Machine Learning for detection of viral sequences in human metagenomic datasets

Extension of the viral ecology in humans using viral profile hidden Markov models

(2018) Zurab Bzhalava et al.   PLoS One

Detection of DNA viruses in prostate cancer

(2016) Vitaly Smelov et al.   Scientific Reports

Viremia during pregnancy and risk of childhood leukemia and lymphomas in the offspring: Nested case-control study

(2015) Davit Bzhalava et al.   INTERNATIONAL JOURNAL OF CANCER

Importance of codon usage for the temporal regulation of viral gene expression

(2015) Young C. Shin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Does human papillomavirus-negative condylomata exist?

(2015) Laila Sara Arroyo Mühr et al.   VIROLOGY

Human papillomavirus type 197 is commonly present in skin tumors

(2014) L. Sara Arroyo Mühr et al.   INTERNATIONAL JOURNAL OF CANCER

Profile Hidden Markov Models for the Detection of Viruses within Metagenomic Sequence Data

(2014) Peter Skewes-Cox et al.   PLoS One

Deep sequencing extends the diversity of human papillomaviruses in human skin

(2014) Davit Bzhalava et al.   Scientific Reports

Previously unknown and highly divergent ssDNA viruses populate the oceans

(2013) Jessica M Labonté et al.   ISME Journal

Unbiased Approach for Virus Detection in Skin Lesions

(2013) Davit Bzhalava et al.   PLoS One

The human virome: new tools and concepts

(2013) Marc Lecuit et al.   TRENDS IN MICROBIOLOGY

Metagenomic sequencing of “HPV-negative” condylomas detects novel putative HPV types

(2013) Hanna Johansson et al.   VIROLOGY

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Next-generation sequencing and large genome assemblies

(2012) Joseph Henson et al.   PHARMACOGENOMICS

Sequence Analysis of the Human Virome in Febrile and Afebrile Children

(2012) Kristine M. Wylie et al.   PLoS One

Human Skin Microbiota: High Diversity of DNA Viruses Identified on the Human Skin by High Throughput Sequencing

(2012) Vincent Foulongne et al.   PLoS One

Emerging view of the human virome

(2012) Kristine M. Wylie et al.   Translational Research

Phylogenetically diverse TT virus viremia among pregnant women

(2012) Davit Bzhalava et al.   VIROLOGY

Next-generation sequencing of cervical DNA detects human papillomavirus types not detected by commercial kits

(2012) Tracy L Meiring et al.   Virology Journal

Large and linked in scientific publishing

(2012) Laurie Goodman et al.   GigaScience

Case Studies of the Spatial Heterogeneity of DNA Viruses in the Cystic Fibrosis Lung

(2011) Dana Willner et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

High throughput sequencing reveals diversity of Human Papillomaviruses in cutaneous lesions

(2011) Johanna Ekström et al.   INTERNATIONAL JOURNAL OF CANCER

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Metagenomic Analysis of Respiratory Tract DNA Viral Communities in Cystic Fibrosis and Non-Cystic Fibrosis Individuals

(2009) Dana Willner et al.   PLoS One

Conditional Variable Importance for Random Forests

(2008) Carolin Strobl et al.   BMC BIOINFORMATICS

Clonal Integration of a Polyomavirus in Human Merkel Cell Carcinoma

(2008) H. Feng et al.   SCIENCE

Newly Discovered Ebola Virus Associated with Hemorrhagic Fever Outbreak in Uganda

(2008) Jonathan S. Towner et al.   PLoS Pathogens

Empirical characterization of random forest variable importance measures

(2007) Kellie J. Archer et al.   COMPUTATIONAL STATISTICS & DATA ANALYSIS