Benjamin D. Singer

Also affiliated with Lung Institute

Biochemistry, Genetics and Molecular BiologyImmunology and MicrobiologyMedicine

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 63 papers. Top paper: “Report of the first seven agents in the I-SPY COVID trial: a phase 2, open label, adaptive platform randomised controlled trial”.

Report of the first seven agents in the I-SPY COVID trial: a phase 2, open label, adaptive platform randomised controlled trial

EClinicalMedicine(2023)10.1016/j.eclinm.2023.101889

N/A

0.787DataRank · unranked

35 citations

Neil R. Aggarwal, Timothy E. Albertson, Sara C. Auld, Jeremy R. Beitler, Paul Berger +86 more

A Call for Rational Intensive Care in the Era of COVID-19

American Journal of Respiratory Cell and Molecular Biology(2020)10.1165/rcmb.2020-0151le

N/A

0.470DataRank · unranked

22 citations

Manu Jain, G. R. Scott Budinger, Richard G. Wunderink, Benjamin D. Singer

A SWI/SNF-dependent transcriptional regulation mediated by POU2AF2/C11orf53 at enhancer

Nature Communications(2024)10.1038/s41467-024-46492-5

N/A

0.442DataRank · unranked

18 citations

Natsumi Tsuboyama, Huijue Lyu, Ping Wang, Oguzhan Beytullahoglu, Te Zhang +5 more

Antibiotic de-escalation patterns and outcomes in critically ill patients with suspected pneumonia as informed by bronchoalveolar lavage results

European Journal of Clinical Microbiology & Infectious Diseases(2025)10.1007/s10096-025-05144-2

N/A

0.386DataRank · unranked

10 citations

Chiagozie I. Pickens, Nikolay S. Markov, Anna Pawlowski, Mengjia Kang, Luke V. Rasmussen +7 more

Advancing Lung Immunology Research: An Official American Thoracic Society Workshop Report

American Journal of Respiratory Cell and Molecular Biology(2022)10.1165/rcmb.2022-0167st

N/A

0.345DataRank · unranked

9 citations

Christina Schofield, Claudia Jakubzick, Shabaana A. Khader, Bart N. Lambrecht, Clare M. Lloyd +7 more

Vimentin modulates regulatory T cell receptor-ligand interactions at distal pole complex, leading to dysregulated host response to viral pneumonia

Cell Reports(2024)10.1016/j.celrep.2024.115056

N/A

0.312DataRank · unranked

7 citations

Andrew D. Prigge, Tatiana P. Ortiz Serrano, Yuan Cheng, Jennifer Davis, Karen F. Lou +9 more

DNA methyltransferase inhibition induces dynamic gene expression changes in lung CD4+ T cells of neonatal mice with E. coli pneumonia

Scientific Reports(2023)10.1038/s41598-023-31285-5

N/A

0.275DataRank · unranked

4 citations

Roland Ndeh, Kathryn A. Helmin, Benjamin D. Singer, Sharon A. McGrath‐Morrow, Nigel S. Michki

Transitions in lung microbiota landscape associate with distinct patterns of pneumonia progression

Cell Host & Microbe(2025)10.1016/j.chom.2025.11.011

N/A

0.269DataRank · unranked

5 citations

Stefanie Huttelmaier, Chiagozie I. Pickens, Anahid A. Moghadam, Hiam Abdala‐Valencia, Jiaxian Shen +95 more

Developing and validating machine learning models to predict next-day extubation

Scientific Reports(2025)10.1038/s41598-025-12264-4

N/A

0.241DataRank · unranked

4 citations

Alec Peltekian, Mengjia Kang, Nikolay S. Markov, Mengou Zhu, Kevin Grudzinski +16 more

Mediator complex subunit 1 architects a tumorigenic Treg cell program independent of inflammation

Cell Reports Medicine(2024)10.1016/j.xcrm.2024.101441

N/A

0.241DataRank · unranked

4 citations

Samuel E. Weinberg, Dongmei Wang, Lenore K. Yalom, Elena Montauti, Radhika Iyer +20 more

Neutrophil percentages in bronchoalveolar lavage fluid: Implications for diagnosing bacterial pneumonia in patients with immunocompromise and neutropenia

medRxiv(2024)10.1101/2024.05.04.24306709

N/A

0.104DataRank · unranked

1 citations

S. Fenske, Alec Peltekian, Nikolay S. Markov, Anna Pawlowski, Mengjia Kang +8 more

Aging imparts cell-autonomous dysfunction to regulatory T cells during recovery from influenza pneumonia

JCI Insight(2021)10.1172/jci.insight.141690

N/A

0DataRank · unranked

80 citations

Kathryn A. Helmin, Manuel A. Torres Acosta, Nikolay S. Markov, Jennifer Yuan-Shih Hu, Anthony M. Joudi +5 more

Age-related Differences in the Nasal Mucosal Immune Response to SARS-CoV-2

American Journal of Respiratory Cell and Molecular Biology(2021)10.1165/rcmb.2021-0292oc

N/A

0DataRank · unranked

48 citations

Andrew D. Prigge, Kishore R. Anekalla, Avani Shukla, Hanh Chi Do Umehara, Leah Setar +13 more

PAX9 Determines Epigenetic State Transition and Cell Fate in Cancer

Cancer Research(2021)10.1158/0008-5472.can-21-1114

N/A

0DataRank · unranked

24 citations

Aileen Patricia Szczepanski, Natsumi Tsuboyama, Hiam Abdala‐Valencia, Young Ah Goo, Benjamin D. Singer +4 more

Technology dictates algorithms: recent developments in read alignment

Genome biology(2021)10.1186/s13059-021-02443-7

N/A

0DataRank · unranked

9 citations

Jeremy Rotman, Dhrithi Deshpande, Kodi Taraszka, Huwenbo Shi, Pelin Icer Baykal +12 more

Aging is associated with a systemic length-associated transcriptome imbalance

Nature Aging(2022)10.1038/s43587-022-00317-6

N/A

0DataRank · unranked

116 citations

Rogan A. Grant, Alexandra C. McQuattie‐Pimentel, Kishore R. Anekalla, Sophia S. Liu, Heliodoro Tejedor-Navarro +14 more

Epigenetic Control of Regulatory T Cell Stability and Function: Implications for Translation

Frontiers in Immunology(2022)10.3389/fimmu.2022.861607

N/A

0DataRank · unranked

51 citations

Carla P. Reyes Flores, Benjamin D. Singer, Anthony M. Joudi

Reduced expression of mitochondrial complex I subunit Ndufs2 does not impact healthspan in mice

Scientific Reports(2022)10.1038/s41598-022-09074-3

N/A

0DataRank · unranked

31 citations

Ram Prosad Chakrabarty, Karis B. D’Alessandro, Yuan‐Shih Hu, Karthik Vasan, Jerica Tan +12 more

Selected Bibliography of Recent Research in COVID-19

American Journal of Respiratory and Critical Care Medicine(2022)10.1164/rccm.202202-0277up

N/A

0DataRank · unranked

3 citations

Sanjay H. Chotirmall, Lindsay Leither, Oliver W. Meldrum, Anthony M. Joudi, Nitin Seam +3 more

Author Correction: Reduced expression of mitochondrial complex I subunit Ndufs2 does not impact healthspan in mice

Scientific Reports(2022)10.1038/s41598-022-12069-9

N/A

0DataRank · unranked

2 citations

Ram Prosad Chakrabarty, Karis B. D’Alessandro, Yuan‐Shih Hu, Karthik Vasan, Jerica Tan +12 more

A machine learning approach identifies unresolving secondary pneumonia as a contributor to mortality in patients with severe pneumonia, including COVID-19

medRxiv(2022)10.1101/2022.09.23.22280118

N/A

0DataRank · unranked

2 citations

Nikolay S. Markov, Thomas Stoeger, Anna Pawlowski, Mengjia Kang, Prasanth Nannapaneni +16 more

Cellular and molecular dynamics in the lungs of neonatal and juvenile mice in response to E. coli

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.09.21.508849

N/A

0DataRank · unranked

1 citations

Jarrett Venezia, Roland Ndeh, Benjamin D. Singer, Raffaello Cimbro, Mark J. Soloski +2 more

An Adjudication Protocol for Severe Bacterial and Viral Pneumonia

medRxiv(2022)10.1101/2022.10.26.22281461

N/A

0DataRank · unranked

1 citations

Catherine A. Gao, James M. Walter, Jacqueline M. Kruser, Helen K. Donnelly, Alvaro Donayre +6 more

DNA methyltransferase inhibition induces dynamic gene expression changes in lung CD4 + T cells of neonatal mice with E. coli pneumonia

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.09.30.510315

N/A

0DataRank · unranked

0 citations

Roland Ndeh, Kathryn A. Helmin, Benjamin D. Singer, Sharon A. McGrath‐Morrow, Nigel S. Michki

Superiority of intranasal over systemic administration of bioengineered soluble ACE2 for survival and brain protection against SARS-CoV-2 infection

OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)(2022)10.1101/2022.12.05.519032

N/A

0DataRank · unranked

0 citations

Jan Wysocki, Jared T. Ahrendsen, Minghao Ye, Ian Gelarden, Vlad Nicolaescu +11 more

Differential roles of regulatory T cells in acute respiratory infections

Journal of Clinical Investigation(2023)10.1172/jci170505

N/A

0DataRank · unranked

56 citations

Nurbek Mambetsariev, Benjamin D. Singer, Luisa Morales‐Nebreda, Milica Jovisic

Machine learning links unresolving secondary pneumonia to mortality in patients with severe pneumonia, including COVID-19

Journal of Clinical Investigation(2023)10.1172/jci170682

N/A

0DataRank · unranked

55 citations

Nikolay S. Markov, Thomas Stoeger, Anna Pawlowski, Mengjia Kang, Prasanth Nannapaneni +15 more

An Adjudication Protocol for Severe Pneumonia

Open Forum Infectious Diseases(2023)10.1093/ofid/ofad336

N/A

0DataRank · unranked

33 citations

Catherine A. Gao, Justin Bodner, James M. Walter, Jacqueline M. Kruser, Helen K. Donnelly +7 more

ELOA3 : A primate-specific RNA polymerase II elongation factor encoded by a tandem repeat gene cluster

Science Advances(2023)10.1126/sciadv.adj1261

N/A

0DataRank · unranked

6 citations

Saeid Mohammad Parast, Marta Iwanaszko, Yuki Aoi, DongAhn Yoo, Zachary J. Dumar +9 more

Intranasal soluble ACE2 improves survival and prevents brain SARS-CoV-2 infection

Life Science Alliance(2023)10.26508/lsa.202301969

N/A

0DataRank · unranked

13 citations

Jan Wysocki, Jared T. Ahrendsen, Minghao Ye, Ian Gelarden, Vlad Nicolaescu +11 more

Temporal correlation between postreperfusion complement deposition and severe primary graft dysfunction in lung allografts

American Journal of Transplantation(2023)10.1016/j.ajt.2023.11.006

N/A

0DataRank · unranked

6 citations

Chitaru Kurihara, Taisuke Kaiho, Takahide Toyoda, Adwaiy Manerikar, Viswajit Kandula +13 more

AMP-activated protein kinase is necessary for Treg cell functional adaptation to microenvironmental stress

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.29.568904

N/A

0DataRank · unranked

2 citations

Nurbek Mambetsariev, Carla P. Reyes Flores, Kathryn A. Helmin, Qianli Liu, Anthony M. Joudi +7 more

Transcriptional profiling of peripheral blood mononuclear cells identifies inflammatory phenotypes in ataxia telangiectasia

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.05.561081

N/A

0DataRank · unranked

0 citations

Benjamin D. Singer, Javier V. Perez, Aaron J. Thomas, Valerie Natale, Kathryn A. Helmin +6 more

Mitochondria regulate proliferation in adult cardiac myocytes

Journal of Clinical Investigation(2024)10.1172/jci165482

N/A

0DataRank · unranked

23 citations

Kimberly A. Smith, Paul T. Mungai, V. Joseph Dudley, Kathryn A. Helmin, Benjamin D. Singer +20 more

Distinctive evolution of alveolar T cell responses is associated with clinical outcomes in unvaccinated patients with SARS-CoV-2 pneumonia

Nature Immunology(2024)10.1038/s41590-024-01914-w

N/A

0DataRank · unranked

17 citations

Ziyou Ren, Karolina J. Senkow, Rogan A. Grant, Catherine A. Gao, Elizabeth S. Malsin +91 more

Prolonged exposure to lung-derived cytokines is associated with activation of microglia in patients with COVID-19

JCI Insight(2024)10.1172/jci.insight.178859

N/A

0DataRank · unranked

20 citations

Taylor A. Poor, Lango Sichizya, Estefani Diaz, Joseph I. Bailey, Sahil Soni +14 more

Transcriptional profiling of peripheral blood mononuclear cells identifies inflammatory phenotypes in Ataxia Telangiectasia

Orphanet Journal of Rare Diseases(2024)10.1186/s13023-024-03073-5

N/A

0DataRank · unranked

2 citations

Benjamin D. Singer, Javier V. Perez, Aaron J. Thomas, Valerie Natale, Kathryn A. Helmin +6 more

Developing and validating a machine learning model to predict successful next-day extubation in the ICU

medRxiv(2024)10.1101/2024.06.28.24309547

N/A

0DataRank · unranked

3 citations

Alec Peltekian, Mengjia Kang, Nikolay S. Markov, Mengou Zhu, Kevin Grudzinski +16 more

Culturing the Future of Medicine: The Imperative of Strengthening the Infectious Diseases Physician-Scientist Pipeline

The Journal of Infectious Diseases(2024)10.1093/infdis/jiae074

N/A

0DataRank · unranked

0 citations

Irini Sereti, Benjamin D. Singer, Boghuma K Titanji

FOXP3+ Regulatory T Cells Require TBET to Regulate Activated CD8+ T Cells During Recovery from Influenza Infection

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.05.30.596295

N/A

0DataRank · unranked

0 citations

Manuel A. Torres Acosta, Qianli Liu, Carla P. Reyes Flores, Anthony M. Joudi, Kathryn A. Helmin +5 more

The Fifth Annual Symposium of the Midwest Aging Consortium

The Journals of Gerontology Series A(2024)10.1093/gerona/glae296

N/A

0DataRank · unranked

0 citations

Lorena Rosas, Bailey A. Knopf, Yang Liu, Diego Alzate‐Correa, Ajay Bhat +30 more

AMPK is necessary for Treg functional adaptation to microenvironmental stress during malignancy and viral pneumonia

Journal of Clinical Investigation(2025)10.1172/jci179572

N/A

0DataRank · unranked

16 citations

Jonathan Gurkan, Qianli Liu, Nurbek Mambetsariev, Carla Reyes Flores, Kathryn A. Helmin +7 more

Maintenance DNA methylation is required for induced Treg reparative function following viral pneumonia in mice

Journal of Clinical Investigation(2025)10.1172/jci192925

N/A

0DataRank · unranked

6 citations

Jonathan Gurkan, Qianli Liu, Elizabeth M. Steinert, Manuel A. Torres Acosta, Kathryn A. Helmin +7 more

An Observational Cohort Study of Bronchoalveolar Lavage Fluid Galactomannan and Aspergillus Culture Positivity in Patients Requiring Mechanical Ventilation

Open Forum Infectious Diseases(2025)10.1093/ofid/ofaf090

N/A

0DataRank · unranked

1 citations

Nikolay S. Markov, Chiagozie I. Pickens, Anna Pawlowski, Mengjia Kang, James M. Walter +3 more

Regulatory T Cells Require TBET to Regulate Activated CD8+ T Cells During Recovery from Influenza

American Journal of Respiratory Cell and Molecular Biology(2025)10.1165/rcmb.2024-0254le

N/A

0DataRank · unranked

1 citations

Manuel A. Torres Acosta, Qianli Liu, Carla P. Reyes Flores, Anthony M. Joudi, Kathryn A. Helmin +5 more

Novel enzyme-based reduced representation method for DNA methylation profiling with low inputs

Nucleic Acids Research(2025)10.1093/nar/gkaf558

N/A

0DataRank · unranked

1 citations

Kathryn A. Helmin, Zachary D. Dortzbach, Carla P. Reyes Flores, Manuel A. Torres Acosta, Jonathan Gurkan +9 more

Large language models accurately identify immunosuppression in intensive care unit patients

Journal of the American Medical Informatics Association(2025)10.1093/jamia/ocaf141

N/A

0DataRank · unranked

1 citations

Mengjia Kang, M. Bak, Steven Tran, Anna Pawlowski, Prasanth Nannapaneni +87 more

Welsh, González, and Negulescu share Lasker Award recognizing transformative treatments for people with cystic fibrosis

Journal of Clinical Investigation(2025)10.1172/jci198727

N/A

0DataRank · unranked

2 citations

G. R. Scott Budinger, Benjamin D. Singer

Multi-omics profiling in severe pneumonia: the importance of robust study design

European Respiratory Journal(2025)10.1183/13993003.00760-2025

N/A

0DataRank · unranked

0 citations

Benjamin D. Singer

Systematic data capture reduces the need for source data verification: exploratory analysis from a phase 2 multicenter randomized controlled platform trial

Communications Medicine(2025)10.1038/s43856-025-01126-9

N/A

0DataRank · unranked

0 citations

Kathleen D. Liu, Derek W. Russell, D. Clark Files, Karl W. Thomas, Fady Yousef +86 more

Age-dependent immune responses and resident cell dynamics in young mice following pneumonia

iScience(2025)10.1016/j.isci.2025.114219

N/A

0DataRank · unranked

0 citations

Javier V. Perez, Dharma A. Varapula, Aaron J. Thomas, Tiffaney L. Vincent, Benjamin D. Singer +3 more

Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation

Genome biology(2020)10.1186/s13059-020-02152-7

N/A

0DataRank · unranked

128 citations

Zhenjia Wang, Cuijuan Han, Stephanie L. Safgren, Kathryn A. Helmin, Emmalee R. Adelman +10 more

Development of a Pilot Machine Learning Model to Predict Successful Short-Term Treatment Success in Critically Ill Patients With Community-Acquired Pneumonia

CHEST Critical Care(2025)10.1016/j.chstcc.2025.100228

N/A

0DataRank · unranked

0 citations

Wan‐Ting Liao, Alec Peltekian, Nikolay S. Markov, Mengjia Kang, Luke V. Rasmussen +10 more

Maintenance DNA methylation is essential for regulatory T cell development and stability of suppressive function

Journal of Clinical Investigation(2020)10.1172/jci137712

N/A

0DataRank · unranked

90 citations

Luisa Morales‐Nebreda, Manuel A. Torres Acosta, Kishore R. Anekalla, Shang-Yang Chen, Hiam Abdala‐Valencia +7 more

DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype

Scientific Reports(2020)10.1038/s41598-020-64514-2

N/A

0DataRank · unranked

38 citations

Roland Ndeh, Kathryn A. Helmin, Basil Khuder, Cynthia Rothblum‐Oviatt, Joseph M. Collaco +5 more

CoRESTed development of regulatory T cells

Journal of Clinical Investigation(2020)10.1172/jci135713

N/A

0DataRank · unranked

6 citations

Kathryn A. Helmin, Benjamin D. Singer, Luisa Morales‐Nebreda

Alveolitis in severe SARS-CoV-2 pneumonia is driven by self-sustaining circuits between infected alveolar macrophages and T cells

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.08.05.238188

N/A

0DataRank · unranked

25 citations

Luisa Morales‐Nebreda, Nikolay S. Markov, Suchitra Swaminathan, Estefany Rios-Guzman, Darryl A. Abbott +30 more

Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.01.17.910687

N/A

0DataRank · unranked

15 citations

Zhenjia Wang, Cuijuan Han, Stephanie L. Safgren, Kathryn A. Helmin, Emmalee R. Adelman +8 more

Maintenance DNA methylation is essential for regulatory T cell development and stability of suppressive function

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.02.03.926949

N/A

0DataRank · unranked

13 citations

Luisa Morales‐Nebreda, Manuel A. Torres Acosta, Kishore R. Anekalla, Shang-Yang Chen, Hiam Abdala‐Valencia +7 more

Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia

Nature(2021)10.1038/s41586-020-03148-w

N/A

0DataRank · unranked

778 citations

Luisa Morales‐Nebreda, Nikolay S. Markov, Suchitra Swaminathan, Melissa Querrey, Estefany Rios-Guzman +59 more

The lung microenvironment shapes a dysfunctional response of alveolar macrophages in aging

Journal of Clinical Investigation(2021)10.1172/jci140299

N/A

0DataRank · unranked

180 citations

Ziyou Ren, Nikita Joshi, Satoshi Watanabe, Thomas Stoeger, Monica Chi +29 more

mTORC1 stimulates cell growth through SAM synthesis and m6A mRNA-dependent control of protein synthesis

Molecular Cell(2021)10.1016/j.molcel.2021.03.009

N/A

0DataRank · unranked

179 citations

Umakant Sahu, Brendan P. O’Hara, Eunüs S. Ali, Kathryn A. Helmin, John M. Asara +4 more

Distinctive features of severe SARS-CoV-2 pneumonia

Journal of Clinical Investigation(2021)10.1172/jci149412

N/A

0DataRank · unranked

88 citations

Alexander V. Misharin, Karen M. Ridge, Benjamin D. Singer, Richard G. Wunderink, G. R. Scott Budinger