T32GM008224

NIH – National Institute of General Medical Sciences

Inverse agonists of retinoic acid receptor/retinoid X receptor signaling as lineage-specific antitumor agents against human adenoid cystic carcinoma

Viragova, S., Aparicio, L., Palmerini, P., Zhao, J., Valencia Salazar, L. E., Schurer, A., Dhuri, A., Sahoo, D., Moskaluk, C. A., Rabadan, R., & Dalerba, P. (2023). Inverse agonists of retinoic acid receptor/retinoid X receptor signaling as lineage-specific antitumor agents against human adenoid cystic carcinoma. JNCI: Journal of the National Cancer Institute, 115(7), 838–852. https://doi.org/10.1093/jnci/djad062

Authors:

Sara Viragova

Luis Aparicio

Pierangela Palmerini

Junfei Zhao

Luis E Valencia Salazar

Alexandra Schurer

Anika Dhuri

Debashis Sahoo

Christopher A Moskaluk

Raul Rabadan

Piero Dalerba

Affiliated Authors:

Sara Viragova

Luis Aparicio

Pierangela Palmerini

Junfei Zhao

Luis E Valencia Salazar

Alexandra Schurer

Anika Dhuri

Raul Rabadan

Piero Dalerba

Columbia Affiliation:

Subjects:

Antineoplastic Agents (MeSH)

Carcinoma, Adenoid Cystic (MeSH)

Receptors, Retinoic Acid (MeSH)

Grants:

P30CA013696 (NIH – National Cancer Institute)

R35CA253126 (NIH – National Cancer Institute)

U01CA261822 (NIH – National Cancer Institute)

UG3TR003355 (NIH – National Center for Advancing Translational Sciences)

TL1TR001875 (NIH – National Center for Advancing Translational Sciences)

UL1TR001873 (NIH – National Center for Advancing Translational Sciences)

R01AI155696 (NIH – National Institute of Allergy and Infectious Diseases)

R01DE028961 (NIH – National Institute of Dental & Craniofacial Research)

RC1DE020687 (NIH – National Institute of Dental & Craniofacial Research)

R01GM138385 (NIH – National Institute of General Medical Sciences)

T32GM008224 (NIH – National Institute of General Medical Sciences)

Publication Type:

Article

Unique ID:

10.1093/jnci/djad062

PMID:

37040084

DOI:

10.1093/jnci/djad062

Journal:

Journal of the National Cancer Institute

Publication Date:

2023-07-06

Data Source:

PubMed

Source Link:

View PubMed Record

View Scopus Record

Record Created:

Friday, August 9, 2024 - 14:05

PrePPI: A Structure Informed Proteome-wide Database of Protein–Protein Interactions

Petrey, D., Zhao, H., Trudeau, S. J., Murray, D., & Honig, B. (2023). PrePPI: A Structure Informed Proteome-wide Database of Protein–Protein Interactions. Journal of Molecular Biology, 435(14), 168052. https://doi.org/10.1016/j.jmb.2023.168052

Authors:

Donald Petrey

Haiqing Zhao

Stephen J. Trudeau

Diana Murray

Barry Honig

Affiliated Authors:

Donald Petrey

Haiqing Zhao

Stephen J. Trudeau

Diana Murray

Barry Honig

Columbia Affiliation:

Subjects:

Databases, Protein (MeSH)

Protein Interaction Mapping (MeSH)

Proteome (MeSH)

Analysis of Gene Interaction Networks (OpenAlex Topic)

Metabolic Engineering and Synthetic Biology (OpenAlex Topic)

Protein Structure Prediction and Analysis (OpenAlex Topic)

Author Keywords:

alphafold models

database

non-structural evidence

protein-protein interactions

structural modeling

Grants:

U54CA209997 (NIH – National Cancer Institute)

R35GM139585 (NIH – National Institute of General Medical Sciences)

T32GM008224 (NIH – National Institute of General Medical Sciences)

T32GM145440 (NIH – National Institute of General Medical Sciences)

Publication Type:

Article

Unique ID:

10.1016/j.jmb.2023.168052

PMID:

36933822

DOI:

10.1016/j.jmb.2023.168052

Journal:

Journal of Molecular Biology

Publication Date:

2023-07-01

Data Source:

OpenAlex

Source Link:

View OpenAlex Record

View PubMed Record

View Scopus Record

Record Created:

Friday, August 9, 2024 - 13:40

PrePCI: A structure- and chemical similarity-informed database of predicted protein compound interactions

Trudeau, S. J., Hwang, H., Mathur, D., Begum, K., Petrey, D., Murray, D., & Honig, B. (2023). PrePCI: A structure‐ and chemical similarity‐informed database of predicted protein compound interactions. Protein Science, 32(4). Portico. https://doi.org/10.1002/pro.4594

Authors:

Stephen J Trudeau

Howook Hwang

Deepika Mathur

Kamrun Begum

Donald Petrey

Diana Murray

Barry Honig

Affiliated Authors:

Stephen J Trudeau

Howook Hwang

Deepika Mathur

Kamrun Begum

Donald Petrey

Diana Murray

Barry Honig

Columbia Affiliation:

Subjects:

Databases, Chemical (MeSH)

Proteins (MeSH)

Author Keywords:

chemical similarity

protein–compound database

protein–compound interactions

structural alignment

protein-compound database

protein-compound interactions

Grants:

U54CA209997 (NIH – National Cancer Institute)

T32GM145440 (NIH – National Institute of General Medical Sciences)

T32GM008224 (NIH – National Institute of General Medical Sciences)

Publication Type:

Article

Unique ID:

10.1002/pro.4594

PMID:

36776141

DOI:

10.1002/pro.4594

Journal:

Protein Science

Publication Date:

2023-04-01

Data Source:

PubMed

Source Link:

View PubMed Record

View Scopus Record

Record Created:

Tuesday, August 13, 2024 - 11:49

A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses

Wang, P., Casner, R. G., Nair, M. S., Yu, J., Guo, Y., Wang, M., Chan, J. F.-W., Cerutti, G., Iketani, S., Liu, L., Sheng, Z., Chen, Z., Yuen, K.-Y., Kwong, P. D., Huang, Y., Shapiro, L., & Ho, D. D. (2021). A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses. Emerging Microbes & Infections, 11(1), 147–157. https://doi.org/10.1080/22221751.2021.2011623

Authors:

Pengfei Wang

Ryan G Casner

Manoj S Nair

Jian Yu

Yicheng Guo

Maple Wang

Jasper F-W Chan

Gabriele Cerutti

Sho Iketani

Lihong Liu

Zizhang Sheng

Zhiwei Chen

Kwok-Yung Yuen

Peter D Kwong

Yaoxing Huang

Lawrence Shapiro

David D Ho

Affiliated Authors:

Pengfei Wang

Ryan G Casner

Manoj S Nair

Jian Yu

Yicheng Guo

Maple Wang

Gabriele Cerutti

Sho Iketani

Lihong Liu

Zizhang Sheng

Peter D Kwong

Yaoxing Huang

Lawrence Shapiro

David D Ho

Columbia Affiliation:

Subjects:

Coronavirus Disease 2019 Research (OpenAlex Topic)

Viral Diseases in Livestock and Poultry (OpenAlex Topic)

Gastrointestinal Viral Infections and Vaccines Development (OpenAlex Topic)

Antibodies, Monoclonal (MeSH)

Antibodies, Neutralizing (MeSH)

Antibodies, Viral (MeSH)

SARS-CoV-2 (MeSH)

Author Keywords:

sars-cov-2

antibody

variants

sarbecovirus

sars-cov

Grants:

T32AI106711 (NIH – National Institute of Allergy and Infectious Diseases)

ZIAAI005022 (NIH – National Institute of Allergy and Infectious Diseases)

ZIAAI005149 (NIH – National Institute of Allergy and Infectious Diseases)

T32GM008224 (NIH – National Institute of General Medical Sciences)

Publication Type:

Article

Unique ID:

10.1080/22221751.2021.2011623

PMID:

34836485

DOI:

10.1080/22221751.2021.2011623

Journal:

Emerging Microbes and Infections

Publication Date:

2022-12-01

Data Source:

PubMed

Source Link:

View PubMed Record

View Web of Science Record

View OpenAlex Record

Record Created:

Friday, September 6, 2024 - 14:52

Transcription factor regulation of eQTL activity across individuals and tissues

Flynn, E. D., Tsu, A. L., Kasela, S., Kim-Hellmuth, S., Aguet, F., Ardlie, K. G., Bussemaker, H. J., Mohammadi, P., & Lappalainen, T. (2022). Transcription factor regulation of eQTL activity across individuals and tissues. PLOS Genetics, 18(1), e1009719. https://doi.org/10.1371/journal.pgen.1009719

Authors:

Elise D. Flynn

Silva Kasela

Sarah Kim-Hellmuth

Harmen Bussemaker

Tuuli Lappalainen

Athena L. Tsu

Francois Aguet

Kristin Ardlie

Pejman Mohammadi

Affiliated Authors:

Elise D. Flynn

Silva Kasela

Sarah Kim-Hellmuth

Harmen Bussemaker

Tuuli Lappalainen

Athena L. Tsu

Columbia Affiliation:

Vagelos College of Physicians and Surgeons
- Department of Systems Biology

Grants:

UL1TR002550 (NIH – National Center for Advancing Translational Sciences)

R01HL142028 (NIH – National Heart, Lung, and Blood Institute)

U41HG009494 (NIH – National Human Genome Research Institute)

R01HG003008 (NIH – National Human Genome Research Institute)

F31HG010580 (NIH – National Human Genome Research Institute)

T32GM008224 (NIH – National Institute of General Medical Sciences)

R01GM140287 (NIH – National Institute of General Medical Sciences)

R01MH106842 (NIH – National Institute of Mental Health)

Publication Type:

Article

Unique ID:

10.1371/journal.pgen.1009719

PMID:

35100260

DOI:

10.1371/journal.pgen.1009719

Journal:

PLOS Genetics

Publication Date:

2022-01-01

Data Source:

Web of Science

Source Link:

View Web of Science Record

Record Created:

Wednesday, February 19, 2025 - 11:45

Contributions of single-particle cryoelectron microscopy toward fighting COVID-19

Rapp, M., Shapiro, L., & Frank, J. (2022). Contributions of single-particle cryoelectron microscopy toward fighting COVID-19. Trends in Biochemical Sciences, 47(2), 117–123. https://doi.org/10.1016/j.tibs.2021.10.005

Authors:

Micah Rapp

Lawrence Shapiro

Joachim Frank

Affiliated Authors:

Micah Rapp

Lawrence Shapiro

Joachim Frank

Columbia Affiliation:

Vagelos College of Physicians and Surgeons
- Department of Biochemistry and Molecular Biophysics

Subjects:

COVID-19 (MeSH)

Spike Glycoprotein, Coronavirus (MeSH)

Author Keywords:

mers-cov

sars-cov-2

antibodies

molecular dynamics

receptor-binding domain

spike protein

Grants:

T32GM008224 (NIH – National Institute of General Medical Sciences)

R35GM139453 (NIH – National Institute of General Medical Sciences)

Publication Type:

Article

Unique ID:

10.1016/j.tibs.2021.10.005

PMID:

34799235

DOI:

10.1016/j.tibs.2021.10.005

Journal:

Trends in Biochemical Sciences

Publication Date:

2021-11-21

Data Source:

PubMed

Source Link:

View PubMed Record

Record Created:

Thursday, May 8, 2025 - 11:43

An autoimmune disease risk variant: A trans master regulatory effect mediated by IRF1 under immune stimulation?

Brandt, M., Kim-Hellmuth, S., Ziosi, M., Gokden, A., Wolman, A., Lam, N., Recinos, Y., Daniloski, Z., Morris, J. A., Hornung, V., Schumacher, J., & Lappalainen, T. (2021). An autoimmune disease risk variant: A trans master regulatory effect mediated by IRF1 under immune stimulation? PLOS Genetics, 17(7), e1009684. https://doi.org/10.1371/journal.pgen.1009684

Authors:

Margot Brandt

Sarah Kim-Hellmuth

Marcello Ziosi

Alper Gokden

Aaron Wolman

Nora Lam

Yocelyn Recinos

Zharko Daniloski

John A. Morris

Tuuli Lappalainen

Veit Hornung

Johannes Schumacher

Affiliated Authors:

Margot Brandt

Sarah Kim-Hellmuth

Nora Lam

Yocelyn Recinos

Tuuli Lappalainen

Columbia Affiliation:

Vagelos College of Physicians and Surgeons
- Department of Systems Biology

Grants:

T32GM008224 (NIH – National Institute of General Medical Sciences)

R01MH106842 (NIH – National Institute of Mental Health)

Publication Type:

Article

Unique ID:

10.1371/journal.pgen.1009684

PMID:

34314424

DOI:

10.1371/journal.pgen.1009684

Journal:

PLOS Genetics

Publication Date:

2021-07-01

Data Source:

Web of Science

Source Link:

View Web of Science Record

Record Created:

Thursday, July 10, 2025 - 15:07