Arjun Raj

Biochemistry, Genetics and Molecular BiologyMedicine

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 100%percentile

0Author DataRank

Indexed papers

1in 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 1 indexed paper 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 →

Papers

Driven by 53 papers. Top paper: “Dynamic enhancer–gene body contacts during transcription elongation”.

Dynamic enhancer–gene body contacts during transcription elongation

Genes & Development(2015)10.1101/gad.255265.114

N/A

3.2DataRank · unranked

84 citations

Chris C.-S. Hsiung, Peng Huang, Arjun Raj, Gerd A. Blobel, Kiwon Lee

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

Proceedings of the National Academy of Sciences(2009)10.1073/pnas.0904715106

N/A

1.2DataRank · unranked

2859 citations

Mitchell Guttman, Maite Huarte, Manuel Garber, Arjun Raj, Dianali Rivea Morales +8 more

Gene regulation gravitates toward either addition or multiplication when combining the effects of two signals

eLife(2020)10.7554/elife.59388

N/A

1.0DataRank · unranked

36 citations

Benjamin Emert, Allison Coté, Arjun Raj, Eric M. Sanford

SAVER: gene expression recovery for single-cell RNA sequencing

Nature Methods(2018)10.1038/s41592-018-0033-z

N/A

1.0DataRank · unranked

851 citations

Jingshu Wang, Eduardo Torre, Hannah Dueck, Sydney Shaffer, Roberto Bonasio +7 more

Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution

Genome Biology(2015)10.1186/s13059-015-0586-4

N/A

0.982DataRank · unranked

695 citations

Margaret C. Dunagin, Patrick D. McClanahan, Andrew Biaesch, Olivia Padovan-Merhar, Prisca Liberali +5 more

Post-transcriptional splicing can occur in a slow-moving zone around the gene

eLife(2023)10.7554/elife.91357

N/A

0.475DataRank · unranked

12 citations

Aoife O'Farrell, Ian Dardani, Margaret C. Dunagin, Chris Coté, Yihan Wan +13 more

Image-based profiling: a powerful and challenging new data type

Biocomputing 2022(2021)10.1142/9789811250477_0038

N/A

0.104DataRank · unranked

1 citations

Hannah Spitzer, Philip Burnham, Arjun Raj, Shantanu Singh, Anne E. Carpenter +2 more

Variability within rare cell states enables multiple paths toward drug resistance

Nature Biotechnology(2021)10.1038/s41587-021-00837-3

N/A

0DataRank · unranked

190 citations

Christopher Coté, Eduardo A. Torre, Ian Dardani, Connie Jiang, Naveen Jain +3 more

p53 mediates target gene association with nuclear speckles for amplified RNA expression

Molecular Cell(2021)10.1016/j.molcel.2021.03.006

N/A

0DataRank · unranked

116 citations

Allison Coté, Son C. Nguyen, Liguo Zhang, Omid Gholamalamdari, Paula A. Agudelo-Garcia +13 more

Genetic screening for single-cell variability modulators driving therapy resistance

Nature Genetics(2021)10.1038/s41588-020-00749-z

N/A

0DataRank · unranked

79 citations

Eri Arai, Sareh Bayatpour, Connie Jiang, Lauren E. Beck, Benjamin Emert +9 more

Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity in vitro

Cell Systems(2021)10.1016/j.cels.2021.07.003

N/A

0DataRank · unranked

23 citations

Hailey I. Edelstein, Rachel Truitt, Yogesh Goyal, Lauren E. Beck, Orsolya Symmons +9 more

CTCF blocks anti-sense transcription initiation at divergent gene promoters

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.30.465508

N/A

0DataRank · unranked

5 citations

Camille M. Syrett, Marit W. Vermunt, Allison Coté, Jacob M. Tome, Haoyue Zhang +13 more

Changes in chromatin accessibility are not concordant with transcriptional changes for single‐factor perturbations

Molecular Systems Biology(2022)10.15252/msb.202210979

N/A

0DataRank · unranked

88 citations

Eric M. Sanford, Yogesh Goyal, Arjun Raj, Karun Kiani

ClampFISH 2.0 enables rapid, scalable amplified RNA detection in situ

Nature Methods(2022)10.1038/s41592-022-01653-6

N/A

0DataRank · unranked

47 citations

Benjamin Emert, Yogesh Goyal, Connie Jiang, Amanpreet Kaur, Jasmine Lee +8 more

CTCF blocks antisense transcription initiation at divergent promoters

Nature Structural & Molecular Biology(2022)10.1038/s41594-022-00855-y

N/A

0DataRank · unranked

28 citations

Marit W. Vermunt, Camille M. Syrett, Allison Coté, Jacob M. Tome, Haoyue Zhang +13 more

Cell type determination for cardiac differentiation occurs soon after seeding of human-induced pluripotent stem cells

Genome biology(2022)10.1186/s13059-022-02654-6

N/A

0DataRank · unranked

25 citations

Yogesh Goyal, Naveen Jain, Qiaohong Wang, Rachel Truitt, Allison Coté +7 more

Systematically quantifying morphological features reveals constraints on organoid phenotypes

Cell Systems(2022)10.1016/j.cels.2022.05.008

N/A

0DataRank · unranked

25 citations

Jasmine Lee, Christopher Coté, Margaret C. Dunagin, Ilya Lukonin, Nikkita Salla +7 more

Allelic correlation is a marker of trade-offs between barriers to transmission of expression variability and signal responsiveness in genetic networks

Cell Systems(2022)10.1016/j.cels.2022.10.008

N/A

0DataRank · unranked

4 citations

Vinay Ayyappan, Lea Schuh, Arjun Raj, Ryan H. Boe

Changes in chromatin accessibility are not concordant with transcriptional changes for single-factor perturbations

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.02.03.478981

N/A

0DataRank · unranked

9 citations

Eric M. Sanford, Yogesh Goyal, Arjun Raj, Karun Kiani

ClonoCluster: a method for using clonal origin to inform transcriptome clustering

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.02.11.480077

N/A

0DataRank · unranked

4 citations

Yogesh Goyal, Connie Jiang, Arjun Raj, Lee P. Richman

fMetastatic potential in clonal melanoma cells is driven by a rare, early-invading subpopulation

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.04.17.488591

N/A

0DataRank · unranked

4 citations

Luciann Cuenca, Karun Kiani, Gianna T. Busch, Dylan Fingerman, Margaret C. Dunagin +9 more

Diverse clonal fates emerge upon drug treatment of homogeneous cancer cells

Nature(2023)10.1038/s41586-023-06342-8

N/A

0DataRank · unranked

182 citations

Gianna T. Busch, Maalavika Pillai, Jingxin Li, Ryan H. Boe, Emanuelle I. Grody +30 more

A subpopulation of lipogenic brown adipocytes drives thermogenic memory

Nature Metabolism(2023)10.1038/s42255-023-00893-w

N/A

0DataRank · unranked

32 citations

Prateek Sharma, Lenka Dohnalová, Kyle Coleman, Giulia T. Uhr, Susanna Kircher +21 more

ClonoCluster: A method for using clonal origin to inform transcriptome clustering

Cell Genomics(2023)10.1016/j.xgen.2022.100247

N/A

0DataRank · unranked

23 citations

Yogesh Goyal, Connie Jiang, Arjun Raj, Lee P. Richman

Retrospective identification of intrinsic factors that mark pluripotency potential in rare somatic cells

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.02.10.527870

N/A

0DataRank · unranked

7 citations

Yogesh Goyal, Margaret C. Dunagin, Christopher Coté, Ian A. Mellis, Benjamin Emert +5 more

Post-transcriptional splicing can occur in a slow-moving zone around the gene

(2023)10.7554/elife.91357.2

N/A

0DataRank · unranked

7 citations

Aoife O’Farrell, Ian Dardani, Margaret C. Dunagin, Chris Coté, Yihan Wan +13 more

Single cell susceptibility to SARS-CoV-2 infection is driven by variable cell states

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.06.547955

N/A

0DataRank · unranked

6 citations

Jesse Miller, Kasirajan Ayyanathan, Margaret C. Dunagin, Naveen Jain, D. Schultz +3 more

Nuclear speckles regulate HIF-2α programs and correlate with patient survival in kidney cancer

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.09.14.557228

N/A

0DataRank · unranked

5 citations

Ruofan Yu, Nicolas Skuli, Nathan J. Coffey, Son C. Nguyen, Christine Faunce +13 more

Reviewer #2 (Public Review): Post-transcriptional splicing can occur in a slow-moving zone around the gene

(2023)10.7554/elife.91357.1.sa0

N/A

0DataRank · unranked

0 citations

Aoife O'Farrell, Ian Dardani, Margaret C. Dunagin, Chris Coté, Yihan Wan +13 more

Post-transcriptional splicing can occur in a slow-moving zone around the gene

(2023)10.7554/elife.91357.1

N/A

0DataRank · unranked

0 citations

Aoife O’Farrell, Ian Dardani, Margaret C. Dunagin, Chris Coté, Yihan Wan +13 more

Author Response: Post-transcriptional splicing can occur in a slow-moving zone around the gene

(2023)10.7554/elife.91357.2.sa3

N/A

0DataRank · unranked

0 citations

Aoife O’Farrell, Ian Dardani, Margaret C. Dunagin, Chris Coté, Yihan Wan +13 more

Reviewer #1 (Public Review): Post-transcriptional splicing can occur in a slow-moving zone around the gene

(2023)10.7554/elife.91357.2.sa1

N/A

0DataRank · unranked

0 citations

Aoife O’Farrell, Ian Dardani, Margaret Dunagin, Chris Coté, Yihan Wan +13 more

Reviewer #2 (Public Review): Post-transcriptional splicing can occur in a slow-moving zone around the gene

(2023)10.7554/elife.91357.2.sa0

N/A

0DataRank · unranked

0 citations

Aoife O'Farrell, Ian Dardani, Margaret C. Dunagin, Chris Coté, Yihan Wan +13 more

Retrospective identification of cell-intrinsic factors that mark pluripotency potential in rare somatic cells

Cell Systems(2024)10.1016/j.cels.2024.01.001

N/A

0DataRank · unranked

29 citations

Yogesh Goyal, Margaret C. Dunagin, Christopher Coté, Ian A. Mellis, Benjamin Emert +7 more

Post-transcriptional splicing can occur in a slow-moving zone around the gene

eLife(2024)10.7554/elife.91357.3

N/A

0DataRank · unranked

14 citations

Aoife O'Farrell, Ian Dardani, Margaret C. Dunagin, Chris Coté, Yihan Wan +13 more

AP-1 Mediates Cellular Adaptation and Memory Formation During Therapy Resistance

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.07.25.604999

N/A

0DataRank · unranked

14 citations

Pavithran T. Ravindran, Aoife O’Farrell, Gianna T. Busch, Ryan H. Boe, Zijian Niu +8 more

Piscis: a novel loss estimator of the F1 score enables accurate spot detection in fluorescence microscopy images via deep learning

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.01.31.578123

N/A

0DataRank · unranked

8 citations

Aoife O’Farrell, Jingxin Li, Sam Reffsin, Naveen Jain, Ian Dardani +3 more

Nuclear speckles regulate functional programs in cancer

Nature Cell Biology(2025)10.1038/s41556-024-01570-0

N/A

0DataRank · unranked

18 citations

Ruofan Yu, Nicolas Skuli, Nathan J. Coffey, Son C. Nguyen, Christine Faunce +13 more

Single-cell susceptibility to viral infection is driven by variable cell states

Cell(2025)10.1016/j.cell.2025.10.021

N/A

0DataRank · unranked

9 citations

Jesse Miller, Kasirajan Ayyanathan, Margaret C. Dunagin, Yael Heyman, Naveen Jain +4 more

Piscis: A loss estimator of the F1 score enables accurate spot detection in fluorescence microscopy images via deep learning

Cell Systems(2025)10.1016/j.cels.2025.101448

N/A

0DataRank · unranked

4 citations

Aoife O'Farrell, Jingxin Li, Sam Reffsin, Naveen Jain, Ian Dardani +3 more

Innate Immune Memory is Stimulus Specific

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.01.22.634275

N/A

0DataRank · unranked

4 citations

Zijian Niu, Jingxin Li, Laura C. Van Eyndhoven, Kavitha Sarma, Arjun Raj +1 more

Gastruloid patterning reflects division of labor among biased stem cell clones

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.07.12.664536

N/A

0DataRank · unranked

2 citations

Catherine G. Triandafillou, Kavitha Sarma, Arjun Raj, Vinay Ayyappan

Heterogeneous therapy-resistant cancer cells have distinct and exploitable drug sensitivity profiles

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.04.25.650475

N/A

0DataRank · unranked

1 citations

Ryan H. Boe, Jingxin Li, Robert F. Gruener, Miles J. Arnett, Pavithran T. Ravindran +4 more

Lineage memory shapes viral resistance barriers in human skin

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.06.27.661951

N/A

0DataRank · unranked

1 citations

Grant Kinsler, Jingchao Zhang, Aoife O’Farrell, Rim Abderrahim, Apurv Srivastav +9 more

Dynamics of Ribosomal RNA Transcription and Abundance in Normal and Leukemic Hematopoiesis

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.08.01.668217

N/A

0DataRank · unranked

0 citations

Victoria K. Feist, Erin M. Gray, Subin S. George, Charles Antony, Jill A. Henrich +14 more

Clonal dynamics shaped by diverse drug-tolerant persister states in melanoma resistance

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.09.16.676608

N/A

0DataRank · unranked

0 citations

Yeqing Chen, Jessica Kaster, M. J. Dunne, Min Xiao, Ling Li +28 more

Single-cell spatial mapping reveals reproducible cell type organization and spatially-dependent gene expression in gastruloids

eLife(2025)10.1101/2025.07.14.664617

N/A

0DataRank · unranked

3 citations

Pranav Sompalle, Yael Heyman, Arjun Raj, Catherine G. Triandafillou

Memory Sequencing Reveals Heritable Single-Cell Gene Expression Programs Associated with Distinct Cellular Behaviors

Cell(2020)10.1016/j.cell.2020.07.003

N/A

0DataRank · unranked

210 citations

Benjamin Emert, Raúl A. Reyes Hueros, Christopher Coté, Guillaume Harmange, Dylan L. Schaff +7 more

Gene Networks with Transcriptional Bursting Recapitulate Rare Transient Coordinated High Expression States in Cancer

Cell Systems(2020)10.1016/j.cels.2020.03.004

N/A

0DataRank · unranked

101 citations

Michael Saint-Antoine, Eric M. Sanford, Benjamin Emert, Abhyudai Singh, Carsten Marr +3 more

Genetic Variation in Type 1 Diabetes Reconfigures the 3D Chromatin Organization of T Cells and Alters Gene Expression

Immunity(2020)10.1016/j.immuni.2020.01.003

N/A

0DataRank · unranked

55 citations

Naomi Goldman, Wenliang Wang, Benjamin Cattau, Yeqiao Zhou, Jelena Petrovic +13 more

Post-transcriptional splicing can occur in a slow-moving zone around the gene

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.06.028092

N/A

0DataRank · unranked

21 citations

Aoife O’Farrell, Ian Dardani, Margaret C. Dunagin, Chris Coté, Yihan Wan +13 more

Gene regulation gravitates towards either addition or multiplication when combining the effects of two signals

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.26.116962

N/A

0DataRank · unranked

4 citations

Benjamin Emert, Allison Coté, Arjun Raj, Eric M. Sanford

Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.11.147207

N/A

0DataRank · unranked

2 citations

Hailey I. Edelstein, Rachel Truitt, Lauren E. Beck, Orsolya Symmons, Yogesh Goyal +7 more