Iain Konigsberg, PhD

Research Scientist, Biomedical Informatics

FacultyPhoto
Graduate School
  • PhD, University of Colorado Health Sciences Center (2021)
Undergraduate School
  • BS, Indiana University–Bloomington (IN) (2016)
Languages
English
Department
Biomedical Informatics

Publications

  • Li X, Chen H, Selvaraj MS, Van Buren E, Zhou H, Wang Y, Sun R, McCaw ZR, Yu Z, Jiang MZ, DiCorpo D, Gaynor SM, Dey R, Arnett DK, Benjamin EJ, Bis JC, Blangero J, Boerwinkle E, Bowden DW, Brody JA, Cade BE, Carson AP, Carlson JC, Chami N, Chen YI, Curran JE, de Vries PS, Fornage M, Franceschini N, Freedman BI, Gu C, Heard-Costa NL, He J, Hou L, Hung YJ, Irvin MR, Kaplan RC, Kardia SLR, Kelly TN, Konigsberg I, Kooperberg C, Kral BG, Li C, Li Y, Lin H, Liu CT, Loos RJF, Mahaney MC, Martin LW, Mathias RA, Mitchell BD, Montasser ME, Morrison AC, Naseri T, North KE, Palmer ND, Peyser PA, Psaty BM, Redline S, Reiner AP, Rich SS, Sitlani CM, Smith JA, Taylor KD, Tiwari HK, Vasan RS, Viali S, Wang Z, Wessel J, Yanek LR, Yu B, Dupuis J, Meigs JB, Auer PL, Raffield LM, Manning AK, Rice KM, Rotter JI, Peloso GM, Natarajan P, Li Z, Liu Z, Lin X. A statistical framework for multi-trait rare variant analysis in large-scale whole-genome sequencing studies. Nat Comput Sci. 2025 Feb 7. [Epub ahead of print] PubMed PMID: 39920506
  • Dalapati T, Wang L, Jones AG, Cardwell J, Konigsberg IR, Bossé Y, Sin DD, Timens W, Hao K, Yang I, Ko DC. Context-specific eQTLs provide deeper insight into causal genes underlying shared genetic architecture of COVID-19 and idiopathic pulmonary fibrosis. HGG Adv. 2025 Jan 27;6(2):100410. [Epub ahead of print] PubMed PMID: 39876559
  • Ferrier K, Graff M, Konigsberg IR, Stanislawski M, Highland HM, Raffield LM, Carson AP, Boerwinkle E, Norris JM, Gignoux CR, Hendricks AE, Raghavan S, North KE, Allison MA, Budoff MJ, Kasela S, Aguet F, Joseph JJ, Kooperberg C, Rich SS, Rotter JI, Lange EM, Lange LA. Epigenome-wide association study meta-analysis of BMI in African American Adults. medRxiv. 2025 Feb 11. PubMed PMID: 39867370
  • Jankowski CM, Konigsberg IR, Wilson MP, Sun J, Brown TT, Julian CG, Erlandson KM. Skeletal muscle DNA methylation: Effects of exercise and HIV. Aging Cell. 2024 Jan;23(1):e14025. PubMed PMID: 37920126
  • Konigsberg IR, Lin NW, Liao SY, Liu C, MacPhail K, Mroz MM, Davidson E, Restrepo CI, Sharma S, Li L, Maier LA, Yang IV. Multi-omic signatures of sarcoidosis and progression in bronchoalveolar lavage cells. Respir Res. 2024 Jul 30;25(1):289. PubMed PMID: 39080656
  • Liu W, Vu T, R Konigsberg I, A Pratte K, Zhuang Y, Kechris KJ. Smccnet 2.0: a comprehensive tool for multi-omics network inference with shiny visualization. BMC Bioinformatics. 2024 Aug 24;25(1):276. PubMed PMID: 39179997
  • Konigsberg IR, Vu T, Liu W, Litkowski EM, Pratte KA, Vargas LB, Gilmore N, Abdel-Hafiz M, Manichaikul A, Cho MH, Hersh CP, DeMeo DL, Banaei-Kashani F, Bowler RP, Lange LA, Kechris KJ. Proteomic networks and related genetic variants associated with smoking and chronic obstructive pulmonary disease. BMC Genomics. 2024 Sep 2;25(1):825. PubMed PMID: 39223457
  • Moll M, Pratte KA, Debban CL, Liu C, Belinsky SA, Picchi M, Konigsberg I, Tern C, Rijhwani H, Hobbs BD, Silverman EK, Tesfaigzi Y, Rich SS, Manichaikul A, Rotter JI, Bowler RP, Cho MH. A protein risk score for all-cause and respiratory-specific mortality in non-Hispanic white and African American individuals who smoke. Sci Rep. 2024 Sep 4;14(1):20618. PubMed PMID: 39232179
  • Moll M, Hecker J, Platig J, Zhang J, Ghosh AJ, Pratte KA, Wang RS, Hill D, Konigsberg IR, Chiles JW 3rd, Hersh CP, Castaldi PJ, Glass K, Dy JG, Sin DD, Tal-Singer R, Mouded M, Rennard SI, Anderson GP, Kinney GL, Bowler RP, Curtis JL, McDonald ML, Silverman EK, Hobbs BD, Cho MH. Polygenic and transcriptional risk scores identify chronic obstructive pulmonary disease subtypes in the COPDGene and ECLIPSE cohort studies. EBioMedicine. 2024 Dec;110:105429. PubMed PMID: 39509750
  • Waldrop SW, Perng W, Konigsberg IR, Borengasser SJ. The potential utility of cord blood DNA methylation in pediatric clinical practice. Epigenomics. 2024 Nov-Nov;16(21-22):1365-1372. PubMed PMID: 39530586
  • Harrall KK, Glueck DH, Lange LA, Litkowski EM, Vanderlinden LA, Konigsberg IR, Cree MG, Perng W, Dabelea D. GLP-1R gene polymorphisms and metabolic traits during childhood and adolescence: The EPOCH study. J Clin Endocrinol Metab. 2024 Dec 18. [Epub ahead of print] PubMed PMID: 39693247
  • Vargas LB, Lange LA, Ferrier K, Aguet F, Ardlie K, Gabriel S, Gupta N, Smith JD, Blackwell TW, Ding J, Durda P, Tracy RP, Liu Y, Taylor KD, Craig Johnson W, Rich SS, Rotter JI, Lange EM, Konigsberg IR. Gene expression associations with body mass index in the Multi-Ethnic Study of Atherosclerosis. Int J Obes (Lond). 2023 Feb;47(2):109-116. PubMed PMID: 36463326
  • Konigsberg IR, Lin NW, Liao SY, Liu C, MacPhail K, Mroz MM, Davidson E, Restrepo CI, Sharma S, Li L, Maier LA, Yang IV. Multi-Omic Signatures of Sarcoidosis and Progression in Bronchoalveolar Lavage Cells. bioRxiv. 2023 Jan 27. PubMed PMID: 36747844
  • Hill AC, Guo C, Litkowski EM, Manichaikul AW, Yu B, Konigsberg IR, Gorbet BA, Lange LA, Pratte KA, Kechris KJ, DeCamp M, Coors M, Ortega VE, Rich SS, Rotter JI, Gerzsten RE, Clish CB, Curtis JL, Hu X, Obeidat ME, Morris M, Loureiro J, Ngo D, O'Neal WK, Meyers DA, Bleecker ER, Hobbs BD, Cho MH, Banaei-Kashani F, Bowler RP. Large scale proteomic studies create novel privacy considerations. Sci Rep. 2023 Jun 7;13(1):9254. PubMed PMID: 37286633
  • Hill EB, Konigsberg IR, Ir D, Frank DN, Jambal P, Litkowski EM, Lange EM, Lange LA, Ostendorf DM, Scorsone JJ, Wayland L, Bing K, MacLean PS, Melanson EL, Bessesen DH, Catenacci VA, Stanislawski MA, Borengasser SJ. The Microbiome, Epigenome, and Diet in Adults with Obesity during Behavioral Weight Loss. Nutrients. 2023 Aug 16;15(16). PubMed PMID: 37630778
  • Abulnoor BA, Attia MH, Konigsberg IR, Konigsberg LW. TestDimorph: An R package for analysis of interpopulation sexual dimorphism differences using summary statistics. Am J Biol Anthropol. 2023 Nov;182(3):487-498. PubMed PMID: 37694912
  • Li X, Chen H, Selvaraj MS, Van Buren E, Zhou H, Wang Y, Sun R, McCaw ZR, Yu Z, Arnett DK, Bis JC, Blangero J, Boerwinkle E, Bowden DW, Brody JA, Cade BE, Carson AP, Carlson JC, Chami N, Chen YI, Curran JE, de Vries PS, Fornage M, Franceschini N, Freedman BI, Gu C, Heard-Costa NL, He J, Hou L, Hung YJ, Irvin MR, Kaplan RC, Kardia SLR, Kelly T, Konigsberg I, Kooperberg C, Kral BG, Li C, Loos RJF, Mahaney MC, Martin LW, Mathias RA, Minster RL, Mitchell BD, Montasser ME, Morrison AC, Palmer ND, Peyser PA, Psaty BM, Raffield LM, Redline S, Reiner AP, Rich SS, Sitlani CM, Smith JA, Taylor KD, Tiwari H, Vasan RS, Wang Z, Yanek LR, Yu B, Rice KM, Rotter JI, Peloso GM, Natarajan P, Li Z, Liu Z, Lin X. A statistical framework for powerful multi-trait rare variant analysis in large-scale whole-genome sequencing studies. bioRxiv. 2023 Nov 2. PubMed PMID: 37961350
  • Liu W, Vu T, Konigsberg IR, Pratte KA, Zhuang Y, Kechris KJ. SmCCNet 2.0: an Upgraded R package for Multi-omics Network Inference. bioRxiv. 2023 Nov 21. PubMed PMID: 38045372
  • Konigsberg IR, Yang IV. Differential Methylation of Chronic Obstructive Pulmonary Disease Lung Macrophage Genes Sheds Light on Disease Pathogenesis. Am J Respir Cell Mol Biol. 2022 Jun;66(6):589-590. PubMed PMID: 35377834
  • Pan J, Li W, Ni J, Wu K, Konigsberg I, Rivera CE, Tincher C, Gregory C, Zhou X, Doak TG, Lee H, Wang Y, Gao X, Lynch M, Long H. Rates of Mutations and Transcript Errors in the Foodborne Pathogen Salmonella enterica subsp. enterica. Mol Biol Evol. 2022 Apr 10;39(4). PubMed PMID: 35446958
  • Borie R, Cardwell J, Konigsberg IR, Moore CM, Zhang W, Sasse SK, Gally F, Dobrinskikh E, Walts A, Powers J, Brancato J, Rojas M, Wolters PJ, Brown KK, Blackwell TS, Nakanishi T, Richards JB, Gerber AN, Fingerlin TE, Sachs N, Pulit SL, Zappala Z, Schwartz DA, Yang IV. Colocalization of Gene Expression and DNA Methylation with Genetic Risk Variants Supports Functional Roles of MUC5B and DSP in Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med. 2022 Nov 15;206(10):1259-1270. PubMed PMID: 35816432
  • Arnold CG, Konigsberg I, Adams JY, Sharma S, Aggarwal N, Hopkinson A, Vest A, Campbell M, Boorgula M, Yang I, Gignoux C, Barnes KC, Monte AA. Epigenetics may characterize asymptomatic COVID-19 infection. Hum Genomics. 2022 Jul 27;16(1):27. PubMed PMID: 35897116
  • Li L, Konigsberg IR, Bhargava M, Liu S, MacPhail K, Mayer A, Davidson EJ, Liao SY, Lei Z, Mroz PM, Fingerlin TE, Yang IV, Maier LA. Multiomic Signatures of Chronic Beryllium Disease Bronchoalveolar Lavage Cells Relate to T-Cell Function and Innate Immunity. Am J Respir Cell Mol Biol. 2022 Dec;67(6):632-640. PubMed PMID: 35972918
  • Vargas LB, Lange LA, Ferrier K, Aguet F, Ardlie K, Gabriel S, Gupta N, Smith JD, Blackwell TW, Ding J, Durda P, Tracy RP, Liu Y, Taylor KD, Craig Johnson W, Rich SS, Rotter JI, Lange EM, Konigsberg IR. Gene expression associations with body mass index in the Multi-Ethnic Study of Atherosclerosis. Int J Obes (Lond). 2022 Dec 3. [Epub ahead of print] PubMed PMID: 36463326
  • Konigsberg IR, Borie R, Walts AD, Cardwell J, Rojas M, Metzger F, Hauck SM, Fingerlin TE, Yang IV, Schwartz DA. Molecular Signatures of Idiopathic Pulmonary Fibrosis. Am J Respir Cell Mol Biol. 2021 Oct;65(4):430-441. PubMed PMID: 34038697
  • Siebert JC, Stanislawski MA, Zaman A, Ostendorf DM, Konigsberg IR, Jambal P, Ir D, Bing K, Wayland L, Scorsone JJ, Lozupone CA, Görg C, Frank DN, Bessesen D, MacLean PS, Melanson EL, Catenacci VA, Borengasser SJ. Multiomic Predictors of Short-Term Weight Loss and Clinical Outcomes During a Behavioral-Based Weight Loss Intervention. Obesity (Silver Spring). 2021 May;29(5):859-869. PubMed PMID: 33811477
  • Konigsberg IR, Maier LA, Yang IV. Epigenetics and sarcoidosis. Eur Respir Rev. 2021 Jun 30;30(160). PubMed PMID: 34168064
  • Liao SY, Atif SM, Mould K, Konigsberg IR, Fu R, Davidson E, Li L, Fontenot AP, Maier LA, Yang IV. Single-cell RNA sequencing identifies macrophage transcriptional heterogeneities in granulomatous diseases. Eur Respir J. 2021 Jun;57(6). PubMed PMID: 33602861
  • Konigsberg IR, Barnes B, Campbell M, Davidson E, Zhen Y, Pallisard O, Boorgula MP, Cox C, Nandy D, Seal S, Crooks K, Sticca E, Harrison GF, Hopkinson A, Vest A, Arnold CG, Kahn MG, Kao DP, Peterson BR, Wicks SJ, Ghosh D, Horvath S, Zhou W, Mathias RA, Norman PJ, Porecha R, Yang IV, Gignoux CR, Monte AA, Taye A, Barnes KC. Host methylation predicts SARS-CoV-2 infection and clinical outcome. Commun Med (Lond). 2021;1(1):42. PubMed PMID: 35072167
  • Furusawa H, Cardwell JH, Okamoto T, Walts AD, Konigsberg IR, Kurche JS, Bang TJ, Schwarz MI, Brown KK, Kropski JA, Rojas M, Cool CD, Lee JS, Wolters PJ, Yang IV, Schwartz DA. Chronic Hypersensitivity Pneumonitis, an Interstitial Lung Disease with Distinct Molecular Signatures. Am J Respir Crit Care Med. 2020 Nov 15;202(10):1430-1444. PubMed PMID: 32602730
  • Konigsberg IR, Yang IV. It's in the (Epi)genetics: Effects of DNA Methylation on Gene Expression in Atopic Asthma?. Chest. 2020 Nov;158(5):1799-1801. PubMed PMID: 33160517
  • Yang IV, Konigsberg I, MacPhail K, Li L, Davidson EJ, Mroz PM, Hamzeh N, Gillespie M, Silveira LJ, Fingerlin TE, Maier LA. DNA Methylation Changes in Lung Immune Cells Are Associated with Granulomatous Lung Disease. Am J Respir Cell Mol Biol. 2019 Jan;60(1):96-105. PubMed PMID: 30141971

Professional Memberships

  • American Society of Human Genetics, Member
  • American Thoracic Society, Member
Public Speaking
Yes
I am comfortable and experienced speaking on topics related to: genetics & genetic disease, omics and multi-omic integration, genetics and omics of lung disease, considerations of use of population descriptors in genetic studies.


School of Medicine

CU Anschutz
Fitzsimons Building

13001 East 17th Place

Aurora, CO 80045

303.724.5375

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General
Students