Next Generation Sequencing Competence Network

Next Generation Sequencing Competence Network

e.g. CCGA
(min 2 characters)

Ivan G Costa

Prof.
RWTH Aachen University
Institute for Computational Genomics
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Hubens WHG, Mai? T, Schnitker M, Bocova L, Puri D, Wessiepe M, Kramer J, Rink L, Koschmieder S, Costa IG, Wagner W. Targeted DNA Methylation Analysis Facilitates Leukocyte Counts in Dried Blood Samples. Clin Chem. 2023 Sep 14. PMID: 37708296.
      Citations:    Fields:    Translation:HumansCells
    2. Costa IG. Dissecting gene regulation with multimodal sequencing. Nat Methods. 2023 09; 20(9):1282-1284. PMID: 37537350.
      Citations: 1     Fields:    
    3. B?low RD, H?lscher DL, Costa IG, Boor P. Extending the landscape of omics technologies by pathomics. NPJ Syst Biol Appl. 2023 08 07; 9(1):38. PMID: 37550386; PMCID: PMC10406938.
      Citations: 8     Fields:    
    4. Jacobi H, Vieri M, B?tow M, Namasu CY, Fl?ter L, Costa IG, Mai? T, Lindemann-Docter K, Chatain N, Beier F, Huber M, Wagner W, Crysandt M, Br?mmendorf TH, Schemionek M. Myelofibrosis at diagnosis is associated with the failure of treatment-free remission in CML patients. Front Pharmacol. 2023; 14:1212392. PMID: 37469867; PMCID: PMC10352620.
      Citations:    
    5. Vucur M, Ghallab A, Schneider AT, Adili A, Cheng M, Castoldi M, Singer MT, B?ttner V, Keysberg LS, K?sgens L, Kohlhepp M, G?rg B, Gallage S, Barragan Avila JE, Unger K, Kordes C, Leblond AL, Albrecht W, Loosen SH, Lohr C, J?rdens MS, Babler A, Hayat S, Schumacher D, Koenen MT, Govaere O, Boekschoten MV, J?rs S, Villacorta-Martin C, Mazzaferro V, Llovet JM, Weiskirchen R, Kather JN, Starlinger P, Trauner M, Luedde M, Heij LR, Neumann UP, Keitel V, Bode JG, Schneider RK, Tacke F, Levkau B, Lammers T, Fluegen G, Alexandrov T, Collins AL, Nelson G, Oakley F, Mann DA, Roderburg C, Longerich T, Weber A, Villanueva A, Samson AL, Murphy JM, Kramann R, Geisler F, Costa IG, Hengstler JG, Heikenwalder M, Luedde T. Sublethal necroptosis signaling promotes inflammation and liver cancer. Immunity. 2023 07 11; 56(7):1578-1595.e8. PMID: 37329888.
      Citations: 12     Fields:    Translation:Humans
    6. Langhammer M, Sch?pf J, Jaquet T, Horn K, Angel M, Spohr C, Christen D, Uhl FM, Mai? T, Jacobi H, Feyerabend TB, Huber J, Panning M, Sitaru C, Costa I, Zeiser R, Aumann K, Becker H, Braunschweig T, Koschmieder S, Shoumariyeh K, Huber M, Schemionek-Reinders M, Brummer T, Halbach S. Mast cell deficiency prevents BCR::ABL1 induced splenomegaly and cytokine elevation in a CML mouse model. Leukemia. 2023 07; 37(7):1474-1484. PMID: 37161070; PMCID: PMC10317838.
      Citations:    Fields:    Translation:HumansAnimalsCells
    7. Torow N, Li R, Hitch TCA, Mingels C, Al Bounny S, van Best N, Stange EL, Simons B, Mai? T, R?ttger L, Gubbi NMKP, Abbott DA, Benabid A, Gadermayr M, Runge S, Treichel N, Merhof D, Rosshart SP, Jehmlich N, Hand TW, von Bergen M, Heymann F, Pabst O, Clavel T, Tacke F, Lelouard H, Costa IG, Hornef MW. M cell maturation and cDC activation determine the onset of adaptive immune priming in the neonatal Peyer's patch. Immunity. 2023 06 13; 56(6):1220-1238.e7. PMID: 37130522; PMCID: PMC10262694.
      Citations:    Fields:    Translation:Cells
    8. B?tow M, Testaquadra FJ, Baumeister J, Mai? T, Chatain N, Jaquet T, Tillmann S, Crysandt M, Costa IG, Br?mmendorf TH, Schemionek M. Targeting cytokine-induced leukemic stem cell persistence in chronic myeloid leukemia by IKK2-inhibition. Haematologica. 2023 04 01; 108(4):1179-1185. PMID: 36453102; PMCID: PMC10071114.
      Citations: 1     Fields:    Translation:HumansCells
    9. Xu H, Li Z, Kuo CC, G?tz K, Look T, de Toledo MAS, Ser? K, Costa IG, Zenke M. A lncRNA identifies Irf8 enhancer element in negative feedback control of dendritic cell differentiation. Elife. 2023 03 14; 12. PMID: 36916882; PMCID: PMC10042546.
      Citations: 1     Fields:    Translation:AnimalsCells
    10. de Toledo MAS, Fu X, Mai? T, Buhl EM, G?tz K, Schmitz S, Kaiser A, Boor P, Braunschweig T, Chatain N, Costa IG, Br?mmendorf TH, Koschmieder S, Zenke M. KIT D816V Mast Cells Derived from Induced Pluripotent Stem Cells Recapitulate Systemic Mastocytosis Transcriptional Profile. Int J Mol Sci. 2023 Mar 09; 24(6). PMID: 36982353; PMCID: PMC10049485.
      Citations: 5     Fields:    Translation:HumansCells
    11. Li Z, Kuo CC, Ticconi F, Shaigan M, Gehrmann J, Gusmao EG, Allhoff M, Manolov M, Zenke M, Costa IG. RGT: a toolbox for the integrative analysis of high throughput regulatory genomics data. BMC Bioinformatics. 2023 Mar 06; 24(1):79. PMID: 36879236; PMCID: PMC9990262.
      Citations:    Fields:    Translation:Cells
    12. Hoeft K, Schaefer GJL, Kim H, Schumacher D, Bleckwehl T, Long Q, Klinkhammer BM, Peisker F, Koch L, Nagai J, Halder M, Ziegler S, Liehn E, Kuppe C, Kranz J, Menzel S, Costa I, Wahida A, Boor P, Schneider RK, Hayat S, Kramann R. Platelet-instructed SPP1+ macrophages drive myofibroblast activation in fibrosis in a CXCL4-dependent manner. Cell Rep. 2023 02 28; 42(2):112131. PMID: 36807143; PMCID: PMC9992450.
      Citations: 14     Fields:    Translation:HumansCells
    13. H?lscher DL, Bouteldja N, Joodaki M, Russo ML, Lan YC, Sadr AV, Cheng M, Tesar V, Stillfried SV, Klinkhammer BM, Barratt J, Floege J, Roberts ISD, Coppo R, Costa IG, B?low RD, Boor P. Next-Generation Morphometry for pathomics-data mining in histopathology. Nat Commun. 2023 01 28; 14(1):470. PMID: 36709324; PMCID: PMC9884209.
      Citations: 19     Fields:    
    14. Li Z, Nagai JS, Kuppe C, Kramann R, Costa IG. scMEGA: single-cell multi-omic enhancer-based gene regulatory network inference. Bioinform Adv. 2023; 3(1):vbad003. PMID: 36698768; PMCID: PMC9853317.
      Citations: 5     
    15. Schreibing F, Hannani MT, Kim H, Nagai JS, Ticconi F, Fewings E, Bleckwehl T, Begemann M, Torow N, Kuppe C, Kurth I, Kranz J, Frank D, Anslinger TM, Ziegler P, Kraus T, Enczmann J, Balz V, Windhofer F, Balfanz P, Kurts C, Marx G, Marx N, Dreher M, Schneider RK, Saez-Rodriguez J, Costa I, Hayat S, Kramann R. Dissecting CD8+ T cell pathology of severe SARS-CoV-2 infection by single-cell immunoprofiling. Front Immunol. 2022; 13:1066176. PMID: 36591270; PMCID: PMC9800604.
      Citations: 7     Fields:    Translation:HumansCells
    16. Barsoum M, Stenzel AT, Bochynska A, Kuo CC, Tsompanidis A, Sayadi-Boroujeni R, Bussmann P, L?scher-Firzlaff J, Costa IG, L?scher B. Loss of the Ash2l subunit of histone H3K4 methyltransferase complexes reduces chromatin accessibility at promoters. Sci Rep. 2022 12 13; 12(1):21506. PMID: 36513698; PMCID: PMC9747801.
      Citations: 2     Fields:    Translation:AnimalsCells
    17. Leisegang MS, Bains JK, Seredinski S, Oo JA, Krause NM, Kuo CC, G?nther S, Sent?rk Cetin N, Warwick T, Cao C, Boos F, Izquierdo Ponce J, Haydar S, Bednarz R, Valasarajan C, Fuhrmann DC, Preussner J, Looso M, Pullamsetti SS, Schulz MH, Jonker HRA, Richter C, Rezende F, Gilsbach R, Pfl?ger-M?ller B, Wittig I, Grummt I, Ribarska T, Costa IG, Schwalbe H, Brandes RP. HIF1a-AS1 is a DNA:DNA:RNA triplex-forming lncRNA interacting with the HUSH complex. Nat Commun. 2022 Nov 02; 13(1):6563. PMID: 36323673; PMCID: PMC9630315.
      Citations: 7     Fields:    Translation:HumansCells
    18. Xu Y, Kuppe C, Perales-Pat?n J, Hayat S, Kranz J, Abdallah AT, Nagai J, Li Z, Peisker F, Saritas T, Halder M, Menzel S, Hoeft K, Kenter A, Kim H, van Roeyen CRC, Lehrke M, Moellmann J, Speer T, Buhl EM, Hoogenboezem R, Boor P, Jansen J, Knopp C, Kurth I, Smeets B, Bindels E, Reinders MEJ, Baan C, Gribnau J, Hoorn EJ, Steffens J, Huber TB, Costa I, Floege J, Schneider RK, Saez-Rodriguez J, Freedman BS, Kramann R. Adult human kidney organoids originate from CD24+ cells and represent an advanced model for adult polycystic kidney disease. Nat Genet. 2022 11; 54(11):1690-1701. PMID: 36303074; PMCID: PMC7613830.
      Citations: 8     Fields:    Translation:Humans
    19. Bochynska A, Stenzel AT, Sayadi Boroujeni R, Kuo CC, Barsoum M, Liang W, Bussmann P, Costa IG, L?scher-Firzlaff J, L?scher B. Induction of senescence upon loss of the Ash2l core subunit of H3K4 methyltransferase complexes. Nucleic Acids Res. 2022 08 12; 50(14):7889-7905. PMID: 35819198; PMCID: PMC9371893.
      Citations: 4     Fields:    Translation:Animals
    20. Kuppe C, Ramirez Flores RO, Li Z, Hayat S, Levinson RT, Liao X, Hannani MT, Tanevski J, W?nnemann F, Nagai JS, Halder M, Schumacher D, Menzel S, Sch?fer G, Hoeft K, Cheng M, Ziegler S, Zhang X, Peisker F, Kaesler N, Saritas T, Xu Y, Kassner A, Gummert J, Morshuis M, Amrute J, Veltrop RJA, Boor P, Klingel K, Van Laake LW, Vink A, Hoogenboezem RM, Bindels EMJ, Schurgers L, Sattler S, Schapiro D, Schneider RK, Lavine K, Milting H, Costa IG, Saez-Rodriguez J, Kramann R. Spatial multi-omic map of human myocardial infarction. Nature. 2022 08; 608(7924):766-777. PMID: 35948637; PMCID: PMC9364862.
      Citations: 77     Fields:    Translation:HumansCells
    21. Li R, Banjanin B, Schneider RK, Costa IG. Detection of cell markers from single cell RNA-seq with sc2marker. BMC Bioinformatics. 2022 Jul 12; 23(1):276. PMID: 35831796; PMCID: PMC9281170.
      Citations: 3     Fields:    
    22. Cheng M, Li Z, Costa IG. MOJITOO: a fast and universal method for integration of multimodal single-cell data. Bioinformatics. 2022 06 24; 38(Suppl 1):i282-i289. PMID: 35758807; PMCID: PMC9235504.
      Citations:    Fields:    Translation:Cells
    23. Dimitrov D, Garrido-Rodriguez M, Burmedi PL, Nagai JS, Boys C, Ramirez Flores RO, Kim H, Szalai B, Costa IG, Valdeolivas A, Saez-Rodriguez J, T?rei D, Dugourd A. Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data. Nat Commun. 2022 06 09; 13(1):3224. PMID: 35680885; PMCID: PMC9184522.
      Citations: 72     Fields:    Translation:Cells
    24. Peisker F, Halder M, Nagai J, Ziegler S, Kaesler N, Hoeft K, Li R, Bindels EMJ, Kuppe C, Moellmann J, Lehrke M, Stoppe C, Schaub MT, Schneider RK, Costa I, Kramann R. Mapping the cardiac vascular niche in heart failure. Nat Commun. 2022 05 31; 13(1):3027. PMID: 35641541; PMCID: PMC9156759.
      Citations: 17     Fields:    Translation:HumansCells
    25. Pellegrino R, Ticconi F, Skawran B, Budczies J, Rose F, Schwab C, Breuhahn K, Neumann UP, Gaisa NT, Costa IG, Longerich T, Castoldi M, Loosen SH, Luedde T. LINC00152 Drives a Competing Endogenous RNA Network in Human Hepatocellular Carcinoma. Cells. 2022 05 03; 11(9). PMID: 35563834; PMCID: PMC9103153.
      Citations: 4     Fields:    Translation:Humans
    26. Daviran D, Roverts R, Kuppe C, Reimer KC, Nagai JS, Drenic V, Costa IG, Endlich N, Schneider RK, Akiva A, Kramann R, Jansen J, van den Berge BT, van den Broek M, Maas RJ, Willemsen B, van der Kruit M, Di Giovanni G, Mooren F, Nlandu Q, Mudde H, Wetzels R, den Braanker D, Parr N, Steenbergen E, Nijenhuis T, Dijkman H, van de Kar NCAJ, Wetzels JFM, van der Vlag J, Schreuder MF, Smeets B. Human pluripotent stem cell-derived kidney organoids for personalized congenital and idiopathic nephrotic syndrome modeling. Development. 2022 05 01; 149(9). PMID: 35417019; PMCID: PMC9148570.
      Citations: 11     Fields:    Translation:HumansCells
    27. Stalmann USA, Banjanin B, Snoeren IAM, Bindels EM, Nagai JS, Leimk?hler NB, Li R, Benabid A, Pritchard JE, Malyaran H, Neuss S, Costa IG, Schneider RK. Single-cell analysis of cultured bone marrow stromal cells reveals high similarity to fibroblasts in situ. Exp Hematol. 2022 06; 110:28-33. PMID: 35341805.
      Citations: 3     Fields:    Translation:AnimalsCells
    28. Stalmann USA, Snoeren IAM, Cowley GS, McConkey ME, Wong AB, Schmitz S, Fuchs SNR, Sood S, Banjanin B, Root D, Pearce JE, Schuppert A, Bindels EMJ, Essers MA, Heckl D, Stiehl T, Ebert BL, Schneider RK, Ticconi F, Li R, Gleitz HFE, Leimk?hler NB, Martinez-H?yer S, Br?mmendorf TH, Costa IG. Genetic barcoding systematically compares genes in del(5q) MDS and reveals a central role for CSNK1A1 in clonal expansion. Blood Adv. 2022 03 22; 6(6):1780-1796. PMID: 35016204; PMCID: PMC8941465.
      Citations: 4     Fields:    Translation:HumansCells
    29. Elsafi Mabrouk MH, Goetzke R, Abagnale G, Salz L, Cypris O, Liesenfelder S, Zeevaert K, Ma Z, Toledo MAS, Pachauri V, Schnakenberg U, Zenke M, Wagner W, Yesilyurt B, Gl?ck P, Li R, Costa IG, Lampert A. The spatial self-organization within pluripotent stem cell colonies is continued in detaching aggregates. Biomaterials. 2022 03; 282:121389. PMID: 35121357.
      Citations: 6     Fields:    Translation:Cells
    30. Jansen J, Reimer KC, Nagai JS, Varghese FS, Overheul GJ, de Beer M, Roverts R, Daviran D, Fermin LAS, Willemsen B, Beukenboom M, Djudjaj S, von Stillfried S, van Eijk LE, Mastik M, Bulthuis M, Dunnen WD, van Goor H, Hillebrands JL, Triana SH, Alexandrov T, Timm MC, van den Berge BT, van den Broek M, Nlandu Q, Heijnert J, Bindels EMJ, Hoogenboezem RM, Mooren F, Kuppe C, Miesen P, Ijzermans T, Steenbergen EJ, Czogalla J, Schreuder MF, Sommerdijk N, Akiva A, Boor P, Puelles VG, Huber TB, COVID Moonshot consortium, van Rij RP, Costa IG, Schneider RK, Smeets B, Kramann R, Gr?nberg K, Floege J. SARS-CoV-2 infects the human kidney and drives fibrosis in kidney organoids. Cell Stem Cell. 2022 02 03; 29(2):217-231.e8. PMID: 35032430; PMCID: PMC8709832.
      Citations: 91     Fields:    Translation:HumansCells
    31. Nagai JS, Schaub MT, Schneider RK, Costa IG, Leimk?hler NB. CrossTalkeR: analysis and visualization of ligand-receptorne tworks. Bioinformatics. 2021 11 18; 37(22):4263-4265. PMID: 35032393; PMCID: PMC9502146.
      Citations: 19     Fields:    Translation:Humans
    32. Heller S, Li Z, Lin Q, Geusz R, Breunig M, Hohwieler M, Zhang X, Nair GG, Seufferlein T, Hebrok M, Sander M, Kleger A, Costa IG, Julier C. Transcriptional changes and the role of ONECUT1 in hPSC pancreatic differentiation. Commun Biol. 2021 11 17; 4(1):1298. PMID: 34789845; PMCID: PMC8599846.
      Citations: 11     Translation:HumansCells
    33. Sonntag R, Penners C, Haas U, Lambertz D, Kroh A, Cramer T, Ticconi F, Costa IG, Gassler N, Trautwein C, Liedtke C, Kohlhepp M, Tacke F. Cyclin E1 in Murine and Human Liver Cancer: A Promising Target for Therapeutic Intervention during Tumour Progression. Cancers (Basel). 2021 Nov 13; 13(22). PMID: 34830835; PMCID: PMC8616292.
      Citations: 4     
    34. Li Z, Kuppe C, Ziegler S, Cheng M, Kabgani N, Menzel S, Zenke M, Kramann R, Costa IG. Chromatin-accessibility estimation from single-cell ATAC-seq data with scOpen. Nat Commun. 2021 11 04; 12(1):6386. PMID: 34737275; PMCID: PMC8568974.
      Citations: 33     Fields:    Translation:Cells
    35. Costa IG, Theocharides A, Buhl EM, Boor P, Zenke M, Olschok K, Han L, de Toledo MAS, B?hnke J, Gra?hoff M, Maurer A, Sch?ler HM, Pannen K, Baumeister J, Kalmer M, Gupta S, Gezer D, Br?mmendorf TH, Chatain N, Koschmieder S. CALR frameshift mutations in MPN patient-derived iPSCs accelerate maturation of megakaryocytes. Stem Cell Reports. 2021 11 09; 16(11):2768-2783. PMID: 34678208; PMCID: PMC8581168.
      Citations: 6     Fields:    Translation:HumansCells
    36. Heller S, Costa IG, Breunig M, Li Z, Kwon G, Russell R, Illing A, Lin Q, Hohwieler M, Zalloua P, Liebau S, Schuster M, Krumm J, Zhang X, Geusz R, Benthuysen JR, Wang A, Chiou J, Gaulton K, Neubauer H, Simon E, Klein T, Wagner M, Nair G, Kuster B, Hebrok M, Seufferlein T, Sander M, Boehm BO, Oswald F, Kleger A, Philippi A, Sen?e V, Degavre A, Besse C, Dandine-Roulland C, Olaso R, Deleuze JF, Nicolino M, Julier C. Mutations and variants of ONECUT1 in diabetes. Nat Med. 2021 11; 27(11):1928-1940. PMID: 34663987; PMCID: PMC9356324.
      Citations: 12     Fields:    Translation:HumansCells
    37. Costa IG, Schneider RK, Leimk?hler NB. From cell to cell: Identification of actionable targets in bone marrow fibrosis using single-cell technologies. Exp Hematol. 2021 12; 104:48-54. PMID: 34601067.
      Citations: 1     Fields:    Translation:HumansAnimalsCells
    38. Muschaweck M, Kopplin L, Ticconi F, Schippers A, Iljazovic A, Abdallah AT, Wagner N, Costa IG, Strowig T, Pabst O, G?lvez EJC. Cognate recognition of microbial antigens defines constricted CD4+ T?cell receptor repertoires in the inflamed colon. Immunity. 2021 11 09; 54(11):2565-2577.e6. PMID: 34582747.
      Citations: 4     Fields:    Translation:HumansCells
    39. Baumeister J, Chatain N, Gan L, Weinbergerova B, de Toledo MAS, Maurer A, Mayer J, Kubesova B, Racil Z, Schuppert A, Costa I, Koschmieder S, Gezer D, Mai? T, Eschweiler J, Br?mmendorf TH. Early and late stage MPN patients show distinct gene expression profiles in CD34+ cells. Ann Hematol. 2021 Dec; 100(12):2943-2956. PMID: 34390367; PMCID: PMC8592960.
      Citations: 6     Fields:    Translation:HumansCells
    40. Kenswil KJG, Pisterzi P, van Dijk C, Lolli A, Knuth C, Vanchin B, Jaramillo AC, Hoogenboezem RM, Sanders MA, Feyen J, Cupedo T, Costa IG, Li R, Lodder K, Blom B, Bos PK, Ten Dijke P, Farrell E, Krenning G, Raaijmakers MHGP, S?nchez-Duffhues G, Bindels EMJ, Goumans MJ. Endothelium-derived stromal cells contribute to hematopoietic bone marrow niche formation. Cell Stem Cell. 2021 04 01; 28(4):653-670.e11. PMID: 33561425.
      Citations: 20     Fields:    Translation:AnimalsCells
    41. Conzelmann C, Merle U, Steinhart J, Weil T, Koepke L, Bozzo CP, Read C, Fois G, Eiseler T, Gehrmann J, Wessbecher IM, Frick M, Costa IG, Breunig M, Peters L, Schuster M, Seufferlein T, Stenger S, Stenzinger A, MacDonald PE, Kirchhoff F, Sparrer KMJ, Walther P, Barth TFE, Wagner M, Heller S, Kleger A, M?ller JA, Gro? R, Kr?ger J, van Vuuren J, Gr?ner B, Liebau S, Lickert H, M?nch J. SARS-CoV-2 infects and replicates in cells of the human endocrine and exocrine pancreas. Nat Metab. 2021 02; 3(2):149-165. PMID: 33536639.
      Citations: 245     Fields:    Translation:HumansCells
    42. Pensold D, Gehrmann J, Pitschelatow G, Walberg A, Braunsteffer K, Reichard J, Ravaei A, Linde J, Lampert A, Costa IG, Zimmer-Bensch G. The Expression of the Cancer-Associated lncRNA Snhg15 Is Modulated by EphrinA5-Induced Signaling. Int J Mol Sci. 2021 Jan 29; 22(3). PMID: 33572758; PMCID: PMC7866228.
      Citations: 3     Fields:    Translation:HumansAnimalsCells
    43. Ronghui L, Snoeren IAM, Fuchs SNR, Nagai JS, Banjanin B, Lam KH, Kuppe C, Stalmann USA, Kreipe H, Krebs P, Banz Y, Boor P, Tai EW, Koschmieder S, Crysandt M, Bindels E, Kramann R, Costa IG, Schneider RK, Leimk?hler NB, Gleitz HFE, Vogl T, B?sche G, G?tgemann I, Br?mmendorf TH. Heterogeneous bone-marrow stromal progenitors drive myelofibrosis via a druggable alarmin axis. Cell Stem Cell. 2021 04 01; 28(4):637-652.e8. PMID: 33301706; PMCID: PMC8024900.
      Citations: 60     Fields:    Translation:HumansAnimalsCells
    44. Schmidt M, Dahl E, Costa IG, Wagner W, Mai? T. Deconvolution of cellular subsets in human tissue based on targeted DNA methylation analysis at individual CpG sites. BMC Biol. 2020 11 24; 18(1):178. PMID: 33234153; PMCID: PMC7687708.
      Citations: 17     Fields:    Translation:HumansCells
    45. Parting O, Langer S, Kuepper MK, Wessling C, Li S, Braunschweig T, Chatain N, Costa IG, Crysandt M, Huber M, Koschmieder S, Schemionek M, Mai? T, Br?mmendorf TH. Therapeutic inhibition of Fc?RIIb signaling targets leukemic stem cells in chronic myeloid leukemia. Leukemia. 2020 10; 34(10):2635-2647. PMID: 32684632; PMCID: PMC7515845.
      Citations: 4     Fields:    Translation:HumansAnimalsCells
    46. Pensold D, Reichard J, Van Loo KMJ, Ciganok N, Hahn A, Bayer C, Liebmann L, Tittelmeier J, Lingner T, Salinas-Riester G, Symmank J, Halfmann C, Urbach A, Gehrmann J, Costa I, Pieler T, Vatter H, Becker AJ, Zimmer-Bensch G, Gro? J, Gonz?lez-Berm?dez L, H?bner CA, Kampa B. DNA Methylation-Mediated Modulation of Endocytosis as Potential Mechanism for Synaptic Function Regulation in Murine Inhibitory Cortical Interneurons. Cereb Cortex. 2020 06 01; 30(7):3921-3937. PMID: 32147726; PMCID: PMC7264686.
      Citations: 20     Fields:    Translation:HumansAnimalsCells
    47. Trembinski DJ, Bink DI, Theodorou K, Sommer J, Fischer A, van Bergen A, Kuo CC, Costa IG, Leisegang MS, Brandes RP, Alekseeva T, Brill B, Wietelmann A, Johnson CN, Spring-Connell A, Kaulich M, Werfel S, Engelhardt S, Hirt MN, Yorgan K, Eschenhagen T, Kirchhof L, Hofmann P, Wittig I, Hamdani N, Bischof C, Krishnan J, Houtkooper RH, Dimmeler S, Boon RA, Sch?rmann C, Ja? N. Aging-regulated anti-apoptotic long non-coding RNA Sarrah augments recovery from acute myocardial infarction. Nat Commun. 2020 04 27; 11(1):2039. PMID: 32341350; PMCID: PMC7184724.
      Citations: 34     Fields:    Translation:HumansAnimalsCells
    48. Costa IG, DEEP consortium, Nordstr?m KJV, Schmidt F, Gasparoni N, Salhab A, Gasparoni G, Kattler K, M?ller F, Ebert P, Pfeifer N, Lengauer T, Schulz MH, Walter J. Unique and assay specific features of NOMe-, ATAC- and DNase I-seq data. Nucleic Acids Res. 2019 11 18; 47(20):10580-10596. PMID: 31584093; PMCID: PMC6847574.
      Citations: 17     Fields:    Translation:HumansCells
    49. Baumeister J, Chatain N, Hubrich A, Costa IG, Denecke B, Han L, Sontag S, Strathmann K, Zenke M, Schuppert A, Kranc KR, Koschmieder S, Gezer D, Mai? T, K?stermann C, Ser? K, Br?mmendorf TH. Hypoxia-inducible factor 1 (HIF-1) is a new therapeutic target in JAK2V617F-positive myeloproliferative neoplasms. Leukemia. 2020 04; 34(4):1062-1074. PMID: 31728053.
      Citations: 29     Fields:    Translation:HumansCells
    50. Herrmann O, Kuepper MK, Costa IG, Appelmann I, Beier F, Luedde T, Braunschweig T, Koschmieder S, Schemionek M, B?tow M, Br?mmendorf TH. Infliximab therapy together with tyrosine kinase inhibition targets leukemic stem cells in chronic myeloid leukemia. BMC Cancer. 2019 Jul 04; 19(1):658. PMID: 31272418; PMCID: PMC6610865.
      Citations: 6     Fields:    Translation:HumansAnimalsCells
    51. Chatain N, Kuo CC, Braunschweig T, Bochynska A, Ullius A, Denecke B, Costa IG, Koschmieder S, L?scher-Firzlaff J, L?scher B. Hematopoietic stem and progenitor cell proliferation and differentiation requires the trithorax protein Ash2l. Sci Rep. 2019 06 04; 9(1):8262. PMID: 31164666; PMCID: PMC6547667.
      Citations: 15     Fields:    Translation:HumansAnimalsCells
    52. Krenkel O, Hundertmark J, Abdallah AT, Kohlhepp M, Puengel T, Roth T, Branco DPP, Mossanen JC, Luedde T, Trautwein C, Costa IG, Tacke F. Myeloid cells in liver and bone marrow acquire a functionally distinct inflammatory phenotype during obesity-related steatohepatitis. Gut. 2020 03; 69(3):551-563. PMID: 31076404.
      Citations: 87     Fields:    Translation:AnimalsCells
    53. Dreschers S, Ohl K, Lehrke M, Denecke B, Costa I, Orlikowsky T, Tenbrock K, M?llmann J, Vogl T, Viemann D, Roth J. Impaired cellular energy metabolism in cord blood macrophages contributes to abortive response toward inflammatory threats. Nat Commun. 2019 04 11; 10(1):1685. PMID: 30976008; PMCID: PMC6459909.
      Citations: 26     Fields:    Translation:HumansCells
    54. Kuo CC, Frank S, Zajzon B, Derks JP, Akhade VS, Ahuja G, Kanduri C, Grummt I, Kurian L, Costa IG, H?nzelmann S, Sent?rk Cetin N. Detection of RNA-DNA binding sites in long noncoding RNAs. Nucleic Acids Res. 2019 04 08; 47(6):e32. PMID: 30698727; PMCID: PMC6451187.
      Citations: 78     Fields:    Translation:HumansCells
    55. Schubert C, Allhoff M, Tillmann S, Costa IG, Lipka DB, Schemionek M, Feldberg K, Baumeister J, Chatain N, Koschmieder S, Mai? T, Br?mmendorf TH. Differential roles of STAT1 and STAT2 in the sensitivity of JAK2V617F- vs. BCR-ABL-positive cells to interferon alpha. J Hematol Oncol. 2019 04 02; 12(1):36. PMID: 30940163; PMCID: PMC6444528.
      Citations: 10     Fields:    Translation:HumansCells
    56. Kuo CC, Ribarska T, Li R, Costa IG, Grummt I, Sent?rk Cetin N. Isolation and genome-wide characterization of cellular DNA:RNA triplex structures. Nucleic Acids Res. 2019 03 18; 47(5):2306-2321. PMID: 30605520; PMCID: PMC6411930.
      Citations: 42     Fields:    Translation:HumansCells
    57. Kuepper MK, Herrmann O, Ziemons J, Chatain N, Maurer A, Kirschner M, Costa IG, Koschmieder S, Schemionek M, B?tow M, Mai? T, Eschweiler J, Br?mmendorf TH, M?ller-Newen G. Stem cell persistence in CML is mediated by extrinsically activated JAK1-STAT3 signaling. Leukemia. 2019 08; 33(8):1964-1977. PMID: 30842608.
      Citations: 24     Fields:    Translation:HumansAnimalsCells
    58. Li Z, Look T, Begemann M, Zenke M, Costa IG, Schulz MH. Identification of transcription factor binding sites using ATAC-seq. Genome Biol. 2019 02 26; 20(1):45. PMID: 30808370; PMCID: PMC6391789.
      Citations: 196     Fields:    Translation:HumansAnimalsCells
    59. Frank S, Ahuja G, Bartsch D, Russ N, Yao W, Kuo JC, Derks JP, Akhade VS, Messling JE, Gramm M, Rehimi R, Vargas NE, Kuroczik A, Yang TP, Sahito RGA, Franzen J, Hescheler J, Sachinidis A, Peifer M, Rada-Iglesias A, Kanduri M, Costa IG, Kanduri C, Kurian L, Kargapolova Y, Georgomanolis T, Brant L, Papantonis A. yylncT Defines a Class of Divergently Transcribed lncRNAs and Safeguards the T-mediated Mesodermal Commitment of Human PSCs. Cell Stem Cell. 2019 02 07; 24(2):318-327.e8. PMID: 30554961.
      Citations: 27     Fields:    Translation:HumansAnimalsCells
    60. Frobel J, Raic A, Ticconi F, Kuo CC, Heilmann-Heimbach S, Goecke TW, Zenke M, Jost E, Costa IG, Wagner W, Bo?ic T. Variants of DNMT3A cause transcript-specific DNA methylation patterns and affect hematopoiesis. Life Sci Alliance. 2018 Dec; 1(6):e201800153. PMID: 30582132; PMCID: PMC6293073.
      Citations: 11     Fields:    
    61. Liepelt A, Wehr A, Kohlhepp M, Mossanen JC, Kreggenwinkel K, Denecke B, Luedde T, Trautwein C, Tacke F, Costa IG. CXCR6 protects from inflammation and fibrosis in NEMOLPC-KO mice. Biochim Biophys Acta Mol Basis Dis. 2019 02 01; 1865(2):391-402. PMID: 30476545.
      Citations: 7     Fields:    Translation:AnimalsCells
    62. Czech J, Cordua S, Weinbergerova B, Baumeister J, Crepcia A, Han L, Costa IG, Denecke B, Maurer A, Schubert C, Feldberg K, Gezer D, Mayer J, Racil Z, Kubesova B, Knudsen T, Skov V, Larsen TS, Hasselbalch HC, Chatain N, Koschmieder S, Mai? T, Br?mmendorf TH, M?ller-Newen G, S?rensen AL, Holmstr?m M, Kj?r L. JAK2V617F but not CALR mutations confer increased molecular responses to interferon-a via JAK1/STAT1 activation. Leukemia. 2019 04; 33(4):995-1010. PMID: 30470838.
      Citations: 31     Fields:    Translation:HumansAnimalsCells
    63. Fahrenkamp D, Gassler N, Abdallah AT, Weiskirchen R, Ticconi F, Costa IG, Sonntag R, Giebeler N, Nevzorova YA, Bangen JM, Lambertz D, Haas U, Hu W, Cubero FJ, M?ller-Newen G, Barbacid M, Trautwein C, Liedtke C. Cyclin E1 and cyclin-dependent kinase 2 are critical for initiation, but not for progression of hepatocellular carcinoma. Proc Natl Acad Sci U S A. 2018 09 11; 115(37):9282-9287. PMID: 30150405; PMCID: PMC6140539.
      Citations: 41     Fields:    Translation:AnimalsCells
    64. Ohl K, Fragoulis A, Klemm P, Baumeister J, Klock W, Verjans E, Lehrke M, Costa I, Denecke B, Schippers A, Wagner N, Wruck C, Tenbrock K, B?ll S, M?llmann J, Roth J. Nrf2 Is a Central Regulator of Metabolic Reprogramming of Myeloid-Derived Suppressor Cells in Steady State and Sepsis. Front Immunol. 2018; 9:1552. PMID: 30034396; PMCID: PMC6043652.
      Citations: 33     Fields:    
    65. Fischer N, Ticconi F, Vastert B, Costa IG, Haas JP, H?gle B, Schippers A, Ohl K, Denecke B, Tenbrock K. Transcription factor motif enrichment in whole transcriptome analysis identifies STAT4 and BCL6 as the most prominent binding motif in systemic juvenile idiopathic arthritis. Arthritis Res Ther. 2018 05 30; 20(1):98. PMID: 29848367; PMCID: PMC5977738.
      Citations: 4     Fields:    Translation:HumansCells
    66. Zirkel A, Nikolic M, Sofiadis K, Mallm JP, Brackley CA, Gothe H, Drechsel O, Becker C, Josipovic N, Georgomanolis T, Brant L, Franzen J, Koker M, Gusmao EG, Costa IG, Ullrich RT, Wagner W, Roukos V, Marenduzzo D, Rippe K, Papantonis A, Altm?ller J, N?rnberg P. HMGB2 Loss upon Senescence Entry Disrupts Genomic Organization and Induces CTCF Clustering across Cell Types. Mol Cell. 2018 05 17; 70(4):730-744.e6. PMID: 29706538.
      Citations: 88     Fields:    Translation:HumansCells
    67. Krenkel O, Puengel T, Govaere O, Abdallah AT, Mossanen JC, Kohlhepp M, Liepelt A, Lefebvre E, Luedde T, Hellerbrand C, Weiskirchen R, Longerich T, Costa IG, Anstee QM, Trautwein C, Tacke F. Therapeutic inhibition of inflammatory monocyte recruitment reduces steatohepatitis and liver fibrosis. Hepatology. 2018 04; 67(4):1270-1283. PMID: 28940700.
      Citations: 203     Fields:    Translation:HumansAnimalsCells
    68. Brylka LJ, Babler A, Kratz B, Denecke B, Yorgan TA, Etich J, Costa IG, Brachvogel B, Boor P, Schinke T, Jahnen-Dechent W, K?ppert S. Post-weaning epiphysiolysis causes distal femur dysplasia and foreshortened hindlimbs in fetuin-A-deficient mice. PLoS One. 2017; 12(10):e0187030. PMID: 29088242; PMCID: PMC5663435.
      Citations: 13     Fields:    Translation:Animals
    69. Jaskowiak PA, Costa IG, Campello RJGB. Clustering of RNA-Seq samples: Comparison study on cancer data. Methods. 2018 01 01; 132:42-49. PMID: 28778489.
      Citations: 9     Fields:    Translation:HumansCells
    70. Abagnale G, Sechi A, Steger M, Zhou Q, Kuo CC, Schalla C, Zenke M, Costa IG, van Rijn P, Gillner A, Wagner W, Aydin G, M?ller-Newen G. Surface Topography Guides Morphology and Spatial Patterning of Induced Pluripotent Stem Cell Colonies. Stem Cell Reports. 2017 08 08; 9(2):654-666. PMID: 28757164; PMCID: PMC5550028.
      Citations: 38     Fields:    Translation:HumansCells
    71. Millstein J, Yang X, Zhang B, Gusmao EG, Shu L, Szabat M, Johnson JD, Derry JMJ, Mecham B, Costa IG, Axelsson AS, Mahdi T, Nenonen HA, Singh T, H?nzelmann S, Wendt A, Bagge A, Reinbothe TM, Tang Y, Wang J, Sal? S, Eliasson L, Artner I, Fex M, Wollheim CB, Sp?gel P, Mulder H, Zhang E, Rosengren AH. Sox5 regulates beta-cell phenotype and is reduced in type 2 diabetes. Nat Commun. 2017 06 06; 8:15652. PMID: 28585545; PMCID: PMC5467166.
      Citations: 14     Fields:    Translation:HumansAnimalsCells
    72. Kolovos P, Georgomanolis T, Koeferle A, Larkin JD, Brant L, Gusmao EG, Zirkel A, Knoch TA, van Ijcken WF, Cook PR, Costa IG, Grosveld FG, Papantonis A, Nikolicc M. Binding of nuclear factor ?B to noncanonical consensus sites reveals its multimodal role during the early inflammatory response. Genome Res. 2016 11; 26(11):1478-1489. PMID: 27633323; PMCID: PMC5088591.
      Citations: 27     Fields:    Translation:HumansCells
    73. Hohwieler M, Illing A, Hermann PC, Mayer T, Stockmann M, Perkhofer L, Eiseler T, Antony JS, Renz S, Kuo CC, Lin Q, Sendler M, Breunig M, Kleiderman SM, Zenker M, Leichsenring M, Rosendahl J, Zenke M, Mayerle J, Costa IG, Seufferlein T, Kormann M, Wagner M, Liebau S, Kleger A, M?ller M, Lechel A, Sainz B. Human pluripotent stem cell-derived acinar/ductal organoids generate human pancreas upon orthotopic transplantation and allow disease modelling. Gut. 2017 03; 66(3):473-486. PMID: 27633923; PMCID: PMC5534761.
      Citations: 111     Fields:    Translation:HumansAnimalsCells
    74. Kalwa M, Otto S, Kuo CC, Franzen J, Joussen S, Fernandez-Rebollo E, Koch C, Hofmann A, Lee SH, Teschendorff AE, Denecke B, Lin Q, Widschwendter M, Weinhold E, Costa IG, Wagner W, H?nzelmann S, Rath B. The lncRNA HOTAIR impacts on mesenchymal stem cells via triple helix formation. Nucleic Acids Res. 2016 12 15; 44(22):10631-10643. PMID: 27634931; PMCID: PMC5159544.
      Citations: 91     Fields:    Translation:HumansCells
    75. Perkhofer L, Walter K, Costa IG, Carrasco MC, Eiseler T, Hafner S, Genze F, Zenke M, Bergmann W, Illing A, Hohwieler M, Lin Q, Holzmann KH, Seufferlein T, Wagner M, Liebau S, Hermann PC, Kleger A, K?hntop R, M?ller M. Tbx3 fosters pancreatic cancer growth by increased angiogenesis and activin/nodal-dependent induction of stemness. Stem Cell Res. 2016 09; 17(2):367-378. PMID: 27632063.
      Citations: 15     Fields:    Translation:HumansCells
    76. Berger AW, Schwerdel D, Costa IG, Hackert T, Strobel O, Lam S, Barth TF, Meining A, Zenke M, Hermann PC, Seufferlein T, Kleger A, Schr?ppel B, B?chler MW. Detection of Hot-Spot Mutations in Circulating Cell-Free DNA From Patients With Intraductal Papillary Mucinous Neoplasms of?the Pancreas. Gastroenterology. 2016 08; 151(2):267-70. PMID: 27343369.
      Citations: 49     Fields:    Translation:HumansCells
    77. Eipel M, Birkhofer C, Gerstenmaier U, Costa IG, Wagner W, Mayer F, Arent T, Ferreira MR, Ritz-Timme S. Epigenetic age predictions based on buccal swabs are more precise in combination with cell type-specific DNA methylation signatures. Aging (Albany NY). 2016 05; 8(5):1034-48. PMID: 27249102; PMCID: PMC4931852.
      Citations: 41     Fields:    Translation:HumansCells
    78. Gusmao EG, Allhoff M, Zenke M, Costa IG. Analysis of computational footprinting methods for DNase sequencing experiments. Nat Methods. 2016 Apr; 13(4):303-9. PMID: 26901649.
      Citations: 80     Fields:    Translation:HumansCells
    79. Zenke M, Costa IG, de Almeida DC, Ferreira MR, Franzen J, Weidner CI, Frobel J, Wagner W. Epigenetic Classification of Human Mesenchymal Stromal Cells. Stem Cell Reports. 2016 Feb 09; 6(2):168-75. PMID: 26862701; PMCID: PMC4750140.
      Citations: 28     Fields:    Translation:HumansCells
    80. Lin Q, Weidner CI, Costa IG, Marioni RE, Ferreira MR, Deary IJ, Wagner W. DNA methylation levels at individual age-associated CpG sites can be indicative for life expectancy. Aging (Albany NY). 2016 Feb; 8(2):394-401. PMID: 26928272; PMCID: PMC4789590.
      Citations: 81     Fields:    Translation:HumansCells
    81. Costa IG, Nascimento AC, Prud?ncio RB. A multiple kernel learning algorithm for drug-target interaction prediction. BMC Bioinformatics. 2016 Jan 22; 17:46. PMID: 26801218; PMCID: PMC4722636.
      Citations: 55     Fields:    Translation:HumansCells
    82. Schemionek M, Herrmann O, Reher MM, Chatain N, Schubert C, Costa IG, Gusmao EG, Kintsler S, Braunschweig T, Hamilton A, Helgason GV, Copland M, Li S, Holyoake TL, Koschmieder S, H?nzelmann S, Schwab A, M?ller-Tidow C, Br?mmendorf TH. Mtss1 is a critical epigenetically regulated tumor suppressor in CML. Leukemia. 2016 Apr; 30(4):823-32. PMID: 26621336.
      Citations: 20     Fields:    Translation:HumansAnimalsCells
    83. Lin Q, Costa IG, Gusmao EG, Mitzka S, Baying B, Klisch T, Moriggl R, Smeets H, Hoffmann K, Benes V, Zenke M, Chauvistr? H, H?nzelmann S, Hennuy B, Ser? K. Epigenetic program and transcription factor circuitry of dendritic cell development. Nucleic Acids Res. 2015 Nov 16; 43(20):9680-93. PMID: 26476451; PMCID: PMC4787753.
      Citations: 27     Fields:    Translation:AnimalsCells
    84. Azoitei N, Eiseler T, Bergmann W, Lin Q, Costa IG, Zenke M, Genze F, Weidgang C, Seufferlein T, Liebau S, Kleger A, M?ller M, Schr?er J, K?hntop R. A time frame permissive for Protein Kinase D2 activity to direct angiogenesis in mouse embryonic stem cells. Sci Rep. 2015 Jul 07; 5:11742. PMID: 26148697; PMCID: PMC4493579.
      Citations: 5     Fields:    Translation:AnimalsCells
    85. Beier F, Gusmao EG, Koch CM, Hummel S, Charapitsa I, Joussen S, Benes V, Reid G, Costa IG, Wagner W, H?nzelmann S, Br?mmendorf TH. Replicative senescence is associated with nuclear reorganization and with DNA methylation at specific transcription factor binding sites. Clin Epigenetics. 2015; 7:19. PMID: 25763115; PMCID: PMC4356053.
      Citations: 31     Fields:    
    86. de Souto MC, Costa IG, Jaskowiak PA. Impact of missing data imputation methods on gene expression clustering and classification. BMC Bioinformatics. 2015 Feb 26; 16:64. PMID: 25888091; PMCID: PMC4350881.
      Citations: 19     Fields:    Translation:Humans
    87. Allhoff M, Lin Q, Zenke M, Costa IG, Ser? K, Chauvistr? H. Detecting differential peaks in ChIP-seq signals with ODIN. Bioinformatics. 2015 Mar 15; 31(6):980. PMID: 25673339.
      Citations: 1     Fields:    
    88. Costa IG, Castelo R, H?nzelmann S, Wang J, G?ney E, Tang Y, Zhang E, Axelsson AS, Nenonen H, Salehi AS, Wollheim CB, Zetterberg E, Berntorp E, Rosengren AH. Thrombin stimulates insulin secretion via protease-activated receptor-3. Islets. 2015; 7(4):e1118195. PMID: 26742564; PMCID: PMC4878264.
      Citations: 8     Fields:    Translation:HumansCells
    89. Allhoff M, Lin Q, Zenke M, Costa IG, Ser? K, Chauvistr? H. Detecting differential peaks in ChIP-seq signals with ODIN. Bioinformatics. 2014 Dec 15; 30(24):3467-75. PMID: 25371479.
      Citations: 16     Fields:    Translation:Animals
    90. Gusmao EG, Dieterich C, Zenke M, Costa IG. Detection of active transcription factor binding sites with the combination of DNase hypersensitivity and histone modifications. Bioinformatics. 2014 Nov 15; 30(22):3143-51. PMID: 25086003.
      Citations: 46     Fields:    Translation:HumansCells
    91. Costa IG, Gusmao EG, Ullius A, L?scher-Firzlaff J, Walsemann G, Forst AH, Kapelle K, Kleine H, Kremmer E, Vervoorts J, L?scher B. The interaction of MYC with the trithorax protein ASH2L promotes gene transcription by regulating H3K27 modification. Nucleic Acids Res. 2014 Jun; 42(11):6901-20. PMID: 24782528; PMCID: PMC4066752.
      Citations: 36     Fields:    Translation:HumansCells
    92. Jaskowiak PA, Campello RJ, Costa IG. On the selection of appropriate distances for gene expression data clustering. BMC Bioinformatics. 2014; 15 Suppl 2:S2. PMID: 24564555; PMCID: PMC4072854.
      Citations: 46     Fields:    Translation:Humans
    93. Weidner CI, Walenda T, Lin Q, Denecke B, Costa IG, Zenke M, Wagner W, W?lfler MM. Hematopoietic stem and progenitor cells acquire distinct DNA-hypermethylation during in vitro culture. Sci Rep. 2013 Nov 28; 3:3372. PMID: 24284763; PMCID: PMC3842544.
      Citations: 19     Fields:    Translation:HumansCells
    94. Costa IG, Jaskowiak PA, Campello RJ. Proximity measures for clustering gene expression microarray data: a validation methodology and a comparative analysis. IEEE/ACM Trans Comput Biol Bioinform. 2013 Jul-Aug; 10(4):845-57. PMID: 24334380.
      Citations: 10     Fields:    Translation:Humans
    95. Allhoff M, Martin M, Costa IG, Rahmann S, Marschall T, Sch?nhuth A. Discovering motifs that induce sequencing errors. BMC Bioinformatics. 2013; 14 Suppl 5:S1. PMID: 23735080; PMCID: PMC3622629.
      Citations: 32     Fields:    Translation:HumansCells
    96. Marschall T, Costa IG, Canzar S, Bauer M, Klau GW, Schliep A, Sch?nhuth A. CLEVER: clique-enumerating variant finder. Bioinformatics. 2012 Nov 15; 28(22):2875-82. PMID: 23060616.
      Citations: 29     Fields:    Translation:Humans
    97. do Rego TG, Roider HG, de Carvalho FA, Costa IG. Inferring epigenetic and transcriptional regulation during blood cell development with a mixture of sparse linear models. Bioinformatics. 2012 Sep 15; 28(18):2297-303. PMID: 22730432.
      Citations: 6     Fields:    Translation:AnimalsCells
    98. Redestig H, Costa IG. Detection and interpretation of metabolite-transcript coresponses using combined profiling data. Bioinformatics. 2011 Jul 01; 27(13):i357-65. PMID: 21685093; PMCID: PMC3117345.
      Citations: 20     Fields:    Translation:Animals
    99. Schilling R, Costa IG, Schliep A. pGQL: A probabilistic graphical query language for gene expression time courses. BioData Min. 2011 Apr 18; 4:9. PMID: 21501515; PMCID: PMC3096586.
      Citations: 2     
    100. Costa IG, Roider HG, do Rego TG, de Carvalho Fde A. Predicting gene expression in T cell differentiation from histone modifications and transcription factor binding affinities by linear mixture models. BMC Bioinformatics. 2011 Feb 15; 12 Suppl 1:S29. PMID: 21342559; PMCID: PMC3044284.
      Citations: 14     Fields:    Translation:Cells
    101. Hafemeister C, Costa IG, Schliep A, Sch?nhuth A. Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions. Bioinformatics. 2011 Apr 01; 27(7):946-52. PMID: 21266444.
      Citations: 7     Fields:    Translation:Animals
    102. Georgi B, Costa IG, Schliep A. PyMix--the python mixture package--a tool for clustering of heterogeneous biological data. BMC Bioinformatics. 2010 Jan 06; 11:9. PMID: 20053276; PMCID: PMC2823712.
      Citations: 5     Fields:    
    103. Rid R, Onder K, Trost A, Bauer J, Hintner H, Ritter M, Jakab M, Costa I, Reischl W, Richter K, MacDonald S, Jendrach M, Breitenbach M, Bereiter-Hahn J. H2O2-dependent translocation of TCTP into the nucleus enables its interaction with VDR in human keratinocytes: TCTP as a further module in calcitriol signalling. J Steroid Biochem Mol Biol. 2010 Jan; 118(1-2):29-40. PMID: 19815065.
      Citations: 11     Fields:    Translation:HumansCells
    104. Costa IG, Hafemeister C, Schliep A, Sch?nhuth A. Constrained mixture estimation for analysis and robust classification of clinical time series. Bioinformatics. 2009 Jun 15; 25(12):i6-14. PMID: 19478017; PMCID: PMC2687976.
      Citations: 10     Fields:    Translation:Humans
    105. de Souto MC, Costa IG, de Araujo DS, Ludermir TB, Schliep A. Clustering cancer gene expression data: a comparative study. BMC Bioinformatics. 2008 Nov 27; 9:497. PMID: 19038021; PMCID: PMC2632677.
      Citations: 81     Fields:    Translation:Humans
    106. Costa IG, Roepcke S, Hafemeister C, Schliep A. Inferring differentiation pathways from gene expression. Bioinformatics. 2008 Jul 01; 24(13):i156-64. PMID: 18586709; PMCID: PMC2718631.
      Citations: 11     Fields:    Translation:Cells
    107. Costa IG, Roepcke S, Schliep A. Gene expression trees in lymphoid development. BMC Immunol. 2007 Oct 09; 8:25. PMID: 17925013; PMCID: PMC2244641.
      Citations: 5     Fields:    Translation:HumansAnimalsCells
    108. Costa IG, Krause R, Opitz L, Schliep A. Semi-supervised learning for the identification of syn-expressed genes from fused microarray and in situ image data. BMC Bioinformatics. 2007; 8 Suppl 10:S3. PMID: 18269697; PMCID: PMC2230504.
      Citations: 9     Fields:    Translation:Animals
    109. Schliep A, Costa IG, Steinhoff C, Sch?nhuth A. Analyzing gene expression time-courses. IEEE/ACM Trans Comput Biol Bioinform. 2005 Jul-Sep; 2(3):179-93. PMID: 17044182.
      Citations: 28     Fields:    
    110. Costa IG, Schliep A, Sch?nhuth A. The Graphical Query Language: a tool for analysis of gene expression time-courses. Bioinformatics. 2005 May 15; 21(10):2544-5. PMID: 15701683.
      Citations: 12     Fields:    

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