Works by Pfeifer, Nico

Results: 35

Inherently interpretable position-aware convolutional motif kernel networks for biological sequencing data.

Published in:

Scientific Reports, 2023, v. 13, n. 1, p. 1, doi. 10.1038/s41598-023-44175-7

By:

Ditz, Jonas C.;
Reuter, Bernhard;
Pfeifer, Nico

Publication type:

Article

Respiratory viruses dynamics and interactions: ten years of surveillance in central Europe.

Published in:

2022

By:

Horemheb-Rubio, Gibran;
Eggeling, Ralf;
Schmeiβer, Norbert;
Pfeifer, Nico;
Lengauer, Thomas;
Gärtner, Barbara C.;
Prifert, Christiane;
Kochanek, Matthias;
Scheid, Christoph;
Adams, Ortwin;
Kaiser, Rolf;
Respiratory Virus Network;
C. Gärtner, Barbara;
Weissbrich, Benedikt;
Berger, Annemarie;
Palupsky, Katrin;
Huzly, Daniela;
Tiemann, Carsten;
Borena, Wegene;
Lindauer, Andreas

Publication type:

journal article

Prediction of HIV-1 sensitivity to broadly neutralizing antibodies shows a trend towards resistance over time.

Published in:

PLoS Computational Biology, 2017, v. 13, n. 10, p. 1, doi. 10.1371/journal.pcbi.1005789

By:

Hake, Anna;
Pfeifer, Nico

Publication type:

Article

EuCARE-hospitalised study protocol: a cohort study of patients hospitalised with COVID-19 in the EuCARE project.

Published in:

BMC Infectious Diseases, 2023, v. 23, n. 1, p. 1, doi. 10.1186/s12879-023-08658-2

By:

Hedberg, Pontus;
Varisco, Benedetta;
Bai, Francesca;
Sönnerborg, Anders;
Naucler, Pontus;
Pfeifer, Nico;
Cozzi-Lepri, Alessandro;
Ceccherini-Silberstein, Francesca;
Naumovas, Daniel;
Drobniewski, Francis;
Jensen, Björn-Erik Ole;
Toscano, Cristina;
Parczewski, Miłosz;
Quintanares, Gibran Horemheb Rubio;
Mwau, Matilu;
Pinto, Jorge A.;
Incardona, Francesca;
Mommo, Chiara;
Marchetti, Giulia

Publication type:

Article

EuCARE-POSTCOVID Study: a multicentre cohort study on long-term post-COVID-19 manifestations.

Published in:

BMC Infectious Diseases, 2023, v. 23, n. 1, p. 1, doi. 10.1186/s12879-023-08595-0

By:

Varisco, Benedetta;
Bai, Francesca;
De Benedittis, Sara;
Tavelli, Alessandro;
Cozzi-Lepri, Alessandro;
Sala, Matteo;
Miraglia, Federica Gaia;
Santoro, Maria Mercedes;
Ceccherini-Silberstein, Francesca;
Shimoni, Yishai;
Ravid, Sivan;
Kozlovski, Tal;
König, Florian;
Pfeifer, Nico;
Shamsara, Elham;
Parczewski, Milosz;
Monforte, Antonella d’Arminio;
Incardona, Francesca;
Mommo, Chiara;
Marchetti, Giulia

Publication type:

Article

Time‐dependent prediction of mortality and cytomegalovirus reactivation after allogeneic hematopoietic cell transplantation using machine learning.

Published in:

American Journal of Hematology, 2022, v. 97, n. 10, p. 1309, doi. 10.1002/ajh.26671

By:

Eisenberg, Lisa;
Brossette, Christian;
Rauch, Jochen;
Grandjean, Andrea;
Ottinger, Hellmut;
Rissland, Jürgen;
Schwarz, Ulf;
Graf, Norbert;
Beelen, Dietrich W.;
Kiefer, Stephan;
Pfeifer, Nico;
Turki, Amin T.

Publication type:

Article

A study on interoperability between two Personal Health Train infrastructures in leukodystrophy data analysis.

Published in:

Scientific Data, 2024, v. 11, n. 1, p. 1, doi. 10.1038/s41597-024-03450-6

By:

Welten, Sascha;
de Arruda Botelho Herr, Marius;
Hempel, Lars;
Hieber, David;
Placzek, Peter;
Graf, Michael;
Weber, Sven;
Neumann, Laurenz;
Jugl, Maximilian;
Tirpitz, Liam;
Kindermann, Karl;
Geisler, Sandra;
Bonino da Silva Santos, Luiz Olavo;
Decker, Stefan;
Pfeifer, Nico;
Kohlbacher, Oliver;
Kirsten, Toralf

Publication type:

Article

Corrigendum to: Family-joining: A fast distance-based method for constructing generally labeled trees.

Published in:

Molecular Biology & Evolution, 2020, v. 37, n. 6, p. 1845, doi. 10.1093/molbev/msz281

By:

Kalaghatgi, Prabhav;
Pfeifer, Nico;
Lengauer, Thomas

Publication type:

Article

Family-Joining: A Fast Distance-Based Method for Constructing Generally Labeled Trees.

Published in:

Molecular Biology & Evolution, 2016, v. 33, n. 10, p. 2720, doi. 10.1093/molbev/msw123

By:

Kalaghatgi, Prabhav;
Pfeifer, Nico;
Lengauer, Thomas

Publication type:

Article

Using drug exposure for predicting drug resistance – A data-driven genotypic interpretation tool.

Published in:

PLoS ONE, 2017, v. 12, n. 4, p. 1, doi. 10.1371/journal.pone.0174992

By:

Pironti, Alejandro;
Pfeifer, Nico;
Walter, Hauke;
Jensen, Björn-Erik O.;
Zazzi, Maurizio;
Gomes, Perpétua;
Kaiser, Rolf;
Lengauer, Thomas

Publication type:

Article

Improving HIV coreceptor usage prediction in the clinic using hints from next-generation sequencing data.

Published in:

Bioinformatics, 2012, v. 28, n. 18, p. i589, doi. 10.1093/bioinformatics/bts373

By:

Pfeifer, Nico;
Lengauer, Thomas

Publication type:

Article

TOPP—the OpenMS proteomics pipeline.

Published in:

Bioinformatics, 2007, v. 23, n. 2, p. e191, doi. 10.1093/bioinformatics/btl299

By:

Oliver Kohlbacher;
Knut Reinert;
Clemens Gröpl;
Eva Lange;
Nico Pfeifer;
Ole Schulz-Trieglaff;
Marc Sturm

Publication type:

Article

Model‐Based Prediction of Clinically Relevant Thrombocytopenia after Allogeneic Hematopoietic Stem Cell Transplantation.

Published in:

Clinical Pharmacology & Therapeutics, 2025, v. 117, n. 5, p. 1413, doi. 10.1002/cpt.3580

By:

Götz, Katharina M.;
Turki, Amin T.;
Och, Katharina;
Selzer, Dominik;
Brossette, Christian;
Graf, Norbert;
Rauch, Jochen;
Theobald, Stefan;
Braun, Yvonne;
Rohm, Kerstin;
Weiler, Gabriele;
Rüdesheim, Simeon;
Schwab, Matthias;
Eisenberg, Lisa;
Pfeifer, Nico;
Kiefer, Stephan;
Schwarz, Ulf;
Riede, Claudia;
Smola, Sigrun;
Beelen, Dietrich W.

Publication type:

Article

OpenMS -- An open-source software framework for mass spectrometry.

Published in:

2008

By:

Sturm, Marc;
Bertsch, Andreas;
Gröpl, Clemens;
Hildebrandt, Andreas;
Hussong, Rene;
Lange, Eva;
Pfeifer, Nico;
Schulz-Trieglaff, Ole;
Zerck, Alexandra;
Reinert, Knut;
Kohlbacher, Oliver

Publication type:

Product Review

Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics.

Published in:

BMC Bioinformatics, 2007, v. 8, p. 468, doi. 10.1186/1471-2105-8-468

By:

Pfeifer, Nico;
Leinenbach, Andreas;
Huber, Christian G.;
Kohlbacher, Oliver

Publication type:

Article

PlasmoFAB: a benchmark to foster machine learning for Plasmodium falciparum protein antigen candidate prediction.

Published in:

Bioinformatics, 2023, v. 39, p. i86, doi. 10.1093/bioinformatics/btad206

By:

Ditz, Jonas C;
Wistuba-Hamprecht, Jacqueline;
Maier, Timo;
Fendel, Rolf;
Pfeifer, Nico;
Reuter, Bernhard

Publication type:

Article

COmic: convolutional kernel networks for interpretable end-to-end learning on (multi-)omics data.

Published in:

Bioinformatics, 2023, v. 39, p. i76, doi. 10.1093/bioinformatics/btad204

By:

Ditz, Jonas C;
Reuter, Bernhard;
Pfeifer, Nico

Publication type:

Article

Efficient privacy-preserving whole-genome variant queries.

Published in:

Bioinformatics, 2022, v. 38, n. 8, p. 2202, doi. 10.1093/bioinformatics/btac070

By:

Akgün, Mete;
Pfeifer, Nico;
Kohlbacher, Oliver

Publication type:

Article

Identifying disease-causing mutations with privacy protection.

Published in:

Bioinformatics, 2020, v. 36, n. 21, p. 5205, doi. 10.1093/bioinformatics/btaa641

By:

Akgün, Mete;
Ünal, Ali Burak;
Ergüner, Bekir;
Pfeifer, Nico;
Kohlbacher, Oliver

Publication type:

Article

Weighted elastic net for unsupervised domain adaptation with application to age prediction from DNA methylation data.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i154, doi. 10.1093/bioinformatics/btz338

By:

Handl, Lisa;
Jalali, Adrin;
Scherer, Michael;
Eggeling, Ralf;
Pfeifer, Nico

Publication type:

Article

Integrating different data types by regularized unsupervised multiple kernel learning with application to cancer subtype discovery.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i268, doi. 10.1093/bioinformatics/btv244

By:

Speicher, Nora K.;
Pfeifer, Nico

Publication type:

Article

Unique and assay specific features of NOMe-, ATAC- and DNase I-seq data.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 20, p. 10580, doi. 10.1093/nar/gkz799

By:

Nordström, Karl J V;
Schmidt, Florian;
Gasparoni, Nina;
Salhab, Abdulrahman;
Gasparoni, Gilles;
Kattler, Kathrin;
Müller, Fabian;
Ebert, Peter;
Costa, Ivan G;
consortium, DEEP;
Pfeifer, Nico;
Lengauer, Thomas;
Schulz, Marcel H;
Walter, Jörn

Publication type:

Article

web-rMKL: a web server for dimensionality reduction and sample clustering of multi-view data based on unsupervised multiple kernel learning.

Published in:

Nucleic Acids Research, 2019, v. 47, n. W1, p. W605, doi. 10.1093/nar/gkz422

By:

Röder, Benedict;
Kersten, Nicolas;
Herr, Marius;
Speicher, Nora K;
Pfeifer, Nico

Publication type:

Article

A dynamic time-to-event model for prediction of acute graft-versus-host disease in patients after allogeneic hematopoietic stem cell transplantation.

Published in:

Cancer Medicine, 2024, v. 13, n. 1, p. 1, doi. 10.1002/cam4.6833

By:

Och, Katharina;
Turki, Amin T.;
Götz, Katharina M.;
Selzer, Dominik;
Brossette, Christian;
Theobald, Stefan;
Braun, Yvonne;
Graf, Norbert;
Rauch, Jochen;
Rohm, Kerstin;
Weiler, Gabriele;
Kiefer, Stephan;
Schwarz, Ulf;
Eisenberg, Lisa;
Pfeifer, Nico;
Ihle, Matthias;
Grandjean, Andrea;
Fix, Sonja;
Riede, Claudia;
Rissland, Jürgen

Publication type:

Article

Molecular Epidemiology of HIV-1 in Eastern Europe and Russia.

Published in:

Viruses (1999-4915), 2022, v. 14, n. 10, p. N.PAG, doi. 10.3390/v14102099

By:

van de Klundert, Maarten A. A.;
Antonova, Anastasiia;
Di Teodoro, Giulia;
Ceña Diez, Rafael;
Chkhartishvili, Nikoloz;
Heger, Eva;
Kuznetsova, Anna;
Lebedev, Aleksey;
Narayanan, Aswathy;
Ozhmegova, Ekaterina;
Pronin, Alexander;
Shemshura, Andrey;
Tumanov, Alexandr;
Pfeifer, Nico;
Kaiser, Rolf;
Saladini, Francesco;
Zazzi, Maurizio;
Incardona, Francesca;
Bobkova, Marina;
Sönnerborg, Anders

Publication type:

Article

Improved therapy-success prediction with GSS estimated from clinical HIV-1 sequences.

Published in:

Journal of the International AIDS Society, 2014, v. 17, p. n/a, doi. 10.7448/IAS.17.4.19743

By:

Pironti, Alejandro;
Pfeifer, Nico;
Kaiser, Rolf;
Walter, Hauke;
Lengauer, Thomas

Publication type:

Article

Interpretable per case weighted ensemble method for cancer associations.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2647-9

By:

Jalali, Adrin;
Pfeifer, Nico

Publication type:

Article

Genetic sequence-based prediction of long-range chromatin interactions suggests a potential role of short tandem repeat sequences in genome organization.

Published in:

BMC Bioinformatics, 2017, v. 18, p. 1, doi. 10.1186/s12859-017-1624-x

By:

Nikumbh, Sarvesh;
Pfeifer, Nico

Publication type:

Article

Clinical use, efficacy, and durability of maraviroc for antiretroviral therapy in routine care: A European survey.

Published in:

PLoS ONE, 2019, v. 14, n. 11, p. 1, doi. 10.1371/journal.pone.0225381

By:

De Luca, Andrea;
Pezzotti, Patrizio;
Boucher, Charles;
Döring, Matthias;
Incardona, Francesca;
Kaiser, Rolf;
Lengauer, Thomas;
Pfeifer, Nico;
Schülter, Eugen;
Vandamme, Anne-Mieke;
Zazzi, Maurizio;
Geretti, Anna Maria

Publication type:

Article

A genotypic method for determining HIV-2 coreceptor usage enables epidemiological studies and clinical decision support.

Published in:

Retrovirology, 2016, v. 13, p. 1, doi. 10.1186/s12977-016-0320-7

By:

Döring, Matthias;
Borrego, Pedro;
Büch, Joachim;
Martins, Andreia;
Friedrich, Georg;
Camacho, Ricardo Jorge;
Eberle, Josef;
Kaiser, Rolf;
Lengauer, Thomas;
Taveira, Nuno;
Pfeifer, Nico

Publication type:

Article

Modelling binding between CCR5 and CXCR4 receptors and their ligands suggests the surface electrostatic potential of the co-receptor to be a key player in the HIV-1 tropism.

Published in:

Retrovirology, 2013, v. 10, n. 1, p. 1, doi. 10.1186/1742-4690-10-130

By:

Kalinina, Olga V.;
Pfeifer, Nico;
Lengauer, Thomas

Publication type:

Article

Insights to HIV-1 coreceptor usage by estimating HLA adaptation with Bayesian generalized linear mixed models.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 12, p. 1, doi. 10.1371/journal.pcbi.1010355

By:

Hake, Anna;
Germann, Anja;
de Beer, Corena;
Thielen, Alexander;
Däumer, Martin;
Preiser, Wolfgang;
von Briesen, Hagen;
Pfeifer, Nico

Publication type:

Article

Predicting functional effects of ion channel variants using new phenotypic machine learning methods.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 3, p. 1, doi. 10.1371/journal.pcbi.1010959

By:

Boßelmann, Christian Malte;
Hedrich, Ulrike B. S.;
Lerche, Holger;
Pfeifer, Nico

Publication type:

Article

Hepatitis C Virus Saint Petersburg Variant Detection With Machine Learning Methods.

Published in:

Journal of Medical Virology, 2025, v. 97, n. 2, p. 1, doi. 10.1002/jmv.70169

By:

Arslan, Nurhan;
Reuter, Bernhard;
Buech, Joachim;
Lengauer, Thomas;
Obermeier, Martin;
Kaiser, Rolf;
Pfeifer, Nico

Publication type:

Article

Machine learning prediction of malaria vaccine efficacy based on antibody profiles.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 6, p. 1, doi. 10.1371/journal.pcbi.1012131

By:

Wistuba-Hamprecht, Jacqueline;
Reuter, Bernhard;
Fendel, Rolf;
Hoffman, Stephen L.;
Campo, Joseph J.;
Felgner, Philip L.;
Kremsner, Peter G.;
Mordmüller, Benjamin;
Pfeifer, Nico

Publication type:

Article