List of works - Konrad Scheffler

A Bayesian Model Comparison Approach to Inferring Positive Selection

article

A model of directional selection applied to the evolution of drug resistance in HIV-1.

scientific article published in February 2007

A random effects branch-site model for detecting episodic diversifying selection.

scientific article published on 13 June 2011

Automatic learning of dialogue strategy using dialogue simulation and reinforcement learning

scholarly article published 2002

Benchmarking multi-rate codon models

scientific article

CodonTest: modeling amino acid substitution preferences in coding sequences

scientific article

Compartmentalized HIV rebound in the central nervous system after interruption of antiretroviral therapy

scientific article published on July 2016

Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial

scientific article

Correcting the bias of empirical frequency parameter estimators in codon models

scientific article

DETECTING MOLECULAR EVIDENCE OF POSITIVE DARWINIAN SELECTION

article

Deep sequencing reveals minor protease resistance mutations in patients failing a protease inhibitor regimen.

scientific article

Detecting individual sites subject to episodic diversifying selection

scientific article

Detecting phylogenetic signal in mutualistic interaction networks using a Markov process model

scientific article

Epitope discovery with phylogenetic hidden Markov models

scientific article

Evidence of HIV-1 adaptation to host HLA alleles following chimp-to-human transmission

scientific article published on 10 October 2009

Evolutionary fingerprinting of genes.

scientific article

Evolutionary origins of human herpes simplex viruses 1 and 2

scientific article

Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences

scientific article published on 23 December 2008

FUBAR: a fast, unconstrained bayesian approximation for inferring selection

scientific article published on 18 February 2013

Frequent toggling between alternative amino acids is driven by selection in HIV-1

scientific article

Gene-wide identification of episodic selection

scientific article published on 19 February 2015

Genome-wide survey of allele-specific splicing in humans

scientific article

IDEPI: rapid prediction of HIV-1 antibody epitopes and other phenotypic features from sequence data using a flexible machine learning platform

scientific article (publication date: September 2014)

Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection

scientific article

Maximum likelihood inference of imprinting and allele-specific expression from EST data

scientific article

Modeling HIV-1 drug resistance as episodic directional selection

scientific article

Models of coding sequence evolution

scientific article published on 29 October 2008

Non-negative matrix factorization for learning alignment-specific models of protein evolution

scientific article

On the validity of evolutionary models with site-specific parameters

scientific article

Phylogenetic relatedness of HIV-1 donor and recipient populations.

scientific article published on 11 January 2013

RELAX: detecting relaxed selection in a phylogenetic framework

scientific article

Robust inference of positive selection from recombining coding sequences

scientific article published on 7 August 2006

Seminal Shedding of CMV and HIV Transmission among Men Who Have Sex with Men.

scientific article published on 7 July 2015

Social and Genetic Networks of HIV-1 Transmission in New York City

scientific article

Standard vaccines increase HIV-1 transcription during antiretroviral therapy.

scientific article published on 16 July 2016

Strelka2: Fast and accurate variant calling for clinical sequencing applications

Strelka2: fast and accurate calling of germline and somatic variants

scholarly article by Sangtae Kim published in July 2018

Using HIV Sequence and Epidemiologic Data to Assess the Effect of Self-referral Testing for Acute HIV Infection on Incident Diagnoses in San Diego, California

scientific article

Very Low Power to Detect Asymmetric Divergence of Duplicated Genes

article

List of works by Konrad Scheffler

A Bayesian Model Comparison Approach to Inferring Positive Selection

A model of directional selection applied to the evolution of drug resistance in HIV-1.

A random effects branch-site model for detecting episodic diversifying selection.

Automatic learning of dialogue strategy using dialogue simulation and reinforcement learning

Benchmarking multi-rate codon models

CodonTest: modeling amino acid substitution preferences in coding sequences

Compartmentalized HIV rebound in the central nervous system after interruption of antiretroviral therapy

Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial

Correcting the bias of empirical frequency parameter estimators in codon models

DETECTING MOLECULAR EVIDENCE OF POSITIVE DARWINIAN SELECTION

Deep sequencing reveals minor protease resistance mutations in patients failing a protease inhibitor regimen.

Detecting individual sites subject to episodic diversifying selection

Detecting phylogenetic signal in mutualistic interaction networks using a Markov process model

Epitope discovery with phylogenetic hidden Markov models

Evidence of HIV-1 adaptation to host HLA alleles following chimp-to-human transmission

Evolutionary fingerprinting of genes.

Evolutionary origins of human herpes simplex viruses 1 and 2

Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences

FUBAR: a fast, unconstrained bayesian approximation for inferring selection

Frequent toggling between alternative amino acids is driven by selection in HIV-1

Gene-wide identification of episodic selection

Genome-wide survey of allele-specific splicing in humans

IDEPI: rapid prediction of HIV-1 antibody epitopes and other phenotypic features from sequence data using a flexible machine learning platform

Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection

Maximum likelihood inference of imprinting and allele-specific expression from EST data

Modeling HIV-1 drug resistance as episodic directional selection

Models of coding sequence evolution

Non-negative matrix factorization for learning alignment-specific models of protein evolution

On the validity of evolutionary models with site-specific parameters

Phylogenetic relatedness of HIV-1 donor and recipient populations.

RELAX: detecting relaxed selection in a phylogenetic framework

Robust inference of positive selection from recombining coding sequences

Seminal Shedding of CMV and HIV Transmission among Men Who Have Sex with Men.

Social and Genetic Networks of HIV-1 Transmission in New York City

Standard vaccines increase HIV-1 transcription during antiretroviral therapy.

Strelka2: Fast and accurate variant calling for clinical sequencing applications

Strelka2: fast and accurate calling of germline and somatic variants

Using HIV Sequence and Epidemiologic Data to Assess the Effect of Self-referral Testing for Acute HIV Infection on Incident Diagnoses in San Diego, California

Very Low Power to Detect Asymmetric Divergence of Duplicated Genes