionally lethal venom in the timber rattlesnake (Crotalus horridus) revealed through comparative venom-gland transcriptomics

(2013) Darin R Rokyta et al.   BMC GENOMICS

Optimizing de novo assembly of short-read RNA-seq data for phylogenomics

(2013) Ya Yang et al.   BMC GENOMICS

Mutant-Bin: Unsupervised Haplotype Estimation of Viral Population Diversity Without Reference Genome

(2013) Shruthi Prabhakara et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Individual Variability in the Venom Proteome of Juvenile Bothrops jararaca Specimens

(2013) Gabriela S. Dias et al.   JOURNAL OF PROTEOME RESEARCH

Intraspecies variation in the venom of the rattlesnake Crotalus simus from Mexico: Different expression of crotoxin results in highly variable toxicity in the venoms of three subspecies

(2013) Edgar Neri Castro et al.   Journal of Proteomics

Deep-Sequencing Analysis of the Association between the Quasispecies Nature of the Hepatitis C Virus Core Region and Disease Progression

(2013) Mika Miura et al.   JOURNAL OF VIROLOGY

Applications and challenges of next-generation sequencing in Brassica species

(2013) Lijuan Wei et al.   PLANTA

Whole Genome Sequencing Reveals Complex Evolution Patterns of Multidrug-Resistant Mycobacterium tuberculosis Beijing Strains in Patients

(2013) Matthias Merker et al.   PLoS One

De Novo Transcriptome Sequencing Reveals Important Molecular Networks and Metabolic Pathways of the Plant, Chlorophytum borivilianum

(2013) Shikha Kalra et al.   PLoS One

Three-Fingered RAVERs: Rapid Accumulation of Variations in Exposed Residues of Snake Venom Toxins

(2013) Kartik Sunagar et al.   Toxins

Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads

(2012) Wei Li et al.   BIOINFORMATICS

Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II.

(2012) John Archer et al.   BMC BIOINFORMATICS

Genetic Variations in Epigenetic Genes Are Predictors of Recurrence in Stage I or II Non-Small Cell Lung Cancer Patients

(2012) K. W. Wagner et al.   CLINICAL CANCER RESEARCH

Intraspecific Variation of Biological Activities in Venoms from Wild and CaptiveBothrops jararaca

(2012) Eduardo Saad et al.   JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH-PART A-CURRENT ISSUES

Differential Evolution and Neofunctionalization of Snake Venom Metalloprotease Domains

(2012) Andreas Brust et al.   MOLECULAR & CELLULAR PROTEOMICS

Reference-free transcriptome assembly in non-model animals from next-generation sequencing data

(2012) V. CAHAIS et al.   Molecular Ecology Resources

Evaluating Characteristics of De Novo Assembly Software on 454 Transcriptome Data: A Simulation Approach

(2012) Marvin Mundry et al.   PLoS One

Candidate Polymorphisms and Severe Malaria in a Malian Population

(2012) Ousmane Toure et al.   PLoS One

Snake venom metalloproteinases

(2012) Francis S. Markland et al.   TOXICON

Complex cocktails: the evolutionary novelty of venoms

(2012) Nicholas R. Casewell et al.   TRENDS IN ECOLOGY & EVOLUTION

Convergence and coevolution of Hepatitis B virus drug resistance

(2012) Hong Thai et al.   Nature Communications

Diversity of metalloproteinases in Bothrops neuwiedi snake venom transcripts: evidences for recombination between different classes of SVMPs

(2011) Ana M Moura-da-Silva et al.   BMC GENETICS

Profiling the venom gland transcriptomes of Costa Rican snakes by 454 pyrosequencing

(2011) Jordi Durban et al.   BMC GENOMICS

Evaluation of short read metagenomic assembly

(2011) Anveshi Charuvaka et al.   BMC GENOMICS

Research strategies to improve snakebite treatment: Challenges and progress

(2011) Robert A. Harrison et al.   Journal of Proteomics

Domain Loss Facilitates Accelerated Evolution and Neofunctionalization of Duplicate Snake Venom Metalloproteinase Toxin Genes

(2011) N. R. Casewell et al.   MOLECULAR BIOLOGY AND EVOLUTION

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation

(2011) J. J. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultra-deep sequencing for the analysis of viral populations

(2011) Niko Beerenwinkel et al.   Current Opinion in Virology

Comparing de novo assemblers for 454 transcriptome data

(2010) Sujai Kumar et al.   BMC GENOMICS

Assembly algorithms for next-generation sequencing data

(2010) Jason R. Miller et al.   GENOMICS

Gene Tree Parsimony of Multilocus Snake Venom Protein Families Reveals Species Tree Conflict as a Result of Multiple Parallel Gene Loss

(2010) Nicholas R. Casewell et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

Comparative analysis of newborn and adult Bothrops jararaca snake venoms

(2010) Thatiane C. Antunes et al.   TOXICON

The Evolutionary Analysis of Emerging Low Frequency HIV-1 CXCR4 Using Variants through Time—An Ultra-Deep Approach

(2010) John Archer et al.   PLoS Computational Biology

The Toxicogenomic Multiverse: Convergent Recruitment of Proteins Into Animal Venoms

(2009) Bryan G. Fry et al.   Annual Review of Genomics and Human Genetics

Comparative venom gland transcriptome surveys of the saw-scaled vipers (Viperidae: Echis) reveal substantial intra-family gene diversity and novel venom transcripts

(2009) Nicholas R Casewell et al.   BMC GENOMICS

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Coevolution of diet and prey-specific venom activity supports the role of selection in snake venom evolution

(2009) A. Barlow et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

The Genome Sequencer FLX™ System—Longer reads, more applications, straight forward bioinformatics and more complete data sets

(2008) Marcus Droege et al.   JOURNAL OF BIOTECHNOLOGY

Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing

(2008) P. J. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Viral Population Estimation Using Pyrosequencing

(2008) Nicholas Eriksson et al.   PLoS Computational Biology