Publications

Check  google scholar for an up-to-date list.

 

Pre-prints

PA Jaskowiak, IG Costa, Clustering Validation with The Area Under Precision-Recall Curves, arXiv preprint arXiv:2304.01450. [paper]

Kalmer, M., Grasshoff, M., Maie, T., … Costa, IG. Koschmieer, S., Deciphering the Complex Clonal Heterogeneity of Polycythemia Vera and the Response to Interferon Alpha. Research Square, https://doi.org/10.21203/rs.3.rs-3490651/v1.

Schmidt, M., Maié, T., Costa, I. G., &Wagner, W. (2024). Cancer- associated fibroblasts reveal aberrant DNA methylation across different types of cancer. BioRxiv, 2024.02.02.578626. [paper]

2023

Joodaki, M., Shaigan, M., Parra, V., Roman, D.B., Nagai. J, Mingbo, C., Barratt, J., Roberts, I.S.D., Coppo, R., Kramann, R., Boor, P., Costa, I.G., 2023. Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport ( PILOT ), Molecular Systems Biology, 20:57-74. [paper | software]

Costa, I.G., 2023. Dissecting gene regulation with multimodal sequencing. Nat Methods. [paper]

Maié T, Schmidt, M., Erz M, Wagner W, Costa IG, CimpleG: Finding simple CpG methylation signatures, Genome Biol 24, 161. [ paper | software].

Li Z, Kuo CC, Ticconi F, Shaigan M, Gehrmann, J., Gusmao, EG, Allhoff, M., Manolov M., Zenke M., Costa I.G. (2023), RGT: a toolbox for the integrative analysis of high throughput regulatory genomics data. BMC Bioinformatics. 2023;24(1):79 [ paper | software].

Li, Z., Nagai, J.S., Kuppe, C., Kramann, R., Costa, I.G., 2023. scMEGA: single-cell multi-omic enhancer-based gene regulatory network inference. Bioinformatics Advances, 3, vbad003 [paper | software ].

Kaesler, N.; Cheng, M.; Nagai, J.; O’Sullivan, J.; Peisker, F.; Bindels, E. M. J.; Babler, A.; Moellmann, J.; Droste, P.; Franciosa, G.; Dugourd, A.; Saez-Rodriguez, J.; Neuss, S.; Lehrke, M.; Boor, P.; Goettsch, C.; Olsen, J. V.; Speer, T.; Lu, T.-S.; Lim, K.; Floege, J.; Denby, L.; Costa, I.G.; Kramann, R. Mapping Cardiac Remodeling in Chronic Kidney Disease. Sci Adv 2023, 9 (47), eadj4846. [ paper | data ].

Hölscher, D.L., Bouteldja, N., Joodaki, M., Russo, M.L., Lan, Y.-C., Sadr, A.V., Cheng, M., Tesar, V., Stillfried, S. V., Klinkhammer, B.M., Barratt, J., Floege, J., Roberts, I.S.D., Coppo, R., Costa, I.G., Bülow, R.D., Boor, P., 2023. Next-Generation Morphometry for pathomics-data mining in histopathology. Nat. Commun. 14, 470. [paper | software]

Bülow, R.D., Hölscher, D.L., Costa, I.G., Boor, P., 2023. Extending the landscape of omics technologies by pathomics. npj Syst Biol Appl 9, 38. [ paper ]

Xu, H., Li, Z., Kuo, C.-C., Goetz, K., Look, T., de Toldeo, M.A., Sere, K., Costa, I.G., Zenke, M., 2023. A lncRNA identifies Irf8 enhancer element in negative feedback control of dendritic cell differentiation. eLife 12, 1–35. [ paper]

Yildiz, C. B.; Kundu, T.; Gehrmann, J.; Koesling, J.; Ravaei, A.; Wolff, P.; Kraft, F.; Maié, T.; Jakovcevski, M.; Pensold, D.; Zimmermann, O.; Rossetti, G.; Costa, I. G.; Zimmer-Bensch, G. EphrinA5 Regulates Cell Motility by Modulating Snhg15/DNA Triplex-Dependent Targeting of DNMT1 to the Ncam1 Promoter. Epigenetics & Chromatin 2023, 16 (1), 42. [ paper ]

Hubens, W. H. G.; Maié, T.; Schnitker, M.; Bocova, L.; Puri, D.; Wessiepe, M.; Kramer, J.; Rink, L.; Koschmieder, S.; Costa, I. G.; Wagner, W. Targeted DNA Methylation Analysis Facilitates Leukocyte Counts in Dried Blood Samples. Clin. Chem. 2023, 69 (11), 1283–1294.

Torow, N., Li, R., Hitch, T.C.A., Mingels, C., Al Bounny, S., van Best, N., Stange, E.L., Simons, B., Maié, T., Rüttger, L., …, Lelouard, H., Costa, I.G., Hornef, M.W., 2023. M cell maturation and cDC activation determine the onset of adaptive immune priming in the neonatal Peyer’s patch. Immunity 56, 1220-1238.e7. [ paper ]

Hoeft, K., Schaefer, G.J.L., Kim, H.,… , Nagai, J., … , Costa, IG., …, Hayat, S., Kramann, R., 2023. Platelet-instructed SPP1+ macrophages drive myofibroblast activation in fibrosis in a CXCL4-dependent manner. Cell reports 42, 112131. [ paper]

Langhammer, M., Schöpf, J., … Maié, T., J... , Costa, I.G., … , M., Schemionek-Reinders, M., Brummer, T., Halbach, S., 2023. Mast cell deficiency prevents BCR::ABL1 induced splenomegaly and cytokine elevation in a CML mouse model. Leukemia. [paper]

Vucur, M., Ghallab, A., Schneider, A.T., Adili, A., Cheng, M., … Geisler, F., Costa, I.G., Hengstler, J.G., Heikenwalder, M., Luedde, T., 2023. Sublethal necroptosis signaling promotes inflammation and liver cancer. Immunity 1–18. [paper]

Bütow, M.; Testaquadra, F. J.; Baumeister, J.; Maié, T.; Chatain, N.; Jaquet, T.; Tillmann, S.; Crysandt, M.; Costa, I. G.; Brümmendorf, T. H.; Schemionek, M. Targeting Cytokine-Induced Leukemic Stem Cell Persistence in Chronic Myeloid Leukemia by IKK2-Inhibition. Haematologica , 108 (4), 1179–1185. [ paper ]

Miguel, V.; Rey-Serra, C.; Tituaña, J.; Sirera, B.; Alcalde-Estévez, E.; Herrero, J. I.; Ranz, I.; Fernández, L.; Castillo, C.; Sevilla, L.; Nagai, J.; Reimer, K. C.; Jansen, J.; Kramann, R.; Costa, I. G.; Castro, A.; Sancho, D.; Rodríguez González-Moro, J. M.; Lamas, S. Enhanced Fatty Acid Oxidation through Metformin and Baicalin as Therapy for COVID-19 and Associated Inflammatory States in Lung and Kidney. Redox Biology, 68, 102957. [ paper ]

2022

Kuppe, C.*, Ramirez Flores*, R.O., Li, Z.*, Hayat, S., Levinson, R.T., Liao, X., Hannani, M.T., Tanevski, J., Wünnemann, F., Nagai, J.S., Halder, M., Schumacher, D., Menzel, S., Schäfer, 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, R.J.A., Boor, P., Klingel, K., Van Laake, L.W., Vink, A., Hoogenboezem, R.M., Bindels, E.M.J., Schurgers, L., Sattler, S., Schapiro, D., Schneider, R.K., Lavine, K., Milting, H., Costa, I.G.*, Saez-Rodriguez, J.*, Kramann, R.*, 2022. Spatial multi-omic map of human myocardial infarction. Nature, 608:766–777 [paper | software | data ]

Cheng, M., Li, Z., Costa, IG, 2022. MOJITOO: a fast and universal method for integration of multimodal single cell data. Bioinformatics (Proc. of ISMB 2022),  32: i282–i289. [paper | software ]

Li, R., Banjanin, B., Schneider, R.K., Costa, I.G., 2022. Detection of cell markers from single cell RNA-seq with sc2marker. BMC Bioinformatics 23, 276. [paper | software ]

Jaskowiak PA, Costa IG, Campello, RJGB, The Area Under the ROC Curve as a Measure of Clustering Quality, Data Mining and Knowledge Discovery, 36, 1219–1245. [paper]

Jansen, J., Reimer, K.C., Nagai, J.S., Varghese, F.S., Overheul, G.J., de Beer, …, van Rij, R.P., Costa, I.G., Schneider, R.K., Smeets, B., Kramann, R. 2022. SARS-CoV-2 infects the human kidney and drives fibrosis in kidney organoids. Cell Stem Cell 29, 217-231.e8. [ paper | data | pre-processed data and scripts ]

Peisker, F., Halder, M., Nagai, J., Ziegler, S., Kaesler, N., Hoeft, K., Li, R., Bindels, E.M.J., Kuppe, C., Moellmann, J., Lehrke, M., Stoppe, C., Schaub, M.T., Schneider, R.K., Costa, I., Kramann, R., 2022. Mapping the cardiac vascular niche in heart failure. Nat. Commun. 13:3027. [paper | data]

Stalmann, U.S.A., Ticconi, F., Snoeren, I.A.M., Li, R., … , Stiehl, T., Costa, I.G., Ebert, B.L., Schneider, R.K., 2022. Genetic barcoding systematically compares genes in del(5q) MDS and reveals a central role for CSNK1A1 in clonal expansion. Blood Adv. 6, 1780–1796. [ paper | data | pre-processed data ]

Stenzel, A.T., Boroujeni, R.S., Kuo, C., Barsoum, M., Liang, W., Bussmann, P., Costa, I.G., Juliane, L., Bernhard, L., 2022. Induction of senescence upon loss of the Ash2l core subunit of H3K4 methyltransferase complexes, Nucleic Acids Research, 50, 7889–7905 [ paper ].

Schreibing, F., Hannani, M.T., Kim, H., Nagai, J.S., Ticconi, F., Fewings, E.,… , Saez-Rodriguez, J., Costa, I.G., Hayat, S., Kramann, R., 2022. Dissecting CD8+ T cell pathology of severe SARS-CoV-2 infection by single-cell immunoprofiling. Front. Immunol. 13, 1–23. [paper]

Dimitrov, D., Türei, D., Garrido-Rodriguez, M., Burmedi, P.L., Nagai, J.S., Boys, C., Ramirez Flores, R.O., Kim, H., Szalai, B., Costa, I.G., Valdeolivas, A., Dugourd, A., Saez-Rodriguez, J., 2022. Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data. Nat. Commun. 13, 3224. [paper]

Leisegang, M.S., Bains, J.K., Seredinski, S., Oo, J.A., Krause, N.M., Kuo, C.C., Günther, S., Sentürk Cetin, N., Warwick, T., Cao, C., Boos, F., Izquierdo Ponce, J., Haydar, S., Bednarz, R., Valasarajan, C., Fuhrmann, D.C., Preussner, J., Looso, M., Pullamsetti, S.S., Schulz, M.H., Jonker, H.R.A., Richter, C., Rezende, F., Gilsbach, R., Pflüger-Müller, B., Wittig, I., Grummt, I., Ribarska, T., Costa, I.G., Schwalbe, H., Brandes, R.P., 2022. HIF1α-AS1 is a DNA:DNA:RNA triplex-forming lncRNA interacting with the HUSH complex. Nat. Commun. 13. [paper]

Xu, Y., Kuppe, C., Perales-Patón, J., Hayat, S., Kranz, J., Abdallah, A.T., Nagai, J., Li, Z., Peisker, F., Saritas, T., Halder, M., Menzel, S., Hoeft, K., Kenter, A., Kim, H., van Roeyen, C.R.C., Lehrke, M., Moellmann, J., Speer, T., Buhl, E.M., Hoogenboezem, R., Boor, P., Jansen, J., Knopp, C., Kurth, I., Smeets, B., Bindels, E., Reinders, M.E.J., Baan, C., Gribnau, J., Hoorn, E.J., Steffens, J., Huber, T.B., Costa, I.G., Floege, J., Schneider, R.K., Saez-Rodriguez, J., Freedman, B.S., Kramann, R., 2022. Adult human kidney organoids originate from CD24+ cells and represent an advanced model for adult polycystic kidney disease. Nat. Genet. 54. [paper]

Stalmann, U.S.A., Banjanin, B., Snoeren, I.A.M., Nagai, J.S., …, Bindels, E., Costa, I.G., Schneider, R.K., 2022. Single cell analysis of cultured bone marrow stromal cells reveals high similarity to fibroblasts in situ. Exp. Hematol., 11028-33. [paper]

Elsafi Mabrouk, M.H., Goetzke, R., Abagnale, G., … , Li, R., Costa, I.G., Lampert, A., Pachauri, V., Schnakenberg, U., Zenke, M., Wagner, W., 2022. The spatial self-organization within pluripotent stem cell colonies is continued in detaching aggregates. Biomaterials 282, 121389. [paper]

Barsoum, M., Stenzel, A.T., Bochyńska, A., Kuo, C.-C., Tsompanidis, A., Sayadi-Boroujeni, R., Bussmann, P., Lüscher-Firzlaff, J., Costa, I.G., Lüscher, B., 2022. Loss of the Ash2l subunit of histone H3K4 methyltransferase complexes reduces chromatin accessibility at promoters. Sci. Rep. 12, 21506. [paper]

Pellegrino, R., Castoldi, M., Ticconi, F., Skawran, B., Budczies, J., Rose, F., Schwab, C., Breuhahn, K., Neumann, U.P., Gaisa, N.T., Loosen, S.H., Luedde, T., Costa, I.G., Longerich, T., 2022. LINC00152 Drives a Competing Endogenous RNA Network in Human Hepatocellular Carcinoma. Cells 11, 1528. [paper]

2021

Li, Z., Kuppe, C., Cheng, M., Menzel, S., Zenke, M., Kramann, R., Costa, I.G.,  scOpen: chromatin-accessibility estimation of single-cell ATAC data. Nature Communications, 12(1),6386. [ paper | software | data | pre-processed data ]

Philippi, A.*, Heller, S.*, Costa, I.G.*, Senée, V.*, Breunig, M., Li, Z., Kwon, …, Nicolino, M., Julier, C., Kleger, A.,  Mutations and variants of ONECUT1 in diabetes. Nature Medicine, 27(11),1928-1940. [ paper | data ]

Leimkühler, N.B.*, Gleitz, H.F.E*., Ronghui, L.*, Snoeren, I.A.M., Fuchs, S.N.R., Nagai, J.S., Banjanin, B.,…., Kramann, R., Costa, I.G.*, Schneider, R.K.*, 2021. Heterogeneous bone-marrow stromal progenitors drive myelofibrosis via a druggable alarmin axis. Cell Stem Cell, 28, 637–652.e8. [paper | data | pre-processed data ]

Nagai, J.S., Leimkühler, N.B., Schaub, M.T., Schneider, R.K., Costa, I.G., CrossTalkeR: Analysis and Visualisation of Ligand Receptor Networks. Bioinformatics, 37(22),4263-4265. [ paper | software ]

Heller, S., Li, Z., Lin, Q., Geusz, R., Breunig, M., Hohwieler, M., Zhang, X., Nair, G.G., Seufferlein, T., Hebrok, M., Sander, M., Julier, C., Kleger, A., Costa, I.G., 2021. Transcriptional changes and the role of ONECUT1 in hPSC pancreatic differentiation. Commun. Biol. 4, 1–12. [paper | data | pre-processed data ]

Leimkühler, N.B., Costa, I.G., Schneider, R.K.,  From cell to cell: Identification of actionable targets in bone marrow fibrosis using single-cell technologies. Exp. Hematol.,  104, 48-54. [paper]

Muschaweck, M., Kopplin, L., Ticconi, F., Schippers, A., Iljazovic, A., Gálvez, E.J.C., Abdallah, A.T., Wagner, N., Costa, I.G., Strowig, T., Pabst, O., 2021. Cognate recognition of microbial antigens defines constricted CD4+ T cell receptor repertoires in the inflamed colon. Immunity 54(11),2565-2577.e6. [paper]

Baumeister, J., Maié, T., Chatain, …., Costa, I.G., Koschmieder, S., Brümmendorf, T.H., Gezer, D., 2021. Early and late stage MPN patients show distinct gene expression profiles in CD34+ cells. Ann. Hematol., 100(12), 2943-2956 [paper | data ]

Olschok, K., Han, L., de Toledo, M.A.S., Böhnke, J., Graßhoff, M., Costa, I.G., Theocharides, A., Maurer, A., … , Brümmendorf, T.H., Zenke, M., Chatain, N., Koschmieder, S., 2021. CALR frameshift mutations in MPN patient-derived iPSCs accelerate maturation of megakaryocytes. Stem Cell Reports 16(11), 2768-2783. [paper]

Karim, M.R., Beyan, O., Zappa, A., Costa, I.G., Rebholz-Schuhmann, D., Cochez, M., Decker, S., 2021. Deep learning-based clustering approaches for bioinformatics. Brief. Bioinform. 22, 393–415. [paper]

Kenswil, K.J.G., Pisterzi, P., Sánchez-Duffhues, G., …, Costa, I.G., Li, R., …, Krenning, G., Raaijmakers, M.H.G.P., 2021. Endothelium-derived stromal cells contribute to hematopoietic bone marrow niche formation. Cell Stem Cell 28, 653–670.e11. [paper]

Müller, J.A., Groß, R., Conzelmann, C., …, Gehrmann, J.,  …, Costa, I.G., …, Münch, J., Heller, S., Kleger, A., 2021. SARS-CoV-2 infects and replicates in cells of the human endocrine and exocrine pancreas. Nature Metabolism 3, 149–165. [paper]

Pensold, D., Gehrmann, J., Pitschelatow, G., Walberg, A., Braunsteffer, K., Reichard, J., Ravaei, A., Linde, J., Lampert, A., Costa, I.G., Zimmer-Bensch, G., 2021. The expression of the cancer-associated lncrna snhg15 is modulated by ephrina5-induced signaling. Int. J. Mol. Sci. , 22(3),1332. [paper]

2020

Schmidt, M.*, Maié, T.*, Dahl, E., Costa, I.G., Wagner, W., 2020. Deconvolution of cellular subsets in human tissue based on targeted DNA methylation analysis at individual CpG sites. BMC Biology, 18, 178. [paper]

Krenkel, O., …, Branco, D.P.P., Mossanen, J.C., Luedde, T., Trautwein, C., Costa, I.G., Tacke, F., 2020. Myeloid cells in liver and bone marrow acquire a functionally distinct inflammatory phenotype during obesity-related steatohepatitis. Gut 69, 551–563. [paper]

Parting, O., Langer, S., … , Maié, T., Costa, I.G., …., Koschmieder, S., Schemionek, M., 2020. Therapeutic inhibition of FcγRIIb signaling targets leukemic stem cells in chronic myeloid leukemia. Leukemia 34, 2635–2647. [paper]

Baumeister, J., Chatain, N., Hubrich, A., Maié, T., Costa, I.G., …, Koschmieder, S., Gezer, D., 2020. Hypoxia-inducible factor 1 (HIF-1) is a new therapeutic target in JAK2V617F-positive myeloproliferative neoplasms. Leukemia 34, 1062–1074. [paper]

Trembinski, D.J., Bink, D.I.,… , Kuo, C.-C., Costa, I.G., …, Dimmeler, S., Boon, R.A., 2020. Aging-regulated anti-apoptotic long non-coding RNA Sarrah augments recovery from acute myocardial infarction. Nat. Communications 11, 2039. [paper]

Pensold, D., … , Gehrmann, J., Costa, I., …, Becker, A.J., Zimmer-Bensch, G., 2020. DNA Methylation-Mediated Modulation of Endocytosis as Potential Mechanism for Synaptic Function Regulation in Murine Inhibitory Cortical Interneurons. Cereb. Cortex 30, 3921–3937. [paper]

2019

Frank S, Ahuja G, Bartsch D, Kuo C.C., …, Costa I.C., Kanduri, C., Papantonis, A., Kurian L. yylncT Defines a Class of Divergently Transcribed lncRNAs and Safeguards the T-mediated Mesodermal Commitment of Human PSCs. Cell Stem Cell,  24(2):318-327.e8 [paper].

Nascimento A.C.A., Prudêncio R.B.C., Costa I.G. A Drug-Target Network-Based Supervised Machine Learning Repurposing Method Allowing the Use of Multiple Heterogeneous Information Sources. Comput. Methods Drug Repurposing.;281–289.

Schubert C, Allhoff M, Tillmann S, Maie T., Costa IG, et al. Differential roles of STAT1 and STAT2 in the sensitivity of JAK2V617F- vs. BCR-ABL-positive cells to interferon alpha. J. Hematol. Oncol. , 12:36 .

Lüscher-Firzlaff J, Chatain N, Kuo C-C, … Costa IG, Koschmieder S, Luscher B, Hematopoietic stem and progenitor cell proliferation and differentiation requires the trithorax protein Ash2l. Sci. Rep. 2019;9(1):8262.

Kuepper MK, Bütow M, Herrmann O, …, Maie. T., Costa IG, … Schemionek M, Stem cell persistence in CML is mediated by extrinsically activated JAK1-STAT3 signaling. Leukemia, 33:1964–1977.

Dreschers S, Ohl K, Lehrke M, …, Costa IG, … Tenbrock K, Impaired cellular energy metabolism in cord blood macrophages contributes to abortive response toward inflammatory threats. Nat. Communications, 10(1):1685.

Liepelt A, Wehr A, Kohlhepp M, …, Costa, I.G.., Luedde, T., Trautwein, C., Tacke, F., CXCR6 protects from inflammation and fibrosis in NEMOLPC-KO mice. Biochim. Biophys. acta. Mol. basis Dis., 1865(2):391–402 [paper].

Herrmann O, Kuepper MK, Bütow M, Costa I.G., et al. Infliximab therapy together with tyrosine kinase inhibition targets leukemic stem cells in chronic myeloid leukemia. BMC Cancer. 2019;19(1):658.

Nordström KJ V, Schmidt F, Gasparoni N, … Costa I.G., , Walter. B., Unique and assay specific features of NOMe-, ATAC- and DNase I-seq data. Nucleic Acids Res. 2019;47(20):10580–10596.

Karim MR, Wicaksono G, Costa IG, Decker S, Beyan O. Prognostically Relevant Subtypes and Survival Prediction for Breast Cancer Based on Multimodal Genomics Data. IEEE Access. 2019;7:133850–133864.

2018

Lorena, A.C., Maciel I.,  de Miranda P.B.C., Costa I.G., Prudêncio, R.B.C., Data Complexity Meta-features for Regression Problems. Machine Learning, 107 (1), 209-246 [paper].

Jaskowiak P.A., Costa, I.G. , Campello, R. J.G.B., Clustering of RNA-Seq Samples: Comparison Study on Cancer Data, Methods ,  132, 42-49 [paper].

Czech J, Cordua S, Weinbergerova B, Baumeister, J. Crepcia, A., Han, L., Maié, T.,  Costa, I.G., et al. JAK2V617F but not CALR mutations confer increased molecular responses to interferon-α via JAK1/STAT1 activation. Leukemia; epub, [paper].

Sonntag R, Giebeler N, Nevzorova YA, … Ticconi F, Costa I.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. 2018;115(37):9282-9287, [paper].

Zirkel, A., Nikolic, M., Sofiadis, K., Mallm, J., Brackley, C.A., Gothe, H., Drechsel, O., Becker, C., Altmüller, J., Josipovic, N., Georgomanolis,T., Brant, L., Franzen, J., Koker, M., Gusmao, E.G., Costa, I.G., Ullrich, R.T., Wagner, W., Roukos, V., Nürnberg, P., Marenduzzo, D., Rippe, K., Papantonis, A., 2018. HMGB2 Loss upon Senescence Entry Disrupts Genomic Organization and Induces CTCF Clustering across Cell Types. Molecular Cell, 70(4):730–744.e6 [paper].

Krenkel O., Puengel T., Govaere O., Abdallah A.T., Mossanen J.C., Kohlhepp M., Liepelt A., Lefebvre E., Luedde T., Hellerbrand C., Weiskirchen R., Longerich T., Costa I.G., Anstee Q.M., Trautwein .C, Tacke F., Therapeutic Inhibition of Inflammatory Monocyte Recruitment Reduces Steatohepatitis and Liver Fibrosis, Hepatology, 67 (4), 1270-1283 [paper].

Božić T, Frobel J, Raic A, Ticconi F, Kuo CC, …, Costa, I.G., Wagner, W., Variants of DNMT3A cause transcript-specific DNA methylation patterns and affect hematopoiesis, Life Science Alliance 1 (6), e201800153. [paper]

Hügle B, Schippers A, Fischer N, …, Ticconi, F., Vastert, B., Costa, I.G., Hass, J.P., 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., 20(1):98 [paper].

Ohl K, Fragoulis A, Klemm P, Baumeister, J., Klock, W., Verjans, E., Böll, S., Möllmann, J., Lehrke, M., Costa, I.G., et al., Nrf2 Is a Central Regulator of Metabolic Reprogramming of Myeloid-Derived Suppressor Cells in Steady State and Sepsis. Front. Immunol.,9 [paper].

2017

Axelsson A.S., Mahdi T. , Nenonen H.A. , Singh T., Hänzelmann S. , … ,  Costa I.G., Zhang E.,  Rosengren A.H., Sox5 regulates beta-cell phenotype and is reduced in type 2 diabetes, Nature Communications, 15652. [paper].

Hohwieler, M., Illing, A., Hermann, P. C., Mayer, T., Stockmann, M., Perkhofer, L., …, Costa, I. G. Seufferlein, T., Kormann, M., Wagner, M., Liebau, S., Kleger, A. (2017). Human pluripotent stem cell-derived acinar/ductal organoids generate human pancreas upon orthotopic transplantation and allow disease modelling. Gut, 66:473:486. [paper]

Abagnale G., Sechi A., Steger M., Zhou Q., Ku C.C., …, Costa I.G. , van Rijn P., Gillner A., Wagner W., Surface Topography Guides Morphology and Spatial Patterning of Induced Pluripotent Stem Cell Colonies, Stem Cell Reports , 9(2) 654–666 [paper].

Brylka L.J., Köppert S., Babler A., Kratz B., Denecke B., Yorgan T.A., Etich J., Costa I.G., Brachvogel B., Boor P., Schinke T., Jahnen-Dechent W., Post-weaning epiphysiolysis causes distal femur dysplasia and foreshortened hindlimbs in fetuin-A-deficient mice. PLoS One, 12(10):e0187030 [paper].

2016

Gusmao E.G., Allhoff, M., Zenke, M.,  Costa, I.G. (2016), Analysis of computational footprinting methods for DNase sequencing experiments, Nature Methods, 13, 303–309 [paper][pre-print][supp].

Kalwa M., Hänzelmann S., Otto S.,  Kuo C.C., Franzen J., … , Elmar Weinhold,  Costa I. G.*, Wagner W.*, The lncRNA HOTAIR impacts on mesenchymal stem cells via triple helix formation, Nucleic Acids Research, 44 (22): 10631-10643. [paper]. (*shared corresponding author).

Allhoff, M., Sere K., Freitas, J., Zenke, M.,  Costa, I.G. (2016), Differential Peak Calling of ChIP-seq Signals with Replicates with THOR, Nucleic Acids Research, 44(20):e153.  [paper][supp][data].

Nascimento, A. C., Prudencio, R.B.C, Costa I.G., A Multiple Kernel Learning algorithm for drug-target interaction prediction, BMC Bioinformatics,17:46 [paper][supp].

Kolovos, P.,  Georgomanolis, T.,  Koeferle A.,  Larkin J. D, Brant L.,  Nikolic M., Gusmao E.G., Zirkel A.,  Knoch T. A., Costa I.G., van Ijcken W. F ,  Cook P. R., Grosveld F. G., Papantonis A., Binding of nuclear factor kappa B to non-canonical consensus sites reveals its multimodal role during the early inflammatory response, Genome Research,  26:1478-1489 [paper].

de Almeida, D., Ferreira, M. R. P., Franzen, J., Weidner, C., Frobel, J., Zenke, M. Costa, I.G., Wagner, W. (2016). Epigenetic Classification of Human Mesenchymal Stromal Cells. Stem Cell Reports, 6(2):68-175 [paper].

Schemionek, M., Herrmann, O., Merle Reher, M., Chatain, N., Schubert, C., Costa, I. G., Gusmao, E.G., … Koschmieder, S. (2015). MTSS1 is a critical epigenetically regulated tumor suppressor in CML. Leukemia, 30(4):823-32. [paper].

Perkhofer L.,  Walter K., Costa I.G., Bergmann W., Eiseler T., Genze F., Hafner S., Zenke M.,  Seufferlein T.,  Hermann P. C.,  Mueller M., Kleger A., TBX3 drives stemness via increased Activin/Nodal-signalling in human pancreatic ductal adenocarcinoma, Stem Cell Research, 17(2):367-378 [paper].

 Lin Q., Weidner C. I., Costa I. G., Marioni, R., Ferreira M. R. P. , Deary I. J., Wagner W., DNA methylation levels at individual age-associated CpG sites can be indicative for life expectancy?, Aging, 8(2):394-401 [paper].

Eipel M., Mayer F., Arent T., Ferreira M. R. P., Birkhofer C., Gerstenmaier W., Costa I.G.,  Ritz- Timme S.,  Wagner W. (2016),Epigenetic age predictions based on buccal swabs are more precise in combination with cell type-specific DNA methylation signatures , Aging, 8(5):1034-48[paper].

Souza, M.R.B., Araujo G., Costa, I.G.,  Oliveira, J.R.O, Combined genome-wide CSF Aβ-42’s associations and simple network properties highlight new risk factors for Alzheimer´s Disease, Journal of Molecular Neuroscience, 58 (1), 120-128.

Berger A.W., Schwerdel, D. Costa I. G. , Hackert T., Giese N.A., Lam S., Barth T. F. ,  Schroppel B., Meining A., Buchler M. W. , Zenke M. ,  Hermann P. C., Seufferlein T. , Kleger A., Circulating cell-free DNA is a reliable tool to detect hot spot mutations in intraductal papillary mucinous neoplasms of the pancreas, Gastroenterology, 51(2):267-270. [paper].

2015

Lin Q*, Chauvistre H*, Costa IG*, Mitzka S, Gusmao EG, Haenzelmann S, Baying B, Hennuy B, Smeets H, Hoffmann K, Benes V, Sere K, Zenke M, Epigenetic and Transcriptional Architecture of Dendritic Cell Development, Nucleic Acids Research, 43:9680-9693, [paper][data][genome tracks] (*shared first co-author).

Haenzelmann S, Beier F., Gusmao EG ,  Koch CM, Hummel S., Charapitsa I, Joussen S, Benes V, Brümmendorf TH , Reid G, Costa, IG*, Wagner, W* (2015) Replicative Senescence is Associated with Nuclear Reorganization and with DNA Methylation at Specific Transcription Factor Binding Sites, Clinical Epigenetics, 7:9 [paper](shared corresponding author).

de Souto M. C. P.,  Jaskowiak P. A., Costa IG , (2015) Impact of Missing Data Imputation Methods on Gene Expression Clustering and Classification Journal, BMC Bioinformatics, 16:64 [paper][supp].

Hanzelmann S, Wang J, Guney E, Tang Y,  Zhang E, Axelsson AS, Nenonen H,  Salehi AS,  Wollheim CB, Zetterberg E, Berntorp E., Costa IG, Castelo R, Rosengren AH, Thrombin stimulates insulin secretion via protease-activated receptor-3, Islets, 7(4):e1118195.

Müller M, Schröer J, Azoitei N, Eiseler T, Bergmann W, Köhntop R, Lin Q, Costa IG, Zenke M, Genze F, Weidgang C, Seufferlein T, Liebau S, Kleger A., A time frame permissive for Protein Kinase D2 activity to direct angiogenesis in mouse embryonic stem cells, Scientific Reports, 5:11742 [paper].

2014

Allhoff, M., Sere, K., Chauvistre, H., Lin, Q., Zenke M, Costa IG, Detecting differential peaks in ChIP-seq signals with ODIN, Bioinformatics, 30, 3467-3475 [paper][data][supp].

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, 30(22):3143-51. [paper] [Supp].

Jaskowiak, PA , Campello, RJGB, Costa, IG., On The Selection of Appropriate Distances for Gene Expression Data Clustering, BMC Bioinformatics, 15(Suppl 2):S2[paper].

Ullius A., Luscher-Firzlaf , Costa IG, Walsemann, G., Forst, A., Gusmao EG, Kapelle, K., Kleine H., Kremmer K., Vervoorts J., Luscher, B, The interaction of MYC with the trithorax protein ASH2L promotes gene transcription by regulating H3K27 modification, Nucleic Acids Research,  42 (11): 6901-6920 [paper].

Gusmao EG, de Souto, MCP, Issues on Sampling Negative Examples for Predicting Prokaryotic Promoters, Proceedings of the IJCNN, 494-501, [paper].

2013

Jaskowiak, PA , Campello, RJGB, Costa, IG., Proximity Measures for Clustering Gene Expression Microarray Data: a Validation Methodology and a Comparative Analysis, IEEE Transaction in Computational Biology and Bioinformatics,  10(4)  , 845-857. [paper].

Weidner CI., Walenda T., Lin Q., Wölfler MM., Denecke B., Costa IG., Zenke M., Wagner W., Hematopoietic Stem and Progenitor Cells Acquire Distinct DNA-Hypermethylation During in vitro Culture, Scientific Reports, 3:3372, 2013.

Allhoff M., Schoenhuth, A.,Martin, M., Costa, IG.,Rahmann, S., Marschall, T, Discovering Context-Specific Sequencing Errors BMC Bioinformatics (RECOMB-Seq 2013) , 14(Supp 5):S1. [paper] .

Hänzelmann, S.,Castelo, R.,Guinney, J., GSVA: gene set variation analysis for microarray and RNA-Seq data BMC Bioinformatics , 14:7,2013. [paper] .

Araujo G., Costa, I.G.,  Souza, M.R.B. Oliveira, J.R.O., Random Forests and Gene Networks for Association of SNPs to Alzheimer’s Disease, Lecture Notes in Bioinformatics, Volume 8213, 104-115.

2012

Marschall, T., Costa, I. G., Canzar, S., Bauer, M., Klau, G., Schliep, A, Schoenhuth, A.. CLEVER: Clique-Enumerating Variant Finder. Bioinformatics, 28(22):2875-2882, 2012. [paper] [F1000].

do Rego, T. G., Roider, H,  de Carvalho, F. A. T., Costa, I.G., Inferring Epigenetic and Transcriptional Regulation during Blood Cell Development with a Mixture of Sparse Linear Models, Bioinformatics, v. 28(18), p.2297-2303, 2012. [paper].

Mahdi T, Hänzelmann S, Salehi A, et. al., Secreted frizzled-related protein 4 reduces insulin secretion and is overexpressed in type 2 diabetes., Cell Metabolism, 7:16(5):625-33, 2012. [paper].

Lorena, A. C., Costa , I. G., Spoloir, N., de Souto, M. C. P. Analysis of Complexity Indices for Classification Problems: Cancer Gene Expression Data. Neurocomputing, v. 75(1), p. 33-42, 2012. [paper]

Gusmao, E. G, Dietrich, C., Costa, I. G.,  Prediction of Transcription Factor Binding Sites by Integrating DNase digestion and Histone Modification, Lecture Notes in Bioinformatics,, v.7409, p.109-119, 2012.

Jaskowiak, P. A., Campelo, R. J. G. B., Costa, I. G. Evaluating Correlation Coefficients for Clustering Gene Expression Profiles of Cancer. Lecture Notes in Bioinformatics, v.7409, p.120-131, 2012.

de Souto, M. C. P., Coelho, A. L. V., Faceli, K., Sakata, T. C., Bonadia, V., Costa, I. G. A comparison of external clustering evaluation indices in the context of imbalanced data sets. Proc. of the Brazilian Symposium on Neural Networks. IEEE, 49-54 , 2012.

Macario Filho, V., de Carvalho, F. A. T, Costa, I. G. Predicting gene functions using semi-supervised clustering algorithms with objective function optimization, Proc. of the Brazilian Symposium on Neural Networks, IEEE, 61-66, 2012.

2011

Redestig, H., Costa, I. G. Detection and interpretation of metabolite-transcript co-responses using combined profiling data. Bioinformatics (Proceedings of ISMB 2011), v. 27(13), p. i357-i365, 2011. [paper].[Supp]

Hafemeister, C., Costa, I. G., Schonhuth, A., Schliep, A.Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions. Bioinformatics, v. 27(7),p. 946-952, 2011. [paper] [Supp]

Costa, I.G., Roider, H, do Rego, T. G., de Carvalho, F. A. T. Predicting Gene Expression in T cell Differentiation from Histone Modifications and Transcription Factor Binding Affinities by Linear Mixture Models, BMC Bioinformatics. , v.12, p.S29, 2011.[paper] [Supp]

Schilling, R , Costa, I. G. ,  Schliep, A. . pGQL: A Probabilistic Graphical Query Language for Gene Expression Time Courses. Biodata Mining, v. 4, p. 9, 2011. [paper] [software]

2010

B. Georgi, I. G. Costa, A. Schliep PyMix – The Python mixture package – a tool for clustering of heterogeneous biological data, BMC Bioinformatics v.11, p.9, 2010, 11:9 [paper].[Supp]

de Souto, M. C. P., Lorena, A. C., Spoloir, N., Costa , I. G. Complexity measures of supervised classifications tasks: A case study for cancer gene expression data , In: Proceedings of the International Joint Conference on Neural Networks (IJCNN). Los Alamitos: IEEE, 2010. p.1-7.

Lorena, A. C., Spoloir, N., Costa , I. G., de Souto, M. C. P. On the Complexity of Gene Marker Selection ,. Proc. of the Brazilian Symposium on Neural Networks. Los Alamitos, EUA: IEEE, 2010.

Ribeiro, C., Costa , I. G., de Carvalho, F. A. T Semi-supervised Approach for Finding Cancer Sub-Classes on Gene Expression Data, Advances in Computational Biology, Lecture Notes in Bioinformatics. Berlin: Springer Verlag, 2010. v.6268. p.24 – 34

2009

Costa I.G., Schoenhut, A., Hafemeister. C, and Schliep, A., Constrained Mixture Estimation for Analysis and Robust Classification of Clinical Time Series. Bioinformatics, v. 25, p. i6-i14, 2009. [paper] [Supp]

I. G. Costa, A. C. Lorena, L. R. M. P. y Peres, M. C. P de Souto, Using Supervised Complexity Measures in the Analysis of Cancer Gene Expression Data sets. In: Lecture Notes on Bionformatics. Berlin : Springer Verlag, 2009 (Best Paper Award).

A.C.A. Nascimento, R.B.C. Prudencio, M.C.P. de Souto, I. G. Costa, Mining rules for selection of clustering methods for cancer gene expression. In: International Conference on Artificial Neural Networks, 2009, Limassol, Cyprus. Proc. of the International Conference on Artificial Neural Networks. Berlin : Springer-Verlag, 2009.

2008

M. C. P. de Souto, I. G. Costa , D. A. S Araujo, T. B. Ludermir, and A. Schliep Clustering cancer gene expression data: a comparative study. BMC Bioinformatics, 9:497, 2008 [paper][Supp].

I. G. Costa, S. Roepcke, C. Hafemeister, and A. Schliep, Inferring Differentiation Pathways from Gene Expression. Bioinformatics, v 24, p. i156-i164, 2008, [paper] [Supp].

de Souto, M. C. P. ; Costa , I. G. ; Lorena, A. C. On the complexity of gene expression classification data sets.  Eighth International Conference on Hybrid Intelligent Systems. Los Alamitos : IEEE, 2008.

M. C. P. de Souto, D. A. S. Araujo, I. G. Costa , R. G. F. Soares, T. B. Ludermir, and A. Schliep Comparative Study on Normalization Procedures for Cluster Analysis of Gene Expression Datasets. Proceedings of the International Joint Conference on Neural Networks, IEEE Computer Society, pages, 3728-3734, 2008 [pre-print].

M. C. P. de Souto, R. B. C. Prudencio, R. G. F. Soares, D. A. S. Araujo, I. G. Costa , T. B. Ludermir, and A. Schliep Ranking and Selecting Clustering Algorithms Using a Meta-learning Approach. Proceedings of the International Joint Conference on Neural Networks, IEEE Computer Society, 2008 [pre-print].

2007

Costa , I. G., Roepcke, S, Schliep, A. Gene Expression Trees in Lymphoid Development . BMC Immunology, v. 8, p. 25, 2007, [paper][Supp].

I. G. Costa, R. Krause, L. Optiz, and A. Schliep Semi-supervised learning for the identification of syn-expressed genes from fused microarray and in situ image data. BMC Bioinformatics 2007, Vol. 8, Pages S3. [paper] [Supp].

I. G. Costa, M. C. P. de Souto, and A. Schliep Validating Gene Clusterings by Selecting Informative Gene Ontology Terms with Mutual Information. Advances in Bioinformatics and Computational Biology, Lecture Notes in Bioinformatics, Pages 81-92, Springer Verlag, 2007 [pre-print].

2006

I. G. Costa, A. Schliep On the Feasibility ofHeterogeneous Analysis of Large Scale Biological Data Proceedings of ECML/PKDD 2006 Workshop on Data and Text Mining for Integrative Biology, ac55-60. [preprint]

A. A. Schönhuth., I. G. Costa, A. Schliep Semi-supervised Clustering of Yeast Gene Expression Data Japanese-German Workshop on data analysis. and classification 2006, Springer,, [pre-print].

2005

A. Schliep, I. G. Costa, C. Steinhoff, A. A. Schönhuth. Analyzing Gene Expression Time-Courses IEEE/ACM Transactions on Computational Biology andBioinformatics ( Special Issue on Machine Learning for Bioinformatics), 2005, 2(3):179-193. [paper]

I. G. Costa, A. Schönhuth, A. Schliep. The Graphical Query Language: a tool for analysis of gene expression time-courses , Bioinformatics, 2005, 21(10):2544-2545. [paper][software]

I. G. Costa, A. Schliep On external indices for mixtures: validating mixtures of genes In From Data and Information Analysis to Knowledge Engineering, Springer 2005, 662-669.

2004

I. G. Costa, F. A. T. de Carvalho, M. C. P. de Souto, Comparative Analysis of Clustering Methods for Gene Expression Time Course Data, Genetics and Molecular Biology, 2004, 27, 4:623-631. [paper]

2003

I. G. Costa, F. A. T. De Carvalho, M. C. P. de Souto Comparative Study on Proximity Indices for Cluster Analysis of Gene Expression Time Series. Journal of Intelligent and Fuzzy Systems, 13(2-4), 133-142, 2003.

2002

Costa, I. G., M. C. P. de Souto, F. A. T. De Carvalho,. A Symbolic Approach to Gene Expression Time Series Analysis VII Brazilian Symposium on Neural Networks. Los Alamitos: IEEE Computer Society Press, 2002, 1,24-30.

I. G. Costa, F. A. T. de Carvalho, M.C.P. de Souto Stability Evaluation of Clustering Algorithms for Time Series Gene Expression Data In: I Brazilian Workshop on Bioinformatics, 2002, 88-90.