Alexis J. Combes

Also affiliated with Clinton Health Access Initiative, Creative Research, University of California San Francisco Medical Center, Universidad Católica de Santa Fe, Solve ME/CFS Initiative, Institute of Biomedical Science, University of San Francisco

Immunology and MicrobiologyMedicineBiochemistry, 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

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 →

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

A Multiomics, Spatiotemporal, and Single Cell Atlas for Mapping Cell-Type-Specific Dysregulation at the Maternal-Fetal Interface

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.01.18.576324

Top 100%

0DataRank

Top 100%0 citations

Yan Zhou, Yuejun Wang, Tuhin K. Guha, Zhida Luo, Tara I. McIntyre +18 more

Papers

Driven by 53 papers — median percentile 0. Top paper: “Dynamic CD8+ T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted in metastatic lymph nodes”.

Dynamic CD8+ T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted in metastatic lymph nodes

Cell(2023)10.1016/j.cell.2023.02.021

N/A

4.9DataRank · unranked

421 citations

Trine Line Hauge Okholm, Kyle B. Jones, Elizabeth McCarthy, Candace C. Liu, Jacqueline L. Yee +18 more

Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis

Nature Communications(2024)10.1038/s41467-024-45665-6

N/A

1.1DataRank · unranked

56 citations

Yang Joon Kim, Gyehyun Lee, I Rusu, Ravi K. Patel, Leah C. Dorman +26 more

Microbial dynamics and pulmonary immune responses in COVID-19 secondary bacterial pneumonia

Nature Communications(2024)10.1038/s41467-024-53566-x

N/A

0.549DataRank · unranked

16 citations

Alexandra Tsitsiklis, Victoria Chu, Hoang Van Phan, Catherine DeVoe, Christina Love +87 more

Dysregulation of CD4+and CD8+resident memory T, myeloid, and stromal cells in steroid-experienced, checkpoint inhibitor colitis

Journal for ImmunoTherapy of Cancer(2024)10.1136/jitc-2023-008628

N/A

0.507DataRank · unranked

15 citations

Yang-Joon Kim, Elvira Mennillo, I Rusu, Jared L. Bain, Arjun A. Rao +17 more

Spatiotemporal co-dependency between macrophages and exhausted CD8 + T cells in cancer

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.09.27.461866

N/A

0.269DataRank · unranked

5 citations

Kenneth H. Hu, Alexis J. Combes, Bushra Samad, Tory Harwin, Arja Ray +10 more

Single-cell omics technologies – Fundamentals on how to create single-cell looking glasses for reproductive health

American Journal of Obstetrics and Gynecology(2025)10.1016/j.ajog.2024.08.041

N/A

0.241DataRank · unranked

4 citations

Brittany Davidson, Gabriela K. Fragiadakis, Marina Sirota, Brice Gaudillière, Alexis J. Combes +1 more

Tracheal aspirate RNA sequencing identifies distinct immunological features of COVID-19 ARDS

Nature Communications(2021)10.1038/s41467-021-25040-5

N/A

0DataRank · unranked

81 citations

Stephanie A. Christenson, Ashley Byrne, Eran Mick, Angela Oliveira Pisco, Catherine DeVoe +89 more

A tumor-specific mechanism of T reg enrichment mediated by the integrin αvβ8

Science Immunology(2021)10.1126/sciimmunol.abf0558

N/A

0DataRank · unranked

29 citations

Kenji Kobayashi, Saburo Ito, Naoki Takasaka, Anthony Cormier, Jillian M. Jespersen +12 more

Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.03.09.434529

N/A

0DataRank · unranked

29 citations

Sara E. Vazquez, George C. Hartoularos, Paul Bastard, Tianna Grant, Raymund Bueno +40 more

Holistic Characterization of Tumor Monocyte-to-Macrophage Differentiation Integrates Distinct Immune Phenotypes in Kidney Cancer

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.07.07.451502

N/A

0DataRank · unranked

10 citations

Alexis J. Combes, Arjun R. Rao, Mikhail Binnewies, Bushra Samad, Jessica Tsui +8 more

Active Surveillance Characterizes Human Intratumoral T Cell Exhaustion

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.05.06.443033

N/A

0DataRank · unranked

8 citations

Jordan Artichoker, Adam Fries, Austin Edwards, Alexis J. Combes, Gabriella C. Reeder +3 more

A Pan-Cancer Census of Dominant Tumor Immune Archetypes

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.04.26.441344

N/A

0DataRank · unranked

4 citations

Bushra Samad, Jessica Tsui, Nayvin W. Chew, Peter Yan, Gabriella C. Reeder +32 more

Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells in cancer

Cancer Cell(2022)10.1016/j.ccell.2022.05.004

N/A

0DataRank · unranked

339 citations

Kenneth H. Hu, Alexis J. Combes, Bushra Samad, Tory Harwin, Arja Ray +10 more

Distinct metabolic states guide maturation of inflammatory and tolerogenic dendritic cells

Nature Communications(2022)10.1038/s41467-022-32849-1

N/A

0DataRank · unranked

119 citations

Paul V. Munson, Felix J. Hartmann, Alexis J. Combes, Philippe Pierre, Matthew F. Krummel +4 more

Tumor-associated macrophage heterogeneity is driven by tissue territories in breast cancer

Cell Reports(2022)10.1016/j.celrep.2022.110865

N/A

0DataRank · unranked

94 citations

Maxime Petit, Eléonore Weber-Delacroix, Alexis J. Combes, Arjun Rao Arkal, Sandrine Barthélémy +6 more

Deep immunophenotyping reveals endometriosis is marked by dysregulation of the mononuclear phagocytic system in endometrium and peripheral blood

BMC Medicine(2022)10.1186/s12916-022-02359-4

N/A

0DataRank · unranked

55 citations

Ashley F. George, Sushmita Sen, Reuben Thomas, Min‐Gyoung Shin, Divyashree Kushnoor +7 more

Holistic Characterization of Tumor Monocyte-to-Macrophage Differentiation Integrates Distinct Immune Phenotypes in Kidney Cancer

Cancer Immunology Research(2022)10.1158/2326-6066.cir-21-0588

N/A

0DataRank · unranked

47 citations

Alexis J. Combes, Arjun A. Rao, Mikhail Binnewies, Bushra Samad, Jessica Tsui +10 more

Deep Immunophenotyping Reveals Endometriosis is Marked by Dysregulation of the Mononuclear Phagocytic System in Endometrium and Peripheral Blood

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.02.02.478809

N/A

0DataRank · unranked

6 citations

Ashley F. George, Sushmita Sen, Reuben Thomas, Min‐Gyoung Shin, Divyashree Kushnoor +7 more

A myeloid program associated with COVID-19 severity is decreased by therapeutic blockade of IL-6 signaling

medRxiv(2022)10.1101/2022.11.07.22282049

N/A

0DataRank · unranked

0 citations

Haridha Shivram, Jason A. Vander Heiden, Christopher C. Overall, Luz D. Orozco, Xia Gao +49 more

Transcriptional space-time mapping identifies concerted immune and stromal cell patterns and gene programs in wound healing and cancer

Cell stem cell(2023)10.1016/j.stem.2023.05.001

N/A

0DataRank · unranked

51 citations

Nicholas F. Kuhn, Tristan Courau, Jessica Tsui, Bushra Samad, Patrick K. Ha +4 more

SARS-CoV-2 infection of airway organoids reveals conserved use of Tetraspanin-8 by Ancestral, Delta, and Omicron variants

Stem Cell Reports(2023)10.1016/j.stemcr.2023.01.011

N/A

0DataRank · unranked

14 citations

Samantha Little, Kayla Kulhanek, Mélia Magnen, Kriti Bahl, Oghenekevwe M. Gbenedio +37 more

A myeloid program associated with COVID-19 severity is decreased by therapeutic blockade of IL-6 signaling

iScience(2023)10.1016/j.isci.2023.107813

N/A

0DataRank · unranked

12 citations

Haridha Shivram, Jason A. Vander Heiden, Christopher C. Overall, Luz D. Orozco, Xia Gao +95 more

High-dimensional immune cell profiling of cerebrospinal fluid from patients with metastatic breast cancer and leptomeningeal disease

npj Breast Cancer(2023)10.1038/s41523-023-00526-1

N/A

0DataRank · unranked

7 citations

Laura A. Huppert, Lev Malevanchik, Hope S. Rugo, Alexis J. Combes, Michael J. Campbell +3 more

Critical role of CD206+ macrophages in promoting a cDC1-NK-CD8 T cell anti-tumor immune axis

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.31.560822

N/A

0DataRank · unranked

10 citations

Kenneth H. Hu, Kelly Kersten, Tristan Courau, Nicholas F. Kuhn, Itzia Zaleta-Linares +4 more

Multimodal delineation of a layer of effector function among exhausted CD8 T cells in tumors

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.09.26.559470

N/A

0DataRank · unranked

5 citations

Molly Bassette, Kenneth H. Hu, Lomax F. Pass, Tristan Courau, Bushra Samad +9 more

Commensal myeloid crosstalk in neonatal skin regulates cutaneous type 17 inflammation

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.09.29.560039

N/A

0DataRank · unranked

4 citations

Ricardo O. Carale, Andrea M. DeRogatis, Henry Rodriguez-Valbuena, Joy N. Okoro, Christina Ekstrand +21 more

Functional haematopoietic progenitor cells in the adult human lung

Research Square(2023)10.21203/rs.3.rs-3576483/v1

N/A

0DataRank · unranked

1 citations

Mélia Magnen, Jessica Tsui, Harrison Wismer, Mohammad Naser, Urmila Venkataramani +11 more

Data from Holistic Characterization of Tumor Monocyte-to-Macrophage Differentiation Integrates Distinct Immune Phenotypes in Kidney Cancer

(2023)10.1158/2326-6066.c.6550550

N/A

0DataRank · unranked

0 citations

Alexis J. Combes, Arjun A. Rao, Mikhail Binnewies, Bushra Samad, Jessica Tsui +10 more

Tumor-associated macrophages restrict CD8+ T cell function through collagen deposition and metabolic reprogramming of the breast cancer microenvironment

Nature Cancer(2024)10.1038/s43018-024-00775-4

N/A

0DataRank · unranked

254 citations

Kelly Kersten, Ori Maller, Greg A. Timblin, Connor Stashko, Fernando P. Canale +12 more

Chromatin remodelling drives immune cell–fibroblast communication in heart failure

Nature(2024)10.1038/s41586-024-08085-6

N/A

0DataRank · unranked

104 citations

Arun Padmanabhan, Tomohiro Nishino, Joshua G. Travers, Lin Ye, Angelo Pelonero +25 more

Targeting CD206+ macrophages disrupts the establishment of a key antitumor immune axis

The Journal of Experimental Medicine(2024)10.1084/jem.20240957

N/A

0DataRank · unranked

44 citations

Kenneth H. Hu, Kelly Kersten, Tristan Courau, Nicholas F. Kuhn, Itzia Zaleta-Linares +4 more

Macrophage and CD8 T cell discordance are associated with acute lung allograft dysfunction progression

The Journal of Heart and Lung Transplantation(2024)10.1016/j.healun.2024.02.007

N/A

0DataRank · unranked

18 citations

Christina Ekstrand, Jonathan P. Singer, Steven R. Hays, Lorriana E. Leard, Rupal Shah +6 more

Distinct pulmonary and systemic effects of dexamethasone in severe COVID-19

Nature Communications(2024)10.1038/s41467-024-49756-2

N/A

0DataRank · unranked

19 citations

Ravi K. Patel, Aartik Sarma, K. Mark Ansel, Stephanie A. Christenson, Michael Adkisson +75 more

Proinflammatory immune cells disrupt angiogenesis and promote germinal matrix hemorrhage in prenatal human brain

Nature Neuroscience(2024)10.1038/s41593-024-01769-2

N/A

0DataRank · unranked

17 citations

Elizabeth E. Crouch, Miriam E. Zawadzki, Kyle A. Jacobs, Lakyn Mayo, Jennifer Ja-Yoon Choi +26 more

Decoding functional hematopoietic progenitor cells in the adult human lung

Research Square(2024)10.21203/rs.3.rs-3576483/v2

N/A

0DataRank · unranked

7 citations

Mélia Magnen, Jessica Tsui, Harrison Wismer, Mohammad Naser, Urmila Venkataramani +11 more

Discovery of a Linked Constellation of Gene Expression Revealed by Local Editing of Fibroblasts in Tumors

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.07.11.603114

N/A

0DataRank · unranked

1 citations

Itzia Zaleta-Linares, William A. Nyberg, Tristan Courau, Brittany Davidson, Tammie Tam +4 more

A Multiomics, Spatiotemporal, and Single Cell Atlas for Mapping Cell-Type-Specific Dysregulation at the Maternal-Fetal Interface

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.01.18.576324

Top 100%

0DataRank

Top 100%0 citations

Yan Zhou, Yuejun Wang, Tuhin K. Guha, Zhida Luo, Tara I. McIntyre +18 more

A conserved subset of cold tumors responsive to immune checkpoint blockade

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.06.583752

N/A

0DataRank · unranked

0 citations

Jim Gkantalis, Inés Guix, William Chou, Kobe Yuen, Ann Lazar +4 more

Single-cell spatial transcriptomics of fixed, paraffin-embedded biopsies reveals colitis-associated cell networks

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.11.11.623014

N/A

0DataRank · unranked

0 citations

Madison L. Lotstein, Gyehyun Lee, Vrinda Johri, Christina Ekstrand, Jessica Tsui +10 more

Tumor cell heterogeneity drives spatial organization of the intratumoral immune response

The Journal of Experimental Medicine(2025)10.1084/jem.20242282

N/A

0DataRank · unranked

18 citations

Lotus Lum, Kenneth H. Hu, Piyush Chaudhary, Savannah Hughes, Cecilia Ledezma-Soto +13 more

Persistent and progressive acute lung allograft dysfunction is linked to cell compositional and transcriptional changes in small airways

The Journal of Heart and Lung Transplantation(2025)10.1016/j.healun.2025.03.010

N/A

0DataRank · unranked

9 citations

Shivaram Yellamilli, Ruyin Guo, R. Mohanty, Allen Duong, Nicholas A. Kolaitis +13 more

Decoding functional hematopoietic progenitor cells in the adult human lung

Blood(2025)10.1182/blood.2024027884

N/A

0DataRank · unranked

15 citations

Mélia Magnen, Jessica Tsui, Harrison Wismer, Mohammad Naser, Urmila Venkataramani +12 more

Identification of a conserved subset of cold tumors responsive to immune checkpoint blockade

Journal for ImmunoTherapy of Cancer(2025)10.1136/jitc-2024-010528

N/A

0DataRank · unranked

8 citations

Jim Gkantalis, Inés Guix, William Chou, Kobe Yuen, Ann Lazar +4 more

KDM6B-dependent epigenetic programming of uterine fibroblasts in early pregnancy regulates parturition timing in mice

Cell(2025)10.1016/j.cell.2024.12.019

N/A

0DataRank · unranked

7 citations

Omar Valdez, N. Kochhar, Brittany Davidson, Bushra Samad, Longhui Qiu +4 more

Single-cell proteomics characterization of bone marrow hematopoiesis with distinct Ras pathway lesions

Blood Advances(2025)10.1182/bloodadvances.2024014411

N/A

0DataRank · unranked

2 citations

Anna‐Marie Finger, Lauren A. Shechtman, Milana Krush, Mengyao Huang, Morgan Prinz +10 more

Anticlustering for sample allocation to minimize batch effects

Cell Reports Methods(2025)10.1016/j.crmeth.2025.101137

N/A

0DataRank · unranked

0 citations

Cheng Wang, Maïgane Diop, Syed Bukhari, Boris Oskotsky, Brittany Davidson +12 more

Global Absence and Targeting of Protective Immune States in Severe COVID-19

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.28.359935

N/A

0DataRank · unranked

25 citations

Tristan Courau, Nicholas F. Kuhn, Kenneth H. Hu, Arja Ray, William S. Chen +34 more

Clinical cure of chronic hepatitis B is dependent on activation and perpetuation of robust CD4 + T cell responses

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.09.29.677401

N/A

0DataRank · unranked

0 citations

Lia Avanesyan, Jean Publicover, Nicholas D. Carey, Ravi K. Patel, Austin Edwards +21 more

Global Absence and Targeting of Protective Immune States in Severe COVID-19.

Research Square(2020)10.21203/rs.3.rs-97042/v1

N/A

0DataRank · unranked

8 citations

Alexis J. Combes, Tristan Courau, Nicholas F. Kuhn, Kenneth H. Hu, Arja Ray +34 more

Global absence and targeting of protective immune states in severe COVID-19

Nature(2021)10.1038/s41586-021-03234-7

N/A

0DataRank · unranked

279 citations

Tristan Courau, Nicholas F. Kuhn, Kenneth H. Hu, Arja Ray, William S. Chen +60 more

Type I interferon autoantibodies are associated with systemic immune alterations in patients with COVID-19

Science Translational Medicine(2021)10.1126/scitranslmed.abh2624

N/A

0DataRank · unranked

239 citations

Sara E. Vazquez, George C. Hartoularos, Paul Bastard, Tianna Grant, Raymund Bueno +40 more

The intersection of COVID-19 and autoimmunity

Journal of Clinical Investigation(2021)10.1172/jci154886

N/A

0DataRank · unranked

218 citations

Roberto Caricchio, Jean-Laurent Casanova, Alexis J. Combes, Betty Diamond, Sharon E. Fox +14 more

Discovering dominant tumor immune archetypes in a pan-cancer census

Cell(2021)10.1016/j.cell.2021.12.004

N/A

0DataRank · unranked

176 citations

Bushra Samad, Jessica Tsui, Nayvin W. Chew, Peter Yan, Gabriella C. Reeder +75 more

Alexis J. Combes

Indexed papers

Top data-sharing exemplar

Papers