Mark Diekhans

Also affiliated with Santa Cruz County Office of Education

Biochemistry, Genetics and Molecular BiologyAgricultural and Biological Sciences

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 1%percentile

154Author DataRank

Indexed papers

37in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 37 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

Initial sequencing and comparative analysis of the mouse genome

Nature(2002)10.1038/nature01262

Top 1%

12.6DataRank

Top 1%7282 citations

Robert H. Waterston, Kerstin Lindblad‐Toh, Julien Lagarde, Josep F. Abril, PANKAJ AGARWAL +189 more

Papers

Driven by 61 papers — median percentile 94. Top paper: “Initial sequencing and comparative analysis of the mouse genome”.

Initial sequencing and comparative analysis of the mouse genome

Nature(2002)10.1038/nature01262

Top 1%

12.6DataRank

Top 1%7282 citations

Robert H. Waterston, Kerstin Lindblad‐Toh, Julien Lagarde, Josep F. Abril, PANKAJ AGARWAL +189 more

GENCODE: The reference human genome annotation for The ENCODE Project

Genome Research(2012)10.1101/gr.135350.111

Top 1%

12.0DataRank

Top 1%5084 citations

Michael G. FitzGerald, Electra Tapanari, Mark Diekhans, Felix Kokocinski, Rizi Ai +42 more

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

Genome Research(2009)10.1101/gr.080531.108

Top 1%

12.0DataRank

Top 1%592 citations

Jennifer Harrow, Rachel A. Harte, Craig Wallin, Mark Diekhans, Bin Ma +52 more

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

Nature(2020)10.1038/s41586-020-2871-y

N/A

8.3DataRank · unranked

643 citations

Hickey, Glenn, Mark Diekhans, Ian T. Fiddes, Adam M. Novak, Alden Deran +16 more

The complete sequence of a human genome

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.05.26.445798

Top 2%

8.2DataRank

Top 2%182 citations

Sergey Koren, Arang Rhie, Allison A. Regier, Andrey V. Bzikadze, Alla Mikheenko +97 more

GENCODE reference annotation for the human and mouse genomes

Nucleic Acids Research(2018)10.1093/nar/gky955

Top 2%

8.2DataRank

Top 2%3533 citations

Mark Diekhans, Anne-Maud Ferreira, Todd A. Johnson, Irwin Jungreis, Jane E Loveland +59 more

The complete sequence of a human genome

Science(2022)10.1126/science.abj6987

Top 3%

7.0DataRank

Top 3%3361 citations

Sergey Koren, Arang Rhie, Allison A. Regier, Andrey V. Bzikadze, Alla Mikheenko +94 more

The GENCODE pseudogene resource

Genome Biology(2012)10.1186/gb-2012-13-9-r51

Top 3%

6.9DataRank

Top 3%353 citations

Cristina Sisu, Michael G. FitzGerald, Cédric Howald, Ryan E. Mills, Xinmeng Jasmine Mu +9 more

GENCODE 2021

Nucleic Acids Research(2020)10.1093/nar/gkaa1087

Top 3%

6.9DataRank

Top 3%1480 citations

Mark Diekhans, Irwin Jungreis, Julien Lagarde, Jane E Loveland, Shinichi Morishita +59 more

Expanded encyclopaedias of DNA elements in the human and mouse genomes

Nature(2020)10.1038/s41586-020-2493-4

Top 3%

6.4DataRank

Top 3%2615 citations

Federico Abascal, Reyes Acosta, Nicholas J. Addleman, Jessika Adrian, Veena Afzal +501 more

The UCSC Genome Browser database: 2021 update

Nucleic Acids Research(2020)10.1093/nar/gkaa1070

Top 3%

6.2DataRank

Top 3%645 citations

Ann S. Zweig, Matthew L Speir, Daniel Schmelter, Kate R. Rosenbloom, Brian J. Raney +18 more

The UCSC Genome Browser database: 2022 update

Nucleic Acids Research(2021)10.1093/nar/gkab959

Top 4%

5.4DataRank

Top 4%309 citations

Galt P Barber, Anna Benet‐Pagès, Jonathan D. Casper, Hiram Clawson, Mark Diekhans +20 more

A draft human pangenome reference

Nature(2023)10.1038/s41586-023-05896-x

Top 4%

5.1DataRank

Top 4%1169 citations

Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness, Hickey, Glenn +95 more

GENCODE: reference annotation for the human and mouse genomes in 2023

Nucleic Acids Research(2022)10.1093/nar/gkac1071

Top 4%

5.1DataRank

Top 4%663 citations

Sílvia Carbonell Sala, Mark Diekhans, Irwin Jungreis, Jane E Loveland, Jonathan M. Mudge +57 more

A comparative genomics multitool for scientific discovery and conservation

Nature(2020)10.1038/s41586-020-2876-6

Top 4%

5.0DataRank

Top 4%447 citations

Aitor Serres, Joel Armstrong, Jeremy Johnson, Voichita D. Marinescu, Eva Murén +43 more

Complete genomic and epigenetic maps of human centromeres

Science(2022)10.1126/science.abl4178

Top 4%

5.0DataRank

Top 4%637 citations

Glennis A. Logsdon, Andrey V. Bzikadze, Pragya Sidhwani, Sasha A. Langley, Gina V. Caldas +54 more

Pangenome graph construction from genome alignments with Minigraph-Cactus

Nature Biotechnology(2023)10.1038/s41587-023-01793-w

N/A

5.0DataRank · unranked

318 citations

Jean Monlong, Jana Ebler, Adam M. Novak, Jordan M. Eizenga, Yan Gao +94 more

Perspectives on ENCODE

Nature(2020)10.1038/s41586-020-2449-8

N/A

4.7DataRank · unranked

227 citations

Reyes Acosta, Nicholas J. Addleman, Jessika Adrian, Veena Afzal, Bronwen Aken +95 more

Segmental duplications and their variation in a complete human genome

Science(2022)10.1126/science.abj6965

Top 5%

4.6DataRank

Top 5%380 citations

Xavi Guitart, Philip C. Dishuck, Ludovica Mercuri, William T. Harvey, Ariel Gershman +15 more

Towards complete and error-free genome assemblies of all vertebrate species

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.22.110833

Top 5%

4.3DataRank

Top 5%195 citations

Shane A McCarthy, Olivier Fédrigo, Joana Damas, Giulio Formenti, Sergey Koren +95 more

The complete sequence of a human Y chromosome

Nature(2023)10.1038/s41586-023-06457-y

Top 5%

4.1DataRank

Top 5%464 citations

Sergey Nurk, Mark J. P. Chaisson, Savannah J. Hoyt, Dylan J. Taylor, Nicolas Altemose +82 more

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

Science(2020)10.1126/science.abc6617

Top 6%

3.6DataRank

Top 6%201 citations

R. Alan Harris, Marina Haukness, Ian T. Fiddes, Shwetha C. Murali, Jason D. Fernandes +55 more

The UCSC Genome Browser database: 2025 update

Nucleic Acids Research(2024)10.1093/nar/gkae974

Top 6%

3.5DataRank

Top 6%588 citations

Galt P Barber, Anna Benet‐Pagès, Jonathan D. Casper, Hiram Clawson, Mark Diekhans +13 more

Evolutionary constraint and innovation across hundreds of placental mammals

Science(2023)10.1126/science.abn3943

Top 7%

3.0DataRank

Top 7%271 citations

Irene M. Kaplow, Diane P. Genereux, Michael X. Dong, Graham M. Hughes, Xue Li +78 more

The Share of Human Genomic DNA under Selection Estimated from Human-Mouse Genomic Alignments

Cold Spring Harbor Symposia on Quantitative Biology(2003)10.1101/sqb.2003.68.245

N/A

2.9DataRank · unranked

63 citations

R.J. WEBER, Bruce A. Roe, Nicholas J. Dickens, Eoghan Harrington, Francesca Chiaromonte +5 more

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

Nature Methods(2024)10.1038/s41592-024-02298-3

Top 8%

2.8DataRank

Top 8%216 citations

Dingjie Wang, Fairlie Reese, Mark Diekhans, Sílvia Carbonell Sala, Brian A. Williams +80 more

GENCODE 2025: reference gene annotation for human and mouse

Nucleic Acids Research(2024)10.1093/nar/gkae1078

Top 8%

2.7DataRank

Top 8%348 citations

Sílvia Carbonell Sala, Mark Diekhans, Jose Gonzalez Martinez, Toby Hunt, Irwin Jungreis +51 more

A high-quality bonobo genome refines the analysis of hominid evolution

Nature(2021)10.1038/s41586-021-03519-x

Top 10%

2.1DataRank

Top 10%92 citations

Claudia Rita Catacchio, LaDeana Hillier, David Porubsky, Ruiyang Li, Arvis Sulovari +34 more

Increased mutation and gene conversion within human segmental duplications

Nature(2023)10.1038/s41586-023-05895-y

N/A

2.1DataRank · unranked

114 citations

Philip C. Dishuck, William T. Harvey, William S. DeWitt, Xavi Guitart, Michael E. Goldberg +108 more

Relating enhancer genetic variation across mammals to complex phenotypes using machine learning

Science(2023)10.1126/science.abm7993

N/A

2.0DataRank · unranked

90 citations

Alyssa J. Lawler, Daniel E. Schäffer, Chaitanya Srinivasan, Heather H. Sestili, Morgan Wirthlin +82 more

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

Science(2023)10.1126/science.abn5856

N/A

1.9DataRank · unranked

106 citations

Megan A. Supple, Ayshwarya Subramanian, Anish Mudide, Ross Swofford, Aitor Serres‐Armero +87 more

Evolution of the ancestral mammalian karyotype and syntenic regions

Proceedings of the National Academy of Sciences(2022)10.1073/pnas.2209139119

Top 12%

1.8DataRank

Top 12%96 citations

Marco Corbo, Kim, Jaebum, Jason Turner-Maier, Marta Farré, Denis M. Larkin +87 more

Segmental duplications and their variation in a complete human genome

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.05.26.445678

Top 14%

1.5DataRank

Top 14%46 citations

Xavi Guitart, Philip C. Dishuck, Ludovica Mercuri, William T. Harvey, Ariel Gershman +15 more

htsget: a protocol for securely streaming genomic data

Bioinformatics(2018)10.1093/bioinformatics/bty492

N/A

1.5DataRank · unranked

28 citations

Mike Lin, C H Albach, Kerstin Lindblad‐Toh, Marina Gourtovaia, David Glazer +26 more

Complete sequencing of ape genomes

Nature(2025)10.1038/s41586-025-08816-3

Top 16%

1.3DataRank

Top 16%128 citations

Arang Rhie, Prajna Hebbar, Francesca Antonacci, Glennis A. Logsdon, Steven J. Solar +123 more

Transcriptional activity and strain-specific history of mouse pseudogenes

Nature Communications(2020)10.1038/s41467-020-17157-w

Top 19%

1.1DataRank

Top 19%38 citations

Paul Muir, Adam Frankish, Ian T. Fiddes, Mark Diekhans, David Thybert +7 more

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.25.550582

Top 20%

0.991DataRank

Top 20%28 citations

Dingjie Wang, Fairlie Reese, Mark Diekhans, Sílvia Carbonell Sala, Brian A. Williams +78 more

Dense sampling of bird diversity increases power of comparative genomics

Nature(2020)10.1038/s41586-020-2873-9

N/A

0.946DataRank · unranked

549 citations

Josefin Stiller, Yuan Deng, Joel Armstrong, Qi Fang, Andrew Hart Reeve +95 more

The complete sequence of a human Y chromosome

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.01.518724

Top 22%

0.934DataRank

Top 22%42 citations

Sergey Nurk, Savannah J. Hoyt, Dylan J. Taylor, Nicolas Altemose, Paul W. Hook +79 more

Complete genomic and epigenetic maps of human centromeres

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.07.12.452052

Top 22%

0.911DataRank

Top 22%17 citations

Glennis A. Logsdon, Andrey V. Bzikadze, Pragya Sidhwani, Sasha A. Langley, Gina V. Caldas +53 more

Integrating gene annotation with orthology inference at scale

Science(2023)10.1126/science.abn3107

N/A

0.804DataRank · unranked

212 citations

Chetan Munegowda, Ekaterina Osipova, David Jebb, Virag Sharma, Moritz Blumer +91 more

The UCSC Genome Browser database: 2026 update

Nucleic Acids Research(2025)10.1093/nar/gkaf1250

Top 27%

0.740DataRank

Top 27%85 citations

Matthew L Speir, Brian J. Raney, Gerardo Perez, Luis R Nassar, Christopher M. Lee +17 more

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

Science(2023)10.1126/science.abn1430

N/A

0.737DataRank · unranked

135 citations

Nicole S. Paulat, Jennifer M. Korstian, Jenna Grimshaw, Michaela K. Halsey, Kevin A. Sullivan +83 more

Leveraging base-pair mammalian constraint to understand genetic variation and human disease

Science(2023)10.1126/science.abn2937

N/A

0.721DataRank · unranked

121 citations

Jennifer R. S. Meadows, Steven Gazal, BaDoi N. Phan, Xue Li, Diane P. Genereux +70 more

Recombination between heterologous human acrocentric chromosomes

Nature(2023)10.1038/s41586-023-05976-y

N/A

0.710DataRank · unranked

113 citations

Silvia Buonaiuto, Leonardo Gomes de Lima, Tamara Potapova, Arang Rhie, Sergey Koren +106 more

Single-cell long-read sequencing-based mapping reveals specialized splicing patterns in developing and adult mouse and human brain

Nature Neuroscience(2024)10.1038/s41593-024-01616-4

N/A

0.701DataRank · unranked

106 citations

Wen Hu, Bei Zhang, Oleksandr Narykov, Mark Diekhans, Jordan Marrocco +10 more

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

Science(2023)10.1126/science.abn2253

N/A

0.657DataRank · unranked

79 citations

Ava Mackay-Smith, Kousuke Mouri, Meilín Fernández García, Michael X. Dong, Jared F. Akers +88 more

GenArk: towards a million UCSC genome browsers

Genome biology(2023)10.1186/s13059-023-03057-x

Top 34%

0.584DataRank

Top 34%16 citations

Brian T. Lee, Brian J. Raney, Galt P Barber, Jonathan D. Casper, Mark Diekhans +18 more

Complete sequencing of ape genomes

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.07.31.605654

Top 34%

0.582DataRank

Top 34%26 citations

Arang Rhie, Prajna Hebbar, Francesca Antonacci, Glennis A. Logsdon, Steven J. Solar +123 more

Chiropterans Are a Hotspot for Horizontal Transfer of DNA Transposons in Mammalia

Molecular Biology and Evolution(2023)10.1093/molbev/msad092

N/A

0.561DataRank · unranked

18 citations

Jessica M. Storer, Diana D. Moreno-Santillán, Austin Osmanski, Kevin A. Sullivan, Jenna Grimshaw +85 more

Vocal learning–associated convergent evolution in mammalian proteins and regulatory elements

Science(2024)10.1126/science.abn3263

N/A

0.542DataRank · unranked

36 citations

Tobias A. Schmid, Julie E. Elie, Xiaomeng Zhang, Amanda Kowalczyk, Ruby Redlich +89 more

Single-cell long-read mRNA isoform regulation is pervasive across mammalian brain regions, cell types, and development

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.04.02.535281

N/A

0.406DataRank · unranked

14 citations

Wen Hu, Bei Zhang, Oleksandr Narykov, Mark Diekhans, Jennifer Balacco +9 more

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

Science(2023)10.1126/science.abn5887

N/A

0.406DataRank · unranked

14 citations

Heather J. Huson, Kathleen M. Morrill, Mingshan Wang, Xue Li, Krishnamoorthy Srikanth +90 more

Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome

Cell Reports Methods(2023)10.1016/j.crmeth.2023.100543

Top 50%

0.352DataRank

Top 50%6 citations

Stephanie Greer, Dmitri S. Pavlichin, Bo Zhou, Alexander E. Urban, Tsachy Weissman +94 more

RNAget: an API to securely retrieve RNA quantifications

Bioinformatics(2023)10.1093/bioinformatics/btad126

N/A

0.241DataRank · unranked

4 citations

Emilio Palumbo, Jeremy Adams, David Bujold, Guillaume Bourque, Jared L. Nedzel +58 more

Using the linear references from the pangenome to discover missing autism variants

Nature Communications(2026)10.1038/s41467-026-68378-4

Top 65%

0.208DataRank

Top 65%3 citations

Jiadong Lin, Michelle D. Noyes, Young-Jun Kwon, Isaac Wong, Nidhi Koundinya +252 more

GENCODE: Creating a Validated Manually Annotated Geneset for the Whole Human Genome

Nature Precedings(2009)10.1038/npre.2009.3155.1

Top 71%

0.128DataRank

Top 71%1 citations

Giulio Formenti, Rizi Ai, Nicholas J. Dickens, Genome Institute at Washington University, Michael Tress +45 more

GenArk: Towards a million UCSC Genome Browsers

Research Square(2023)10.21203/rs.3.rs-2697398/v1

N/A

0.104DataRank · unranked

1 citations

Brian T. Lee, Galt P Barber, Jonathan D. Casper, Mark Diekhans, Clay Fischer +17 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.18.389049

N/A

0DataRank · unranked

4 citations

Madalee G. Wulf, Ira Schildkraut, George Tzertzinis, J. A. Buswell, Miten Jain +6 more

The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.30.569198

N/A

0DataRank · unranked

24 citations

Brandon D. Pickett, Robert S. Harris, Gabrielle A. Hartley, Monika Čechová, Karol Pal +78 more

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

RNA(2021)10.1261/rna.078703.121

N/A

0DataRank · unranked

29 citations

Madalee G. Wulf, Ira Schildkraut, George Tzertzinis, J. A. Buswell, Miten Jain +6 more

Mark Diekhans

Indexed papers

Top data-sharing exemplar

Papers