Mark Diekhans

62.3k total citations · 4 hit papers
52 papers, 6.7k citations indexed

About

Mark Diekhans is a scholar working on Molecular Biology, Genetics and Plant Science. According to data from OpenAlex, Mark Diekhans has authored 52 papers receiving a total of 6.7k indexed citations (citations by other indexed papers that have themselves been cited), including 45 papers in Molecular Biology, 17 papers in Genetics and 11 papers in Plant Science. Recurrent topics in Mark Diekhans's work include Genomics and Phylogenetic Studies (29 papers), RNA and protein synthesis mechanisms (19 papers) and Chromosomal and Genetic Variations (11 papers). Mark Diekhans is often cited by papers focused on Genomics and Phylogenetic Studies (29 papers), RNA and protein synthesis mechanisms (19 papers) and Chromosomal and Genetic Variations (11 papers). Mark Diekhans collaborates with scholars based in United States, United Kingdom and Germany. Mark Diekhans's co-authors include David Haussler, Robert Baertsch, Mario Stanke, Tommi Jaakkola, Rachel Karchin, Hiram Clawson, Robert M. Kuhn, Jonathan D. Casper, W. James Kent and Melissa Cline and has published in prestigious journals such as Science, Proceedings of the National Academy of Sciences and Nucleic Acids Research.

In The Last Decade

Mark Diekhans

51 papers receiving 6.6k citations

Hit Papers

align trajectories

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

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

2008 1.5k citations Mario Stanke, Mark Diekhans et al. profile →
The UCSC Genome Browser database: 2019 update

2018 547 citations Maximilian Haeussler, Matthew L Speir et al. Nucleic Acids Research profile →
Segmental duplications and their variation in a complete human genome

2022 152 citations Mitchell R. Vollger, Xavi Guitart et al. Science profile →
The UCSC Genome Browser database: 2025 update

2024 113 citations Galt P Barber, Anna Benet‐Pagès et al. Nucleic Acids Research profile →

Peers

Countries citing papers authored by Mark Diekhans

Since Specialization

Citations

This map shows the geographic impact of Mark Diekhans's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Mark Diekhans with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Mark Diekhans more than expected).

Fields of papers citing papers by Mark Diekhans

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Mark Diekhans. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Mark Diekhans. The network helps show where Mark Diekhans may publish in the future.

Co-authorship network of co-authors of Mark Diekhans

This figure shows the co-authorship network connecting the top 25 collaborators of Mark Diekhans. A scholar is included among the top collaborators of Mark Diekhans based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with Mark Diekhans. Mark Diekhans is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

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20 of 20 papers shown

#	Work	Indexed citations
1	Making genomic data FAIR through effective Data Portals 2025 ·Scientific Data ·Matthew L Speir, (unknown), Marc D. Perry, Richard D. Schwartz, (unknown), Tim Harris, Clay Fischer, Mark Diekhans, (unknown), Benedict Paten, W. James Kent, Maximilian Haeussler	0
2	The UCSC Genome Browser database: 2025 update breakdown → 2024 ·Nucleic Acids Research ·(unknown), Galt P Barber, Anna Benet‐Pagès, Jonathan D. Casper, Hiram Clawson, Mark Diekhans, Clay Fischer, Jairo Navarro Gonzalez, Angie S. Hinrichs, Christopher M. Lee, Luis R Nassar, Brian J. Raney, Matthew L Speir, Marijke J. van Baren, Charles Vaske, D. Haussler, W. James Kent, Maximilian Haeussler	113
3	Single-cell long-read sequencing-based mapping reveals specialized splicing patterns in developing and adult mouse and human brain 2024 ·Nature Neuroscience ·Anoushka Joglekar, Wen Hu, Bei Zhang, Oleksandr Narykov, Mark Diekhans, Jordan Marrocco, Jennifer Balacco, Lishomwa C. Ndhlovu, Teresa A. Milner, Olivier Fédrigo, Erich D. Jarvis, Gloria Sheynkman, Dmitry Korkin, M. Elizabeth Ross, Hagen Tilgner	29
4	Segmental duplications and their variation in a complete human genome breakdown → 2022 ·Science ·Mitchell R. Vollger, Xavi Guitart, Philip C. Dishuck, Ludovica Mercuri, William T. Harvey, Ariel Gershman, Mark Diekhans, Arvis Sulovari, Katherine M. Munson, Alexandra P. Lewis, Kendra Hoekzema, David Porubský, (unknown), Sergey Nurk, Sergey Koren, Karen H. Miga, Adam M. Phillippy, Winston Timp, Mario Ventura, Evan E. Eichler	152
5	Identification of high-confidence human poly(A) RNA isoform scaffolds using nanopore sequencing 2021 ·RNA ·Logan Mulroney, (unknown), Ira Schildkraut, George Tzertzinis, J. A. Buswell, Miten Jain, Hugh E. Olsen, Mark Diekhans, Ivan R. Corrêa, Mark Akeson, Laurence Ettwiller	17
6	AMELIE speeds Mendelian diagnosis by matching patient phenotype and genotype to primary literature 2020 ·Science Translational Medicine ·Johannes Birgmeier, Maximilian Haeussler, Cole A. Deisseroth, Ethan Steinberg, Karthik A. Jagadeesh, Alexander Ratner, Harendra Guturu, Aaron M. Wenger, Mark Diekhans, Peter D. Stenson, D.N. Cooper, Christopher Ré, Alan H. Beggs, Jonathan A. Bernstein, Gill Bejerano	56
7	Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation 2018 ·Genome Research ·Ian T. Fiddes, Joel Armstrong, Mark Diekhans, (unknown), Zev Kronenberg, Jason G. Underwood, David Gordon, Dent Earl, Thomas Keane, Evan E. Eichler, David Haussler, Mario Stanke, Benedict Paten	60
8	Long-read sequence assembly of the gorilla genome 2016 ·Science ·David Gordon, John Huddleston, Mark Chaisson, C. Hill, Zev Kronenberg, Katherine M. Munson, Maika Malig, Archana N. Raja, Ian T. Fiddes, LaDeana Hillier, Christopher Dunn, Carl Baker, Joel Armstrong, Mark Diekhans, Benedict Paten, Jay Shendure, Richard K. Wilson, David Haussler, Chen-Shan Chin, Evan E. Eichler	218
9	Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes 2014 ·Human Molecular Genetics ·Iakes Ezkurdia, David Juan, José Manuel Rodrı́guez, Adam Frankish, Mark Diekhans, Jennifer Harrow, Jesús Vázquez, Alfonso Valencia, Michael L. Tress	334
10	The UCSC Cancer Genomics Browser: update 2013 2012 ·Nucleic Acids Research ·Mary J. Goldman, Brian Craft, Teresa Swatloski, Kyle Ellrott, Melissa Cline, Mark Diekhans, Singer Ma, (unknown), Joshua M. Stuart, David Haussler, Jingchun Zhu	129
11	Cactus Graphs for Genome Comparisons 2011 ·Journal of Computational Biology ·Benedict Paten, Mark Diekhans, Dent Earl, John St. John, Jian Ma, Bernard Suh, David Haussler	55
12	Retrocopy contributions to the evolution of the human genome 2008 ·BMC Genomics ·Robert Baertsch, Mark Diekhans, W. James Kent, David Haussler, Jürgen Brosius	78
13	Targeted discovery of novel human exons by comparative genomics 2007 ·Genome Research ·Adam Siepel, Mark Diekhans, Broňa Brejová, Laura Langton, Michael Stevens, (unknown), Colleen Davis, Brent Ewing, Shelly Oommen, Christopher Lau, Hung‐Chun Yu, Jianfeng Li, Bruce A. Roe, Phil Green, Daniela S. Gerhard, Gary Temple, David Haussler, Michael R. Brent	33
14	Comparative Genomics Search for Losses of Long-Established Genes on the Human Lineage 2007 ·PLoS Computational Biology ·Jingchun Zhu, Zack Sanborn, Mark Diekhans, Craig B. Lowe, (unknown), David Haussler	80
15	Analysis of Human mRNAs With the Reference Genome Sequence Reveals Potential Errors, Polymorphisms, and RNA Editing 2004 ·Genome Research ·Terrence S. Furey, Mark Diekhans, Yontao Lu, Tina Graves, (unknown), (unknown), LaDeana W. Hillier, Richard K. Wilson, David Haussler	29
16	The Share of Human Genomic DNA under Selection Estimated from Human-Mouse Genomic Alignments 2003 ·Cold Spring Harbor Symposia on Quantitative Biology ·Francesca Chiaromonte, R. Weber, Krishna M. Roskin, Mark Diekhans, W. James Kent, David Haussler	45
17	Global Predictions and Tests of Erythroid Regulatory Regions 2003 ·Cold Spring Harbor Symposia on Quantitative Biology ·Ross C. Hardison, Francesca Chiaromonte, Diana L. Kolbe, (unknown), Hanna M. Petrykowska, Laura Elnitski, Shan Yang, Belinda Giardine, Ying Zhang, Cathy Riemer, Scott Schwartz, David Haussler, Krishna M. Roskin, R. Weber, Mark Diekhans, W. James Kent, Mitchell J. Weiss, John J. Welch, Webb Miller	7
18	Combining local-structure, fold-recognition, and new fold methods for protein structure prediction 2003 ·Proteins Structure Function and Bioinformatics ·Kevin Karplus, Rachel Karchin, Jenny Draper, Jonathan D. Casper, Yael Mandel‐Gutfreund, Mark Diekhans, Richard Hughey	235
19	What is the value added by human intervention in protein structure prediction? 2001 ·Proteins Structure Function and Bioinformatics ·Kevin Karplus, Rachel Karchin, Christian Barrett, (unknown), Melissa Cline, Mark Diekhans, Leslie R. Grate, Jonathan D. Casper, Richard Hughey	102
20	Tcl/Tk tools 1997 ·(unknown), (unknown), De A. Clarke, (unknown), Mark Diekhans, Saul Greenberg, (unknown), (unknown), (unknown), Don Libes, Michael McLennan, John K. Ousterhout, (unknown), Mark Roseman, Lawrence A. Rowe, (unknown), (unknown)	7

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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