🏆 Finalist — NIH Data Sharing Index (“S-Index”) Challenge

Mihaela Pertea

Johns Hopkins University

ORCID: 0000-0003-0762-8637

Also affiliated with Johns Hopkins Medicine, University of Baltimore

Biochemistry, Genetics and Molecular Biology

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
13.9Author DataRank

Indexed papers

13in 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 13 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 →

Top data-sharing exemplar

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

The status of the human gene catalogue

Nature(2023)10.1038/s41586-023-06490-x
Top 8%
2.9DataRank
Top 8%171 citations

Sílvia Carbonell Sala, Francisco M. De La Vega, Tiago Faial, Adam Frankish, T Gingeras +16 more

Papers

Driven by 37 papers — median percentile 78. Top paper: “GFF Utilities: GffRead and GffCompare”.

GFF Utilities: GffRead and GffCompare

F1000Research(2020)10.12688/f1000research.23297.1
N/A
9.8DataRank · unranked
1500 citations

Mihaela Pertea, Geo Pertea

The status of the human gene catalogue

Nature(2023)10.1038/s41586-023-06490-x
Top 8%
2.9DataRank
Top 8%171 citations

Sílvia Carbonell Sala, Francisco M. De La Vega, Tiago Faial, Adam Frankish, T Gingeras +16 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

Assembly and annotation of an Ashkenazi human reference genome

Genome biology(2020)10.1186/s13059-020-02047-7
Top 10%
2.2DataRank
Top 10%70 citations

Aleksey V. Zimin, Rachel M. Sherman, Daniela Puiu, Justin Wagner, Nathan D. Olson +5 more

CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure

Genome biology(2023)10.1186/s13059-023-03088-4
Top 14%
1.5DataRank
Top 14%58 citations

Markus J. Sommer, Beril Erdogdu, Ida Shinder, Ilia Minkin, Kuan-Hao Chao +10 more

Structure-guided isoform identification for the human transcriptome

eLife(2022)10.7554/elife.82556
N/A
1.4DataRank · unranked
50 citations

Sooyoung Cha, Ales Varabyou, Natalia Rincon, Sukhwan Park, Ilia Minkin +4 more

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

Nature Protocols(2016)10.1038/nprot.2016.095
N/A
1.3DataRank · unranked
7503 citations

Daehwan Kim, Jeffrey T. Leek, Steven L. Salzberg, Reenal Pattni, Mihaela Pertea

GFF Utilities: GffRead and GffCompare

F1000Research(2020)10.12688/f1000research.23297.2
N/A
1.1DataRank · unranked
1161 citations

Mihaela Pertea, Geo Pertea

The first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual

G3 Genes Genomes Genetics(2023)10.1093/g3journal/jkac321
Top 19%
1.0DataRank
Top 19%26 citations

Aleksey V. Zimin, Mihaela Pertea, Steven L. Salzberg, Kuan-Hao Chao

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

A reference-quality, fully annotated genome from a Puerto Rican individual

Genetics(2021)10.1093/genetics/iyab227
Top 22%
0.910DataRank
Top 22%31 citations

Alaina Shumate, Ida Shinder, Jakob Heinz, Daniela Puiu, Mihaela Pertea +2 more

Assembly and Annotation of an Ashkenazi Human Reference Genome

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.03.18.997395
Top 33%
0.593DataRank
Top 33%9 citations

Aleksey V. Zimin, Rachel M. Sherman, Daniela Puiu, Justin Wagner, Nathan D. Olson +5 more

Effects of transcriptional noise on estimates of gene and transcript expression in RNA sequencing experiments

Genome Research(2020)10.1101/gr.266213.120
N/A
0.587DataRank · unranked
49 citations

Steven L. Salzberg, Mihaela Pertea, Ales Varabyou

Rapid detection of inter-clade recombination in SARS-CoV-2 with Bolotie

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.09.21.300913
N/A
0.477DataRank · unranked
23 citations

Christopher Pockrandt, Steven L. Salzberg, Mihaela Pertea, Ales Varabyou

Translon: a single term for translated regions

Nature Methods(2025)10.1038/s41592-025-02810-3
N/A
0.389DataRank · unranked
11 citations

Jack A. S. Tierney, M. Mar Albà, Dmitry E. Andreev, Julie L. Aspden, John F. Atkins +164 more

CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.21.521274
Top 48%
0.371DataRank
Top 48%9 citations

Markus J. Sommer, Beril Erdogdu, Ida Shinder, Ilia Minkin, Kuan-Hao Chao +10 more

The first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.08.08.503226
Top 50%
0.350DataRank
Top 50%6 citations

Aleksey V. Zimin, Mihaela Pertea, Steven L. Salzberg, Kuan-Hao Chao

A reference-quality, fully annotated genome from a Puerto Rican individual

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.06.10.447952
Top 52%
0.330DataRank
Top 52%8 citations

Alaina Shumate, Ida Shinder, Jakob Heinz, Daniela Puiu, Mihaela Pertea +2 more

Detecting differential transcript usage in complex diseases with SPIT

Cell Reports Methods(2024)10.1016/j.crmeth.2024.100736
N/A
0.315DataRank · unranked
5 citations

Ales Varabyou, Stephanie C. Hicks, Steven L. Salzberg, Mihaela Pertea, Beril Erdogdu

EASTR: Identifying and eliminating systematic alignment errors in multi-exon genes

Nature Communications(2023)10.1038/s41467-023-43017-4
N/A
0.241DataRank · unranked
4 citations

Richard Hu, Hyun Joo Ji, Kuan-Hao Chao, Mihaela Pertea, Ida Shinder

Detecting differential transcript usage in complex diseases with SPIT

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.10.548289
N/A
0.104DataRank · unranked
1 citations

Ales Varabyou, Stephanie C. Hicks, Steven L. Salzberg, Mihaela Pertea, Beril Erdogdu

Major data analysis errors invalidate cancer microbiome findings

mBio(2023)10.1128/mbio.01607-23
N/A
0DataRank · unranked
205 citations

Yuchen Ge, Jennifer Lu, Daniela Puiu, Amanda Xu, Colin S. Cooper +4 more

Highly accurate isoform identification for the human transcriptome

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.06.08.495354
N/A
0DataRank · unranked
3 citations

Sooyoung Cha, Ales Varabyou, Natalia Rincon, Sukhwan Park, Ilia Minkin +4 more

Major data analysis errors invalidate cancer microbiome findings

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.28.550993
N/A
0DataRank · unranked
38 citations

Yuchen Ge, Jennifer Lu, Daniela Puiu, Amanda Xu, Colin S. Cooper +4 more

Improved Transcriptome Assembly Using a Hybrid of Long and Short Reads with StringTie

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.12.08.471868
N/A
0DataRank · unranked
15 citations

Brandon Wong, Geo Pertea, Mihaela Pertea, Alaina Shumate

Investigating Open Reading Frames in Known and Novel Transcripts using ORFanage

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.23.533704
N/A
0DataRank · unranked
3 citations

Beril Erdogdu, Steven L. Salzberg, Mihaela Pertea, Ales Varabyou

The status of the human gene catalogue

arXiv (Cornell University)(2023)10.48550/arxiv.2303.13996
Top 100%
0DataRank
Top 100%0 citations

Sílvia Carbonell Sala, Francisco M. De La Vega, Tiago Faial, Adam Frankish, T Gingeras +16 more

EASTR: Correcting systematic alignment errors in multi-exon genes

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.10.540179
N/A
0DataRank · unranked
0 citations

Richard Hu, Hyun Joo Ji, Kuan-Hao Chao, Mihaela Pertea, Ida Shinder

TieBrush: an efficient method for aggregating and summarizing mapped reads across large datasets

Bioinformatics(2021)10.1093/bioinformatics/btab342
N/A
0DataRank · unranked
27 citations

Geo Pertea, Christopher Pockrandt, Mihaela Pertea, Ales Varabyou

Splam: a deep-learning-based splice site predictor that improves spliced alignments

Genome biology(2024)10.1186/s13059-024-03379-4
N/A
0DataRank · unranked
20 citations

Alan Mao, Steven L. Salzberg, Mihaela Pertea, Kuan-Hao Chao

Rapid detection of inter-clade recombination in SARS-CoV-2 with Bolotie

Genetics(2021)10.1093/genetics/iyab074
N/A
0DataRank · unranked
72 citations

Christopher Pockrandt, Steven L. Salzberg, Mihaela Pertea, Ales Varabyou

Combining DNA and protein alignments to improve genome annotation with LiftOn

Genome Research(2024)10.1101/gr.279620.124
N/A
0DataRank · unranked
20 citations

Jakob Heinz, Celine Hoh, Alan Mao, Alaina Shumate, Mihaela Pertea +2 more

Enhancing transcriptome expression quantification through accurate assignment of long RNA sequencing reads with TranSigner

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.04.13.589356
N/A
0DataRank · unranked
3 citations

Mihaela Pertea, Hyun Joo Ji

Enhancing transcriptome expression quantification through accurate assignment of long RNA sequencing reads with TranSigner

Genome biology(2025)10.1186/s13059-025-03723-2
N/A
0DataRank · unranked
1 citations

Mihaela Pertea, Hyun Joo Ji

Assembly and quantification of transcripts from noisy long reads with NIFFLR

F1000Research(2025)10.12688/f1000research.164583.1
N/A
0DataRank · unranked
0 citations

Mihaela Pertea, Aleksey V. Zimin, Alina Guo

Investigating open reading frames in known and novel transcripts using ORFanage

Nature Computational Science(2023)10.1038/s43588-023-00496-1
N/A
0DataRank · unranked
34 citations

Beril Erdogdu, Steven L. Salzberg, Mihaela Pertea, Ales Varabyou

Comprehensive Transcriptome Annotation of Thousands of HIV-1 Genomes

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.09.24.675449
Top 100%
0DataRank
Top 100%0 citations

Mykhaylo Artamonov, Sophia Cheng, Diane L. Bolton, Steven L. Salzberg, Mihaela Pertea +1 more