PuSH - Publikationsserver des Helmholtz Zentrums München

An, Y. ; Bergant, V.* ; Grünke, C.* ; Bonnal, B.* ; Henrici, A.* ; Pichlmair, A. ; Schubert, B. ; Marsico, A.

TransFactor-Prediction of pro-viral SARS-CoV-2 host factors using a protein language model.

Bioinformatics 41:btaf491 (2025)

Ouologuem, S. ; Martens, L.D. ; Schaar, A. ; Shulman, M. ; Gagneur, J. ; Theis, F.J.

Spatial transcriptomics deconvolution methods generalize well to spatial chromatin accessibility data.

Bioinformatics 41, i314-i322 (2025)

Ali, M. ; Kuijs, M. ; Hediyeh-Zadeh, S. ; Treis, T. ; Hrovatin, K. ; Palla, G. ; Schaar, A. ; Theis, F.J.

GraphCompass: Spatial metrics for differential analyses of cell organization across conditions.

Bioinformatics 40, i548-i557 (2024)

Astaburuaga-García, R.* ; Sell, T.* ; Mutlu, S.* ; Sieber, A.* ; Lauber, K. ; Blüthgen, N.*

RUCova: Removal of unwanted covariance in mass cytometry data.

Bioinformatics 40:btae669 (2024)

Dorešić, D. ; Grein, S.* ; Hasenauer, J.

Efficient parameter estimation for ODE models of cellular processes using semi-quantitative data.

Bioinformatics 40, i558-i566 (2024)

Hagenberg, J. ; Budde, M.* ; Pandeva, T. ; Kondofersky, I. ; Schaupp, S.K.* ; Theis, F.J. ; Schulze, T.G.* ; Müller, N.S. ; Heilbronner, U.* ; Batra, R. ; Knauer-Arloth, J.

longmixr: A tool for robust clustering of high-dimensional cross-sectional and longitudinal variables of mixed data types.

Bioinformatics 40:btae137 (2024)

Heumos, S.* ; Heuer, M.L.* ; Hanssen, F.* ; Heumos, L. ; Guarracino, A.* ; Heringer, P.* ; Ehmele, P. ; Prins, P.* ; Garrison, E.* ; Nahnsen, S.*

Cluster-efficient pangenome graph construction with nf-core/pangenome.

Bioinformatics 40:btae609 (2024)

Stock, M. ; Popp, N. ; Fiorentino, J. ; Scialdone, A.

Topological benchmarking of algorithms to infer Gene Regulatory Networks from Single-Cell RNA-seq Data.

Bioinformatics 40:btae267 (2024)

Wang, J.* ; Horlacher, M. ; Cheng, L.* ; Winther, O.*

DeepLocRNA: An interpretable deep learning model for predicting RNA subcellular localisation with domain-specific transfer-learning.

Bioinformatics 40:btae065 (2024)

Alamoudi, E.* ; Schälte, Y. ; Müller, R.* ; Starruß, J.* ; Bundgaard, N.* ; Graw, F.* ; Brusch, L.* ; Hasenauer, J.

FitMultiCell: simulating and parameterizing computational models of multi-scale and multi-cellular processes.

Bioinformatics 39:btad674 (2023)

Hecker, D.* ; Behjati Ardakani, F.* ; Karollus, A.* ; Gagneur, J. ; Schulz, M.H.*

The adapted activity-by-contact model for enhancer-gene assignment and its application to single-cell data.

Bioinformatics 39:btad062 (2023)

Heumos, L. ; Ehmele, P.* ; Kuhn Cuellar, L.* ; Menden, K.* ; Miller, E.* ; Lemke, S.* ; Gabernet, G.* ; Nahnsen, S.*

mlf-core: A framework for deterministic machine learning.

Bioinformatics 39:8 (2023)

Huth, M. ; Arruda, J.* ; Gusinow, R. ; Contento, L.* ; Tacconelli, E.* ; Hasenauer, J.*

Accessibility of covariance information creates vulnerability in Federated Learning frameworks.

Bioinformatics 39:9 (2023)

Kardell, O. ; Breimann, S.* ; Hauck, S.M.

mpwR: An R package for comparing performance of mass spectrometry-based proteomic workflows.

Bioinformatics 39:3 (2023)

Schälte, Y. ; Fröhlich, F.* ; Jost, P.J.* ; Vanhoefer, J.* ; Pathirana, D.* ; Stapor, P. ; Lakrisenko, P. ; Wang, D. ; Raimundez-Alvarez, E. ; Merkt, S.* ; Schmiester, L. ; Städter, P. ; Grein, S.* ; Dudkin, E.* ; Doresic, D.* ; Weindl, D. ; Hasenauer, J.

pyPESTO: A modular and scalable tool for parameter estimation for dynamic models.

Bioinformatics 39:btad711 (2023)

Vilov, S. ; Heinig, M.

DeepSom: A CNN-based approach to somatic variant calling in WGS samples without a matched normal.

Bioinformatics 39:9 (2023)

Weidner, L. ; Hemmler, D. ; Rychlik, M.* ; Schmitt-Kopplin, P.

DBDIpy: A Python library for processing of untargeted datasets from real-time plasma ionization mass spectrometry.

Bioinformatics 39:2 (2023)

Yuzeir, A.* ; Bejarano, D.A.* ; Grein, S.* ; Hasenauer, J. ; Schlitzer, A.* ; Yu, J.*

IntestLine: A shiny-based application to map the rolled intestinal tissue onto a line.

Bioinformatics 39:2 (2023)

Chetnik, K.* ; Benedetti, E.* ; Gomari, D.P. ; Schweickart, A.* ; Batra, R.* ; Buyukozkan, M.* ; Wang, Z.* ; Arnold, M. ; Zierer, J.* ; Suhre, K.* ; Krumsiek, J.*

maplet: An extensible R toolbox for modular and reproducible metabolomics pipelines.

Bioinformatics 38, 1168-1170 (2022)

Habermann, D.* ; Kharimzadeh, H.* ; Walker, A.* ; Li, Y.* ; Yang, R.* ; Kaiser, R.* ; Brumme, Z.L.* ; Timm, J.* ; Roggendorf, M. ; Hoffmann, D.*

HAMdetector: A Bayesian regression model that integrates information to detect HLA-associated mutations.

Bioinformatics 38, 2428-2436 (2022)

Ogris, C. ; Castresana-Aguirre, M.* ; Sonnhammer, E.L.L.*

PathwAX II: Network-based pathway analysis with interactive visualization of network crosstalk.

Bioinformatics 38, 2659-2660 (2022)

Salzer, L. ; Witting, M. ; Schmitt-Kopplin, P.

MobilityTransformR: An R package for effective mobility transformation of CE-MS data.

Bioinformatics 38, 4044-4045 (2022)

Fröhlich, F.* ; Weindl, D. ; Schälte, Y. ; Pathirana, D.* ; Paszkowski, L.* ; Lines, G.T.* ; Stapor, P. ; Hasenauer, J.

AMICI: High-performance sensitivity analysis for large ordinary differential equation models.

Bioinformatics 37, 3676-3677 (2021)

Schmiester, L. ; Weindl, D. ; Hasenauer, J.

Efficient gradient-based parameter estimation for dynamic models using qualitative data.

Bioinformatics 37, 4493-4500 (2021)

Angerer, P. ; Fischer, D.S. ; Theis, F.J. ; Scialdone, A. ; Marr, C.

Automatic identification of relevant genes from low-dimensional embeddings of single-cell RNA-seq data.

Bioinformatics 36, 4291-4295 (2020)

Dorigatti, E. ; Schubert, B.

Joint epitope selection and spacer design for string-of-beads vaccines.

Bioinformatics 36, 2, i643-i650 (2020)

Haselimashhadi, H.* ; Mason, J.C.* ; Muñoz-Fuentes, V.* ; López-Gómez, F.* ; Babalola, K.* ; Acar, E.F.* ; Kumar, V.* ; White, J.* ; Flenniken, A.M.* ; King, R.* ; Straiton, E.* ; Seavitt, J.R.* ; Gaspero, A.* ; Garza, A.* ; Christianson, A.E.* ; Hsu, C.-W.* ; Reynolds, C.L.* ; Lanza, D.G.* ; Lorenzo, I.* ; Green, J.R.* ; Gallegos, J.J.* ; Bohat, R.* ; Samaco, R.C.* ; Veeraragavan, S.* ; Kim, J.K.* ; Miller, G. ; Fuchs, H. ; Garrett, L. ; Becker, L. ; Kang, Y.K.* ; Clary, D.* ; Cho, S.Y.* ; Tamura, M.* ; Tanaka, N.* ; Soo, K.D.* ; Bezginov, A.* ; About, G.B.* ; Champy, M.-F.* ; Vasseur, L.* ; Leblanc, S.* ; Meziane, H.* ; Selloum, M.* ; Reilly, P.T.* ; Spielmann, N. ; Maier, H. ; Gailus-Durner, V. ; Sorg, T.* ; Hiroshi, M.* ; Yuichi, O.* ; Heaney, J.D.* ; Dickinson, M.E.* ; Wurst, W. ; Tocchini-Valentini, G.P.* ; Lloyd, K.C.K.* ; McKerlie, C.* ; Seong, J.K.* ; Herault, Y.* ; Hrabě de Angelis, M. ; Brown, S.D.M.* ; Smedley, D.* ; Flicek, P.* ; Mallon, A.-M.* ; Parkinson, H.* ; Meehan, T.F.*

Soft windowing application to improve analysis of high-throughput phenotyping data.

Bioinformatics 36, 1492-1500 (2020)

Lotfollahi, M. ; Naghipourfar, M. ; Theis, F.J. ; Wolf, F.A.

Conditional out-of-distribution generation for unpaired data using transfer VAE.

Bioinformatics 36, 2, i610-i617 (2020)

Porubsky, D.* ; Sanders, A.D.* ; Taudt, A. ; Colomé-Tatché, M. ; Lansdorp, P.M.* ; Guryev, V.*

breakpointR: An R/Bioconductor package to localize strand state changes in Strand-seq data.

Bioinformatics 36, 1260-1261 (2020)

Schälte, Y. ; Hasenauer, J.

Efficient exact inference for dynamical systems with noisy measurements using sequential approximate Bayesian computation.

Bioinformatics 36, 1, 551-559 (2020)

Schmiester, L. ; Schälte, Y. ; Fröhlich, F. ; Hasenauer, J. ; Weindl, D.

Efficient parameterization of large-scale dynamic models based on relative measurements.

Bioinformatics 36, 594-602 (2020)

Solovey, M. ; Scialdone, A.

COMUNET: A tool to explore and visualize intercellular communication.

Bioinformatics 36, 4296-4300 (2020)

Do, K.T. ; Rasp, D.J.N.P. ; Kastenmüller, G. ; Suhre, K. ; Krumsiek, J.

MoDentify: Phenotype-driven module identification in metabolomics networks at different resolutions.

Bioinformatics 35, 532-534 (2019)

Gilly, A. ; Southam, L.* ; Suveges, D.* ; Kuchenbaecker, K.* ; Moore, R.* ; Melloni, G.E.M.* ; Hatzikotoulas, K. ; Farmaki, A.E.* ; Ritchie, G.* ; Schwartzentruber, J.* ; Danecek, P.* ; Kilian, B.* ; Pollard, M.O.* ; Ge, X.* ; Tsafantakis, E.* ; Dedoussis, G.* ; Zeggini, E.

Very low-depth whole-genome sequencing in complex trait association studies.

Bioinformatics 35, 2555-2561 (2019)

Hamad, S. ; Adornetto, G. ; Naveja, J.J. ; Ravindranath, A.C. ; Raffler, J. ; Campillos, M.

HitPickV2: A web server to predict targets of chemical compounds.

Bioinformatics 35, 1239-1240 (2019)

Hass, H.* ; Loos, C. ; Raimundez-Alvarez, E. ; Timmer, J.* ; Hasenauer, J. ; Kreutz, C.*

Benchmark problems for dynamic modeling of intracellular processes.

Bioinformatics 35, 3073-3082 (2019)

Jeske, T. ; Huypens, P. ; Stirm, L. ; Höckele, S. ; Wurmser, C.M.* ; Böhm, A. ; Weigert, C. ; Staiger, H. ; Klein, C.* ; Beckers, J. ; Hastreiter, M.

DEUS: An R package for accurate small RNA profiling based on differential expression of unique sequences.

Bioinformatics 35, 4834-4836 (2019)

Villaverde, A.F.* ; Fröhlich, F. ; Weindl, D. ; Hasenauer, J. ; Banga, J.R.*

Benchmarking optimization methods for parameter estimation in large kinetic models.

Bioinformatics 35, 830-838 (2019)

Ballnus, B. ; Schaper, S.* ; Theis, F.J. ; Hasenauer, J.

Bayesian parameter estimation for biochemical reaction networks using region-based adaptive parallel tempering.

Bioinformatics 34, 494-501 (2018)

Klinger, E. ; Rickert, D. ; Hasenauer, J.

pyABC: Distributed, likelihood-free inference.

Bioinformatics 34, 3591-3593 (2018)

Loos, C. ; Krause, S. ; Hasenauer, J.

Hierarchical optimization for the efficient parametrization of ODE models.

Bioinformatics 34, 4266-4273 (2018)

Stapor, P. ; Weindl, D. ; Ballnus, B. ; Hug, S. ; Loos, C. ; Fiedler, A. ; Krause, S. ; Hross, S. ; Fröhlich, F. ; Hasenauer, J.

PESTO: Parameter EStimation TOolbox.

Bioinformatics 34, 705-707 (2018)

Stapor, P. ; Fröhlich, F. ; Hasenauer, J.

Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis.

Bioinformatics 34, 151-159 (2018)

Chlis, N.-K. ; Wolf, F.A. ; Theis, F.J.

Model-based branching point detection in single-cell data by K-Branches clustering.

Bioinformatics 33, 3211-3219 (2017)

Dirmeier, S.* ; Fuchs, C. ; Müller, N.S. ; Theis, F.J.

netReg: Network-regularized linear models for biological association studies.

Bioinformatics 34, 896-898 (2017)

Fröhlich, F. ; Theis, F.J. ; Rädler, J.O.* ; Hasenauer, J.

Parameter estimation for dynamical systems with discrete events and logical operations.

Bioinformatics 33, 1049-1056 (2017)

Hastreiter, M. ; Jeske, T. ; Hoser, J.D.S. ; Kluge, M. ; Ahomaa, K. ; Friedl, M.-S. ; Kopetzky, S.J. ; Quell, J. ; Mewes, H.-W. ; Küffner, R.

KNIME4NGS: A comprehensive toolbox for next generation sequencing analysis.

Bioinformatics 33, 1565-1567 (2017)

Hilsenbeck, O.* ; Schwarzfischer, M. ; Loeffler, D.* ; Dimopoulos, S.* ; Hastreiter, S.* ; Marr, C. ; Theis, F.J. ; Schroeder, T.*

fastER: A user-friendly tool for ultrafast and robust cell segmentation in large-scale microscopy.

Bioinformatics 33, 2020-2028 (2017)

Jaravine, V.* ; Raffegerst, S.* ; Schendel, D.J.* ; Frishman, D.

Assessment of cancer and virus antigens for cross-reactivity in human tissues.

Bioinformatics 33, 104-111 (2017)

Kazeroonian, A. ; Theis, F.J. ; Hasenauer, J.

A scalable moment-closure approximation for large-scale biochemical reaction networks.

Bioinformatics 33, i293-i300 (2017)

Ligon, T.S.* ; Fröhlich, F. ; Chi, O.T.* ; Banga, J.R.* ; Balsa-Canto, E.* ; Hasenauer, J.

GenSSI 2.0: Multi-experiment structural identifiability analysis of SBML models.

Bioinformatics 34, 1421-1423 (2017)

Maier, C. ; Loos, C. ; Hasenauer, J.

Robust parameter estimation for dynamical systems from outlier-corrupted data.

Bioinformatics 33, 1-8 (2017)

Zheng, J.* ; Erzurumluoglu, A.M.* ; Elsworth, B.L.* ; Kemp, J.P.* ; Howe, L.* ; Haycock, P.C.* ; Hemani, G.* ; Tansey, K.* ; Laurin, C.* ; St. Pourcain, B.* ; Warrington, N.M.* ; Finucane, H.K.* ; Price, A.L.* ; Bulik-Sullivan, B.* ; Anttila, V.* ; Paternoster, L.* ; Gaunt, T.R.* ; Evans, D.M* ; Neale, B.M.* ; EUMODIC Consortium (Heinrich, J.)

LD Hub: A centralized database and web interface to perform LD score regression that maximizes the potential of summary level GWAS data for SNP heritability and genetic correlation analysis.

Bioinformatics 33, 272-279 (2017)

Angerer, P. ; Haghverdi, L. ; Büttner, M. ; Theis, F.J. ; Marr, C. ; Buettner, F.

Destiny: Diffusion maps for large-scale single-cell data in R.

Bioinformatics 32, 1241-1243 (2016)

Geissen, E.M.* ; Hasenauer, J. ; Heinrich, S.* ; Hauf, S.* ; Theis, F.J. ; Radde, N.*

MEMO - multi-experiment mixture model analysis of censored data.

Bioinformatics 32, 2464-2472 (2016)

Hross, S. ; Hasenauer, J.

Analysis of CFSE time-series data using division-, age- and label-structured population models.

Bioinformatics 32, 2321-2329 (2016)

Arnold, M. ; Raffler, J. ; Pfeufer, A. ; Suhre, K. ; Kastenmüller, G.

SNiPA: An interactive, genetic variant-centered annotation browser.

Bioinformatics 31, 1334-1336 (2015)

Haase, K.* ; Raffegerst, S.H. ; Schendel, D.J. ; Frishman, D.

Expitope: A web server for epitope expression.

Bioinformatics 31, 1854-1856 (2015)

Haghverdi, L. ; Buettner, F. ; Theis, F.J.

Diffusion maps for high-dimensional single-cell analysis of differentiation data.

Bioinformatics 31, 2989-2998 (2015)

Kim, D.K.* ; Lee, J.* ; Kim, S.R.* ; Choi, D.S.* ; Yoon, Y.J.* ; Kim, J.H.* ; Go, G.* ; Nhung, D.* ; Hong, K.* ; Jang, S.C.* ; Kim, S.H.* ; Park, K.S.* ; Kim, O.Y.* ; Park, H.T.* ; Seo, J.H.* ; Aikawa, E.* ; Baj-Krzyworzeka, M.* ; van Balkom, B.W.* ; Belting, M.* ; Blanc, L.* ; Bond, V.* ; Bongiovanni, A.* ; Borràs, F.E.* ; Buée, L.* ; Buzás, E.I.* ; Cheng, L.* ; Clayton, A.* ; Cocucci, E.* ; Dela Cruz, C.S.* ; Desiderio, D.M.* ; di Vizio, D.* ; Ekström, K.* ; Falcón-Pérez, J.M.* ; Gardiner, C.* ; Giebel, B.* ; Greening, D.W.* ; Gross, J.C.* ; Gupta, D.* ; Hendrix, A.* ; Hill, A.F.* ; Hill, M.M.* ; Nolte-'t Hoen, E.* ; Hwang, D.W.* ; Inal, J.* ; Jagannadham, M.V.* ; Jayachandran, M.* ; Jee, Y.K.* ; Jørgensen, M.* ; Kim, K.P.* ; Kim, Y.K.* ; Kislinger, T.* ; Lässer, C.* ; Lee, D.S.* ; Lee, H.* ; van Leeuwen, J.* ; Lener, T.* ; Liu, M.L.* ; Lötvall, J.* ; Marcilla, A.* ; Mathivanan, S. ; Möller, A.* ; Morhayim, J.* ; Mullier, F.* ; Nazarenko, I.* ; Nieuwland, R.* ; Nunes, D.N.* ; Pang, K.* ; Park, J.* ; Patel, T.* ; Pocsfalvi, G.* ; del Portillo, H.* ; Putz, U.* ; Ramirez, M.I.* ; Rodrigues, M.L.* ; Roh, T.Y.* ; Royo, F.* ; Sahoo, S.* ; Schiffelers, R.* ; Sharma, S.* ; Siljander, P.* ; Simpson, R.J.* ; Soekmadji, C.* ; Stahl, P.* ; Stensballe, A.* ; Stępień, E.* ; Tahara, H.* ; Trummer, A.* ; Valadi, H.* ; Vella, L.J.* ; Wai, S.N.* ; Witwer, K.* ; Yáñez-Mó, M.* ; Youn, H.* ; Zeidler, R. ; Gho, Y.S.*

EVpedia: A community web portal for extracellular vesicles research.

Bioinformatics 31, 933-939 (2015)

Matos, M.R.* ; Knapp, B. ; Kaderali, L.*

lpNet: A linear programming approach to reconstruct signal transduction networks.

Bioinformatics 31, 3231-3233 (2015)

Ocone, A. ; Haghverdi, L. ; Müller, N.S. ; Theis, F.J.

Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data.

Bioinformatics 31, i89-i96 (2015)

Petri, T.* ; Altmann, S.* ; Geistlinger, L.* ; Zimmer, R.* ; Küffner, R.

Addressing false discoveries in network inference.

Bioinformatics 31, 2836-2843 (2015)

Raue, A.* ; Steiert, B.* ; Schelker, M.* ; Kreutz, C.* ; Maiwald, T.* ; Hass, H.* ; Vanlier, J.* ; Tönsing, C.* ; Adlung, L.* ; Engesser, R.* ; Mader, W.* ; Heinemann, T.* ; Hasenauer, J. ; Schilling, M.* ; Höfer, T.* ; Klipp, E.* ; Theis, F.J. ; Klingmüller, U.* ; Schöberl, B.* ; Timmer, J.*

Data2Dynamics: A modeling environment tailored to parameter estimation in dynamical systems.

Bioinformatics 31, 3558-3560 (2015)

Sass, S. ; Buettner, F. ; Müller, N.S. ; Theis, F.J.

RAMONA: A web application for gene set analysis on multilevel omics data.

Bioinformatics 31, 128-130 (2015)

Andor, N. ; Harness, J.V.* ; Müller, S.* ; Mewes, H.-W. ; Petritsch, C.*

EXPANDS: Expanding ploidy and allele frequency on nested subpopulations.

Bioinformatics 30, 50-60 (2014)

Buettner, F. ; Moignard, V.* ; Göttgens, B.* ; Theis, F.J.

Probabilistic PCA of censored data: Accounting for uncertainties in the visualisation of high-throughput single-cell qPCR data.

Bioinformatics 30, 1867-1875 (2014)

Liu, X. ; Campillos, M.

Unveiling new biological relationships using shared hits of chemical screening assay pairs.

Bioinformatics 30, i579-i586 (2014)

März, M.* ; Beerenwinkel, N.* ; Drosten, C.* ; Fricke, M.* ; Frishman, D. ; Hofacker, I.L.* ; Hoffmann, D.* ; Middendorf, M.* ; Rattei, T.* ; Stadler, P.F.* ; Töpfer, A.*

Challenges in RNA virus bioinformatics.

Bioinformatics 30, 1793-1799 (2014)

Nussbaumer, T. ; Kugler, K.G. ; Bader, K.C. ; Sharma, S. ; Seidel, M. ; Mayer, K.F.X.

RNASeqExpressionBrowser - a web interface to browse and visualize high-throughput expression data.

Bioinformatics 30, 2519-2520 (2014)

Vogt, I. ; Prinz, J. ; Worf, K.* ; Campillos, M.

Systematic analysis of gene properties influencing organ system phenotypes in mammalian perturbations.

Bioinformatics 30, 3093-3100 (2014)

Liu, X. ; Vogt, I. ; Haque, T. ; Campillos, M.

HitPick: A web server for hit identification and target prediction of chemical screenings.

Bioinformatics 29, 1910-1912 (2013)

Rivas, M.A.* ; Pirinen, M.* ; Neville, M.J.* ; Gaulton, K.J.* ; Moutsianas, L.* ; GoT2D Consortium (Gieger, C. ; Grallert, H. ; Hrabě de Angelis, M. ; Huth, C. ; Kriebel, J. ; Meisinger, C. ; Meitinger, T. ; Müller-Nurasyid, M. ; Peters, A. ; Rathmann, W. ; Ried, J.S. ; Strauch, K. ; Donnelly, P.) ; Lindgren, C.M.* ; Karpe, F.* ; McCarthy, M.I.*

Assessing association between protein truncating variants and quantitative traits.

Bioinformatics 29, 2419-2426 (2013)

Buettner, F. ; Theis, F.J.

A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst.

Bioinformatics 28, i626-i632 (2012)

Seifert, M.* ; Cortijo, S.* ; Colomé-Tatché, M. ; Johannes, F.* ; Roudier, F.* ; Colot, V.*

MeDIP-HMM: Genome-wide identification of distinct DNA methylation states from high-density tiling arrays.

Bioinformatics 28, 2930-2939 (2012)

Ellwanger, D.C. ; Büttner, F.A. ; Mewes, H.-W. ; Stuempflen, V.

The sufficient minimal set of miRNA seed types.

Bioinformatics 27, 1346-1350 (2011)

Götz, S.* ; Arnold, R.* ; Sebastián-León, P.* ; Martín-Rodríguez, S.* ; Tischler, P.* ; Jehl, M.A.* ; Dopazo, J.* ; Rattei, T.* ; Conesa, A.*

B2G-FAR, a species-centered GO annotation repository.

Bioinformatics 27, 919-924 (2011)

Johannes, F.* ; Wardenaar, R.* ; Colomé-Tatché, M. ; Mousson, F.* ; de Graaf, P.* ; Mokry, M.* ; Guryev, V.* ; Timmers, H.T.* ; Cuppen, E.* ; Jansen, R.C.*

Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq.

Bioinformatics 26, 1000-1006 (2010)

Smialowski, P. ; Frishman, D. ; Kramer, S.*

Pitfalls of supervised feature selection.

Bioinformatics 26, 440-443 (2010)

Dietmann, S. ; Georgii, E.* ; Antonov, A.* ; Tsuda, K.* ; Mewes, H.-W.

The DICS repository: Module-assisted analysis of disease-related gene lists.

Bioinformatics 25, 830-831 (2009)

Georgii, E.* ; Dietmann, S. ; Uno, T.* ; Pagel, P. ; Tsuda, K.*

Enumeration of condition-dependent dense modules in protein interaction networks.

Bioinformatics 25, 933-940 (2009)

Rieber, N.* ; Knapp, B.* ; Eils, R.* ; Kaderali, L.*

RNAither, an automated pipeline for the statistical analysis of high-throughput RNAi screens.

Bioinformatics 25, 678-679 (2009)

Wägele, B. ; Dunger-Kaltenbach, I. ; Fobo, G. ; Montrone, C. ; Mewes, H.-W. ; Ruepp, A.

CRONOS: The cross-reference navigation server.

Bioinformatics 25, 141-143 (2009)

Kastenmüller, G. ; Gasteiger, J.* ; Mewes, H.-W.

An environmental perspective on large-scale genome clustering based on metabolic capabilities.

Bioinformatics 24, i56-i62 (2008)

Krumsiek, J.* ; Friedel, C.C.* ; Zimmer, R.*

ProCope - protein complex prediction and evaluation.

Bioinformatics 24, 2115-2116 (2008)

Schachtner, R.* ; Lutter, D. ; Knollmüller, P.* ; Tomé, A.M.* ; Theis, F.J. ; Schmitz, G.* ; Stetter, M.* ; Vilda, P.G.* ; Lang, E.W.*

Knowledge-based gene expression classification via matrix factorization.

Bioinformatics 24, 1688-1697 (2008)

Tetko, I.V. ; Rodchenkov, I. ; Walter, M.C. ; Rattei, T.* ; Mewes, H.-W.

Beyond the 'best' match: Machine learning annotation of protein sequences by integration of different sources of information.

Bioinformatics 24, 621-628 (2008)

Krumsiek, J. ; Arnold, R. ; Rattei, T.*

Gepard: A rapid and sensitive tool for creating dotplots on genome scale.

Bioinformatics 23, 1026-1028 (2007)

Pagel, P. ; Oesterheld, M. ; Stuempflen, V. ; Frishman, D.

The DIMA web resource-exploring the protein domain network.

Bioinformatics 22, 997-998 (2006)

Wang, Y. ; Hindemitt, T. ; Mayer, K.F.X.

Significant sequence similarities in promoters and precursors of Arabidopsis thaliana non-conserved microRNAs.

Bioinformatics 22, 2585-2589 (2006)

Arnold, R. ; Rattei, T.* ; Tischler, P. ; Truong, M.-D. ; Stuempflen, V. ; Mewes, H.-W.

Bioinformatics 21, 42-46 (2005)

Artamonova, I.I. ; Frishman, G. ; Gelfand, M.S.* ; Frishman, D.

Mining sequence annotation databanks for association patterns.

Bioinformatics 21, 3, 49-57 (2005)

Friedel, C.C.* ; Jahn, K.H.* ; Sommer, S.* ; Rudd, S.* ; Mewes, H.-W. ; Tetko, I.V.

Support vector machines for separation of mixed plant-pathogen EST collections based on codon usage.

Bioinformatics 21, 1383-1388 (2005)

Hindemitt, T. ; Mayer, K.F.X.

CREDO: A web-based tool for computational detection of conserved sequence motifs in noncoding sequences.

Bioinformatics 21, 4304-4306 (2005)

Pagel, P. ; Kovac, S. ; Oesterheld, M. ; Brauner, B. ; Dunger-Kaltenbach, I. ; Frishman, G. ; Montrone, C. ; Mark, P.* ; Stuempflen, V. ; Mewes, H.-W. ; Ruepp, A.

The MIPS mammalian protein-protein interaction database.

Bioinformatics 21, 832-834 (2005)

Tetko, I.V. ; Brauner, B. ; Dunger-Kaltenbach, I. ; Frishman, G. ; Montrone, C. ; Fobo, G. ; Ruepp, A. ; Antonov, A.V.

MIPS bacterial genomes functional annotation benchmark dataset.

Bioinformatics 21, 2520-2521 (2005)

Wahl, M.B. ; Heinzmann, U. ; Imai, K.

LongSAGE analysis significantly improves genome annotation: identifications of novel genes and alternative transcripts in the mouse.

Bioinformatics 21, 1393-1400 (2005)

Wahl, M.B. ; Heinzmann, U. ; Imai, K.

LongSAGE analysis revealed the presence of a large number of novel antisense genes in the mouse genome.

Bioinformatics 21, 1389-1392 (2005)

Antonov, A.V. ; Tetko, I.V. ; Mader, M.T. ; Budczies, J. ; Mewes, H.-W.