Research

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Highlighted

Proteomic Networks and Related Genetic Variants Associated with Smoking and Chronic Obstructive Pulmonary Disease

Iain R Konigsberg, Thao Vu, Weixuan Liu, Elizabeth M Litkowski, Katherine A Pratte, …, Dawn L DeMeo, Farnoush Banaei-Kashani, Russell P Bowler, Leslie A Lange, Katerina J Kechris

Cold Spring Harbor Laboratory  ·  28 Feb 2024  ·  doi:10.1101/2024.02.26.24303069

We identified sparse networks of proteins associated with FEV1, emphysema, and smoking status in the COPDGene study. We performed genome-wide association studies on summary measures of these networks.

COPD proteomics genetics

All

2024

Admix-kit: an integrated toolkit and pipeline for genetic analyses of admixed populations

Kangcheng Hou, Stephanie Gogarten, Joohyun Kim, Xing Hua, Julie-Alexia Dias, …, Jonathan Shortt, Jibril Hirbo, Yun Li, Bogdan Pasaniuc, Haoyu Zhang

Bioinformatics  ·  15 Mar 2024  ·  doi:10.1093/bioinformatics/btae148

genetics

Proteomic Networks and Related Genetic Variants Associated with Smoking and Chronic Obstructive Pulmonary Disease

Iain R Konigsberg, Thao Vu, Weixuan Liu, Elizabeth M Litkowski, Katherine A Pratte, …, Dawn L DeMeo, Farnoush Banaei-Kashani, Russell P Bowler, Leslie A Lange, Katerina J Kechris

Cold Spring Harbor Laboratory  ·  28 Feb 2024  ·  doi:10.1101/2024.02.26.24303069

We identified sparse networks of proteins associated with FEV1, emphysema, and smoking status in the COPDGene study. We performed genome-wide association studies on summary measures of these networks.

COPD proteomics genetics

2023

SmCCNet 2.0: A Comprehensive Tool for Multi-omics Network Inference with Shiny Visualization

Weixuan Liu, Thao Vu, Iain Konigsberg, Katherine Pratte, Yonghua Zhuang, Katerina Kechris

Cold Spring Harbor Laboratory  ·  21 Nov 2023  ·  doi:10.1101/2023.11.20.567893

Skeletal muscle DNA methylation: Effects of exercise and HIV

Catherine M. Jankowski, Iain R. Konigsberg, Melissa P. Wilson, Jing Sun, Todd T. Brown, Colleen G. Julian, Kristine M. Erlandson

Aging Cell  ·  03 Nov 2023  ·  doi:10.1111/acel.14025

A statistical framework for powerful multi-trait rare variant analysis in large-scale whole-genome sequencing studies

Xihao Li, Han Chen, Margaret Sunitha Selvaraj, Eric Van Buren, Hufeng Zhou, …, Gina M. Peloso, Pradeep Natarajan, Zilin Li, Zhonghua Liu, Xihong Lin

Cold Spring Harbor Laboratory  ·  02 Nov 2023  ·  doi:10.1101/2023.10.30.564764

TestDimorph: An R package for analysis of interpopulation sexual dimorphism differences using summary statistics

Bassam A. Abulnoor, MennattAllah Hassan Attia, Iain R. Konigsberg, Lyle W. Konigsberg

American Journal of Biological Anthropology  ·  11 Sep 2023  ·  doi:10.1002/ajpa.24842

The Microbiome, Epigenome, and Diet in Adults with Obesity during Behavioral Weight Loss

Emily B. Hill, Iain R. Konigsberg, Diana Ir, Daniel N. Frank, Purevsuren Jambal, …, Edward L. Melanson, Daniel H. Bessesen, Victoria A. Catenacci, Maggie A. Stanislawski, Sarah J. Borengasser

Nutrients  ·  16 Aug 2023  ·  doi:10.3390/nu15163588

Large scale proteomic studies create novel privacy considerations

Andrew C. Hill, Claire Guo, Elizabeth M. Litkowski, Ani W. Manichaikul, Bing Yu, …, Eugene R. Bleecker, Brian D. Hobbs, Michael H. Cho, Farnoush Banaei-Kashani, Russell P. Bowler

Scientific Reports  ·  07 Jun 2023  ·  doi:10.1038/s41598-023-34866-6

Multi-Omic Signatures of Sarcoidosis and Progression in Bronchoalveolar Lavage Cells

Iain R. Konigsberg, Nancy W. Lin, Shu-Yi Liao, Cuining Liu, Kristyn MacPhail, …, Clara I. Restrepo, Sunita Sharma, Li Li, Lisa A. Maier, Ivana V. Yang

Cold Spring Harbor Laboratory  ·  27 Jan 2023  ·  doi:10.1101/2023.01.26.525601

2022

Gene expression associations with body mass index in the Multi-Ethnic Study of Atherosclerosis

Luciana B. Vargas, Leslie A. Lange, Kendra Ferrier, François Aguet, Kristin Ardlie, …, W. Craig Johnson, Stephen S. Rich, Jerome I. Rotter, Ethan M. Lange, Iain R. Konigsberg

International Journal of Obesity  ·  03 Dec 2022  ·  doi:10.1038/s41366-022-01240-x

Multiomic Signatures of Chronic Beryllium Disease Bronchoalveolar Lavage Cells Relate to T-Cell Function and Innate Immunity

Li Li, Iain R. Konigsberg, Maneesh Bhargava, Sucai Liu, Kristyn MacPhail, …, Zhe Lei, Peggy M. Mroz, Tasha E. Fingerlin, Ivana V. Yang, Lisa A. Maier

American Journal of Respiratory Cell and Molecular Biology  ·  01 Dec 2022  ·  doi:10.1165/rcmb.2022-0077OC

Colocalization of Gene Expression and DNA Methylation with Genetic Risk Variants Supports Functional Roles of MUC5B and DSP in Idiopathic Pulmonary Fibrosis

Raphael Borie, Jonathan Cardwell, Iain R. Konigsberg, Camille M. Moore, Weiming Zhang, …, Norman Sachs, Sara L. Pulit, Zachary Zappala, David A. Schwartz, Ivana V. Yang

American Journal of Respiratory and Critical Care Medicine  ·  15 Nov 2022  ·  doi:10.1164/rccm.202110-2308OC

Epigenetics may characterize asymptomatic COVID-19 infection

Cosby G. Arnold, Iain Konigsberg, Jason Y. Adams, Sunita Sharma, Neil Aggarwal, …, Meher Boorgula, Ivana Yang, Christopher Gignoux, Kathleen C. Barnes, Andrew A. Monte

Human Genomics  ·  27 Jul 2022  ·  doi:10.1186/s40246-022-00401-3

Differential Methylation of Chronic Obstructive Pulmonary Disease Lung Macrophage Genes Sheds Light on Disease Pathogenesis

Iain R. Konigsberg, Ivana V. Yang

American Journal of Respiratory Cell and Molecular Biology  ·  01 Jun 2022  ·  doi:10.1165/rcmb.2022-0125ED

Rates of Mutations and Transcript Errors in the Foodborne PathogenSalmonella entericasubsp.enterica

Jiao Pan, Weiyi Li, Jiahao Ni, Kun Wu, Iain Konigsberg, …, Heewook Lee, Yan Wang, Xiang Gao, Michael Lynch, Hongan Long

Molecular Biology and Evolution  ·  01 Apr 2022  ·  doi:10.1093/molbev/msac081

2021

Host methylation predicts SARS-CoV-2 infection and clinical outcome

Iain R. Konigsberg, Bret Barnes, Monica Campbell, Elizabeth Davidson, Yingfei Zhen, …, Ivana V. Yang, Christopher R. Gignoux, Andrew A. Monte, Alem Taye, Kathleen C. Barnes

Communications Medicine  ·  26 Oct 2021  ·  doi:10.1038/s43856-021-00042-y

Molecular Signatures of Idiopathic Pulmonary Fibrosis

Iain R. Konigsberg, Raphael Borie, Avram D. Walts, Jonathan Cardwell, Mauricio Rojas, Fabian Metzger, Stefanie M. Hauck, Tasha E. Fingerlin, Ivana V. Yang, David A. Schwartz

American Journal of Respiratory Cell and Molecular Biology  ·  01 Oct 2021  ·  doi:10.1165/rcmb.2020-0546OC

Epigenetics and sarcoidosis

Iain R. Konigsberg, Lisa A. Maier, Ivana V. Yang

European Respiratory Review  ·  23 Jun 2021  ·  doi:10.1183/16000617.0076-2021

Multiomic Predictors of Short‐Term Weight Loss and Clinical Outcomes During a Behavioral‐Based Weight Loss Intervention

Janet C. Siebert, Maggie A. Stanislawski, Adnin Zaman, Danielle M. Ostendorf, Iain R. Konigsberg, …, Daniel Bessesen, Paul S. MacLean, Edward L. Melanson, Victoria A. Catenacci, Sarah J. Borengasser

Obesity  ·  03 Apr 2021  ·  doi:10.1002/oby.23127

Single-cell RNA sequencing identifies macrophage transcriptional heterogeneities in granulomatous diseases

Shu-Yi Liao, Shaikh M. Atif, Kara Mould, Iain R. Konigsberg, Rui Fu, Elizabeth Davidson, Li Li, Andrew P. Fontenot, Lisa A. Maier, Ivana V. Yang

European Respiratory Journal  ·  18 Feb 2021  ·  doi:10.1183/13993003.03794-2020

2020

Chronic Hypersensitivity Pneumonitis, an Interstitial Lung Disease with Distinct Molecular Signatures

Haruhiko Furusawa, Jonathan H. Cardwell, Tsukasa Okamoto, Avram D. Walts, Iain R. Konigsberg, …, Carlyne D. Cool, Joyce S. Lee, Paul J. Wolters, Ivana V. Yang, David A. Schwartz

American Journal of Respiratory and Critical Care Medicine  ·  15 Nov 2020  ·  doi:10.1164/rccm.202001-0134OC

It’s in the (Epi)genetics

Iain R. Konigsberg, Ivana V. Yang

Chest  ·  01 Nov 2020  ·  doi:10.1016/j.chest.2020.07.050

2019

Author Correction: Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations

Michelle Daya, Nicholas Rafaels, Tonya M. Brunetti, Sameer Chavan, Albert M. Levin, …, Gloria Varela, Olga Marina Vasquez, Francisco M. De La Vega, Lorraine B. Ware, Maria Yazdanbakhsh

Nature Communications  ·  04 Sep 2019  ·  doi:10.1038/s41467-019-12158-w

Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations

Michelle Daya, Nicholas Rafaels, Tonya M. Brunetti, Sameer Chavan, Albert M. Levin, …, Gloria Varela, Olga Marina Vasquez, Francisco M. De La Vega, Lorraine B. Ware, Maria Yazdanbakhsh

Nature Communications  ·  20 Feb 2019  ·  doi:10.1038/s41467-019-08469-7

DNA Methylation Changes in Lung Immune Cells Are Associated with Granulomatous Lung Disease

Ivana V. Yang, Iain Konigsberg, Kristyn MacPhail, Li Li, Elizabeth J. Davidson, …, Nabeel Hamzeh, May Gillespie, Lori J. Silveira, Tasha E. Fingerlin, Lisa A. Maier

American Journal of Respiratory Cell and Molecular Biology  ·  01 Jan 2019  ·  doi:10.1165/rcmb.2018-0177OC