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List of works by Mark Diekhans

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

scientific article (publication date: December 2007)

A draft human pangenome reference

scientific article published on 10 May 2023

AMELIE speeds Mendelian diagnosis by matching patient phenotype and genotype to primary literature

scientific article published on 01 May 2020

Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing

scientific article published on October 2004

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

scientific article

Author Correction: Dense sampling of bird diversity increases power of comparative genomics

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer

scientific article

CRAVAT: cancer-related analysis of variants toolkit

scientific article published on 16 January 2013

Cactus Graphs for Genome Comparisons

scientific article (publication date: 2010)

Cactus graphs for genome comparisons

scientific article published in March 2011

Cactus: Algorithms for genome multiple sequence alignment

scientific article published on 10 June 2011

Combining local-structure, fold-recognition, and new fold methods for protein structure prediction.

scientific article

Comparative Annotation Toolkit (CAT) - simultaneous clade and personal genome annotation

article published in 2017

Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation

Comparative analysis of pseudogenes across three phyla

scientific article

Comparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs ⬇️

Comparative genomics search for losses of long-established genes on the human lineage

scientific article published in December 2007

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

Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation

scientific article

Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution

scientific article

Current status and new features of the Consensus Coding Sequence database

scientific article

Dense sampling of bird diversity increases power of comparative genomics

scientific article published on 11 November 2020

ENCODE data in the UCSC Genome Browser: year 5 update

scientific article

ENCODE whole-genome data in the UCSC Genome Browser: update 2012.

scientific article

Evaluating recovery potential of the northern white rhinoceros from cryopreserved somatic cells.

scientific article published on 24 May 2018

Evolutionary constraint and innovation across hundreds of placental mammals

scientific article published on 28 April 2023

GENCODE 2021 ⬇️

scientific article published on 03 December 2020

GENCODE reference annotation for the human and mouse genomes

scientific article published on 01 January 2019

GENCODE: the reference human genome annotation for The ENCODE Project

scientific article

Genomic legacy of the African cheetah, Acinonyx jubatus

scientific article

High-resolution comparative analysis of great ape genomes

scientific article published in Science

Identification of high-confidence human poly(A) RNA isoform scaffolds using nanopore sequencing

scientific article published on 02 November 2021

Initial sequencing and comparative analysis of the mouse genome

scientific article

Insights into mammalian TE diversity through the curation of 248 genome assemblies ⬇️

Integrating gene annotation with orthology inference at scale ⬇️

scientific article published on 28 April 2023

LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures.

scientific article

LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources.

scientific article

Long-read sequence assembly of the gorilla genome

scientific article published on April 2016

Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges.

scientific article published on 23 May 2017

MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures

scientific article

Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes

scientific article (publication date: 15 November 2014)

Multiple laboratory mouse reference genomes define strain specific haplotypes and novel functional loci

Progressive Cactus is a multiple-genome aligner for the thousand-genome era

scientific article published on 11 November 2020

Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era

scientific article published on 9 August 2019

Pseudogenes in the mouse lineage: transcriptional activity and strain-specific history

Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in SCN1A

scientific article published on 02 December 2019

Regions of extreme synonymous codon selection in mammalian genes

scientific article

Retrocopy contributions to the evolution of the human genome

scientific article

Score functions for determining regional conservation in two-species local alignments

scientific article published in January 2004

Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility

scientific article

Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci

scientific article published on 01 October 2018

Targeted discovery of novel human exons by comparative genomics

scientific article

The GENCODE pseudogene resource

scientific article

The NIH BD2K center for big data in translational genomics

scientific article

The UCSC Cancer Genomics Browser: update 2013.

scientific article

The UCSC Cancer Genomics Browser: update 2015

scientific article

The UCSC Genome Browser database: 2014 update

scientific article

The UCSC Genome Browser database: 2015 update

scientific article

The UCSC Genome Browser database: 2016 update

scientific article

The UCSC Genome Browser database: 2017 update

scientific article

The UCSC Genome Browser database: 2018 update

scientific article published on 2 November 2017

The UCSC Genome Browser database: 2019 update

scientific article published on 01 January 2019

The UCSC Genome Browser database: 2021 update

scientific article published on 22 November 2020

The UCSC Genome Browser database: extensions and updates 2011.

scientific article

The UCSC Genome Browser database: extensions and updates 2013.

scientific article

The UCSC Genome Browser database: update 2010

scientific article (publication date: 2010)

The UCSC Genome Browser database: update 2011

scientific article

The UCSC Known Genes

scientific article

The UCSC Proteome Browser

scientific article

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 completion of the Mammalian Gene Collection (MGC).

scientific article published on 18 September 2009

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes

scientific article

The contribution of historical processes to contemporary extinction risk in placental mammals ⬇️

The functional and evolutionary impacts of human-specific deletions in conserved elements ⬇️

Three-dimensional genome rewiring in loci with human accelerated regions ⬇️

scientific article published on 28 April 2023

Tracking and coordinating an international curation effort for the CCDS Project

scientific article

Transcriptional activity and strain-specific history of mouse pseudogenes

scientific article published on 29 July 2020

UCSC Genome Browser enters 20th year

scientific article published on 01 January 2020

Using native and syntenically mapped cDNA alignments to improve de novo gene finding.

scientific article

Whole-Genome Alignment and Comparative Annotation

scientific article published on 31 October 2018

halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments

scientific article published on 01 June 2020

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