ViraMiner: Deep learning on raw DNA sequences for identifying viral genomes in human samples

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

(2018) Zurab Bzhalava et al.   PLoS One

Machine Learning for detection of viral sequences in human metagenomic datasets

(2018) Zurab Bzhalava et al.   BMC BIOINFORMATICS

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

(2017) Jie Ren et al.   Microbiome

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks

(2016) David R. Kelley et al.   GENOME RESEARCH

Deep learning for computational biology

(2016) Christof Angermueller et al.   Molecular Systems Biology

Detection of DNA viruses in prostate cancer

(2016) Vitaly Smelov et al.   Scientific Reports

Large-scale machine learning for metagenomics sequence classification

(2015) Kévin Vervier et al.   BIOINFORMATICS

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

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

Does human papillomavirus-negative condylomata exist?

(2015) Laila Sara Arroyo Mühr et al.   VIROLOGY

16S Classifier: A Tool for Fast and Accurate Taxonomic Classification of 16S rRNA Hypervariable Regions in Metagenomic Datasets

(2015) Nikhil Chaudhary et al.   PLoS One

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

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

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

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

(2012) Y. Peng et al.   BIOINFORMATICS

No evidence of enteroviruses in the intestine of patients with type 1 diabetes

(2012) A. Mercalli et al.   DIABETOLOGIA

Deep Neural Networks for Acoustic Modeling in Speech Recognition: The Shared Views of Four Research Groups

(2012) Geoffrey Hinton et al.   IEEE SIGNAL PROCESSING MAGAZINE

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

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo 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

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

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 short read alignment with Burrows-Wheeler transform

(2009) H. 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

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