Naftali Kaminski

Medicine

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

14.2Author DataRank

Indexed papers

6in 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 6 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.

The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

Science(2022)10.1126/science.abl4896

Top 4%

5.3DataRank

Top 4%1018 citations

Robert C. Jones, Jim Karkanias, Naftali Kaminski, Angela Oliveira Pisco, Stephen R. Quake +181 more

Papers

Driven by 120 papers — median percentile 92. Top paper: “SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues”.

SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues

Cell(2020)10.1016/j.cell.2020.04.035

N/A

14.1DataRank · unranked

2492 citations

Samuel J. Allon, Sarah K. Nyquist, Ian Mbano, Vincent N. Miao, Constantine N. Tzouanas +92 more

The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

Science(2022)10.1126/science.abl4896

Top 4%

5.3DataRank

Top 4%1018 citations

Robert C. Jones, Jim Karkanias, Naftali Kaminski, Angela Oliveira Pisco, Stephen R. Quake +181 more

An integrated cell atlas of the lung in health and disease

Nature Medicine(2023)10.1038/s41591-023-02327-2

Top 4%

5.0DataRank

Top 4%781 citations

Ciro Ramírez-Suástegui, Tessa E. Gillett, Luke Zappia, Elo Madissoon, Nikolay S. Markov +87 more

An integrated cell atlas of the human lung in health and disease

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.03.10.483747

Top 8%

2.8DataRank

Top 8%97 citations

Daniel Strobl, Luke Zappia, Nikolay S. Markov, Laure-Emmanuelle Zaragosi, Marie-Jeanne Arguel +77 more

Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity

Nature Communications(2021)10.1038/s41467-021-24467-0

N/A

2.0DataRank · unranked

43 citations

Nichelle I. Winters, Mei-i Chung, Chitra Joseph, Austin J. Gutierrez, Arun C. Habermann +67 more

Lung Microenvironments and Disease Progression in Fibrotic Hypersensitivity Pneumonitis

American Journal of Respiratory and Critical Care Medicine(2021)10.1164/rccm.202103-0569oc

N/A

1.5DataRank · unranked

37 citations

John E. McDonough, Jonas C. Schupp, Xiting Yan, Arno Vanstapel, Anke Van Herck +21 more

MicroRNA miR-24-3p reduces DNA damage responses, apoptosis, and susceptibility to chronic obstructive pulmonary disease

JCI Insight(2020)10.1172/jci.insight.134218

N/A

1.4DataRank · unranked

40 citations

Feng Wan, Eric Finnemore, Willy Roque, Sojin Kim, Isabel Bazán +15 more

Transcriptomics of bronchoalveolar lavage cells identifies new molecular endotypes of sarcoidosis

European Respiratory Journal(2021)10.1183/13993003.02950-2020

N/A

1.2DataRank · unranked

58 citations

Xiting Yan, Kevin F. Gibson, Mridu Gulati, Jonas C. Schupp, Giuseppe DeIuliis +24 more

Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis

Science Advances(2020)10.1126/sciadv.aba1983

N/A

1.1DataRank · unranked

1447 citations

Jonas C. Schupp, Sergio Poli, Ehab Ayaub, Nir Neumark, Farida Ahangari +13 more

Integrated Single Cell Atlas of Endothelial Cells of the Human Lung

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.21.347914

Top 19%

1.1DataRank

Top 19%32 citations

Taylor Adams, Carlos Cosme, Micha Sam Brickman Raredon, Norihito Omote, Sergio Poli +22 more

Characterization of the COPD alveolar niche using single-cell RNA sequencing

Nature Communications(2022)10.1038/s41467-022-28062-9

N/A

0.816DataRank · unranked

229 citations

John E. McDonough, Taylor Adams, Neeharika Kothapalli, Thomas Bärnthaler, Rhiannon B. Werder +21 more

Reconstructed Single-Cell Fate Trajectories Define Lineage Plasticity Windows during Differentiation of Human PSC-Derived Distal Lung Progenitors

Cell stem cell(2020)10.1016/j.stem.2019.12.009

N/A

0.766DataRank · unranked

164 citations

Jun Ding, Carlos Villacorta-Martín, Michael J. Herriges, Anjali Jacob, Marall Vedaie +18 more

Type I interferon transcriptional network regulates expression of coinhibitory receptors in human T cells

Nature Immunology(2022)10.1038/s41590-022-01152-y

N/A

0.763DataRank · unranked

161 citations

Shai Dulberg, Jonas C. Schupp, Matthew R. Lincoln, Helen A. Stillwell, Pierre‐Paul Axisa +7 more

Expression of SARS-CoV-2 receptor ACE2 and coincident host response signature varies by asthma inflammatory phenotype

Journal of Allergy and Clinical Immunology(2020)10.1016/j.jaci.2020.05.051

N/A

0.724DataRank · unranked

124 citations

Marc Gauthier, Naftali Kaminski, Anuradha Ray, Sally E. Wenzel, Matthew Camiolo

Saracatinib, a Selective Src Kinase Inhibitor, Blocks Fibrotic Responses in Preclinical Models of Pulmonary Fibrosis

American Journal of Respiratory and Critical Care Medicine(2022)10.1164/rccm.202010-3832oc

N/A

0.718DataRank · unranked

119 citations

Christine Becker, Daniel G. Foster, Maurizio Chioccioli, Meghan Nelson, K.M. Beke +29 more

Single-Cell Profiling Reveals Immune Aberrations in Progressive Idiopathic Pulmonary Fibrosis

American Journal of Respiratory and Critical Care Medicine(2024)10.1164/rccm.202306-0979oc

N/A

0.659DataRank · unranked

80 citations

Amy Zhao, Nir Neumark, Jonas C. Schupp, Farida Ahangari, Carlos Cosme +12 more

microRNA-33 deficiency in macrophages enhances autophagy, improves mitochondrial homeostasis, and protects against lung fibrosis

JCI Insight(2023)10.1172/jci.insight.158100

N/A

0.624DataRank · unranked

63 citations

Nathan L. Price, Shipra Malik, Maurizio Chioccioli, Thomas Bärnthaler, Taylor Adams +22 more

Emergence of division of labor in tissues through cell interactions and spatial cues

Cell Reports(2023)10.1016/j.celrep.2023.112412

N/A

0.604DataRank · unranked

55 citations

Noa Moriel, Aleksandrina Goeva, Inbal Avraham‐Davidi, Simon Mages, Taylor Adams +6 more

Cutting Edge: Distinct B Cell Repertoires Characterize Patients with Mild and Severe COVID-19

The Journal of Immunology(2021)10.4049/jimmunol.2100135

N/A

0.578DataRank · unranked

46 citations

Palaniappan Ramanathan, Avraham Unterman, Tomokazu S. Sumida, Hiromitsu Asashima, David A. Hafler +6 more

Integrated transcriptomic analysis of human tuberculosis granulomas and a biomimetic model identifies therapeutic targets

Journal of Clinical Investigation(2021)10.1172/jci148136

N/A

0.568DataRank · unranked

43 citations

Liku B. Tezera, Andrés F. Vallejo, Milica Vukmirovic, Rui Xiao, James B. Reynolds +10 more

Mechanisms of Hypoxia-Induced Pulmonary Arterial Stiffening in Mice Revealed by a Functional Genetics Assay of Structural, Functional, and Transcriptomic Data

Frontiers in Physiology(2021)10.3389/fphys.2021.726253

N/A

0.556DataRank · unranked

16 citations

Abhay B. Ramachandra, Jonas C. Schupp, Cristina Cavinato, Micha Sam Brickman Raredon, Thomas Bärnthaler +6 more

Precision-Cut Lung Slices: Emerging Tools for Preclinical and Translational Lung Research: An Official American Thoracic Society Workshop Report

American Journal of Respiratory Cell and Molecular Biology(2024)10.1165/rcmb.2024-0479st

N/A

0.542DataRank · unranked

36 citations

Ramaswamy Krishnan, Jennifer M. S. Sucre, Hrishikesh S. Kulkarni, Ricardo Pineda, Christopher D. Anderson +29 more

Lung Cell Atlases in Health and Disease

Annual Review of Physiology(2022)10.1146/annurev-physiol-032922-082826

N/A

0.515DataRank · unranked

30 citations

Arnaud Marlier, Naftali Kaminski, Taylor Adams

Connectome : computation and visualization of cell-cell signaling topologies in single-cell systems data

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.21.427529

N/A

0.494DataRank · unranked

26 citations

Junchen Yang, James Garritano, Meng Wang, Dan Kushnir, Jonas C. Schupp +8 more

Mast-cell expressed membrane protein-1 is expressed in classical monocytes and alveolar macrophages in idiopathic pulmonary fibrosis and regulates cell chemotaxis, adhesion, and migration in a TGFβ-dependent manner

American Journal of Physiology-Cell Physiology(2024)10.1152/ajpcell.00563.2023

N/A

0.477DataRank · unranked

23 citations

Τheodoros Karampitsakos, Avraham Unterman, Taylor Adams, K. Marlin, Alyssa Arsenault +7 more

Single-cell transcriptomic analysis of human pleura reveals stromal heterogeneity and informsin vitromodels of mesothelioma

European Respiratory Journal(2024)10.1183/13993003.00143-2023

N/A

0.466DataRank · unranked

12 citations

José Antonio Valer, Reshma Nibhani, Taylor Adams, Jonas C. Schupp, Niki Veale +14 more

A deep generative model for deciphering cellular dynamics and in silico drug discovery in complex diseases

Nature Biomedical Engineering(2025)10.1038/s41551-025-01423-7

N/A

0.457DataRank · unranked

20 citations

Jonas C. Schupp, Taylor Adams, Gérémy Clair, A. Justet, Farida Ahangari +17 more

Pulmonary Fibrosis Stakeholder Summit: A Joint NHLBI, Three Lakes Foundation, and Pulmonary Fibrosis Foundation Workshop Report

American Journal of Respiratory and Critical Care Medicine(2023)10.1164/rccm.202307-1154ws

N/A

0.434DataRank · unranked

17 citations

Christian R. Gómez, Michael F. Beers, Robert Brown, Ishanu Chattopadhyay, Kevin R. Flaherty +29 more

Type I Interferon Transcriptional Network Regulates Expression of Coinhibitory Receptors in Human T cells

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.30.362947

N/A

0.416DataRank · unranked

15 citations

Shai Dulberg, Jonas C. Schupp, Helen A. Stillwell, Pierre‐Paul Axisa, Michela Comi +7 more

A Pulmonary Vascular Model From Endothelialized Whole Organ Scaffolds

Frontiers in Bioengineering and Biotechnology(2021)10.3389/fbioe.2021.760309

N/A

0.406DataRank · unranked

14 citations

Katherine L. Leiby, Allison M. Greaney, Micha Sam Brickman Raredon, Hong Qian, Jonas C. Schupp +10 more

Keratinocytes as active regulators of cutaneous and mucosal immunity: a systematic review across inflammatory epithelial disorders

Frontiers in Immunology(2025)10.3389/fimmu.2025.1694066

N/A

0.396DataRank · unranked

13 citations

Yizhuo Shen, Federico Repetto, Stav Brown, Leonard Knoedler, Christine J. Ko +10 more

A Picture Worth a Thousand Words, Created with One Sentence: Using Artificial Intelligence–created Art to Enhance Medical Education

ATS Scholar(2023)10.34197/ats-scholar.2022-0141ps

N/A

0.396DataRank · unranked

13 citations

Naftali Kaminski, John C. Huston

Microenvironmental Sensing by Fibroblasts Controls Macrophage Population Size

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.01.18.476683

N/A

0.373DataRank · unranked

11 citations

Ruth A. Franklin, Miri Adler, Trevor S. Carter, Emily Condiff, Taylor Adams +6 more

Alveolar epithelial cell plasticity and injury memory in human pulmonary fibrosis

10.1101/2025.06.10.658504

N/A

0.373DataRank · unranked

11 citations

Jonas C. Schupp, Agshin Balayev, Johad Khoury, Aurélien Justet, Fadi Nikola +15 more

Gene coexpression networks reveal novel molecular endotypes in alpha-1 antitrypsin deficiency

Thorax(2020)10.1136/thoraxjnl-2019-214301

N/A

0.345DataRank · unranked

9 citations

Wenlan Zang, Milica Vukmirovic, Xiting Yan, Taylor Adams, Giuseppe DeIuliis +20 more

SDePER: a hybrid machine learning and regression method for cell-type deconvolution of spatial barcoding-based transcriptomic data

Genome biology(2024)10.1186/s13059-024-03416-2

N/A

0.330DataRank · unranked

8 citations

Ningshan Li, Ji Qi, Gang Xu, Jiayi Zhao, Nating Wang +12 more

A lung targeted miR-29 Mimic as a Therapy for Pulmonary Fibrosis

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.12.22.473724

N/A

0.330DataRank · unranked

8 citations

Subhadeep Roy, Kevin M. Rigby, Rachel Newell, Oliver Dansereau, Linda Pestano +14 more

Integrative genetic and genomic networks identify microRNA associated with COPD and ILD

Scientific Reports(2023)10.1038/s41598-023-39751-w

N/A

0.312DataRank · unranked

7 citations

Carly B. Garrison, Lingqi Luo, Gang Liu, Daniel G. Taub, Xiao‐Jun Ji +13 more

Understanding the Added Value of High-Resolution CT Beyond Chest X-Ray in Determining Extent of Physiologic Impairment

CHEST Journal(2024)10.1016/j.chest.2024.04.031

N/A

0.292DataRank · unranked

6 citations

William Lippitt, Isabel O. Cortopassi, G.K. Balasubramani, Eduardo J. Mortani Barbosa, Wonder P. Drake +11 more

Single Cell Transcriptional Archetypes of Airway Inflammation in Cystic Fibrosis

medRxiv(2020)10.1101/2020.03.06.20032292

N/A

0.292DataRank · unranked

6 citations

Sara Khanal, José L. Gómez, Maor Sauler, Taylor Adams, Geoffrey Chupp +10 more

A statistical framework to identify cell types whose genetically regulated proportions are associated with complex diseases

PLoS Genetics(2023)10.1371/journal.pgen.1010825

N/A

0.275DataRank · unranked

3 citations

Wenxuan Deng, Ming Chen, Zihan Dong, Biqing Zhu, Zhaolong Yu +8 more

Emergence of division of labor in tissues through cell interactions and spatial cues

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.16.516540

N/A

0.269DataRank · unranked

5 citations

Noa Moriel, Aleksandrina Goeva, Inbal Avraham‐Davidi, Simon Mages, Taylor Adams +6 more

Single-cell RNA Sequencing Analysis of Sputum Cell Transcriptomes Reveals Pathways and Communication Networks That Contribute to the Pathogenesis of Asthma

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.03.31.646405

N/A

0.241DataRank · unranked

3 citations

Qing Liu, Taylor Adams, Jonas C. Schupp, Sihan Li, Stark Huang +9 more

Toll-Like-Receptor 5 protects against pulmonary fibrosis by reducing lung dysbiosis

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.04.30.591719

N/A

0.208DataRank · unranked

3 citations

Emma Wiley, Alma Solis, Collin G. Johnson, Xianglin Meng, Salik Hussain +30 more

A Markov Random Field Model for Network-based Differential Expression Analysis of Single-cell RNA-seq Data

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.11.378976

N/A

0.168DataRank · unranked

2 citations

Biqing Zhu, Zhichao Xu, Taylor Adams, Naftali Kaminski, Luca Pinello +1 more

Dendritic Cell – Fibroblast Crosstalk via TLR9 and AHR Signaling Drives Lung Fibrogenesis

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.15.584457

N/A

0.165DataRank · unranked

2 citations

Rita Medina Costa, Taylor Adams, Talon M. Gilchrist, Claire E. Emch, Monica Bame +7 more

An integrated cell atlas of the human lung in health and disease

Research Square(2022)10.21203/rs.3.rs-1438584/v1

Top 71%

0.127DataRank

Top 71%1 citations

Avi Srivastava, Daniel Strobl, Luke Zappia, Elo Madissoon, Nikolay S. Markov +80 more

A Statistical Framework to Identify Cell Types Whose Genetically Regulated Proportions are Associated with Complex Diseases

Research Square(2021)10.21203/rs.3.rs-275314/v1

N/A

0.104DataRank · unranked

1 citations

Wei Liu, Wenxuan Deng, Ming Chen, Zihan Dong, Biqing Zhu +7 more

PINK1 mediates the protective effects of thyroid hormone T3 in hyperoxia-induced lung injury

American Journal of Physiology-Lung Cellular and Molecular Physiology(2021)10.1152/ajplung.00598.2020

N/A

0DataRank · unranked

16 citations

Guoying Yu, Naftali Kaminski, Patty J. Lee, Yi Zhang

Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19

Nature Communications(2022)10.1038/s41467-021-27716-4

N/A

0DataRank · unranked

188 citations

Tomokazu S. Sumida, Nima Nouri, Xiting Yan, Amy Zhao, Victor Gasque +47 more

Elevated plasma level of Pentraxin 3 is associated with emphysema and mortality in smokers

Thorax(2021)10.1136/thoraxjnl-2020-215356

N/A

0DataRank · unranked

17 citations

John Tedrow, Mehdi Nouraie, Xiaoyun Li, Divay Chandra, Jessica Bon +7 more

Airway basal cells show a dedifferentiated KRT17highPhenotype and promote fibrosis in idiopathic pulmonary fibrosis

Nature Communications(2022)10.1038/s41467-022-33193-0

N/A

0DataRank · unranked

146 citations

Jonas C. Schupp, Linda Plappert, Oliver Terwolbeck, Nataliia Artysh, Gian Kayser +14 more

Computation and visualization of cell–cell signaling topologies in single-cell systems data using Connectome

Scientific Reports(2022)10.1038/s41598-022-07959-x

N/A

0DataRank · unranked

140 citations

Junchen Yang, James Garritano, Meng Wang, Dan Kushnir, Jonas C. Schupp +8 more

Comprehensive visualization of cell–cell interactions in single-cell and spatial transcriptomics with NICHES

Bioinformatics(2022)10.1093/bioinformatics/btac775

N/A

0DataRank · unranked

123 citations

Junchen Yang, Neeharika Kothapalli, Wesley Lewis, Naftali Kaminski, Laura E. Niklason +2 more

Machine learning implicates the IL-18 signaling axis in severe asthma

JCI Insight(2021)10.1172/jci.insight.149945

N/A

0DataRank · unranked

33 citations

Xiuxia Zhou, Qi Wei, Humberto E. Trejo Bittar, Naftali Kaminski, Anuradha Ray +2 more

CD38 Mediates Lung Fibrosis by Promoting Alveolar Epithelial Cell Aging

American Journal of Respiratory and Critical Care Medicine(2022)10.1164/rccm.202109-2151oc

N/A

0DataRank · unranked

69 citations

Na Xie, Sami Banerjee, Tapan Dey, Rui-Ming Liu, Veena B. Antony +7 more

Longitudinal lung function and gas transfer in individuals with idiopathic pulmonary fibrosis: a genome-wide association study

The Lancet Respiratory Medicine(2022)10.1016/s2213-2600(22)00251-x

N/A

0DataRank · unranked

66 citations

Justin M. Oldham, David Jenkins, Olivia C. Leavy, Beatriz Guillén‐Guío, Carl Melbourne +26 more

Single-cell RNA-seq uncovers cellular heterogeneity and provides a signature for paediatric sleep apnoea

European Respiratory Journal(2022)10.1183/13993003.01465-2022

N/A

0DataRank · unranked

30 citations

Taylor Adams, K. Cataldo, Justin Hummel, Naftali Kaminski, David Gozal +2 more

Fibroblasts positive for meflin have anti-fibrotic properties in pulmonary fibrosis

European Respiratory Journal(2021)10.1183/13993003.03397-2020

N/A

0DataRank · unranked

53 citations

Naozumi Hashimoto, Koji Sakamoto, Atsushi Enomoto, Taylor Adams, Toyoharu Yokoi +15 more

BAL Transcriptomes Characterize Idiopathic Pulmonary Fibrosis Endotypes With Prognostic Impact

CHEST Journal(2022)10.1016/j.chest.2021.12.668

N/A

0DataRank · unranked

23 citations

Stijn E. Verleden, Jonas C. Schupp, John E. McDonough, Tinne Goos, Jonas Yserbyt +6 more

FK506-Binding Protein 11 Is a Novel Plasma Cell-Specific Antibody Folding Catalyst with Increased Expression in Idiopathic Pulmonary Fibrosis

Cells(2022)10.3390/cells11081341

N/A

0DataRank · unranked

21 citations

Yoshihiro Ishikawa, Elisabeth Hennen, Stephan Winklmeier, Jonas C. Schupp, Larissa Knüppel +19 more

From COVID to fibrosis: lessons from single-cell analyses of the human lung

Human Genomics(2022)10.1186/s40246-022-00393-0

N/A

0DataRank · unranked

19 citations

Amy Zhao, Naftali Kaminski, A. Justet

Integrative analyses for the identification of idiopathic pulmonary fibrosis-associated genes and shared loci with other diseases

Thorax(2022)10.1136/thorax-2021-217703

N/A

0DataRank · unranked

11 citations

Yiliang Zhang, Taylor Adams, Dingjue Ji, Wei Jiang, Louise V. Wain +4 more

CINS: Cell Interaction Network inference from Single cell expression data

PLoS Computational Biology(2022)10.1371/journal.pcbi.1010468

N/A

0DataRank · unranked

10 citations

Carlos Cosme, Taylor Adams, Jonas C. Schupp, Koji Sakamoto, Nikos Xylourgidis +5 more

Comprehensive visualization of cell-cell interactions in single-cell and spatial transcriptomics with NICHES

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.01.23.477401

N/A

0DataRank · unranked

19 citations

Junchen Yang, Neeharika Kothapalli, Wesley Lewis, Naftali Kaminski, Laura E. Niklason +2 more

Macrophage-derived netrin-1 drives adrenergic nerve–associated lung fibrosis

Journal of Clinical Investigation(2021)10.1172/jci136542

N/A

0DataRank · unranked

114 citations

Xueyan Peng, Carrighan Perry, Huanxing Sun, Aglaia Ntokou, Changwan Ryu +15 more

Saracatinib, a Selective Src Kinase Inhibitor, Blocks Fibrotic Responses in In Vitro, In Vivo and Ex Vivo Models of Pulmonary Fibrosis

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.01.04.474955

N/A

0DataRank · unranked

1 citations

Christine Becker, Daniel G. Foster, Maurizio Chioccioli, Meghan Nelson, K.M. Beke +24 more

iDESC: Identifying differential expression in single-cell RNA sequencing data with multiple subjects

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.02.07.479293

N/A

0DataRank · unranked

1 citations

Ningya Wang, Taylor Adams, Jonas C. Schupp, Weimiao Wu, John E. McDonough +5 more

In vitro engineering of the lung alveolus

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.03.13.484143

N/A

0DataRank · unranked

1 citations

Yifan Yuan, Ronald Ng, Micha Sam Brickman Raredon, Taylor Adams, Pavlina Baevova +6 more

Integrative genetic and genomic networks identify microRNA associated with COPD and ILD

medRxiv(2022)10.1101/2022.08.07.22278496

N/A

0DataRank · unranked

0 citations

Carly B. Garrison, Lingqi Luo, Gang Liu, Daniel G. Taub, Xiao‐Jun Ji +13 more

Immune dysregulation and autoreactivity correlate with disease severity in SARS-CoV-2-associated multisystem inflammatory syndrome in children

Immunity(2021)10.1016/j.immuni.2021.04.003

N/A

0DataRank · unranked

261 citations

Nina N. Brodsky, Tomokazu S. Sumida, Michela Comi, Hiromitsu Asashima, Kenneth B. Hoehn +27 more

PD-1highCXCR5–CD4+ peripheral helper T cells promote CXCR3+ plasmablasts in human acute viral infection

Cell Reports(2023)10.1016/j.celrep.2022.111895

N/A

0DataRank · unranked

44 citations

Subhasis Mohanty, Michela Comi, William Ruff, Kenneth B. Hoehn, Patrick Wong +19 more

SRC and TKS5 mediated podosome formation in fibroblasts promotes extracellular matrix invasion and pulmonary fibrosis

Nature Communications(2023)10.1038/s41467-023-41614-x

N/A

0DataRank · unranked

27 citations

Paraskevi Kanellopoulou, Dionysiοs Fanidis, Dimitris Nastos, Eleftheria-Dimitra Ntouskou, Apostolos Galaris +10 more

Rational engineering of lung alveolar epithelium

npj Regenerative Medicine(2023)10.1038/s41536-023-00295-2

N/A

0DataRank · unranked

26 citations

Yifan Yuan, Ronald Ng, Micha Sam Brickman Raredon, Taylor Adams, Pavlina Baevova +7 more

Increased expression of CXCL6 in secretory cells drives fibroblast collagen synthesis and is associated with increased mortality in idiopathic pulmonary fibrosis

European Respiratory Journal(2023)10.1183/13993003.00088-2023

N/A

0DataRank · unranked

21 citations

Jiangning Tan, Rosa Marie Apel, Benjamin Seeliger, Jonas C. Schupp, Xiaoyun Li +24 more

Decreased miR-24-3p potentiates DNA damage responses and increases susceptibility to COPD

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.22.108688

N/A

0DataRank · unranked

2 citations

Feng Wan, Eric Finnemore, Willy Roque, Sojin Kim, Isabel Bazán +13 more

Alveolar Vascular Remodeling in Nonspecific Interstitial Pneumonia: Replacement of Normal Lung Capillaries with COL15A1 -Positive Endothelial Cells

American Journal of Respiratory and Critical Care Medicine(2023)10.1164/rccm.202303-0544le

N/A

0DataRank · unranked

13 citations

Edward P. Manning, Maurizio Chioccioli, Jan C. Kamp, Leonard Christian, Changwan Ryu +7 more

An AI-powered patient triage platform for future viral outbreaks using COVID-19 as a disease model

Human Genomics(2023)10.1186/s40246-023-00521-4

N/A

0DataRank · unranked

13 citations

Reza Aalizadeh, Álvaro J. Santos‐Neto, Wan Ying Tan, Emily A. Davidson, Varvara Nikolopoulou +82 more

Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity

Research Square(2020)10.21203/rs.3.rs-119865/v1

N/A

0DataRank · unranked

4 citations

Nichelle I. Winters, Mei-i Chung, Chitra Joseph, Austin J. Gutierrez, Arun C. Habermann +16 more

Genetic analyses of chr11p15.5 region identify MUC5AC-MUC5B associated with asthma-related phenotypes

Journal of Asthma(2023)10.1080/02770903.2023.2193631

N/A

0DataRank · unranked

6 citations

Huashi Li, Stephanie A. Christenson, Mario Castro, Loren C. Denlinger, Serpil C. Erzurum +15 more

Transcriptomics of Bronchoalveolar Lavage Cells Identifies New Molecular Endotypes of Sarcoidosis

medRxiv(2020)10.1101/2020.07.24.20161448

N/A

0DataRank · unranked

5 citations

Xiting Yan, Kevin F. Gibson, Mridu Gulati, Jonas C. Schupp, Giuseppe DeIuliis +24 more

iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects

BMC Bioinformatics(2023)10.1186/s12859-023-05432-8

N/A

0DataRank · unranked

13 citations

Jiayi Zhao, Taylor Adams, Ningya Wang, Jonas C. Schupp, Weimiao Wu +6 more

Thyroid hormone modulates hyperoxic neonatal lung injury and mitochondrial function

JCI Insight(2023)10.1172/jci.insight.160697

N/A

0DataRank · unranked

11 citations

Teodora Nicola, Rui Li, Snehashis Hazra, Sadis Matalon, Naftali Kaminski +3 more

SH2 Domain-Containing Phosphatase-SHP2 Attenuates Fibrotic Responses through Negative Regulation of Mitochondrial Metabolism in Lung Fibroblasts

Diagnostics(2023)10.3390/diagnostics13061166

N/A

0DataRank · unranked

6 citations

Apostolos Galaris, Ilianna Barbayianni, Giuseppe DeIuliis, Farida Ahangari, Fotis Sampsonas +10 more

Circulating Mitochondrial DNA Is Associated With High Levels of Fatigue in Two Independent Sarcoidosis Cohorts

CHEST Journal(2023)10.1016/j.chest.2023.11.020

N/A

0DataRank · unranked

2 citations

Buqu Hu, Ying Sun, Sheeline Yu, John McGovern, Shifa Gandhi +10 more

Single-cell profiling reveals immune aberrations in progressive idiopathic pulmonary fibrosis

medRxiv(2023)10.1101/2023.04.29.23289296

N/A

0DataRank · unranked

12 citations

Amy Zhao, Nir Neumark, Jonas C. Schupp, Farida Ahangari, Carlos Cosme +12 more

A hybrid machine learning and regression method for cell type deconvolution of spatial barcoding-based transcriptomic data

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.24.554722

N/A

0DataRank · unranked

3 citations

Ningshan Li, Ji Qi, Gang Xu, Jiayi Zhao, Nating Wang +11 more

Mast-Cell Expressed Membrane Protein-1 (MCEMP1) is expressed in classical monocytes and alveolar macrophages in Idiopathic Pulmonary Fibrosis and regulates cell chemotaxis, adhesion, and migration in a TGFβ dependent manner

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.07.561349

N/A

0DataRank · unranked

2 citations

Τheodoros Karampitsakos, Avraham Unterman, Taylor Adams, K. Marlin, Alyssa Arsenault +7 more

A novel Bayesian framework for harmonizing information across tissues and studies to increase cell type deconvolution accuracy

Briefings in Bioinformatics(2023)10.1093/bib/bbac616

N/A

0DataRank · unranked

0 citations

Bolun Li, Jiawei Wang, Wei Jiang, Xiting Yan, Ningshan Li +5 more

Association study of human leukocyte antigen (HLA) variants and idiopathic pulmonary fibrosis

medRxiv(2023)10.1101/2023.07.20.23292940

N/A

0DataRank · unranked

0 citations

Megan L. Paynton, Richard J. Allen, D Chin, Lauren J. Donoghue, Amy Stockwell +42 more

Airway Basal Cells show a dedifferentiated KRT17 high Phenotype and promote Fibrosis in Idiopathic Pulmonary Fibrosis

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.09.04.283408

N/A

0DataRank · unranked

7 citations

Jonas C. Schupp, Linda Plappert, Oliver Terwolbeck, Gian Kayser, Peggy Engelhard +13 more

Single-Cell Analysis Reveals Novel Immune Perturbations in Fibrotic Hypersensitivity Pneumonitis

American Journal of Respiratory and Critical Care Medicine(2024)10.1164/rccm.202401-0078oc

N/A

0DataRank · unranked

42 citations

Avraham Unterman, Nebal Abu Hussein, Prapti Sharma, Fadi Nikola, Jasper Flint +20 more

Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.20.347187

N/A

0DataRank · unranked

9 citations

Nichelle I. Winters, Mei-i Chung, Chitra Joseph, Austin J. Gutierrez, Arun C. Habermann +17 more

Stem cell migration drives lung repair in living mice

Developmental Cell(2024)10.1016/j.devcel.2024.02.003

N/A

0DataRank · unranked

26 citations

Shuyu Liu, Sumner Magruder, Aleksandra Tata, Lucia Borriello, John E. McDonough +14 more

Suppression of NLRX1 in chronic obstructive pulmonary disease

UNC Libraries(2020)10.17615/nhwa-g117

N/A

0DataRank · unranked

2 citations

Chang-Min Lee, Bo Hye Kim, Maor Sauler, Chun Geun Lee, Woo Jin Kim +13 more

Postinfectious Pulmonary Complications: Establishing Research Priorities to Advance the Field: An Official American Thoracic Society Workshop Report

Annals of the American Thoracic Society(2024)10.1513/annalsats.202406-651st

N/A

0DataRank · unranked

22 citations

Ajay Sheshadri, Jennifer Alexander‐Brett, Yael Aschner, Amy K. Barczak, Maria C. Basil +29 more

Retrograde signaling by a mtDNA-encoded non-coding RNA preserves mitochondrial bioenergetics

Communications Biology(2020)10.1038/s42003-020-01322-4

N/A

0DataRank · unranked

27 citations

Raul Jobava, Ilya Bederman, A. J. Degar, Harshavardhan Kenche, Bo Guan +19 more

Dedifferentiated early postnatal lung myofibroblasts redifferentiate in adult disease

Frontiers in Cell and Developmental Biology(2024)10.3389/fcell.2024.1335061

N/A

0DataRank · unranked

9 citations

Taylor Adams, Inamul Kabir, Eunate Gallardo‐Vara, Naftali Kaminski, Brigitte N. Gomperts +2 more

Platform Effects on Regeneration by Pulmonary Basal Cells as Evaluated by Single-Cell RNA Sequencing

Cell Reports(2020)10.1016/j.celrep.2020.03.004

N/A

0DataRank · unranked

54 citations

Taylor Adams, Micha Sam Brickman Raredon, Elise Gubbins, Jonas C. Schupp, Alexander J. Engler +5 more

Predicting lung aging using scRNA-Seq data

PLoS Computational Biology(2024)10.1371/journal.pcbi.1012632

N/A

0DataRank · unranked

2 citations

A Singh, John E. McDonough, Taylor Adams, Robin Vos, Ruben De Man +10 more

Genetic analyses identify GSDMB associated with asthma severity, exacerbations, and antiviral pathways

Journal of Allergy and Clinical Immunology(2020)10.1016/j.jaci.2020.07.030

N/A

0DataRank · unranked

93 citations

Stephanie A. Christenson, Brian D. Modena, Huashi Li, William W. Busse, Mario Castro +15 more

Genome-wide SNP-sex interaction analysis of susceptibility to idiopathic pulmonary fibrosis

medRxiv(2024)10.1101/2024.01.12.24301204

N/A

0DataRank · unranked

2 citations

Anne F Goemans, Amy Stockwell, Richard J. Allen, Beatriz Guillén‐Guío, Tamara Hernández-Beeftink +39 more

Small airways pathology in idiopathic pulmonary fibrosis: a retrospective cohort study

The Lancet Respiratory Medicine(2020)10.1016/s2213-2600(19)30356-x

N/A

0DataRank · unranked

125 citations

Naoya Tanabe, John E. McDonough, Dragoş M. Vasilescu, Feng Xu, Wim A. Wuyts +18 more

CD103+ dendritic cell–fibroblast crosstalk via TLR9, TDO2, and AHR signaling drives lung fibrogenesis

JCI Insight(2025)10.1172/jci.insight.177072

N/A

0DataRank · unranked

14 citations

Rita Medina Costa, Taylor Adams, Talon M. Gilchrist, Claire E. Emch, Monica Bame +8 more

Epigenetic age acceleration in idiopathic pulmonary fibrosis revealed by DNA methylation clocks

American Journal of Physiology-Lung Cellular and Molecular Physiology(2025)10.1152/ajplung.00171.2024

N/A

0DataRank · unranked

10 citations

Farida Ahangari, Taylor Adams, Ruben De Man, Jessica Tang, Marianne Carlon +9 more

Dysregulated alveolar type 2 epithelial cell proteostasis promotes fibrogenic macrophage migration inhibitory factor–CD74 signaling

Science Translational Medicine(2025)10.1126/scitranslmed.adr2277

N/A

0DataRank · unranked

4 citations

Jessica Nouws, Jannik Ruwisch, Gavitt A. Woodard, Joseph Cooley, Johad Khoury +21 more

The transcriptome of CD14 + CD163 − HLA-DR low monocytes predicts mortality in idiopathic pulmonary fibrosis

European Respiratory Journal(2025)10.1183/13993003.00804-2025

N/A

0DataRank · unranked

2 citations

Minxue Jia, Bochra Tourki, Zainab Fatima, Bogdan Visinescu, Carole Y. Perrot +19 more

Racial, Ethnic, Sex, and Gender Equity for Inclusive Interstitial Lung Disease Research: An Official American Thoracic Society Research Statement

American Journal of Respiratory and Critical Care Medicine(2025)10.1164/rccm.202509-2336st

N/A

0DataRank · unranked

2 citations

Ayodeji Adegunsoye, Yet H. Khor, Francesco Bonella, Raphaël Borie, Ivette Buendía-Roldán +13 more

Predicting lung aging using scRNA-Seq data

UNC Libraries(2025)10.17615/ka9b-3z04

N/A

0DataRank · unranked

0 citations

Vanaudenaerde B.M, Ceulemans L.J, Naftali Kaminski, Jonas C. Schupp, Vos R +10 more

Sex-specific genetic effects on susceptibility to idiopathic pulmonary fibrosis

ERJ Open Research(2025)10.1183/23120541.00200-2025

N/A

0DataRank · unranked

0 citations

Anne F Goemans, Tamara Hernández-Beeftink, Amy Stockwell, Richard J. Allen, Beatriz Guillén‐Guío +36 more

Matrix metalloproteinases and disease severity among PIMZ and PIZZ individuals in the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) cohort

BMJ Open Respiratory Research(2025)10.1136/bmjresp-2025-003585

N/A

0DataRank · unranked

0 citations

Russell P. Bowler, Karina A. Serban, Katherine Pratte, Victor E. Ortega, James K. Stoller +3 more

Long noncoding RNA TINCR is a novel regulator of human bronchial epithelial cell differentiation state

Physiological Reports(2021)10.14814/phy2.14727

N/A

0DataRank · unranked

10 citations

Koji Sakamoto, Qin Li, Jonas C. Schupp, Taylor Adams, Farida Ahangari +6 more

Identification of Lupus Immune Complex-Driven Pathogenic Pro-inflammatory Monocytes and Macrophages in Systemic Lupus Erythematosus

bioRxiv (Cold Spring Harbor Laboratory)(2026)10.64898/2026.01.21.700902

N/A

0DataRank · unranked

0 citations

Min Shin, Sang Jin Lee, Helen Cai, Won Jae Seong, Hyoungsu Kim +25 more

Type I Interferon Transcriptional Network Regulates Expression of Coinhibitory Receptors in Human T cells

Research Square(2021)10.21203/rs.3.rs-133494/v1

N/A

0DataRank · unranked

8 citations

Tomokazu S. Sumida, Shai Dulberg, Jonas C. Schupp, Helen A. Stillwell, Pierre‐Paul Axisa +7 more

A Markov random field model for network-based differential expression analysis of single-cell RNA-seq data

BMC Bioinformatics(2021)10.1186/s12859-021-04412-0

N/A

0DataRank · unranked

13 citations

Biqing Zhu, Zhichao Xu, Taylor Adams, Naftali Kaminski, Luca Pinello +1 more

PD-1 high CXCR5 – CD4 + Peripheral Helper T (Tph) cells Promote Tissue-Homing Plasmablasts in COVID-19

medRxiv(2021)10.1101/2021.03.13.21253527

N/A

0DataRank · unranked

5 citations

Subhasis Mohanty, Michela Comi, William Ruff, Kenneth B. Hoehn, Patrick Wong +15 more

CINS: Cell Interaction Network inference from Single cell expression data

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.02.22.432206

N/A

0DataRank · unranked

4 citations

Carlos Cosme, Taylor Adams, Jonas C. Schupp, Koji Sakamoto, Nikos Xylourgidis +4 more

A Statistical Framework to Identify Cell Types Whose Genetically Regulated Proportions are Associated with Complex Diseases

medRxiv(2021)10.1101/2021.02.25.21252462

N/A

0DataRank · unranked

1 citations

Wenxuan Deng, Ming Chen, Zihan Dong, Biqing Zhu, Zhaolong Yu +7 more

High CXCL6 drives matrix expression and correlate with markers of poor outcome in IPF

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.06.22.449424

N/A

0DataRank · unranked

1 citations

Jiangning Tan, Rosa Marie Apel, Benjamin Seeliger, Xiaoyun Li, Ting‐Yun Chen +19 more

Cell-Specific Transcriptome of the COPD Alveolar Niche

Research Square(2021)10.21203/rs.3.rs-276195/v1

N/A

0DataRank · unranked

0 citations

John E. McDonough, Taylor Adams, Neeharika Kotahpalli, Jonas C. Schupp, Thomas Bärnthaler +19 more

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