Publications 2024
Assessing computational predictions of antimicrobial resistance phenotypes from microbial genomes. Hu, K., F. Meyer, Z. L. Deng, E. Asgari, T. H. Kuo, P. C. Münch, and A. C. McHardy. 2024. Brief Bioinform 25.
Shared and Distinct Gut Microbiota in Spondyloarthritis, Acute Anterior Uveitis, and Crohn’s Disease.Essex, M., V. Rios Rodriguez, J. Rademacher, F. Proft, U. Lober, L. Marko, U. Pleyer, T. Strowig, J. Marchand, J. A. Kirwan, B. Siegmund, S. K. Forslund, and D. Poddubnyy. 2024. Arthritis Rheumatol 76: 48-58.
Publications 2023
Spondyloarthritis, acute anterior uveitis, and Crohn’s disease have both shared and distinct gut microbiota. Essex M, Rios Rodriguez V, Rademacher J, Proft F, Löber U, Markó L, Pleyer U, Strowig T, Marchand J, Kirwan JA, Siegmund B, Forslund SK, Poddubnyy D. Arthritis Rheumatol. 2023 Jul 20.
Brief report: Assessment of mucosal barrier integrity using serological biomarkers in preclinical stages of rheumatoid arthritis. Gilbert BTP, Lamacchia C, Amend L, Strowig T, Rodriguez E, Palmer G, Finckh A. Front Immunol. 2023 Feb 16;14:1117742.
The link between rheumatic disorders and inborn errors of immunity. Sogkas G, Witte T. EBioMedicine. 2023 Mar 2;90:104501.
The natural product chlorotonil A preserves colonization resistance and prevents relapsing Clostridioides difficile infection. Bublitz A, Brauer M, Wagner S, Hofer W, Müsken M, Deschner F, Lesker TR, Neumann-Schaal M, Paul LS, Nübel U, Bartel J, Kany AM, Zühlke D, Bernecker S, Jansen R, Sievers S, Riedel K, Herrmann J, Müller R, Fuchs TM, Strowig T. Cell Host Microbe. 2023 Apr 18:S1931-3128(23)00147-6.
Pulsed antibiotic treatments of gnotobiotic mice manifest in complex bacterial community dynamics and resistance effects. Münch PC, Eberl C, Woelfel S, Ring D, Fritz A, Herp S, Lade I, Geffers R, Franzosa EA, Huttenhower C, McHardy AC, Stecher B. Pulsed antibiotic treatments of gnotobiotic mice manifest in complex bacterial community dynamics and resistance effects. Cell Host Microbe. 2023 Jun 14;31(6):1007-1020.e4.
MAGT1 Deficiency Dysregulates Platelet Cation Homeostasis and Accelerates Arterial Thrombosis and Ischemic Stroke in Mice. Gotru SK, Mammadova-Bach E, Sogkas G, Schuhmann MK, Schmitt K, Kraft P, Herterich S, Mamtimin M, Pinarci A, Beck S, Stritt S, Han C, Ren P, Freund JN, Klemann C, Ringshausen FC, Heemskerk JWM, Dietrich A, Nieswandt B, Stoll G, Gudermann T, Braun A. Arterioscler Thromb Vasc Biol. 2023 Aug;43(8):1494-1509. doi: 10.1161/ATVBAHA.122.318115. Epub 2023 Jun 29. PMID: 37381987.
Publications 2022
Critical Assessment of Metagenome Interpretation: the second round of challenges. Meyer F, Fritz A, Deng ZL, Koslicki D, Lesker TR, Gurevich A, Robertson G, Alser M, Antipov D, Beghini F, Bertrand D, Brito JJ, Brown CT, Buchmann J, Buluç A, Chen B, Chikhi R, Clausen PTLC, Cristian A, Dabrowski PW, Darling AE, Egan R, Eskin E, Georganas E, Goltsman E, Gray MA, Hansen LH, Hofmeyr S, Huang P, Irber L, Jia H, Jørgensen TS, Kieser SD, Klemetsen T, Kola A, Kolmogorov M, Korobeynikov A, Kwan J, LaPierre N, Lemaitre C, Li C, Limasset A, Malcher-Miranda F, Mangul S, Marcelino VR, Marchet C, Marijon P, Meleshko D, Mende DR, Milanese A, Nagarajan N, Nissen J, Nurk S, Oliker L, Paoli L, Peterlongo P, Piro VC, Porter JS, Rasmussen S, Rees ER, Reinert K, Renard B, Robertsen EM, Rosen GL, Ruscheweyh HJ, Sarwal V, Segata N, Seiler E, Shi L, Sun F, Sunagawa S, Sørensen SJ, Thomas A, Tong C, Trajkovski M, Tremblay J, Uritskiy G, Vicedomini R, Wang Z, Wang Z, Wang Z, Warren A, Willassen NP, Yelick K, You R, Zeller G, Zhao Z, Zhu S, Zhu J, Garrido-Oter R, Gastmeier P, Hacquard S, Häußler S, Khaledi A, Maechler F, Mesny F, Radutoiu S, Schulze-Lefert P, Smit N, Strowig T, Bremges A, Sczyrba A, McHardy AC. Nat Methods. 2022 Apr;19(4):429-440. doi: 10.1038/s41592-022-01431-4. Epub 2022 Apr 8. PMID: 35396482.
Strain Identification and Quantitative Analysis in Microbial Communities. Ghazi AR, Münch PC, Chen D, Jensen J, Huttenhower C. J Mol Biol. 2022 Aug; Epub 2022 Apr 7.
Primary antibody deficiency-associated arthritis shares features with spondyloarthritis and enteropathic arthritis. Pott NM, Atschekzei F, Pott CC, Ernst D, Witte T, Sogkas G. RMD Open. 2022 Dec
Publications 2021
Klebsiella oxytoca causes colonization resistance against multidrug-resistant K. pneumoniae in the gut via cooperative carbohydrate competition. Osbelt L, Wende M, Almási É, Derksen E, Muthukumarasamy U, Lesker TR, Galvez EJC, Pils MC, Schalk E, Chhatwal P, Färber J, Neumann-Schaal M, Fischer T, Schlüter D, Strowig T. Cell Host Microbe.
Novel aspects of regulatory T cell dysfunction as a therapeutic target in giant cell arteritis. Adriawan IR, Atschekzei F, Dittrich-Breiholz O, Garantziotis P, Hirsch S, Risser LM, Kosanke M, Schmidt RE, Witte T, Sogkas G. Ann Rheum Dis.
B cell depletion impairs vaccination-induced CD8+ T cell responses in a type I interferon-dependent manner. Graalmann T, Borst K, Manchanda H, Vaas L, Bruhn M, Graalmann L, Koster M, Verboom M, Hallensleben M, Guzmán CA, Sutter G, Schmidt RE, Witte T, Kalinke U. Ann Rheum Dis.
Haploflow: strain-resolved de novo assembly of viral genomes. Genome Biol 22:212. Fritz A, Bremges A, Deng Z-L, Lesker TR, Götting J, Ganzenmueller T, Sczyrba A, Dilthey A, Klawonn F, McHardy AC. 2021.
Anti-CD74 IgA autoantibodies in radiographic axial spondyloarthritis: a longitudinal Swedish study. Do L, Granåsen G, Hellman U, Lejon K, Geijer M, Baraliakos X, Witte T, Forsblad-d’Elia H. Rheumatology (Oxford). 2021 Sep 1;60(9):4085-4093. doi: 10.1093/rheumatology/keaa882. PMID: 33369649; PMCID: PMC8410007.
Perturbation of the gut microbiome by Prevotella spp. enhances host susceptibility to mucosal inflammation. Iljazovic A, Roy U, Gálvez EJC, Lesker TR, Zhao B, Gronow A, Amend L, Will SE, Hofmann JD, Pils MC, Schmidt-Hohagen K, Neumann-Schaal M, Strowig T. Mucosal Immunol. 2021 Jan;14(1):113-124. doi: 10.1038/s41385-020-0296-4. Epub 2020 May 20. PMID: 32433514; PMCID: PMC7790746.
Single-cell chromatin accessibility landscape identifies tissue repair program in human regulatory T cells. Delacher M, Simon M, Sanderink L, Hotz-Wagenblatt A, Wuttke M, Schambeck K, Schmidleithner L, Bittner S, Pant A, Ritter U, Hehlgans T, Riegel D, Schneider V, Groeber-Becker FK, Eigenberger A, Gebhard C, Strieder N, Fischer A, Rehli M, Hoffmann P, Edinger M, Strowig T, Huehn J, Schmidl C, Werner JM, Prantl L, Brors B, Imbusch CD, Feuerer M. Immunity. 2021 Apr 13;54(4):702-720.e17. doi: 10.1016/j.immuni.2021.03.007. Epub 2021 Mar 30. PMID: 33789089; PMCID: PMC8050210.
Publications 2020
Strategic Anti-SARS-CoV-2 Serology Testing in a Low Prevalence Setting: The COVID-19 Contact (CoCo) Study in Healthcare Professionals. Behrens GMN, Cossmann A, Stankov MV, Schulte B, Streeck H, Förster R, Bosnjak B, Willenzon S, Boeck AL, Thu Tran A, Thiele T, Graalmann T, Kayser MZ, Zychlinsky Scharff A, Dopfer C, Horke A, Pink I, Witte T, Wetzke M, Ernst D, Jablonka A, Happle C. Infect Dis Ther. 2020 Dec;9(4):837-849. doi: 10.1007/s40121-020-00334-1. Epub 2020 Sep 4. PMID: 32886335; PMCID: PMC7472691.
An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome. Lesker TR, Durairaj AC, Gálvez EJC, Lagkouvardos I, Baines JF, Clavel T, Sczyrba A, McHardy AC, Strowig T. Cell Rep. 2020 Mar 3;30(9):2909-2922.e6. doi: 10.1016/j.celrep.2020.02.036. PMID: 32130896; PMCID: PMC7059117.
Peripheral Blood Lymphocyte Phenotype Differentiates Secondary Antibody Deficiency in Rheumatic Disease from Primary Antibody Deficiency. Jablonka A, Etemadi H, Adriawan IR, Ernst D, Jacobs R, Buyny S, Witte T, Schmidt RE, Atschekzei F, Sogkas G. J Clin Med. 2020 Apr 7;9(4):1049. doi: 10.3390/jcm9041049. PMID: 32272789; PMCID: PMC7230453.
Distinct Polysaccharide Utilization Determines Interspecies Competition between Intestinal Prevotella spp. Gálvez EJC, Iljazovic A, Amend L, Lesker TR, Renault T, Thiemann S, Hao L, Roy U, Gronow A, Charpentier E, Strowig T. Cell Host Microbe. 2020 Dec 9;28(6):838-852.e6. doi: 10.1016/j.chom.2020.09.012. Epub 2020 Oct 27. PMID: 33113351.
Identification of Natural CRISPR Systems and Targets in the Human Microbiome. Cell Host Microbe. Münch PC, Franzosa EA, Stecher B, McHardy AC, Huttenhower C. 2021 Jan 13;29(1):94-106.e4. doi: 10.1016/j.chom.2020.10.010. Epub 2020 Nov 19. PMID: 33217332; PMCID: PMC7813156.
Dietary Short-Term Fiber Interventions in Arthritis Patients Increase Systemic SCFA Levels and Regulate Inflammation. Dürholz K, Hofmann J, Iljazovic A, Häger J, Lucas S, Sarter K, Strowig T, Bang H, Rech J, Schett G, Zaiss MM. Nutrients. 2020 Oct 20;12(10):3207. doi: 10.3390/nu12103207. PMID: 33092271; PMCID: PMC7589100.
The Role of Ames Dwarfism and Calorie Restriction on Gut Microbiota. Wiesenborn DS, Gálvez EJC, Spinel L, Victoria B, Allen B, Schneider A, Gesing A, Al-Regaiey KA, Strowig T, Schäfer KH, Masternak MM. J Gerontol A Biol Sci Med Sci. 2020 Jun 18;75(7):e1-e8. doi: 10.1093/gerona/glz236. PMID: 31665244; PMCID: PMC7302176.
Perturbation of the gut microbiome by Prevotella spp. enhances host susceptibility to mucosal inflammation. Iljazovic A, Roy U, Gálvez EJC, Lesker TR, Zhao B, Gronow A, Amend L, Will SE, Hofmann JD, Pils MC, Schmidt-Hohagen K, Neumann-Schaal M, Strowig T. Mucosal Immunol. 2021 Jan;14(1):113-124. doi: 10.1038/s41385-020-0296-4. Epub 2020 May 20. PMID: 32433514; PMCID: PMC7790746.
Clinical, Radiological, and Laboratory Features of Spinal Cord Involvement in Primary Sjögren’s Syndrome. Butryn M, Neumann J, Rolfes L, Bartels C, Wattjes MP, Mahmoudi N, Seeliger T, Konen FF, Thiele T, Witte T, Meuth SG, Skripuletz T, Pawlitzki M. J Clin Med. 2020 May 14;9(5):1482. doi: 10.3390/jcm9051482. PMID: 32423153; PMCID: PMC7290729.
Anti-CD74 IgA autoantibodies in radiographic axial spondyloarthritis; a longitudinal Swedish study. Do L, Granasen G, Hellman U, Lejon K, Geijer M, Baraliakos X, Witte T, Forsblad-d’Elia H. Rheumatology (Oxford) 2020
High frequency of variants in genes associated with primary immunodeficiencies in patients with rheumatic diseases with secondary hypogammaglobulinaemia Sogkas G, Dubrowinskaja N, Adriawan IR, Anim M, Witte T, Schmidt RE, Atschekzei F. Ann Rheum Dis 2020
Repertoire characterization and validation of gB-specific human IgGs directly cloned from humanized mice vaccinated with dendritic cells and protected against HCMV. Theobald SJ, Kreer C, Khailaie S, Bonifacius A, Eiz-Vesper B, Figueiredo C, Mach M, Backovic M, Ballmaier M, Koenig J, Olbrich H, Schneider A, Volk V, Danisch S, Gieselmann L, Ercanoglu MS, Messerle M, Kaisenberg CV, Witte T, Klawonn F, Meyer-Hermann M, Klein F, Stripecke R. PLoS Pathog. 2020 Jul 15;16(7):e1008560. doi: 10.1371/journal.ppat.1008560. PMID: 32667948; PMCID: PMC7363084.
Publications 2019
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkıran A, Cetin Atalay R, Zhang C, Hurto RL, Freddolino PL, Zhang Y, Bhat P, Supek F, Fernández JM, Gemovic B, Perovic VR, Davidović RS, Sumonja N, Veljkovic N, Asgari E, Mofrad MRK, Profiti G, Savojardo C, Martelli PL, Casadio R, Boecker F, Schoof H, Kahanda I, Thurlby N, McHardy AC, Renaux A, Saidi R, Gough J, Freitas AA, Antczak M, Fabris F, Wass MN, Hou J, Cheng J, Wang Z, Romero AE, Paccanaro A, Yang H, Goldberg T, Zhao C, Holm L, Törönen P, Medlar AJ, Zosa E, Borukhov I, Novikov I, Wilkins A, Lichtarge O, Chi PH, Tseng WC, Linial M, Rose PW, Dessimoz C, Vidulin V, Dzeroski S, Sillitoe I, Das S, Lees JG, Jones DT, Wan C, Cozzetto D, Fa R, Torres M, Warwick Vesztrocy A, Rodriguez JM, Tress ML, Frasca M, Notaro M, Grossi G, Petrini A, Re M, Valentini G, Mesiti M, Roche DB, Reeb J, Ritchie DW, Aridhi S, Alborzi SZ, Devignes MD, Koo DCE, Bonneau R, Gligorijević V, Barot M, Fang H, Toppo S, Lavezzo E, Falda M, Berselli M, Tosatto SCE, Carraro M, Piovesan D, Ur Rehman H, Mao Q, Zhang S, Vucetic S, Black GS, Jo D, Suh E, Dayton JB, Larsen DJ, Omdahl AR, McGuffin LJ, Brackenridge DA, Babbitt PC, Yunes JM, Fontana P, Zhang F, Zhu S, You R, Zhang Z, Dai S, Yao S, Tian W, Cao R, Chandler C, Amezola M, Johnson D, Chang JM, Liao WH, Liu YW, Pascarelli S, Frank Y, Hoehndorf R, Kulmanov M, Boudellioua I, Politano G, Di Carlo S, Benso A, Hakala K, Ginter F, Mehryary F, Kaewphan S, Björne J, Moen H, Tolvanen MEE, Salakoski T, Kihara D, Jain A, Šmuc T, Altenhoff A, Ben-Hur A, Rost B, Brenner SE, Orengo CA, Jeffery CJ, Bosco G, Hogan DA, Martin MJ, O’Donovan C, Mooney SD, Greene CS, Radivojac P, Friedberg I. Genome Biol. 2019 Nov 19;20(1):244.
Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX). Asgari E, McHardy AC, Mofrad MRK. Sci Rep. 2019 Mar 5;9(1):3577. doi: 10.1038/s41598-019-38746-w. PMID: 30837494; PMCID: PMC6401088.