Publications

NCBench: providing an open, reproducible, transparent, adaptable, and continuous benchmark approach for DNA-sequencing-based variant calling. Hanssen F, Gabernet G, Bäuerle F, Stöcker B, Wiegand F, Smith NH, Mertes C, Neogi AG, Brandhoff L, Ossowski A, Altmueller J, Becker K, Petzold A, Sturm M, Stöcker T, Sivalingam S, Brand F, Schmidt A, Buness A, Probst AJ, Motameny S, Köster J.F1000Res. 2024 Sep 12;12:1125. doi: 10.12688/f1000research.140344.1. eCollection 2023.

Retention of ES cell-derived 129S genome drives NLRP1 hypersensitivity and transcriptional deregulation in Nlrp3^tm1Flv mice. Weiss FD, Alvarez Y, Shakeri F, Sahu A, Leka P, Dernst A, Rollheiser J, Vasconcelos M, Geraci A, Duthie F, Stahl R, Lee HE, Gellner AK, Buness A, Latz E, Meissner F.Cell Death Differ. 2024 Sep 17. doi: 10.1038/s41418-024-01379-2.

The vast majority of somatic mutations in plants are layer-specific. Goel M, Campoy JA, Krause K, Baus LC, Sahu A, Sun H, Walkemeier B, Marek M, Beaudry R, Ruiz D, Huettel B, Schneeberger K.Genome Biol. 2024 Jul 24;25(1):194. doi: 10.1186/s13059-024-03337-0.

Next-generation phenotyping integrated in a national framework for patients with ultrarare disorders improves genetic diagnostics and yields new molecular findings. Nat Genet. 2024 Jul 22. doi: 10.1038/s41588-024-01836-1.

Neuropilin2 in Mesenchymal Stromal Cells as a Potential Novel Therapeutic Target in Myelofibrosis. Vosbeck K, Förster S, Mayr T, Sahu A, Haddouti EM, Al-Adilee O, Körber RM, Bisht S, Muders MH, Nesic S, Buness A, Kristiansen G, Schildberg FA, Gütgemann I.Cancers (Basel). 2024 May 18;16(10):1924. doi: 10.3390/cancers16101924.

Gene regulatory network analysis identifies MYL1, MDH2, GLS, and TRIM28 as the principal proteins in the response of mesenchymal stem cells to Mg²⁺ ions. Nourisa J, Passemiers A, Shakeri F, Omidi M, Helmholz H, Raimondi D, Moreau Y, Tomforde S, Schlüter H, Luthringer-Feyerabend B, Cyron CJ, Aydin RC, Willumeit-Römer R, Zeller-Plumhoff B.Comput Struct Biotechnol J. 2024 Apr 14;23:1773-1785. doi: 10.1016/j.csbj.2024.04.033.

Enhancing Variant Prioritization in VarFish through On-Premise Computational Facial Analysis. Bhasin MA, Knaus A, Incardona P, Schmid A, Holtgrewe M, Elbracht M, Krawitz PM, Hsieh TC.Genes (Basel). 2024 Mar 17;15(3):370. doi: 10.3390/genes15030370.

Analysis of 72,469 UK Biobank exomes links rare variants to male-pattern hair loss. Henne SK, Aldisi R, Sivalingam S, Hochfeld LM, Borisov O, Krawitz PM, Maj C, Nöthen MM, Heilmann-Heimbach S.Nat Commun. 2023 Sep 22;14(1):5492. doi: 10.1038/s41467-023-41186-w.

Gene-based burden scores identify rare variant associations for 28 blood biomarkers. Aldisi R, Hassanin E, Sivalingam S, Buness A, Klinkhammer H, Mayr A, Fröhlich H, Krawitz P, Maj C.BMC Genom Data. 2023 Sep 4;24(1):50. doi: 10.1186/s12863-023-01155-0.

Altered Notch signalling in Dowling-Degos disease: A transcriptomic insight into disease pathogenesis. Kumar S, Hausen J, Sivalingam S, Humbatova A, Buness A, Frank J, Ralser DJ, Betz RC.Br J Dermatol. 2023 Aug 25:ljad306. doi: 10.1093/bjd/ljad306.

Machine Learning for Decision-Support in Acute Abdominal Pain – Proof of Concept and Central Considerations. Henn J, Hatterscheidt S, Sahu A, Buness A, Dohmen J, Arensmeyer J, Feodorovici P, Sommer N, Schmidt J, Kalff JC, Matthaei H.Zentralbl Chir. 2023 Aug;148(4):376-383. doi: 10.1055/a-2125-1559. Epub 2023 Aug 10.

Identification of de novo variants in nonsyndromic cleft lip with/without cleft palate patients with low polygenic risk scores. Ishorst N, Henschel L, Thieme F, Drichel D, Sivalingam S, Mehrem SL, Fechtner AC, Fazaal J, Welzenbach J, Heimbach A, Maj C, Borisov O, Hausen J, Raff R, Hoischen A, Dixon M, Rada-Iglesias A, Bartusel M, Rojas-Martinez A, Aldhorae K, Braumann B, Kruse T, Kirschneck C, Spanier G, Reutter H, Nowak S, Gölz L, Knapp M, Buness A, Krawitz P, Nöthen MM, Nothnagel M, Becker T, Ludwig KU, Mangold E.Mol Genet Genomic Med. 2022 Dec 5:e2109. doi: 10.1002/mgg3.2109.

Deficiency for SAMHD1 activates MDA5 in a cGAS/STING-dependent manner. Schumann T, Ramon SC, Schubert N, Mayo MA, Hega M, Maser KI, Ada SR, Sydow L, Hajikazemi M, Badstübner M, Müller P, Ge Y, Shakeri F, Buness A, Rupf B, Lienenklaus S, Utess B, Muhandes L, Haase M, Rupp L, Schmitz M, Gramberg T, Manel N, Hartmann G, Zillinger T, Kato H, Bauer S, Gerbaulet A, Paeschke K, Roers A, Behrendt R.J Exp Med. 2023 Jan 2;220(1):e20220829. doi: 10.1084/jem.20220829. Epub 2022 Nov 8.

Genome-wide identification of disease-causing copy number variations in 450 individuals with anorectal malformations. Fabian J, Dworschak GC, Waffenschmidt L, Schierbaum L, Bendixen C, Heilmann-Heimbach S, Sivalingam S, Buness A, Schwarzer N, Boemers TM, Schmiedeke E, Neser J, Leonhardt J, Kosch F, Weih S, Gielen HM, Hosie S, Kabs C, Palta M, Märzheuser S, Bode LM, Lacher M, Schäfer FM, Stehr M, Knorr C, Ure B, Kleine K, Rolle U, Zaniew M, Phillip G, Zwink N, Jenetzky E, Reutter H, Hilger AC.Eur J Hum Genet. 2022 Nov 1. doi: 10.1038/s41431-022-01216-5

Next-generation phenotyping contributing to the identification of a 4.7 kb deletion in KANSL1 causing Koolen-de Vries Syndrome. Brand F, Vijayananth A, Hsieh TC, Schmidt A, Peters S, Mangold E, Cremer K, Bender T, Sivalingam S, Hundertmark H, Knaus A, Engels H, Krawitz PM, Perne C.Hum Mutat. 2022 Sep 14. doi: 10.1002/humu.24467

A novel serum extracellular vesicle protein signature to monitor glioblastoma tumor progression. Tzaridis T, Weller J, Bachurski D, Shakeri F, Schaub C, Hau P, Buness A, Schlegel U, Steinbach JP, Seidel C, Goldbrunner R, Schäfer N, Wechsler-Reya RJ, Hallek M, Scheffler B, Glas M, Haeberle L, Herrlinger U, Coch C, Reiners KS, Hartmann G.Int J Cancer. 2022 Aug 27. doi: 10.1002/ijc.34261

PFN4 is required for manchette development and acrosome biogenesis during mouse spermiogenesis. Umer N, Phadke S, Shakeri F, Arévalo L, Lohanadan K, Kirfel G, Sylvester M, Buness A, Schorle H.Development. 2022 Aug 15;149(16):dev200499. doi: 10.1242/dev.200499. Epub 2022 Aug 22.

Induction of Interferon-Stimulated Genes Correlates with Reduced Growth of Influenza A Virus in Lungs after RIG-I Agonist Treatment of Ferrets. Schwab LSU, Londrigan SL, Brooks AG, Hurt AC, Sahu A, Deng YM, Moselen J, Coch C, Zillinger T, Hartmann G, Reading PC.J Virol. 2022 Aug 2:e0055922. doi: 10.1128/jvi.00559-22.

Effects of different ratios of omega-6:omega-3 fatty acids in the diet of sows on the proteome of milk-derived extracellular vesicles. Ferreira RF, Blees T, Shakeri F, Buness A, Sylvester M, Savoini G, Agazzi A, Mrljak V, Sauerwein H.J Proteomics. 2022 May 26:104632. doi: 10.1016/j.jprot.2022.104632.

Reconstruction of the origin of the first major SARS-CoV-2 outbreak in Germany. Korencak M, Sivalingam S, Sahu A, Dressen D, Schmidt A, Brand F, Krawitz P, Hart L, Maria Eis-Hübinger A, Buness A, Streeck H.Comput Struct Biotechnol J. 2022;20:2292-2296. doi: 10.1016/j.csbj.2022.05.011. Epub 2022 May 10.

GenRisk: A tool for comprehensive genetic risk modeling. Aldisi R, Hassanin E, Sivalingam S, Buness A, Klinkhammer H, Mayr A, Fröhlich H, Krawitz P, Maj C. Bioinformatics. 2022 Mar 10:btac152. doi: 10.1093/bioinformatics/btac152.

GestaltMatcher facilitates rare disease matching using facial phenotype descriptors. Hsieh TC, Bar-Haim A, Moosa S, Ehmke N, Gripp KW, Pantel JT, Danyel M, Mensah MA, Horn D, Rosnev S, Fleischer N, Bonini G, Hustinx A, Schmid A, Knaus A, Javanmardi B, Klinkhammer H, Lesmann H, Sivalingam S, Kamphans T, Meiswinkel W, Ebstein F, Krüger E, Küry S, Bézieau S, Schmidt A, Peters S, Engels H, Mangold E, Kreiß M, Cremer K, Perne C, Betz RC, Bender T, Grundmann-Hauser K, Haack TB, Wagner M, Brunet T, Bentzen HB, Averdunk L, Coetzer KC, Lyon GJ, Spielmann M, Schaaf CP, Mundlos S, Nöthen MM, Krawitz PM. Nat Genet. 2022 Mar;54(3):349-357. doi: 10.1038/s41588-021-01010-x. Epub 2022 Feb 10.

Overexpression of Parkin in clear cell renal cell carcinoma decreases tumor aggressiveness by regulating CKS2 levels. Esser LK, Branchi V, Shakeri F, Simon AG, Stephan C, Kristiansen G, Buness A, Schorle H, Toma MI. Int J Oncol. 2022 Feb;60(2):20. doi: 10.3892/ijo.2022.5310. Epub 2022 Jan 21.

Iron Deficiency Caused by Intestinal Iron Loss-Novel Candidate Genes for Severe Anemia. Huettmann C, Stelljes M, Sivalingam S, Fobker M, Vrachimis A, Exler A, Wenning C, Wempe C, Penke M, Buness A, Ludwig KU, Muckenthaler MU, Steinbicker AU. Genes (Basel). 2021 Nov 24;12(12):1869. doi: 10.3390/genes12121869.

Variant profiling of colorectal adenomas from three patients of two families with MSH3-related adenomatous polyposis. Perne C, Peters S, Cartolano M, Horpaopan S, Grimm C, Altmüller J, Sommer AK, Hillmer AM, Thiele H, Odenthal M, Möslein G, Adam R, Sivalingam S, Kirfel J, Schweiger MR, Peifer M, Spier I, Aretz S. PLoS One. 2021 Nov 29;16(11):e0259185. doi: 10.1371/journal.pone.0259185. eCollection 2021.

Genome-Wide Survey for Microdeletions or -Duplications in 155 Patients with Lower Urinary Tract Obstructions (LUTO). Schierbaum LM, Schneider S, Herms S, Sivalingam S, Fabian J, Reutter H, Weber S, Merz WM, Tkaczyk M, Miklaszewska M, Sikora P, Szmigielska A, Krzemien G, Zachwieja K, Szczepanska M, Taranta-Janusz K, Kroll P, Polok M, Zaniew M, Hilger AC. Genes (Basel). 2021 Sep 20;12(9):1449. doi: 10.3390/genes12091449.

Machine learning to guide clinical decision-making in abdominal surgery-a systematic literature review. Henn J, Buness A, Schmid M, Kalff JC, Matthaei H. Langenbecks Arch Surg. 2021 Oct 29. doi: 10.1007/s00423-021-02348-w.

Comparative proteome profiling in exosomes derived from porcine colostrum versus mature milk reveals distinct functional proteomes. Ferreira RF, Blees T, Shakeri F, Buness A, Sylvester M, Savoini G, Agazzi A, Mrljak V, Sauerwein H.J Proteomics. 2021 Jul 31:104338. doi: 10.1016/j.jprot.2021.104338.

TBK1 and TNFRSF13B mutations and an autoinflammatory disease in a child with lethal COVID-19. Schmidt A, Peters S, Knaus A, Sabir H, Hamsen F, Maj C, Fazaal J, Sivalingam S, Savchenko O, Mantri A, Holzinger D, Neudorf U, Müller A, Ludwig KU, Krawitz PM, Engels H, Nöthen MM, Bagci S.NP J Genom Med. 2021 Jul 1;6(1):55. doi: 10.1038/s41525-021-00220-w.

Extending the allelic spectrum at noncoding risk loci of orofacial clefting. Thieme F, Henschel L, Hammond NL, Ishorst N, Hausen J, Adamson AD, Biedermann A, Bowes J, Zieger HK, Maj C, Kruse T, Buness A, Hoischen A, Gilissen C, Kreusch T, Jäger A, Gölz L, Braumann B, Aldhorae K, Rojas-Martinez A, Krawitz PM, Mangold E, Dixon MJ, Ludwig KU. Hum Mutat. 2021 May 18. doi: 10.1002/humu.24219.

Differential proteome between ejaculate and epididymal sperm represents a key factor for sperm freezability in wild small ruminants. Martínez-Fresneda L, Sylvester M, Shakeri F, Bunes A, Del Pozo JC, García-Vázquez FA, Neuhoff C, Tesfaye D, Schellander K, Santiago-Moreno J. Cryobiology. 2021 Apr;99:64-77. doi: 10.1016/j.cryobiol.2021.01.012.

Prognostic Gene Expression, Stemness and Immune Microenvironment in Pediatric Tumors. Stahl D, Knoll R, Gentles AJ, Vokuhl C, Buness A, Gütgemann I. Cancers (Basel). 2021 Feb 18;13(4):854. doi: 10.3390/cancers13040854.

Macrophage frequency in the bone marrow correlates with morphologic subtype of myeloproliferative neoplasm. Molitor DCA, Boor P, Buness A, Schneider RK, Teichmann LL, Körber RM, Horvath GL, Koschmieder S, Gütgemann I. Ann Hematol. 2021 Jan;100(1):97-104. doi: 10.1007/s00277-020-04304-y.

High-Dimensional Analysis of Immune Cell Composition Predicts Periprosthetic Joint Infections and Dissects Its Pathophysiology. Korn MF, Stein RR, Dolf A, Shakeri F, Buness A, Hilgers C, Masson W, Gravius S, Kohlhof H, Burger C, Wirtz DC, Randau TM, Schildberg FA. Biomedicines. 2020 Sep 17;8(9):358. doi: 10.3390/biomedicines8090358.

Protamine-2 Deficiency Initiates a Reactive Oxygen Species (ROS)-Mediated Destruction Cascade during Epididymal Sperm Maturation in Mice. Schneider S, Shakeri F, Trötschel C, Arévalo L, Kruse A, Buness A, Poetsch A, Steger K, Schorle H. Cells. 2020 Jul 27;9(8):1789. doi: 10.3390/cells9081789.

Mutations in SREBF1, Encoding Sterol Regulatory Element Binding Transcription Factor 1, Cause Autosomal-Dominant IFAP Syndrome. Wang H, Humbatova A, Liu Y, Qin W, Lee M, Cesarato N, Kortüm F, Kumar S, Romano MT, Dai S, Mo R, Sivalingam S, Motameny S, Wu Y, Wang X, Niu X, Geng S, Bornholdt D, Kroisel PM, Tadini G, Walter SD, Hauck F, Girisha KM, Calza AM, Bottani A, Altmüller J, Buness A, Yang S, Sun X, Ma L, Kutsche K, Grzeschik KH, Betz RC, Lin Z. Am J Hum Genet. 2020 Jul 2;107(1):34-45. doi: 10.1016/j.ajhg.2020.05.006. Epub 2020 Jun 3.

A high-salt diet compromises antibacterial neutrophil responses through hormonal perturbation. Jobin K, Stumpf NE, Schwab S, Eichler M, Neubert P, Rauh M, Adamowski M, Babyak O, Hinze D, Sivalingam S, Weisheit C, Hochheiser K, Schmidt SV, Meissner M, Garbi N, Abdullah Z, Wenzel U, Hölzel M, Jantsch J, Kurts C. Sci Transl Med. 2020 Mar 25;12(536):eaay3850. doi: 10.1126/scitranslmed.aay3850.

Altered Notch Signaling in Dowling-Degos Disease: Additional Mutations in POGLUT1 and Further Insights into Disease Pathogenesis. Ralser DJ, Takeuchi H, Fritz G, Basmanav FB, Effern M, Sivalingam S, El-Shabrawi-Caelen L, Degirmentepe EN, Kocatürk E, Singh M, Booken N, Spierings NMK, Schnabel V, Heineke A, Knuever J, Wolf S, Wehner M, Tronnier M, Leverkus M, Tantcheva-Poór I, Wenzel J, Oji V, Has C, Hölzel M, Frank J, Haltiwanger RS, Betz RC. J Invest Dermatol. 2019 Apr;139(4):960-964. doi: 10.1016/j.jid.2018.10.030. Epub 2018 Nov 9.