Aly A. Khan

Also affiliated with Chan Zuckerberg Biohub San Francisco

Biochemistry, Genetics and Molecular BiologyImmunology and Microbiology

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 17 papers. Top paper: “Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction”.

Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction

Cell(2020)10.1016/j.cell.2020.09.015

N/A

0.945DataRank · unranked

543 citations

Marit M. van Buuren, Kristen K. Dang, Vanessa M. Hubbard-Lucey, Kathleen C. F. Sheehan, Katie M. Campbell +95 more

Androgens contribute to sex bias of autoimmunity in mice by T cell-intrinsic regulation of Ptpn22 phosphatase expression

Nature Communications(2024)10.1038/s41467-024-51869-7

N/A

0.311DataRank · unranked

6 citations

Leonid Yurkovetskiy, Derek Reiman, Lara Frommer, Zoe Strong, Anthony Chang +4 more

Genome-wide association study of delay discounting identifies 11 loci and reveals transdiagnostic associations across mental and physical health

Molecular Psychiatry(2025)10.1038/s41380-025-03356-8

N/A

0.208DataRank · unranked

3 citations

Renata B. Cupertino, Shreya R. Pakala, Pierre Fontanillas, Mariela Jennings, Jane Yang +75 more

Improved integration of single-cell transcriptome and surface protein expression by LinQ-View

Cell Reports Methods(2021)10.1016/j.crmeth.2021.100056

N/A

0DataRank · unranked

13 citations

Haley L. Dugan, Christopher T. Stamper, Linda Yu-Ling Lan, Nicholas Asby, Matthew Knight +17 more

Gut commensal bacteria enhance pathogenesis of a tumorigenic murine retrovirus

Cell Reports(2022)10.1016/j.celrep.2022.111341

N/A

0DataRank · unranked

8 citations

Aly A. Khan, Sophie Lara, Kelly O’Grady, Jessica Wilks, Sandeep Gurbuxani +6 more

Gut commensal bacteria enhance pathogenesis of a tumorigenic murine retrovirus

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.02.02.478820

N/A

0DataRank · unranked

3 citations

Sophie Lara, Aly A. Khan, Kelly O’Grady, Jessica Wilks, Sandeep Gurbuxani +6 more

Deploying synthetic coevolution and machine learning to engineer protein-protein interactions

Science(2023)10.1126/science.adh1720

N/A

0DataRank · unranked

44 citations

Kevin M. Jude, Ben Lai, Mason Minot, Anna Kocyła, Caleb R. Glassman +6 more

Microbiota-dependent proteolysis of gluten subverts diet-mediated protection against type 1 diabetes

Cell Host & Microbe(2023)10.1016/j.chom.2022.12.009

N/A

0DataRank · unranked

12 citations

Leonid Yurkovetskiy, Andrey Kuznetsov, Derek Reiman, Camilla Hartmann Friis Hansen, Katharine I. Senter +10 more

Computational prediction of protein interactions on single cells by proximity sequencing

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.27.550388

N/A

0DataRank · unranked

1 citations

Hoang Van Phan, Luke Vistain, Mengjie Chen, Aly A. Khan, Savaş Tay +1 more

ATAT: Automated Tissue Alignment and Traversal in Spatial Transcriptomics with Self-Supervised Learning

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.12.08.570839

N/A

0DataRank · unranked

1 citations

Emaan Mohsin, Renyu Zhang, Andrey Kuznetsov, Le Shen, Robert L. Grossman +3 more

TRIBAL: Tree Inference of B cell Clonal Lineages

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.27.568874

N/A

0DataRank · unranked

0 citations

Derek Reiman, Mrinmoy Saha Roddur, Yuanyuan Qi, Mohammed El-Kebir, Aly A. Khan +1 more

Isotype-aware inference of B cell clonal lineage trees from single-cell sequencing data

Cell Genomics(2024)10.1016/j.xgen.2024.100637

N/A

0DataRank · unranked

4 citations

Derek Reiman, Mrinmoy Saha Roddur, Yuanyuan Qi, Mohammed El-Kebir, Aly A. Khan +1 more

Computational prediction of protein interactions in single cells by proximity sequencing

PLoS Computational Biology(2024)10.1371/journal.pcbi.1011915

N/A

0DataRank · unranked

3 citations

Hoang Van Phan, Luke Vistain, Mengjie Chen, Aly A. Khan, Savaş Tay +1 more

Virtual CRISPR: Can LLMs Predict CRISPR Screen Results?

(2025)10.18653/v1/2025.bionlp-1.30

N/A

0DataRank · unranked

1 citations

Abdalla Abdrabou, Asmita Dabholkar, Kastan Day, Pavan Dharmoju, Jason Perera +3 more

AI-assisted Diagnosis of Nonmelanoma Skin Cancer in Resource-Limited Settings

Cancer Epidemiology Biomarkers & Prevention(2025)10.1158/1055-9965.epi-25-0132

N/A

0DataRank · unranked

0 citations

Steven Song, Derek Reiman, Xuan Hui, Renyu Zhang, Hasan Shahriar +7 more

FiberAI: A Deep Learning model for automated analysis of nascent DNA Fibers

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.28.397430

N/A

0DataRank · unranked

5 citations

Stephen Arnovitz, Aly A. Khan, Fotini Gounari, Azam Mohsin

Innate-like self-reactive B cells infiltrate human renal allografts during transplant rejection

Nature Communications(2021)10.1038/s41467-021-24615-6

N/A

0DataRank · unranked

57 citations

Joe Daccache, Dharmendra Jain, Kichul Ko, Andrew J Kinloch, Margaret Veselits +10 more