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Author Details

Konrad Scheffler
Illumina Inc.
2005
42
24
PMIDPaper TitleJournal TitlePublished Year
36417740Extrapolation of System Matrices in Magnetic Particle Imaging.IEEE Trans Med Imaging2023
35948990REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats.Genome Med2022
33737402Timing the SARS-CoV-2 index case in Hubei province.Science2021
33269353Timing the SARS-CoV-2 Index Case in Hubei Province.bioRxiv2020
31134279ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions.Bioinformatics2019
30013048Strelka2: fast and accurate calling of germline and somatic variants.Nat Methods2018
28068413Social and Genetic Networks of HIV-1 Transmission in New York City.PLoS Pathog2017
27882678A molecular transmission network of recent hepatitis C infection in people with and without HIV: Implications for targeted treatment strategies.J Viral Hepat2017
27174704Using HIV Sequence and Epidemiologic Data to Assess the Effect of Self-referral Testing for Acute HIV Infection on Incident Diagnoses in San Diego, California.Clin Infect Dis2016
27774305Compartmentalized HIV rebound in the central nervous system after interruption of antiretroviral therapy.Virus Evol2016
27427877Standard vaccines increase HIV-1 transcription during antiretroviral therapy.AIDS2016
25540451RELAX: detecting relaxed selection in a phylogenetic framework.Mol Biol Evol2015
26431315Comparative Analysis of Cell-Associated HIV DNA Levels in Cerebrospinal Fluid and Peripheral Blood by Droplet Digital PCR.PLoS One2015
26198239Seminal Shedding of CMV and HIV Transmission among Men Who Have Sex with Men.Int J Environ Res Public Health2015
25701167Gene-wide identification of episodic selection.Mol Biol Evol2015
25646817Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial.PLoS Comput Biol2015
25697341Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection.Mol Biol Evol2015
24722425On the validity of evolutionary models with site-specific parameters.PLoS One2014
25254639IDEPI: rapid prediction of HIV-1 antibody epitopes and other phenotypic features from sequence data using a flexible machine learning platform.PLoS Comput Biol2014
25294947Detecting phylogenetic signal in mutualistic interaction networks using a Markov process model.Oikos2014
24916030Evolutionary origins of human herpes simplex viruses 1 and 2.Mol Biol Evol2014
23315327Phylogenetic relatedness of HIV-1 donor and recipient populations.J Infect Dis2013
23420840FUBAR: a fast, unconstrained bayesian approximation for inferring selection.Mol Biol Evol2013
22589711Modeling HIV-1 drug resistance as episodic directional selection.PLoS Comput Biol2012
22807683Detecting individual sites subject to episodic diversifying selection.PLoS Genet2012
22457522Deep sequencing reveals minor protease resistance mutations in patients failing a protease inhibitor regimen.J Virol2012
21670087A random effects branch-site model for detecting episodic diversifying selection.Mol Biol Evol2011
22216138Non-negative matrix factorization for learning alignment-specific models of protein evolution.PLoS One2011
20089717Epitope discovery with phylogenetic hidden Markov models.Mol Biol Evol2010
20808876CodonTest: modeling amino acid substitution preferences in coding sequences.PLoS Comput Biol2010
20689581Correcting the bias of empirical frequency parameter estimators in codon models.PLoS One2010
20657773Benchmarking multi-rate codon models.PLoS One2010
19864470Evolutionary fingerprinting of genes.Mol Biol Evol2010
18971241Models of coding sequence evolution.Brief Bioinform2009
19818146Evidence of HIV-1 adaptation to host HLA alleles following chimp-to-human transmission.Virol J2009
18518984Genome-wide survey of allele-specific splicing in humans.BMC Genomics2008
19105834Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences.Virol J2008
19096508Frequent toggling between alternative amino acids is driven by selection in HIV-1.PLoS Pathog2008
17272680A model of directional selection applied to the evolution of drug resistance in HIV-1.Mol Biol Evol2007
16895925Robust inference of positive selection from recombining coding sequences.Bioinformatics2006
17038342Maximum likelihood inference of imprinting and allele-specific expression from EST data.Bioinformatics2006
16120799A Bayesian model comparison approach to inferring positive selection.Mol Biol Evol2005
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Collaborators

Sergei L Kosakovsky Pond
Co-authored papers 22
Joel O Wertheim
University of California
Co-authored papers 11
Davey M Smith
University of California San Diego
Co-authored papers 11
Michael Worobey
University of Arizona
Co-authored papers 2
Susan J Little
Co-authored papers 2
Ronald J Ellis
University of California
Co-authored papers 2
Michael A Eberle
Illumina Inc.
Co-authored papers 2
Kristina Iba??ez
William Harvey Research Institute, Queen Mary University of London
Co-authored papers 2
Jonathan E Pekar
University of California San Diego
Co-authored papers 2
Douglas D Richman
Center for AIDS Research, University of California San Diego
Co-authored papers 2
Peter Krusche
Novartis Pharma AG
Co-authored papers 2
Simon D W Frost
Co-authored papers 2
Niema Moshiri
Bonita Vista High School, University of California San Diego, University of California, San Diego
Co-authored papers 2
Victoria Nembaware
University of Cape Town
Co-authored papers 2
Scott L Letendre
University of California, university of california san diego
Co-authored papers 2
Winston Hide
Harvard Medical School
Co-authored papers 1
Frances Lucy Raymond
University of Cambridge, UK Cambridge University Hospitals NHS Foundation Trust
Co-authored papers 1
Mark F Bennett
Co-authored papers 1
Ivelin S Georgiev
Co-authored papers 1
Dorothea Emig
Departments of Bioinformatics and Clinical Genomics, Illumina Inc.
Co-authored papers 1
Sangtae Kim
Co-authored papers 1
Raphael Gottardo
Fred Hutchinson Cancer Center
Co-authored papers 1
Jonathan M Carlson
Co-authored papers 1
David R Bentley
Illumina Cambridge Ltd.
Co-authored papers 1
Ben Weisburd
Broad Institute of MIT and Harvard
Co-authored papers 1
Anthony Aylward
Co-authored papers 1
Bryan R Lajoie
NASA Ames Research Center
Co-authored papers 1
Aaron L Halpern
Illumina Inc.
Co-authored papers 1
Heidi L Rehm
The Broad Institute of MIT and Harvard
Co-authored papers 1
Peter D Kwong
Co-authored papers 1
Release 1.2