Ali Mortazavi

Biochemistry, Genetics and Molecular BiologyNeuroscience

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

22.7Author DataRank

Indexed papers

9in 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 9 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.

A comparative encyclopedia of DNA elements in the mouse genome

Nature(2014)10.1038/nature13992

Top 2%

7.9DataRank

Top 2%1946 citations

Yong Cheng, Alessandra Breschi, Jost Vielmetter, Weisheng Wu, Tyrone Ryba +150 more

Papers

Driven by 60 papers — median percentile 85. Top paper: “A comparative encyclopedia of DNA elements in the mouse genome”.

A comparative encyclopedia of DNA elements in the mouse genome

Nature(2014)10.1038/nature13992

Top 2%

7.9DataRank

Top 2%1946 citations

Yong Cheng, Alessandra Breschi, Jost Vielmetter, Weisheng Wu, Tyrone Ryba +150 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

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

The ENCODE Uniform Analysis Pipelines

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.04.04.535623

Top 11%

2.0DataRank

Top 11%102 citations

Jin-Wook Lee, Otto Jolanki, Meenakshi S. Kagda, Keenan Graham, Paul Sud +55 more

Predicting gene expression in massively parallel reporter assays: A comparative study

Human Mutation(2017)10.1002/humu.23197

N/A

1.7DataRank · unranked

52 citations

Haoyang Zeng, Matthew D. Edwards, Gamze Gürsoy, Kevin Tian, R. Alan Harris +20 more

The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models

Cell(2023)10.1016/j.cell.2023.02.018

Top 15%

1.4DataRank

Top 15%82 citations

Jiahao Gao, Beatrice Borsari, Yucheng T. Yang, Timur R. Galeev, Gamze Gürsoy +95 more

Landscape of transcription in human cells

Nature(2012)10.1038/nature11233

N/A

1.3DataRank · unranked

5354 citations

Qi Dai, Angelika Merkel, Timo Lassmann, Shinichi Morishita, Andrea Tanzer +91 more

Deciphering the impact of genomic variation on function

Nature(2024)10.1038/s41586-024-07510-0

N/A

1.1DataRank · unranked

89 citations

Jesse M. Engreitz, Heather A. Lawson, Harinder Singh, Lea M. Starita, Gary C. Hon +95 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

C5aR1 antagonism suppresses inflammatory glial responses and alters cellular signaling in an Alzheimer’s disease mouse model

Nature Communications(2024)10.1038/s41467-024-51163-6

N/A

0.911DataRank · unranked

50 citations

Heidi Yahan Liang, Klébea Carvalho, Shu‐Hui Chu, Adrian Mendoza‐Arvilla, Tiffany J. Petrisko +4 more

Integration of high-resolution promoter profiling assays reveals novel, cell type–specific transcription start sites across 115 human cell and tissue types

Genome Research(2021)10.1101/gr.275723.121

Top 30%

0.670DataRank

Top 30%15 citations

Xiao‐Ou Zhang, Shaimae I. Elhajjajy, Kaili Fan, Henry Pratt, Fairlie Reese +3 more

Uncovering the mesendoderm gene regulatory network through multi-omic data integration

Cell Reports(2022)10.1016/j.celrep.2022.110364

N/A

0.586DataRank · unranked

16 citations

Kitt Paraiso, Jeff Jiajing Zhou, Ira L. Blitz, Margaret B. Fish, Rebekah M. Charney +11 more

An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.12.26.629296

Top 45%

0.416DataRank

Top 45%12 citations

Henry Pratt, Kaili Fan, Nishigandha Phalke, Jonathan Fisher, Shaimae I. Elhajjajy +37 more

Systematic cell-type resolved transcriptomes of 8 tissues in 8 lab and wild-derived mouse strains capture global and local expression variation

Cell Genomics(2025)10.1016/j.xgen.2025.101108

Top 70%

0.165DataRank

Top 70%2 citations

Ryan Weber, Elnaz Abdollahzadeh, Nikhila Swarna, Delaney K. Sullivan, Diane Trout +21 more

Transcriptome analysis of heterogeneity in mouse model of metastatic breast cancer

Breast Cancer Research(2021)10.1186/s13058-021-01468-x

N/A

0DataRank · unranked

38 citations

Gabriela Balderrama-Gutierrez, Krystian J. Ibanez, Steve Huy D. Phan, Angelique N. Cortez, Ali Mortazavi +2 more

Coordinated Gene Expression and Chromatin Regulation during Hydra Head Regeneration

Genome Biology and Evolution(2021)10.1093/gbe/evab221

N/A

0DataRank · unranked

32 citations

Aide Macias-Muñoz, Ashley Wong, Ricardo Martínez‐García, Ali Mortazavi, Rabi Murad

Disruption of β-Catenin–Dependent Wnt Signaling in Colon Cancer Cells Remodels the Microenvironment to Promote Tumor Invasion

Molecular Cancer Research(2021)10.1158/1541-7786.mcr-21-0349

N/A

0DataRank · unranked

27 citations

Delia F. Tifrea, Rabi Murad, Amber N. Habowski, Yung Lyou, Madeleine Duong +5 more

An Infection-Tolerant Mammalian Reservoir for Several Zoonotic Agents Broadly Counters the Inflammatory Effects of Endotoxin

mBio(2021)10.1128/mbio.00588-21

N/A

0DataRank · unranked

26 citations

Ana Milovic, Vanessa J. Cook, M. Nurul Islam, Youwen Zhang, Hippokratis Kiaris +4 more

Transcriptome and chromatin landscape changes associated with trastuzumab resistance in HER2+ breast cancer cells

Gene(2021)10.1016/j.gene.2021.145808

N/A

0DataRank · unranked

23 citations

Arabo A. Avanes, Xinyi Ma, Shuhui Geng, Ali Mortazavi, Jamil Momand +1 more

Linking Chromosomal Silencing With Xist Expression From Autosomal Integrated Transgenes

Frontiers in Cell and Developmental Biology(2021)10.3389/fcell.2021.693154

N/A

0DataRank · unranked

16 citations

Benjamin Lin, Chiu-Ho T. Webb, Shan Jiang, Sarah Carmona, Wenzhu Liu +3 more

Diverse functional elements in RNA predicted transcriptome-wide by orthogonal RNA structure probing

Nucleic Acids Research(2021)10.1093/nar/gkab885

N/A

0DataRank · unranked

8 citations

Chao Feng, Whitney England, Dana Wyman, Ryan A. Flynn, Xiuye Wang +4 more

Uncovering the Gene Regulatory Networks Underlying Macrophage Polarization Through Comparative Analysis of Bulk and Single-Cell Data

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.20.427499

N/A

0DataRank · unranked

16 citations

Elisabeth Rebboah, Camden Jansen, Katherine Williams, Andrew Dowey, Cassandra McGill +2 more

Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.04.26.441522

N/A

0DataRank · unranked

5 citations

Fairlie Reese, Katherine Williams, Gabriela Balderrama-Gutierrez, Cassandra McGill, Diane Trout +5 more

Systematic phenotyping and characterization of the 3xTg-AD mouse model of Alzheimer’s Disease

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.01.462640

N/A

0DataRank · unranked

5 citations

Kristine M. Tran, Jimmy Phan, Edna E. Hingco, Enikö A. Kramár, Celia Da Cunha +15 more

Subventricular zone/white matter microglia reconstitute the empty adult microglial niche in a dynamic wave

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.02.17.431594

N/A

0DataRank · unranked

2 citations

Allison R. Najafi, Yasamine Ghorbanian, Neelakshi Soni, Joshua Crapser, Dario X. Figueroa Velez +9 more

Muscle group specific transcriptomic and DNA methylation differences related to developmental patterning in FSHD

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.09.28.462147

N/A

0DataRank · unranked

2 citations

Xiangduo Kong, Nam Viet Nguyen, Cassandra McGill, Rabi Tawil, Kyoko Yokomori +2 more

Systematic Phenotyping and Characterization of the 3xTg-AD Mouse Model of Alzheimer’s Disease

Frontiers in Neuroscience(2022)10.3389/fnins.2021.785276

N/A

0DataRank · unranked

213 citations

Kristine M. Tran, Jimmy Phan, Edna E. Hingco, Enikö A. Kramár, Celia Da Cunha +17 more

Modulation of C5a–C5aR1 signaling alters the dynamics of AD progression

Journal of Neuroinflammation(2022)10.1186/s12974-022-02539-2

N/A

0DataRank · unranked

63 citations

Nicole D. Schartz, Gabriela Balderrama-Gutierrez, Heidi Yahan Liang, Shu‐Hui Chu, Purnika Selvan +6 more

Heterogeneous Skeletal Muscle Cell and Nucleus Populations Identified by Single-Cell and Single-Nucleus Resolution Transcriptome Assays

Frontiers in Genetics(2022)10.3389/fgene.2022.835099

N/A

0DataRank · unranked

43 citations

Kyoko Yokomori, Ali Mortazavi, Katherine Williams

Analysis of alternative polyadenylation from long-read or short-read RNA-seq with LAPA

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.08.515683

N/A

0DataRank · unranked

16 citations

Ali Mortazavi, Muhammed Hasan Çelik

PyWGCNA: A Python package for weighted gene co-expression network analysis

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.08.22.504852

N/A

0DataRank · unranked

12 citations

Fairlie Reese, Ali Mortazavi, Narges Rezaie

Modulation of C5a-C5aR1 signaling alters the dynamics of AD progression

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.04.01.486759

N/A

0DataRank · unranked

5 citations

Nicole D. Schartz, Gabriela Balderrama-Gutierrez, Heidi Yahan Liang, Shu‐Hui Chu, Purnika Selvan +6 more

Engineered SMCHD1 and D4Z4 mutations reveal roles of D4Z4 heterochromatin disruption and feedforward DUX4 network activation in FSHD

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.10.14.512332

N/A

0DataRank · unranked

0 citations

Nam Viet Nguyen, Yumeng Li, Jasmine Sakr, Katherine Williams, Sheila Sharifi +9 more

A Trem2R47H mouse model without cryptic splicing drives age- and disease-dependent tissue damage and synaptic loss in response to plaques

Molecular Neurodegeneration(2023)10.1186/s13024-023-00598-4

N/A

0DataRank · unranked

51 citations

Shimako Kawauchi, Enikö A. Kramár, Narges Rezaie, Heidi Yahan Liang, Jasmine Sakr +24 more

PyWGCNA: a Python package for weighted gene co-expression network analysis

Bioinformatics(2023)10.1093/bioinformatics/btad415

N/A

0DataRank · unranked

75 citations

Fairlie Reese, Ali Mortazavi, Narges Rezaie

The ENCODE Uniform Analysis Pipelines

Research Square(2023)10.21203/rs.3.rs-3111932/v1

N/A

0DataRank · unranked

39 citations

Jin-Wook Lee, Otto Jolanki, Meenakshi S. Kagda, Keenan Graham, Paul Sud +57 more

C5aR1 antagonism suppresses inflammatory glial gene expression and alters cellular signaling in an aggressive Alzheimer’s model

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.22.554306

N/A

0DataRank · unranked

5 citations

Heidi Yahan Liang, Klébea Carvalho, Shu‐Hui Chu, Adrian Mendoza‐Arvilla, Tiffany J. Petrisko +4 more

Within-subject changes in methylome profile identify individual signatures of early-life adversity, with a potential to predict neuropsychiatric outcome

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.12.16.571594

N/A

0DataRank · unranked

0 citations

Ryan Weber, Noriko Kamei, Christina Wilcox Thai, Hina Arora, Ali Mortazavi +4 more

Individual longitudinal changes in DNA-methylome identify signatures of early-life adversity and correlate with later outcome

Neurobiology of Stress(2024)10.1016/j.ynstr.2024.100652

N/A

0DataRank · unranked

17 citations

Ryan Weber, Noriko Kamei, Christina Wilcox Thai, Hina Arora, Ali Mortazavi +4 more

Genetic diversity promotes resilience in a mouse model of Alzheimer's disease

Alzheimer s & Dementia(2024)10.1002/alz.13753

N/A

0DataRank · unranked

16 citations

Lindsay A. Hohsfield, Kristine M. Tran, Shimako Kawauchi, Amber Walker, Dominic I. Javonillo +17 more

Engineered FSHD mutations results in D4Z4 heterochromatin disruption and feedforward DUX4 network activation

iScience(2024)10.1016/j.isci.2024.109357

N/A

0DataRank · unranked

9 citations

Nam Viet Nguyen, Yumeng Li, Jasmine Sakr, K. Williams, Sheila Sharifi +9 more

BIN1K358R suppresses glial response to plaques in mouse model of Alzheimer's disease

Alzheimer s & Dementia(2024)10.1002/alz.13767

N/A

0DataRank · unranked

9 citations

Zechuan Shi, Ian F. Smith, Enikö A. Kramár, Katelynn Tran, Shimako Kawauchi +22 more

Long-read sequencing transcriptome quantification with lr-kallisto

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.07.19.604364

N/A

0DataRank · unranked

14 citations

Delaney K. Sullivan, A. Sina Booeshaghi, Fairlie Reese, Elisabeth Rebboah, Jasmine Sakr +12 more

Unlocking the regulatory code of RNA: launching the Human RNome Project

Genome biology(2025)10.1186/s13059-025-03824-y

N/A

0DataRank · unranked

7 citations

Etienne Boileau, Janusz M. Bujnicki, Vivian G. Cheung, Silvestro G. Conticello, Peter C. Dedon +14 more

Dogme: A nextflow pipeline for reprocessing nanopore RNA and DNA modifications

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.06.04.657941

N/A

0DataRank · unranked

1 citations

Ali Mortazavi, Elnaz Abdollahzadeh

Determining gene specificity from multivariate single-cell RNA sequencing data

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.11.21.689845

N/A

0DataRank · unranked

1 citations

A. Sina Booeshaghi, Elisabeth Rebboah, M. Grace Gordon, Pooja Kathail, Taibo Li +6 more

Probing the roles of developmentally active neurons, in early-life adversity induced disruptions of adult behaviors

Frontiers in Neuroscience(2025)10.3389/fnins.2025.1671495

N/A

0DataRank · unranked

0 citations

Ali Mortazavi, Tallie Z. Baram, Amalia Floriou‐Servou, Ryan Weber

Slug regulates the Dll4-Notch-VEGFR2 axis to control endothelial cell activation and angiogenesis

Nature Communications(2020)10.1038/s41467-020-18633-z

N/A

0DataRank · unranked

101 citations

Jennifer S. Fang, Mary E. Ziegler, Ricardo N. Ramírez, Duc T. T. Phan, Michaela M.S. Hatch +8 more

Unexpected Transcriptional Programs Contribute to Hippocampal Memory Deficits and Neuronal Stunting after Early-Life Adversity

Cell Reports(2020)10.1016/j.celrep.2020.108511

N/A

0DataRank · unranked

46 citations

Anton Schulmann, Megan M. Curran, Limor Regev, Yuncai Chen, Noriko Kamei +8 more

Swan: a library for the analysis and visualization of long-read transcriptomes

Bioinformatics(2020)10.1093/bioinformatics/btaa836

N/A

0DataRank · unranked

34 citations

Ali Mortazavi, Fairlie Reese

Swan: a library for the analysis and visualization of long-read transcriptomes

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.09.143024

N/A

0DataRank · unranked

4 citations

Ali Mortazavi, Fairlie Reese

Comparative Transcriptomics of heads and tails between Steinernema carpocapsae and Caenorhabditis elegans

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.08.20.259739

N/A

0DataRank · unranked

4 citations

Lorrayne Serra Clague, Cassandra McGill, Bryan Rodriguez, Ali Mortazavi, Isaryhia Rodriguez

Uncovering the mesendoderm gene regulatory network through multi-omic data integration

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.01.362053

N/A

0DataRank · unranked

3 citations

Kitt Paraiso, Jeff Jiajing Zhou, Ira L. Blitz, Margaret B. Fish, Rebekah M. Charney +11 more

Transcriptome-Wide Combinatorial RNA Structure Probing in Living Cells

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.03.24.006866

N/A

0DataRank · unranked

2 citations

Chao Feng, Whitney England, Dana Wyman, Ryan A. Flynn, Xiuye Wang +4 more

Relationship of DUX4 and target gene expression in FSHD myocytes

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.24.109710

N/A

0DataRank · unranked

0 citations

Xiangduo Kong, Nam Viet Nguyen, Katherine Williams, Rabi Tawil, Tohru Kiyono +3 more

The infection-tolerant mammalian reservoir of Lyme disease and other zoonoses broadly counters the inflammatory effects of endotoxin

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.13.422519

N/A

0DataRank · unranked

0 citations

Ana Milovic, Vanessa J. Cook, M. Nurul Islam, Youwen Zhang, Hippokratis Kiaris +4 more

Generation of a humanized Aβ expressing mouse demonstrating aspects of Alzheimer’s disease-like pathology

Nature Communications(2021)10.1038/s41467-021-22624-z

N/A

0DataRank · unranked

116 citations

Stefânia Forner, Lena Cai, Alessandra Cadete Martini, Laura Trujillo‐Estrada, Vivek Swarup +30 more

Microglial dyshomeostasis drives perineuronal net and synaptic loss in a CSF1R +/− mouse model of ALSP, which can be rescued via CSF1R inhibitors

Science Advances(2021)10.1126/sciadv.abg1601

N/A

0DataRank · unranked

96 citations

Neelakshi Soni, Joshua Crapser, Lindsay A. Hohsfield, Monica R. P. Elmore, Dina P. Matheos +5 more

Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq

Genome biology(2021)10.1186/s13059-021-02505-w

N/A

0DataRank · unranked

64 citations

Fairlie Reese, Katherine Williams, Gabriela Balderrama-Gutierrez, Cassandra McGill, Diane Trout +5 more

Single-Cell Transcriptional Changes in Hypothalamic Corticotropin-Releasing Factor–Expressing Neurons After Early-Life Adversity Inform Enduring Alterations in Vulnerabilities to Stress

Biological Psychiatry Global Open Science(2021)10.1016/j.bpsgos.2021.12.006

N/A

0DataRank · unranked

46 citations

Christina Wilcox Thai, Yuncai Chen, Noriko Kamei, Aidan L. Pham, Matthew T. Birnie +4 more

Ali Mortazavi

Indexed papers

Top data-sharing exemplar

Papers