Justin B. Kinney

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 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 28 papers. Top paper: “Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time”.

Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time

eLife(2020)10.7554/elife.55308

N/A

1.7DataRank · unranked

78 citations

Suzannah M. Beeler, Emanuel Flores‐Bautista, Nicholas S. McCarty, Tom Röschinger, Nathan M. Belliveau +5 more

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

Nature Biotechnology(2012)10.1038/nbt.2137

N/A

0.978DataRank · unranked

677 citations

Anand Murugan, Xiaolan Zhang, Tiberiu Tesileanu, Li Wang, Peter Rogov +9 more

Specificity, synergy, and mechanisms of splice-modifying drugs

Nature Communications(2024)10.1038/s41467-024-46090-5

N/A

0.571DataRank · unranked

44 citations

Mandy S. Wong, Carlos Martí‐Gómez, Andalus Ayaz, Mahdi Kooshkbaghi, Sonya M. Hanson +4 more

MAVE-NN: learning genotype-phenotype maps from multiplex assays of variant effect

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.14.201475

N/A

0.406DataRank · unranked

14 citations

Mahdi Kooshkbaghi, Anna Posfai, William T. Ireland, David M. McCandlish, Justin B. Kinney +1 more

Deciphering the regulatory genome of Escherichia coli , one hundred promoters at a time

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.01.18.910323

N/A

0.371DataRank · unranked

5 citations

Suzannah M. Beeler, Emanuel Flores‐Bautista, Nathan M. Belliveau, Michael J. Sweredoski, Annie Moradian +3 more

Specificity, synergy, and mechanisms of splice-modifying drugs

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.30.522303

N/A

0.345DataRank · unranked

9 citations

Mandy S. Wong, Carlos Martí‐Gómez, Andalus Ayaz, Mahdi Kooshkbaghi, Sonya M. Hanson +4 more

Gauge fixing for sequence-function relationships

PLoS Computational Biology(2025)10.1371/journal.pcbi.1012818

N/A

0.330DataRank · unranked

8 citations

Juannan Zhou, David M. McCandlish, Justin B. Kinney, Anna Posfai

MAVE-NN: learning genotype-phenotype maps from multiplex assays of variant effect

Genome biology(2022)10.1186/s13059-022-02661-7

N/A

0DataRank · unranked

89 citations

Mahdi Kooshkbaghi, Anna Posfai, William T. Ireland, David M. McCandlish, Justin B. Kinney +1 more

Higher-order epistasis and phenotypic prediction

Proceedings of the National Academy of Sciences(2022)10.1073/pnas.2204233119

N/A

0DataRank · unranked

55 citations

Mandy S. Wong, Wei-Chia Chen, Adrian R. Krainer, Justin B. Kinney, David M. McCandlish +1 more

Structural and mechanistic basis of σ-dependent transcriptional pausing

Proceedings of the National Academy of Sciences(2022)10.1073/pnas.2201301119

N/A

0DataRank · unranked

15 citations

Vadim Molodtsov, Mahdi Kooshkbaghi, Ammar Tareen, Hoa Vu, Kyle S. Skalenko +7 more

Structural and mechanistic basis of σ-dependent transcriptional pausing

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.01.24.477500

N/A

0DataRank · unranked

4 citations

Vadim Molodtsov, Mahdi Kooshbaghi, Ammar Tareen, Hoa Vu, Kyle S. Skalenko +7 more

Interpreting cis -regulatory mechanisms from genomic deep neural networks using surrogate models

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.14.567120

N/A

0DataRank · unranked

11 citations

David M. McCandlish, Justin B. Kinney, Peter K. Koo, E. Seitz

Interpreting cis-regulatory mechanisms from genomic deep neural networks using surrogate models

Nature Machine Intelligence(2024)10.1038/s42256-024-00851-5

N/A

0DataRank · unranked

28 citations

David M. McCandlish, Justin B. Kinney, Peter K. Koo, E. Seitz

Gauge fixing for sequence-function relationships

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.05.12.593772

N/A

0DataRank · unranked

4 citations

Juannan Zhou, David M. McCandlish, Justin B. Kinney, Anna Posfai

Symmetry, gauge freedoms, and the interpretability of sequence-function Relationships

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.05.12.593774

N/A

0DataRank · unranked

3 citations

David M. McCandlish, Justin B. Kinney, Anna Posfai

Algebraic and Diagrammatic Methods for the Rule-Based Modeling of Multiparticle Complexes

PRX Life(2025)10.1103/prxlife.3.023004

N/A

0DataRank · unranked

1 citations

Justin B. Kinney, Rebecca J. Rousseau

Structural basis of DNA-dependent coactivator recruitment by the tuft cell master regulator POU2F3

Cell Reports(2025)10.1016/j.celrep.2025.116572

N/A

0DataRank · unranked

1 citations

Jonathan J. Ipsaro, Damianos Skopelitis, Sujay Pal, Frank S. Chung, Shannon L. Carpenter +12 more

Symmetry, gauge freedoms, and the interpretability of sequence-function relationships

Physical Review Research(2025)10.1103/physrevresearch.7.023005

N/A

0DataRank · unranked

1 citations

David M. McCandlish, Justin B. Kinney, Anna Posfai

Inference and visualization of complex genotype-phenotype maps with gpmap-tools

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.03.09.642267

N/A

0DataRank · unranked

4 citations

Juannan Zhou, Wei-Chia Chen, Arlin Stoltzfus, Justin B. Kinney, David M. McCandlish +1 more

Uncovering the Mechanistic Landscape of Regulatory DNA with Deep Learning

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.10.07.681052

N/A

0DataRank · unranked

3 citations

David M. McCandlish, Justin B. Kinney, Peter K. Koo, E. Seitz

HENMT1 restricts endogenous retrovirus activity by methylation of 3’-tRNA fragments

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.05.12.650695

N/A

0DataRank · unranked

1 citations

Helene Sertznig, John J. Desmarais, Jenna Wilken, David Sánz-Rubio, Matthew Peacey +3 more

GaugeFixer: overcoming parameter non-identifiability in models of sequence-function relationships

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.64898/2025.12.08.693054

N/A

0DataRank · unranked

1 citations

David M. McCandlish, Justin B. Kinney, Carlos Martí‐Gómez

Evolution of DNA replication origin specification and gene silencing mechanisms

Nature Communications(2020)10.1038/s41467-020-18964-x

N/A

0DataRank · unranked

45 citations

Ammar Tareen, Yi-Jun Sheu, William T. Ireland, Christian Speck, Huilin Li +4 more

Evolution of DNA Replication Origin Specification and Gene Silencing Mechanisms

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.04.187286

N/A

0DataRank · unranked

6 citations

Ammar Tareen, Yi-Jun Sheu, William T. Ireland, Christian Speck, Huilin Li +4 more

Higher-order epistasis and phenotypic prediction

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.14.339804

N/A

0DataRank · unranked

1 citations

Mandy S. Wong, Wei-Chia Chen, Adrian R. Krainer, Justin B. Kinney, David M. McCandlish +1 more

Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli

Proceedings of the National Academy of Sciences(2021)10.1073/pnas.2106388118

N/A

0DataRank · unranked

13 citations

Lingting Li, Yuanchao Zhang, Irina O. Vvedenskaya, Jared T. Winkelman, Alexander L. Cope +7 more

Field-theoretic density estimation for biological sequence space with applications to 5′ splice site diversity and aneuploidy in cancer

Proceedings of the National Academy of Sciences(2021)10.1073/pnas.2025782118

N/A

0DataRank · unranked

13 citations

Juannan Zhou, Jason M. Sheltzer, Justin B. Kinney, David M. McCandlish, Wei-Chia Chen

Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.04.06.438613

N/A

0DataRank · unranked

0 citations

Lingting Li, Yuanchao Zhang, Irina O. Vvedenskaya, Jared T. Winkelman, Alexander L. Cope +7 more