Benedict Paten

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

46.2Author DataRank

Indexed papers

19in 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 19 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.

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

Papers

Driven by 96 papers — median percentile 90. Top paper: “Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes”.

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

Nature Biotechnology(2020)10.1038/s41587-020-0503-6

N/A

12.8DataRank · unranked

655 citations

Trevor Pesout, Ryan Lorig-Roach, Marina Haukness, Hugh E. Olsen, Colleen M. Bosworth +27 more

Telomere-to-telomere assembly of a complete human X chromosome

Nature(2020)10.1038/s41586-020-2547-7

N/A

11.3DataRank · unranked

835 citations

Sergey Koren, Arang Rhie, Mitchell R. Vollger, Ariel Gershman, Andrey V. Bzikadze +48 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

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

A complete reference genome improves analysis of human genetic variation

Science(2022)10.1126/science.abl3533

Top 5%

4.4DataRank

Top 5%437 citations

Stephanie M. Yan, Daniela C. Soto, Melanie Kirsche, Samantha Zarate, Pavel Avdeyev +28 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

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

Cell Genomics(2022)10.1016/j.xgen.2021.100085

N/A

3.9DataRank · unranked

132 citations

Anthony Philippakis, Enis Afgan, Eric Banks, Vincent J. Carey, Robert J. Carroll +95 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

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

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

Genetic effects on gene expression across human tissues

UNC Libraries(2020)10.17615/p82n-gb73

Top 8%

2.6DataRank

Top 8%63 citations

Yuan He, Lin Chen, Emmanouil T. Dermitzakis, Philip A. Branton, Andrew B. Nobel +95 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

precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.13.380741

Top 11%

2.0DataRank

Top 11%67 citations

Justin Wagner, Jennifer McDaniel, Sarah H. Stephens, Samuel T. Westreich, Anish G. Prasanna +68 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

Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling

eLife(2022)10.7554/elife.76562

N/A

1.6DataRank · unranked

46 citations

Jason Talkish, Hongxu Ding, Haller Igel, Alejandra Durán, Shreya Mantripragada +3 more

Structurally divergent and recurrently mutated regions of primate genomes

Cell(2024)10.1016/j.cell.2024.01.052

Top 15%

1.4DataRank

Top 15%72 citations

William T. Harvey, David Porubsky, Katherine M. Munson, Kendra Hoekzema, Alexandra P. Lewis +29 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

Pangenome Graphs

Annual Review of Genomics and Human Genetics(2020)10.1146/annurev-genom-120219-080406

N/A

0.882DataRank · unranked

356 citations

Adam M. Novak, Jonas A. Sibbesen, Simon Heumos, Ali Ghaffaari, Hickey, Glenn +11 more

Genotyping structural variants in pangenome graphs using the vg toolkit

Genome biology(2020)10.1186/s13059-020-1941-7

N/A

0.877DataRank · unranked

346 citations

David N. Heller, Jean Monlong, Jonas A. Sibbesen, Jouni Sirén, Jordan M. Eizenga +5 more

Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References

Annual Review of Genomics and Human Genetics(2024)10.1146/annurev-genom-021623-081639

Top 23%

0.864DataRank

Top 23%42 citations

Jordan M. Eizenga, Qiuhui Li, Arun Das, Katharine M. Jenike, Eimear E. Kenny +6 more

Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads

Nature Biotechnology(2020)10.1038/s41587-020-0719-5

N/A

0.815DataRank · unranked

228 citations

Peter Ebert, Peter A. Audano, Mitchell R. Vollger, William T. Harvey, Pierre Marijon +16 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

Bridging the rodent to human translational gap: Marmosets as model systems for the study of Alzheimer's disease

Alzheimer s & Dementia Translational Research & Clinical Interventions(2023)10.1002/trc2.12417

N/A

0.751DataRank · unranked

35 citations

Gregg E. Homanics, David J. Schaeffer, Lauren K Hayrynen Schaeffer, Jung Eun Park, Julia Oluoch +13 more

Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation

Nature Methods(2023)10.1038/s41592-023-01993-x

N/A

0.747DataRank · unranked

144 citations

Kimberley J. Billingsley, Mira Mastoras, Melissa Meredith, Jean Monlong, Ryan Lorig-Roach +25 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

Identification of constrained sequence elements across 239 primate genomes

Nature(2023)10.1038/s41586-023-06798-8

N/A

0.713DataRank · unranked

115 citations

Jacob C. Ulirsch, Sabrina Mohd Rashid, Mohamed Ameen, Laksshman Sundaram, Hickey, Glenn +87 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

Structurally divergent and recurrently mutated regions of primate genomes

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.07.531415

Top 32%

0.624DataRank

Top 32%14 citations

William T. Harvey, David Porubsky, Katherine M. Munson, Kendra Hoekzema, Alexandra P. Lewis +22 more

Gaps and complex structurally variant loci in phased genome assemblies

Genome Research(2023)10.1101/gr.277334.122

N/A

0.621DataRank · unranked

62 citations

Mitchell R. Vollger, William T. Harvey, Allison N. Rozanski, Peter Ebert, Hickey, Glenn +8 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

Efficient dynamic variation graphs

Bioinformatics(2020)10.1093/bioinformatics/btaa640

N/A

0.550DataRank · unranked

38 citations

Adam M. Novak, Emily Kobayashi, Flavia Villani, Cecilia Cisar, Simon Heumos +5 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

A strategy for building and using a human reference pangenome

F1000Research(2021)10.12688/f1000research.19630.2

N/A

0.533DataRank · unranked

10 citations

Giuseppe Narzisi, Valérie Schneider, Peter A. Audano, Evan Biederstedt, Lon Blauvelt +35 more

Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing

Nature Biotechnology(2025)10.1038/s41587-025-02618-8

N/A

0.505DataRank · unranked

28 citations

Asher Bryant, Tanveer Ahmad, Byunggil Yoo, Sergey Aganezov, Anton Goretsky +36 more

A 3-way hybrid approach to generate a new high-quality chimpanzee reference genome (Pan_tro_3.0)

GigaScience(2017)10.1093/gigascience/gix098

Top 40%

0.483DataRank

Top 40%24 citations

Chad Tomlinson, LaDeana W Hillier, Annabel Tran, Ian T Fiddes, Joel Armstrong +21 more

Local read haplotagging enables accurate long-read small variant calling

Nature Communications(2024)10.1038/s41467-024-50079-5

N/A

0.457DataRank · unranked

20 citations

Daniel E. Cook, Maria Nattestad, Lucas Brambrink, Brandy McNulty, John E. Gorzynski +9 more

Distance indexing and seed clustering in sequence graphs

Bioinformatics(2020)10.1093/bioinformatics/btaa446

N/A

0.457DataRank · unranked

20 citations

Jordan M. Eizenga, Adam M. Novak, Jouni Sirén, Benedict Paten, Xian Chang

Building a collaborative cloud platform to accelerate heart, lung, blood, and sleep research

Journal of the American Medical Informatics Association(2023)10.1093/jamia/ocad048

N/A

0.442DataRank · unranked

18 citations

Paul Avillach, Rebecca Boyles, Kira Bradford, Steven J. Cox, Brandi N. Davis‐Dusenbery +53 more

Phased nanopore assembly with Shasta and modular graph phasing with GFAse

Genome Research(2024)10.1101/gr.278268.123

N/A

0.434DataRank · unranked

17 citations

Melissa Meredith, Jean Monlong, Miten Jain, Hugh E. Olsen, Brandy McNulty +18 more

Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair

Scientific Data(2025)10.1038/s41597-025-05438-2

Top 44%

0.421DataRank

Top 44%10 citations

Vaidehi Patel, Nathan D. Olson, Hua‐Jun He, Anthony Schmitt, Kenneth D. Cole +80 more

Genetic regulation of TERT splicing affects cancer risk by altering cellular longevity and replicative potential

Nature Communications(2025)10.1038/s41467-025-56947-y

N/A

0.416DataRank · unranked

15 citations

Michelle Ho, Maxwell H. Hogshead, Brenen W. Papenberg, Chia‐Han Lee, Kaitlin Forsythe +18 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

Phased nanopore assembly with Shasta and modular graph phasing with GFAse

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.02.21.529152

N/A

0.396DataRank · unranked

13 citations

Melissa Meredith, Jean Monlong, Miten Jain, Hugh E. Olsen, Brandy McNulty +18 more

A phenome-wide association study of methylated GC-rich repeats identifies a GCC repeat expansion in AFF3 associated with intellectual disability

Nature Genetics(2024)10.1038/s41588-024-01917-1

N/A

0.373DataRank · unranked

11 citations

Paras Garg, Joke J.F.A. van Vugt, Kristina Ibáñez, Delia Gagliardi, William Lee +19 more

Increased mutation rate and interlocus gene conversion within human segmental duplications

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.07.06.498021

N/A

0.330DataRank · unranked

8 citations

William S. DeWitt, Philip C. Dishuck, William T. Harvey, Xavi Guitart, Michael E. Goldberg +13 more

Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.09.18.613544

Top 54%

0.314DataRank

Top 54%6 citations

Vaidehi Patel, Nathan D. Olson, Hua‐Jun He, Kenneth D. Cole, Alexander A. Gooden +78 more

Local read haplotagging enables accurate long-read small variant calling

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.09.07.556731

N/A

0.241DataRank · unranked

4 citations

Daniel E. Cook, Maria Nattestad, Brandy McNulty, John E. Gorzynski, Sneha D. Goenka +8 more

Efficient indexing and querying of annotations in a pangenome graph

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.10.12.618009

N/A

0.241DataRank · unranked

4 citations

Dickson Chung, Hickey, Glenn, Sarah Djebali, Toshiyuki Yokoyama, Erik Garrison +4 more

A Complete Pedigree-Based Graph Workflow for Rare Candidate Variant Analysis

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.11.24.469912

N/A

0.165DataRank · unranked

2 citations

Charles Huang, Álex Rodríguez, Andrew Carroll, Pi-Chuan Chang, Jordan M. Eizenga +4 more

Haplotype-Resolved DNA Methylation at the APOE Locus identifies Allele-Specific Epigenetic Signatures Relevant to Alzheimer’s Disease Risk

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.07.01.662592

N/A

0.104DataRank · unranked

1 citations

Melissa Meredith, Abraham Moller, Cory A. Weller, Kensuke Daida, Alexis Ayuketah +18 more

GBZ file format for pangenome graphs

Bioinformatics(2022)10.1093/bioinformatics/btac656

N/A

0DataRank · unranked

32 citations

Benedict Paten, Jouni Sirén

Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing

Nature Biotechnology(2022)10.1038/s41587-022-01221-5

N/A

0DataRank · unranked

121 citations

John E. Gorzynski, Kishwar Shafin, Dianna G. Fisk, Trevor Pesout, Tanner Jensen +24 more

Haplotype-aware pantranscriptome analyses using spliced pangenome graphs

Nature Methods(2023)10.1038/s41592-022-01731-9

N/A

0DataRank · unranked

82 citations

Jordan M. Eizenga, Adam M. Novak, Jouni Sirén, Xian Chang, Erik Garrison +2 more

Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies

Nature Methods(2022)10.1038/s41592-022-01440-3

N/A

0DataRank · unranked

125 citations

Kishwar Shafin, Michael Alonge, Andrey V. Bzikadze, Giulio Formenti, Arkarachai Fungtammasan +15 more

Optimal gap-affine alignment in O ( s ) space

Bioinformatics(2023)10.1093/bioinformatics/btad074

N/A

0DataRank · unranked

63 citations

Jordan M. Eizenga, Andrea Guarracino, Benedict Paten, Erik Garrison, Miquel Moretó +1 more

Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.12.16.472988

N/A

0DataRank · unranked

1 citations

Jason Talkish, Hongxu Ding, Haller Igel, Alejandra Durán, Shreya Mantripragada +3 more

Inversion polymorphism in a complete human genome assembly

Genome biology(2023)10.1186/s13059-023-02919-8

N/A

0DataRank · unranked

33 citations

William T. Harvey, Allison N. Rozanski, Jana Ebler, Wolfram Höps, Hufsah Ashraf +7 more

Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.07.02.450803

N/A

0DataRank · unranked

16 citations

Kishwar Shafin, Michael Alonge, Andrey V. Bzikadze, Giulio Formenti, Arkarachai Fungtammasan +15 more

Haplotype-aware pantranscriptome analyses using spliced pangenome graphs

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.03.26.437240

N/A

0DataRank · unranked

18 citations

Jordan M. Eizenga, Adam M. Novak, Jouni Sirén, Xian Chang, Erik Garrison +2 more

A unified pipeline for FISH spatial transcriptomics

Cell Genomics(2023)10.1016/j.xgen.2023.100384

N/A

0DataRank · unranked

14 citations

Nicholas Keener, Mathew Ruffalo, Benedict Paten, Cecilia Cisar

Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies

Research Square(2021)10.21203/rs.3.rs-712747/v1

N/A

0DataRank · unranked

20 citations

Ann M. Mc Cartney, Kishwar Shafin, Michael Alonge, Andrey V. Bzikadze, Giulio Formenti +15 more

Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.01.12.523790

N/A

0DataRank · unranked

31 citations

Kimberley J. Billingsley, Mira Mastoras, Melissa Meredith, Jean Monlong, Ryan Lorig-Roach +25 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

Haplotype-aware variant calling enables high accuracy in nanopore long-reads using deep neural networks

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.03.04.433952

N/A

0DataRank · unranked

32 citations

Trevor Pesout, Pi-Chuan Chang, Maria Nattestad, Alexey Kolesnikov, Sidharth Goel +8 more

Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans

Genome Research(2021)10.1101/gr.275989.121

N/A

0DataRank · unranked

43 citations

Joel Armstrong, Alden Deran, Carolyn J. Khoury, Benedict Paten, David Haussler +2 more

A phenome-wide association study of methylated GC-rich repeats identifies a GCC repeat expansion in AFF3 as a significant cause of intellectual disability

medRxiv(2023)10.1101/2023.05.03.23289461

N/A

0DataRank · unranked

7 citations

Paras Garg, Joke J.F.A. van Vugt, Kristina Ibáñez, Delia Gagliardi, William Lee +16 more

Personalized Pangenome References

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.12.13.571553

N/A

0DataRank · unranked

4 citations

Parsa Eskandar, Matteo Tommaso Ungaro, Hickey, Glenn, Jordan M. Eizenga, Adam M. Novak +7 more

Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures

Nature Communications(2021)10.1038/s41467-021-26929-x

N/A

0DataRank · unranked

10 citations

Ioannis N. Anastopoulos, Andrew D. Bailey, Joshua M. Stuart, Benedict Paten, Hongxu Ding

The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols

Nucleic Acids Research(2021)10.1093/nar/gkab346

N/A

0DataRank · unranked

38 citations

Louise Cabansay, Andrew Duncan, Gary Luu, Gregory Hogue, Charles Overbeck +13 more

Pervasive cis effects of variation in copy number of large tandem repeats on local DNA methylation and gene expression

The American Journal of Human Genetics(2021)10.1016/j.ajhg.2021.03.016

N/A

0DataRank · unranked

47 citations

Alejandro Martin-Trujillo, Oscar L. Rodriguez, Scott J Gies, Elina Hadelia, Bharati Jadhav +4 more

Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads

Nature Methods(2021)10.1038/s41592-021-01299-w

N/A

0DataRank · unranked

332 citations

Trevor Pesout, Pi-Chuan Chang, Maria Nattestad, Alexey Kolesnikov, Sidharth Goel +9 more

Personalized pangenome references

Nature Methods(2024)10.1038/s41592-024-02407-2

N/A

0DataRank · unranked

30 citations

Parsa Eskandar, Matteo Tommaso Ungaro, Hickey, Glenn, Jordan M. Eizenga, Adam M. Novak +7 more

Pangenomics enables genotyping of known structural variants in 5202 diverse genomes

Science(2021)10.1126/science.abg8871

N/A

0DataRank · unranked

419 citations

Jean Monlong, Xian Chang, Adam M. Novak, Jordan M. Eizenga, Charles Markello +15 more

A survey of rare epigenetic variation in 23,116 human genomes identifies disease-relevant epivariations and novel CGG expansions

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.03.25.007864

N/A

0DataRank · unranked

0 citations

Bharati Jadhav, Oscar L. Rodriguez, Nihir Patel, Alejandro Martin-Trujillo, Miten Jain +8 more

Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads

medRxiv(2024)10.1101/2024.03.22.24304756

N/A

0DataRank · unranked

21 citations

Asher Bryant, Tanveer Ahmad, Byunggil Yoo, Sergey Aganezov, Anton Goretsky +33 more

DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.08.16.608331

N/A

0DataRank · unranked

19 citations

Daniel E. Cook, Pi-Chuan Chang, Alexey Kolesnikov, Lucas Brambrink, Juan Carlos Mier +26 more

Towards Inferring Nanopore Sequencing Ionic Currents from Nucleotide Chemical Structures

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.30.404947

N/A

0DataRank · unranked

2 citations

Ioannis N. Anastopoulos, Andrew D. Bailey, Joshua M. Stuart, Benedict Paten, Hongxu Ding

Succinct dynamic variation graphs

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.23.056317

N/A

0DataRank · unranked

4 citations

Adam M. Novak, Emily Kobayashi, Flavia Villani, Cecilia Cisar, Simon Heumos +5 more

Genetic regulation of TERT splicing contributes to reduced or elevated cancer risk by altering cellular longevity and replicative potential

medRxiv(2024)10.1101/2024.11.04.24316722

N/A

0DataRank · unranked

0 citations

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0DataRank · unranked

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0DataRank · unranked

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0DataRank · unranked

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0DataRank · unranked

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Genome Research(2025)10.1101/gr.280149.124

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0DataRank · unranked

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0DataRank · unranked

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0DataRank · unranked

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0DataRank · unranked

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0DataRank · unranked

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0DataRank · unranked

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0DataRank · unranked

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0DataRank · unranked

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