Comprehensive Analysis of Transcriptome Variation Uncovers Known and Novel Driver Events in T-Cell Acute Lymphoblastic Leukemia

Assessing identity, redundancy and confounds in Gene Ontology annotations over time

(2013) Jesse Gillis et al.   BIOINFORMATICS

New MLLT10 gene recombinations in pediatric T-acute lymphoblastic leukemia

(2013) L. Brandimarte et al.   BLOOD

Discovery of somatic STAT5b mutations in large granular lymphocytic leukemia

(2013) H. L. M. Rajala et al.   BLOOD

Bivalent promoter marks and a latent enhancer may prime the leukaemia oncogene LMO1 for ectopic expression in T-cell leukaemia

(2013) S H Oram et al.   LEUKEMIA

Development of Strategies for SNP Detection in RNA-Seq Data: Application to Lymphoblastoid Cell Lines and Evaluation Using 1000 Genomes Data

(2013) Emma M. Quinn et al.   PLoS One

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Extensive molecular mapping of TCR / - and TCR -involved chromosomal translocations reveals distinct mechanisms of oncogene activation in T-ALL

(2012) S. Le Noir et al.   BLOOD

Mutation of the receptor tyrosine phosphatase PTPRC (CD45) in T-cell acute lymphoblastic leukemia

(2012) M. Porcu et al.   BLOOD

Chimeric RNAs as potential biomarkers for tumor diagnosis

(2012) Jianhua Zhou et al.   BMB Reports

Hotspot Mutations in H3F3A and IDH1 Define Distinct Epigenetic and Biological Subgroups of Glioblastoma

(2012) Dominik Sturm et al.   CANCER CELL

From oncogene to tumor suppressor

(2012) Iris Uribesalgo et al.   CELL CYCLE

Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events

(2012) J. Liu et al.   GENOME RESEARCH

The transcriptional landscape and mutational profile of lung adenocarcinoma

(2012) J.-S. Seo et al.   GENOME RESEARCH

The molecular basis of T cell acute lymphoblastic leukemia

(2012) Pieter Van Vlierberghe et al.   JOURNAL OF CLINICAL INVESTIGATION

Newly described activating JAK3 mutations in T-cell acute lymphoblastic leukemia

(2012) T Bains et al.   LEUKEMIA

Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma

(2012) Jeremy Schwartzentruber et al.   NATURE

The genetic basis of early T-cell precursor acute lymphoblastic leukaemia

(2012) Jinghui Zhang et al.   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

The difficult calls in RNA editing

(2012) Brenda Bass et al.   NATURE BIOTECHNOLOGY

Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas

(2012) Gang Wu et al.   NATURE GENETICS

Exome sequencing identifies mutation in CNOT3 and ribosomal genes RPL5 and RPL10 in T-cell acute lymphoblastic leukemia

(2012) Kim De Keersmaecker et al.   NATURE GENETICS

Exome RNA sequencing reveals rare and novel alternative transcripts

(2012) Jonatan Halvardson et al.   NUCLEIC ACIDS RESEARCH

ExPASy: SIB bioinformatics resource portal

(2012) P. Artimo et al.   NUCLEIC ACIDS RESEARCH

JAK/STAT signaling in hematological malignancies

(2012) W Vainchenker et al.   ONCOGENE

High Accuracy Mutation Detection in Leukemia on a Selected Panel of Cancer Genes

(2012) Zeynep Kalender Atak et al.   PLoS One

SomaticSniper: identification of somatic point mutations in whole genome sequencing data

(2011) David E. Larson et al.   BIOINFORMATICS

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

FERM domain mutations induce gain of function in JAK3 in adult T-cell leukemia/lymphoma

(2011) N. E. Elliott et al.   BLOOD

GC-Content Normalization for RNA-Seq Data

(2011) Davide Risso et al.   BMC BIOINFORMATICS

Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples

(2011) Serban Nacu et al.   BMC Medical Genomics

Gain-of-function mutations ininterleukin-7 receptor-α(IL7R) in childhood acute lymphoblastic leukemias

(2011) Chen Shochat et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma

(2011) Ryan D. Morin et al.   NATURE

MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers

(2011) Christian Steidl et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Oncogenic IL7R gain-of-function mutations in childhood T-cell acute lymphoblastic leukemia

(2011) Priscila P Zenatti et al.   NATURE GENETICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

SMART 7: recent updates to the protein domain annotation resource

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

Mutant p53 drives multinucleation and invasion through a process that is suppressed by ANKRD11

(2011) J E Noll et al.   ONCOGENE

Proline-Rich Tyrosine Kinase 2 (Pyk2) Promotes Cell Motility of Hepatocellular Carcinoma through Induction of Epithelial to Mesenchymal Transition

(2011) Chris K. Sun et al.   PLoS One

Mutations in CIC and FUBP1 Contribute to Human Oligodendroglioma

(2011) C. Bettegowda et al.   SCIENCE

Regulatory gene network circuits underlying T cell development from multipotent progenitors

(2011) Hao Yuan Kueh et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data

(2011) Andrew McPherson et al.   PLoS Computational Biology

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

(2010) William McLaren et al.   BIOINFORMATICS

SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors

(2010) Rodrigo Goya et al.   BIOINFORMATICS

Expression of tenascin-C and its isoforms in the breast

(2010) David S. Guttery et al.   CANCER AND METASTASIS REVIEWS

Integrative analysis of the melanoma transcriptome

(2010) M. F. Berger et al.   GENOME RESEARCH

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

PHF6 mutations in T-cell acute lymphoblastic leukemia

(2010) Pieter Van Vlierberghe et al.   NATURE GENETICS

Advances in understanding cancer genomes through second-generation sequencing

(2010) Matthew Meyerson et al.   NATURE REVIEWS GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Transcriptome sequencing to detect gene fusions in cancer

(2009) Christopher A. Maher et al.   NATURE

The transcriptional network for mesenchymal transformation of brain tumours

(2009) Maria Stella Carro et al.   NATURE

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays

(2009) R. Drmanac et al.   SCIENCE

A comprehensive analysis of the CDKN2A gene in childhood acute lymphoblastic leukemia reveals genomic deletion, copy number neutral loss of heterozygosity, and association with specific cytogenetic subgroups

(2008) S. Sulong et al.   BLOOD

Proline-rich tyrosine kinase 2 (Pyk2) promotes proliferation and invasiveness of hepatocellular carcinoma cells through c-Src/ERK activation

(2008) C. K. Sun et al.   CARCINOGENESIS

Somatically acquiredJAK1mutations in adult acute lymphoblastic leukemia

(2008) Elisabetta Flex et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Cooperative genetic defects in TLX3 rearranged pediatric T-ALL

(2008) P Van Vlierberghe et al.   LEUKEMIA

Alternative Splicing in Colon, Bladder, and Prostate Cancer Identified by Exon Array Analysis

(2008) Kasper Thorsen et al.   MOLECULAR & CELLULAR PROTEOMICS

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Biology and Treatment of Acute Lymphoblastic Leukemia

(2008) Rob Pieters et al.   PEDIATRIC CLINICS OF NORTH AMERICA