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List of works by Michael C. Schatz

16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model

scientific article published on 15 June 2017

16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model

A diploid assembly-based benchmark for variants in the major histocompatibility complex

scientific article published on 22 September 2020

A master regulator of regeneration

scientific article published on 01 March 2019

A multi-task convolutional deep neural network for variant calling in single molecule sequencing

scientific article published on 01 March 2019

A plasmid locus associated with Klebsiella clinical infections encodes a microbiome-dependent gut fitness factor

scientific article published on 30 April 2021

A robust benchmark for detection of germline large deletions and insertions

scientific article published on 15 June 2020

Abstract 850: Comprehensive genome and transcriptome structural analysis of a breast cancer cell line using single molecule sequencing

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

scientific article published on 12 August 2019

Accurate de novo and transmitted indel detection in exome-capture data using microassembly

scientific article

Accurate detection of complex structural variations using single-molecule sequencing

article by Fritz Sedlazeck et al published June 2018 in Nature Methods

Addressing confounding artifacts in reconstruction of gene co-expression networks

article

Addressing confounding artifacts in reconstruction of gene co-expression networks

Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L

scientific article published on 08 October 2018

Aluminum tolerance in maize is associated with higher MATE1 gene copy number

scientific article published on 11 March 2013

Antibiotic pressure on the acquisition and loss of antibiotic resistance genes in Klebsiella pneumoniae.

scientific article published on 10 April 2018

Applying Rapid Whole Genome Sequencing to Predict Phenotypic Antimicrobial Susceptibility Testing Results Among Carbapenem-Resistant Clinical Isolates

scientific article published on 21 December 2018

Assemblathon 1: a competitive assessment of de novo short read assembly methods

scientific article

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

scientific article

Assembly complexity of prokaryotic genomes using short reads

scientific article

Assembly of large genomes using second-generation sequencing

scientific article published on 27 May 2010

Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop

scientific article published on 01 December 2019

Assemblytics: a web analytics tool for the detection of variants from an assembly.

scientific article published on 17 June 2016

Author Correction: A robust benchmark for detection of germline large deletions and insertions

scientific article published on 22 July 2020

Author Correction: Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato

scientific article published on 01 August 2019

Automated correction of genome sequence errors

scientific article published on 26 January 2004

Big Data: Astronomical or Genomical?

scientific article published on 7 July 2015

Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding

scientific article

Clonal Hematopoiesis Before, During, and After Human Spaceflight

scientific article published in 2020

Cloud computing and the DNA data race

scientific article

CloudBurst: highly sensitive read mapping with MapReduce

scientific article published on 08 April 2009

Comparative genomics of mutualistic viruses of Glyptapanteles parasitic wasps

scientific article published on 30 December 2008

Complete Sequence of a 641-kb Insertion of Mitochondrial DNA in the Arabidopsis thaliana Nuclear Genome

scientific article published on 01 May 2022

Complete genomic and epigenetic maps of human centromeres

scientific article published in April 2022

Complete genomic and epigenetic maps of human centromeres

scientific article published on 13 July 2021

Complex microbiome underlying secondary and primary metabolism in the tunicate-Prochloron symbiosis

scientific article published on 28 November 2011

Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line

scientific article published on 28 June 2018

Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing

scientific article published on 04 September 2020

Computational thinking in the era of big data biology ⬇️

scientific article published on November 29, 2012

Conservation Genomics of the Declining North American Bumblebee Reveals Inbreeding and Selection on Immune Genes

article

Correction: Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding.

scientific article published on 9 December 2016

Current challenges in de novo plant genome sequencing and assembly

scientific article

De Novo Gene Disruptions in Children on the Autistic Spectrum

scientific article (publication date: April 2012)

De novo genome assembly of Candida glabrata reveals cell wall protein complement and structure of dispersed tandem repeat arrays

scientific article published on 18 February 2020

Draft genome of the filarial nematode parasite Brugia malayi

scientific article

Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis

scientific article

Dual functions of Macpiwi1 in transposon silencing and stem cell maintenance in the flatworm Macrostomum lignano

scientific article

Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato

scientific article published on 06 May 2019

Erratum to: The advantages of SMRT sequencing

scientific article published on 16 August 2017

Establishing Physalis as a Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome ⬇️

scientific article published on 21 October 2022

Evolution of genes and genomes on the Drosophila phylogeny

scientific article

Extending reference assembly models

scientific article

Fast and accurate reference-guided scaffolding of draft genomes

article published in 2019

First near complete haplotype phased genome assembly of River buffalo (Bubalus bubalis)

From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

scientific article published in April 2022

From telomere to telomere: the transcriptional and epigenetic state of human repeat elements

scientific article published on 12 July 2021

GAGE: A critical evaluation of genome assemblies and assembly algorithms

scientific article published on 6 January 2012

Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet

scientific article published in 2023

Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano.

scientific article

Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius

scientific article published on 2 February 2016

Genome assembly forensics: finding the elusive mis-assembly

scientific article

Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.)

scientific article

Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A

article

Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A.

scientific article

Genome sequence of Aedes aegypti, a major arbovirus vector

scientific article

GenomeScope: Fast reference-free genome profiling from short reads.

scientific article

Genome‐wide patterns of transposon proliferation in an evolutionary young hybrid fish

scientific article published on 06 February 2019

Genomic Diversity of SARS-CoV-2 During Early Introduction into the United States National Capital Region

scientific article published on 15 August 2020

Genomic analyses of the microsporidian Nosema ceranae, an emergent pathogen of honey bees

scientific article published in June 2009

Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score ⬇️

scientific article published on June 4, 2012

Genomic diversity of SARS-CoV-2 during early introduction into the Baltimore-Washington metropolitan area

scientific article published on 22 March 2021

Genomic survey of the ectoparasitic mite Varroa destructor, a major pest of the honey bee Apis mellifera

scientific article

Genotyping in the Cloud with Crossbow ⬇️

scientific article published on September 1, 2012

Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies

scientific article published on 23 December 2011

Hawkeye: an interactive visual analytics tool for genome assemblies

scientific article published on January 2007

High-coverage sequencing and annotated assemblies of the budgerigar genome

scientific article

High-throughput sequence alignment using Graphics Processing Units

scientific article

Highly-accurate long-read sequencing improves variant detection and assembly of a human genome: Supplementary Material

article

Hybrid assembly with long and short reads improves discovery of gene family expansions

scientific article

Hybrid error correction and de novo assembly of single-molecule sequencing reads

scientific article

In memory of James Taylor: the birth of Galaxy

scientific article published on 30 April 2020

Indel variant analysis of short-read sequencing data with Scalpel.

scientific article

Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida.

scientific article published on 27 May 2016

Integrated microbial survey analysis of prokaryotic communities for the PhyloChip microarray

scientific article

Interactive analysis and assessment of single-cell copy-number variations

scientific article published on 7 September 2015

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space

scientific article published on 13 January 2022

KBase: The United States Department of Energy Systems Biology Knowledgebase

article

LRSim: A Linked-Reads Simulator Generating Insights for Better Genome Partitioning

scientific article published on 9 November 2017

Local adaptation and archaic introgression shape global diversity at human structural variant loci

scientific article published in 2021

Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato

scientific article published on 08 June 2020

Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species

scientific article published in January 2005

Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud

scientific article published on 31 March 2020

Metassembler: merging and optimizing de novo genome assemblies

scientific article

Molecular genetic diversity and characterization of conjugation genes in the fish parasite Ichthyophthirius multifiliis

scientific article

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis

scientific article published in 2010

Natural Genetic Diversity in Tomato Flavor Genes

scientific article published on 04 June 2021

Optimizing Data Intensive GPGPU Computations for DNA Sequence Alignment

scientific article

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome

scientific article

Paragraph: a graph-based structural variant genotyper for short-read sequence data

scientific article published on 19 December 2019

Parliament2: Accurate structural variant calling at scale

scientific article published on 01 December 2020

Parrot Genomes and the Evolution of Heightened Longevity and Cognition

scientific article published on 06 December 2018

Phased diploid genome assembly with single-molecule real-time sequencing.

scientific article

Piercing the dark matter: bioinformatics of long-range sequencing and mapping. ⬇️

scientific article

Publisher Correction: Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L

scientific article published on 01 December 2018

Quake: quality-aware detection and correction of sequencing errors

scientific article

RaGOO: fast and accurate reference-guided scaffolding of draft genomes

scientific article published on 28 October 2019

Rate of meristem maturation determines inflorescence architecture in tomato

scientific article

Recovering rearranged cancer chromosomes from karyotype graphs

scientific article published on 17 December 2019

Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma

scientific article published on 8 May 2017

Reducing INDEL calling errors in whole genome and exome sequencing data

scientific article

Reference Quality Assembly of the 3.5 Gb genome ofCapsicum annuumfrom a Single Linked-Read Library

Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library

scientific article published on 12 January 2018

Revealing biological modules via graph summarization

scientific article

Ribbon: Intuitive visualization for complex genomic variation

scientific article published on 07 August 2020

Samovar: Single-Sample Mosaic Single-Nucleotide Variant Calling with Linked Reads

scientific article published on 29 May 2019

Sapling: Accelerating Suffix Array Queries with Learned Data Models

scientific article published on 27 October 2020

Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy

scholarly article

Scikit-ribo Enables Accurate Estimation and Robust Modeling of Translation Dynamics at Codon Resolution

scientific article published on 17 January 2018

Scikit-ribo: Accurate estimation and robust modeling of translation dynamics at codon resolution

Searching for SNPs with cloud computing

scientific article

Sixty years of genome biology

scientific article published on 25 April 2013

Skyhawk: An Artificial Neural Network-based discriminator for reviewing clinically significant genomic variants

scholarly article published 1 May 2018

SplitMEM: a graphical algorithm for pan-genome analysis with suffix skips

scientific article

Structure and evolution of a proviral locus of Glyptapanteles indiensis bracovirus

scientific article published on 26 June 2007

TGF-β reduces DNA ds-break repair mechanisms to heighten genetic diversity and adaptability of CD44+/CD24- cancer cells.

scientific article published on 16 January 2017

Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED

scientific article published on 30 November 2020

Teaser: Individualized benchmarking and optimization of read mapping results for NGS data.

scientific article published on 22 October 2015

The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes

preprint article published in December 2023

The DNA Data Deluge: Fast, efficient genome sequencing machines are spewing out more data than geneticists can analyze

scientific article

The DNA60IFX contest

scientific article

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update

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

scientific article published on 20 May 2024

The advantages of SMRT sequencing

scientific article (publication date: 3 July 2013)

The bracteatus pineapple genome and domestication of clonally propagated crops

scientific article published on 30 September 2019

The challenge of small-scale repeats for indel discovery

scientific article

The complete sequence and comparative analysis of ape sex chromosomes

scholarly article published in June 2024

The complete sequence of a human Y chromosome

The complete sequence of a human genome

scientific article published in April 2022

The complete sequence of a human genome

scientific article published on 27 May 2021

The contribution of de novo coding mutations to autism spectrum disorder

scientific article

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).

scientific article

The evolution of inflorescence diversity in the nightshades and heterochrony during meristem maturation

scientific article

The genome of the Wollemi pine, a critically endangered “living fossil” unchanged since the Cretaceous, reveals extensive ancient transposon activity

The genomic basis of evolutionary differentiation among honey bees

scientific article published on 04 May 2021

The missing graphical user interface for genomics

scientific article

The pineapple genome and the evolution of CAM photosynthesis

scientific article published on 2 November 2015

The rise of a digital immune system

scientific article

Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp.

scientific article

Vargas: heuristic-free alignment for assessing linear and graph read aligners

scientific article published on 22 April 2020

Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica

scientific article

iGenomics: Comprehensive DNA sequence analysis on your Smartphone

scientific article published on 01 December 2020

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