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List of works by Anton Nekrutenko

28-way vertebrate alignment and conservation track in the UCSC Genome Browser

scientific article (publication date: December 2007)

A High-Resolution View of Adaptive Event Dynamics in a Plasmid

scientific article published on 01 October 2019

A first look at ARFome: dual-coding genes in mammalian genomes

scientific article

A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly

scientific article

A massively parallel sequencing approach uncovers ancient origins and high genetic variability of endangered Przewalski's horses

scientific article (publication date: 2011)

A reference model for deploying applications in virtualized environments

A single-cell RNA-sequencing training and analysis suite using the Galaxy framework

scientific article published on 01 October 2020

A sustainable national gateway for biological computation

An evolutionary approach reveals a high protein-coding capacity of the human genome

scientific article

Assessment of compositional heterogeneity within and between eukaryotic genomes

scientific article

Biology Needs Evolutionary Software Tools: Let's Build Them Right.

scientific article published on 23 April 2018

Bottleneck and selection in the germline and maternal age influence transmission of mitochondrial DNA in human pedigrees

scientific article published on 22 November 2019

Child Weight Gain Trajectories Linked To Oral Microbiota Composition

scientific article published in Scientific Reports

Community-Driven Data Analysis Training for Biology

scientific article published on 01 June 2018

Comparative genomics

scientific article published in January 2004

Complete Khoisan and Bantu genomes from southern Africa

scientific article

Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach

scientific article

Densities, length proportions, and other distributional features of repetitive sequences in the human genome estimated from 430 megabases of genomic sequence

article

Detection of gene duplications and block duplications in eukaryotic genomes

scientific article

Dissemination of scientific software with Galaxy ToolShed

scientific article (publication date: 20 February 2014)

Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study

scientific article published on 23 June 2011

ETOPE: Evolutionary test of predicted exons

scientific article

Enhancing pre-defined workflows with ad hoc analytics using Galaxy, Docker and Jupyter

Erratum: The anatomy of successful computational biology software

article

Evolutionary Dynamics of Oncogenes and Tumor Suppressor Genes: Higher Intensities of Purifying Selection than Other Genes

article

Evolutionary analyses of the human genome

scientific article (publication date: 15 February 2001)

Family reunion via error correction: an efficient analysis of duplex sequencing data

scientific article published on 04 March 2020

Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring

scientific article

Functionality of unspliced XBP1 is required to explain evolution of overlapping reading frames

scientific article published on 10 October 2006

Galaxy CloudMan: delivering cloud compute clusters

scientific article

Galaxy: A Gateway to Tools in e-Science

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences ⬇️

scientific article published on August 25, 2010

Galaxy: a platform for interactive large-scale genome analysis

scientific article

Galaxy: a web-based genome analysis tool for experimentalists

scientific article

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

scientific article

Harnessing cloud computing with Galaxy Cloud

scientific article published on 8 November 2011

High-resolution mapping of evolutionary trajectories in a phage

scientific article published on 11 August 2009

HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies

scientific article published on 01 January 2020

Identification of novel exons from rat-mouse comparisons

scientific article

In memory of James Taylor: the birth of Galaxy

scientific article published on 30 April 2020

Increased yields of duplex sequencing data by a series of quality control tools

scientific article published on 09 February 2021

Integrating diverse databases into an unified analysis framework: a Galaxy approach

scientific article (publication date: 2011)

Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace

scientific article published on 18 January 2016

Isolation of binary species-specific PCR-based markers and their value for diagnostic applications

scientific article published in May 2000

Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers.

scientific article

Lessons learned from Galaxy, a Web-based platform for high-throughput genomic analyses

Making whole genome multiple alignments usable for biologists

scientific article (publication date: September 2011)

Manipulation of FASTQ data with Galaxy

scientific article

Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA.

scientific article published on 13 October 2014

NGS analyses by visualization with Trackster

scientific article

Next-generation sequencing data interpretation: enhancing reproducibility and accessibility ⬇️

scientific article published on September 1, 2012

No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics

scientific article published on 13 August 2020

No more business as usual: agile and effective responses to emerging pathogen threats require open data and open analytics

scientific article published on 22 February 2020

Online resources for genomic analysis using high-throughput sequencing

scientific article published on 5 February 2015

Oscillating evolution of a mammalian locus with overlapping reading frames: an XLalphas/ALEX relay

scientific article

Practical Computational Reproducibility in the Life Sciences

scientific article published on 01 June 2018

Practical computational reproducibility in the life sciences

scientific article published on 10 October 2017

Predicting runtimes of bioinformatics tools based on historical data: five years of Galaxy usage

scientific article published on 01 September 2019

RNA-DNA differences in human mitochondria restore ancestral form of 16S ribosomal RNA

scientific article published on 02 August 2013

Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network

scientific article

Rapid asymmetric evolution of a dual-coding tumor suppressor INK4a/ARF locus contradicts its function

scientific article

Reconciling the numbers: ESTs versus protein-coding genes

scientific article published on 19 March 2004

Representational difference analysis to distinguish cryptic species

scientific article published in 1999

Reproducible and accessible analysis of transposon insertion sequencing in Galaxy for qualitative essentiality analyses

scientific article

Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function

scientific article published on 01 April 2022

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

scientific article

Sequencing error profiles of Illumina sequencing instruments

scientific article

Signatures of domain shuffling in the human genome

scientific article published on November 2002

Streamlined analysis of duplex sequencing data with Du Novo

scientific article

StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo.

scientific article

Subgenome-specific markers in allopolyploid cotton Gossypium hirsutum: implications for evolutionary analysis of polyploids

article

Ten simple rules for reproducible computational research

scientific article

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

scientific article

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update.

scientific article published in July 2018

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update

scientific article published on 01 June 2020

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update

a correction published on 25 June 2020

The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

scientific article published on 20 May 2024

The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study

scientific article

The anatomy of successful computational biology software

scientific article

The elastic analysis with galaxy on the cloud.

scientific article published on 11 October 2010

Toward the commoditization of translational genomic research: Design and implementation features of the Galaxy genomic workbench

scientific article

Transcriptome of embryonic and neonatal mouse cortex by high-throughput RNA sequencing.

scholarly article

Transposable elements are found in a large number of human protein-coding genes

article

Using Galaxy to perform large-scale interactive data analyses

scientific article

Using galaxy to perform large-scale interactive data analyses

scientific article

Web-based analysis of (Epi-) genome data using EpiGRAPH and Galaxy

scientific article

Web-based visual analysis for high-throughput genomics

scientific article

Wheels within wheels: clues to the evolution of the Gnas and Gnal loci

scientific article published on 8 October 2008

Windshield splatter analysis with the Galaxy metagenomic pipeline

scientific article published on 09 October 2009

Wrangling Galaxy's reference data

scientific article

mNSC1 shows no evidence of protein-coding capacity

scientific article

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