Cis-perturbation of cancer drivers by the HTLV-1/BLV proviruses is an early determinant of leukemogenesis

Retrovirus Integration Database (RID): a public database for retroviral insertion sites into host genomes

(2016) Wei Shao et al.   Retrovirology

Characterization of novel Bovine Leukemia Virus (BLV) antisense transcripts by deep sequencing reveals constitutive expression in tumors and transcriptional interaction with viral microRNAs

(2016) Keith Durkin et al.   Retrovirology

FOXR2 Interacts with MYC to Promote Its Transcriptional Activities and Tumorigenesis

(2016) Xu Li et al.   Cell Reports

HTLV-1 bZIP Factor RNA and Protein Impart Distinct Functions on T-cell Proliferation and Survival

(2015) Y. Mitobe et al.   CANCER RESEARCH

RNA sequencing ofSleeping Beautytransposon-induced tumors detects transposon-RNA fusions in forward genetic cancer screens

(2015) Nuri A. Temiz et al.   GENOME RESEARCH

Mutations of ASXL1 and TET2 in aplastic anemia

(2015) J. Huang et al.   HAEMATOLOGICA

SPSB1, a Novel Negative Regulator of the Transforming Growth Factor-β Signaling Pathway Targeting the Type II Receptor

(2015) Sheng Liu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Integrated molecular analysis of adult T cell leukemia/lymphoma

(2015) Keisuke Kataoka et al.   NATURE GENETICS

Ubiquitination by March-I prevents MHC class II recycling and promotes MHC class II turnover in antigen-presenting cells

(2015) Kyung-Jin Cho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mutations of ASXL1 and TET2 in aplastic anemia

(2015) J. Huang et al.   HAEMATOLOGICA

The role of HTLV-1 clonality, proviral structure, and genomic integration site in adult T-cell leukemia/lymphoma

(2014) L. B. Cook et al.   BLOOD

Viral-Human Chimeric Transcript Predisposes Risk to Liver Cancer Development and Progression

(2014) Chi-Chiu Lau et al.   CANCER CELL

Identification of FoxR2 as an Oncogene in Medulloblastoma

(2014) Hideto Koso et al.   CANCER RESEARCH

Options for the control of bovine leukemia virus in dairy cattle

(2014) Paul C. Bartlett et al.   JAVMA-JOURNAL OF THE AMERICAN VETERINARY MEDICAL ASSOCIATION

Human T-cell leukaemia virus type I and adult T-cell leukaemia-lymphoma

(2014) Kenji Ishitsuka et al.   LANCET ONCOLOGY

The E3 ligase Cbl-b and TAM receptors regulate cancer metastasis via natural killer cells

(2014) Magdalena Paolino et al.   NATURE

Novel principles of gamma-retroviral insertional transcription activation in murine leukemia virus-induced end-stage tumors

(2014) Martin Sokol et al.   Retrovirology

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution

(2013) Jing-Woei Li et al.   BIOINFORMATICS

The Lipid Transfer Protein StarD7: Structure, Function, and Regulation

(2013) Jésica Flores-Martin et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Deep sequencing reveals abundant noncanonical retroviral microRNAs in B-cell leukemia/lymphoma

(2013) N. Rosewick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HTLV-1 clonality in adult T-cell leukaemia and non-malignant HTLV-1 infection

(2013) Charles R.M. Bangham et al.   SEMINARS IN CANCER BIOLOGY

Human T-cell leukemia virus type 1: replication, proliferation and propagation by Tax and HTLV-1 bZIP factor

(2013) Masao Matsuoka et al.   Current Opinion in Virology

Genome-wide Determinants of Proviral Targeting, Clonal Abundance and Expression in Natural HTLV-1 Infection

(2013) Anat Melamed et al.   PLoS Pathogens

Massive Depletion of Bovine Leukemia Virus Proviral Clones Located in Genomic Transcriptionally Active Sites during Primary Infection

(2013) Nicolas A. Gillet et al.   PLoS Pathogens

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

Integrated genomic analyses identify ARID1A and ARID1B alterations in the childhood cancer neuroblastoma

(2012) Mark Sausen et al.   NATURE GENETICS

Epidemiological Aspects and World Distribution of HTLV-1 Infection

(2012) Antoine Gessain et al.   Frontiers in Microbiology

BamTools: a C++ API and toolkit for analyzing and managing BAM files

(2011) D. W. Barnett et al.   BIOINFORMATICS

The host genomic environment of the provirus determines the abundance of HTLV-1-infected T-cell clones

(2011) N. A. Gillet et al.   BLOOD

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Bovine leukemia virus integration site selection in cattle that develop leukemia

(2011) Hironobu Murakami et al.   VIRUS RESEARCH

HTLV-1 bZIP Factor Induces T-Cell Lymphoma and Systemic Inflammation In Vivo

(2011) Yorifumi Satou et al.   PLoS Pathogens

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Cytotoxic responses to BLV tax oncoprotein do not prevent leukemogenesis in sheep

(2010) Anne Van den Broeke et al.   LEUKEMIA RESEARCH

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

The immune control of HTLV-1 infection: selection forces and dynamics

(2009) Charles et al.   Frontiers in Bioscience-Landmark

Loss of TLE1 and TLE4 from the del(9q) commonly deleted region in AML cooperates with AML1-ETO to affect myeloid cell proliferation and survival

(2008) F. Dayyani et al.   BLOOD

PI3K pathway alterations in cancer: variations on a theme

(2008) T L Yuan et al.   ONCOGENE

A genome-wide RNAi screen for Wnt/ -catenin pathway components identifies unexpected roles for TCF transcription factors in cancer

(2008) W. Tang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Rag GTPases Bind Raptor and Mediate Amino Acid Signaling to mTORC1

(2008) Y. Sancak et al.   SCIENCE