PuSH - Publikationsserver des Helmholtz Zentrums München

Ratajczak, F. ; Joblin, M.* ; Ringsquandl, M.* ; Hildebrandt, M.*

Task-driven knowledge graph filtering improves prioritizing drugs for repurposing.

BMC Bioinformatics 23:84 (2022)

Amrhein, L. ; Fuchs, C.

stochprofML: Stochastic profiling using maximum likelihood estimation in R.

BMC Bioinformatics 22:123 (2021)

Waibel, D.J.E. ; Shetab Boushehri, S. ; Marr, C.

InstantDL: An easy-to-use deep learning pipeline for image segmentation and classification.

BMC Bioinformatics 22:103 (2021)

Dony, L. ; He, F.* ; Stumpf, M.P.H.*

Parametric and non-parametric gradient matching for network inference: A comparison.

BMC Bioinformatics 20:52 (2019)

Thiel, D.* ; Conrad, N.D.* ; Ntini, E.* ; Peschutter, R.X.* ; Siebert, H.* ; Marsico, A.

Identifying lncRNA-mediated regulatory modules via ChIA-PET network analysis.

BMC Bioinformatics 20:292 (2019)

Keilwagen, J.* ; Hartung, F.* ; Paulini, M.* ; Twardziok, S.O. ; Grau, J.*

Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi.

BMC Bioinformatics 19:189 (2018)

Molnos, S. ; Baumbach, C. ; Wahl, S. ; Müller-Nurasyid, M. ; Strauch, K. ; Wang-Sattler, R. ; Waldenberger, M. ; Meitinger, T. ; Adamski, J. ; Kastenmüller, G. ; Suhre, K. ; Peters, A. ; Grallert, H. ; Theis, F.J. ; Gieger, C.

pulver: An R package for parallel ultra-rapid p-value computation for linear regression interaction terms.

BMC Bioinformatics 18:429 (2017)

Hahn, K.R. ; Massopust, P. ; Prigarin, S.M.*

A new method to measure complexity in binary or weighted networks and applications to functional connectivity in the human brain.

BMC Bioinformatics 17:87 (2016)

Karapiperis, C.* ; Kempf, S.J. ; Quintens, R.* ; Azimzadeh, O. ; Vidal, V.L.* ; Pazzaglia, S.* ; Bazyka, D.* ; Mastroberardino, P.G.* ; Scouras, Z.G.* ; Tapio, S. ; Benotmane, M.A.* ; Ouzounis, C.A.*

Brain Radiation Information Data Exchange (BRIDE): Integration of experimental data from low-dose ionising radiation research for pathway discovery.

BMC Bioinformatics 17:212 (2016)

Liu, Y. ; Smirnov, K. ; Lucio, M. ; Gougeon, R.D.* ; Alexandre, H.* ; Schmitt-Kopplin, P.

MetICA: Independent component analysis for high-resolution mass-spectrometry based non-targeted metabolomics.

BMC Bioinformatics 17:114 (2016)

Weinhold, L.* ; Wahl, S. ; Pechlivanis, S.* ; Hoffmann, P.* ; Schmid, M.*

A statistical model for the analysis of beta values in DNA methylation studies.

BMC Bioinformatics 17:480 (2016)

Heinig, M.* ; Colomé-Tatché, M.* ; Taudt, A.* ; Rintisch, C.* ; Schäfer, S.* ; Pravenec, M.* ; Hubner, N.* ; Vingron, M.* ; Johannes, F.*

histoneHMM: Differential analysis of histone modifications with broad genomic footprints.

BMC Bioinformatics 16:60 (2015)

Kristensen, D.M.* ; Saeed, U. ; Frishman, D. ; Koonin, E.V.*

A census of α-helical membrane proteins in double-stranded DNA viruses infecting bacteria and archaea.

BMC Bioinformatics 16:380 (2015)

Feigelman, J. ; Theis, F.J. ; Marr, C.

MCA: Multiresolution Correlation Analysis, a graphical tool for subpopulation identification in single-cell gene expression data.

BMC Bioinformatics 15:240 (2014)

Wahl, S. ; Fenske, N.* ; Zeilinger, S. ; Suhre, K. ; Gieger, C. ; Waldenberger, M. ; Grallert, H. ; Schmid, M.*

On the potential of models for location and scale for genome-wide DNA methylation data.

BMC Bioinformatics 15:232 (2014)

Buggenthin, F. ; Marr, C. ; Schwarzfischer, M. ; Hoppe, P.S. ; Hilsenbeck, O. ; Schroeder, T. ; Theis, F.J.

An automatic method for robust and fast cell detection in bright field images from high-throughput microscopy.

BMC Bioinformatics 14:297 (2013)

Hock, S. ; Hasenauer, J. ; Theis, F.J.

Modeling of 2D diffusion processes based on microscopy data: Parameter estimation and practical identifiability analysis.

BMC Bioinformatics 14:S7 (2013)

Vehlow, C.* ; Hasenauer, J. ; Krämer, A.* ; Raue, A. ; Hug, S. ; Timmer, J.* ; Radde, N.* ; Theis, F.J. ; Weiskopf, D.*

iVUN: Interactive Visualization of Uncertain biochemical reaction Networks.

BMC Bioinformatics 14:S2 (2013)

Petersen, A.-K. ; Krumsiek, J. ; Wägele, B. ; Theis, F.J. ; Wichmann, H.-E. ; Gieger, C. ; Suhre, K.

On the hypothesis-free testing of metabolite ratios in genome-wide and metabolome-wide association studies.

BMC Bioinformatics 13:120 (2012)

van Wieringen, W.N.* ; Unger, K. ; Leday, G.G.R.* ; Krijgsman, O.* ; de Menezes, R.X.* ; Ylstra, B.* ; van de Wiel, M.A.*

Matching of array CGH and gene expression microarray features for the purpose of integrative genomic analyses.

BMC Bioinformatics 13:80 (2012)

Hasenauer, J.* ; Waldherr, S.* ; Doszczak, M.* ; Radde, N.* ; Scheurich, P.* ; Allgöwer, F.*

Identification of models of heterogeneous cell populations from population snapshot data.

BMC Bioinformatics 12:125 (2011)

Knapp, B.* ; Rebhan, I.* ; Kumar, A.* ; Matula, P.* ; Kiani, N.A.* ; Binder, M.* ; Erfle, H.* ; Rohr, K.B.* ; Eils, R.* ; Bartenschlager, R.* ; Kaderali, L.*

Normalizing for individual cell population context in the analysis of high-content cellular screens.

BMC Bioinformatics 12:485 (2011)

Forer, L.* ; Schönherr, S.* ; Weissensteiner, H.* ; Haider, F.* ; Kluckner, T.* ; Gieger, C. ; Wichmann, H.-E. ; Specht, G.* ; Kronenberg, F.* ; Kloss-Brandstätter, A.*

CONAN: Copy number variation analysis software for genome-wide association studies.

BMC Bioinformatics 11:318 (2010)

Hartsperger, M.L. ; Blöchl, F. ; Stuempflen, V. ; Theis, F.J.

Structuring heterogeneous biological information using fuzzy clustering of k-partite graphs.

BMC Bioinformatics 11:522 (2010)

Kowarsch, A. ; Blöchl, F. ; Bohl, S.* ; Saile, M.* ; Gretz, N.* ; Klingmüller, U.* ; Theis, F.J.

Knowledge-based matrix factorization temporally resolves the cellular responses to IL-6 stimulation.

BMC Bioinformatics 11:585 (2010)

Krumsiek, J. ; Pölsterl, S. ; Wittmann, D.M. ; Theis, F.J.

Odefy - from discrete to continuous models.

BMC Bioinformatics 11, 1-10:233 (2010)

Sturm, M. ; Hackenberg, M.* ; Langenberger, D.* ; Frishman, D.