Publications by authors named "Dmitrij Frishman"

100Publications

Experimental determination and data-driven prediction of homotypic transmembrane domain interfaces.

Comput Struct Biotechnol J 2020 7;18:3230-3242. Epub 2020 Oct 7.

Center for Integrated Protein Science Munich (CIPSM) at the Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany.

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http://dx.doi.org/10.1016/j.csbj.2020.09.035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7649602PMC
October 2020

Reply to the Letter of Charre et al. "Mis-Genotyping of Some Hepatitis D Virus Genotype 2 and 5 Sequences Using HDVdb".

Viruses 2020 Nov 9;12(11). Epub 2020 Nov 9.

Institute of Virology, Technische Universität München, 81675 Munich, Germany.

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http://dx.doi.org/10.3390/v12111278DOI Listing
November 2020

Neuronal Differentiation of LUHMES Cells Induces Substantial Changes of the Proteome.

Proteomics 2020 Sep 19:e2000174. Epub 2020 Sep 19.

German Center for Neurodegenerative Diseases (DZNE), Feodor-Lynen-Straße 17, München, 81377, Germany.

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http://dx.doi.org/10.1002/pmic.202000174DOI Listing
September 2020

MPTherm-Pred: Analysis and Prediction of Thermal Stability Changes upon Mutations in Transmembrane Proteins.

J Mol Biol 2020 Sep 10. Epub 2020 Sep 10.

Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, Indian Institute of Technology Madras, Chennai 600 036, Tamilnadu, India. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2020.09.005DOI Listing
September 2020

Mutations in transmembrane proteins: diseases, evolutionary insights, prediction and comparison with globular proteins.

Brief Bioinform 2020 Jul 16. Epub 2020 Jul 16.

Department of Bioinformatics at the TUM School of Life Sciences Weihenstephan in Freising, Germany.

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http://dx.doi.org/10.1093/bib/bbaa132DOI Listing
July 2020

DeepHelicon: Accurate prediction of inter-helical residue contacts in transmembrane proteins by residual neural networks.

J Struct Biol 2020 Oct 11;212(1):107574. Epub 2020 Jul 11.

Department of Bioinformatics, Wissenschaftzentrum Weihenstephan, Technische Universität München, 85354 Freising, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.jsb.2020.107574DOI Listing
October 2020

AllesTM: predicting multiple structural features of transmembrane proteins.

BMC Bioinformatics 2020 Jun 12;21(1):242. Epub 2020 Jun 12.

Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, 85354, Freising, Germany.

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http://dx.doi.org/10.1186/s12859-020-03581-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7291640PMC
June 2020

HDVdb: A Comprehensive Hepatitis D Virus Database.

Viruses 2020 05 14;12(5). Epub 2020 May 14.

Institute of Virology, Technische Universität München, 81675 Munich, Germany.

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http://dx.doi.org/10.3390/v12050538DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7290977PMC
May 2020

Edgetic perturbation signatures represent known and novel cancer biomarkers.

Sci Rep 2020 03 9;10(1):4350. Epub 2020 Mar 9.

Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, 85354, Freising, Germany.

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http://dx.doi.org/10.1038/s41598-020-61422-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7062722PMC
March 2020

Pred-MutHTP: Prediction of disease-causing and neutral mutations in human transmembrane proteins.

Hum Mutat 2020 03 10;41(3):581-590. Epub 2019 Dec 10.

Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, Indian Institute of Technology Madras, Chennai, Tamilnadu, India.

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http://dx.doi.org/10.1002/humu.23961DOI Listing
March 2020

Machine Learning for Cancer Immunotherapies Based on Epitope Recognition by T Cell Receptors.

Front Genet 2019 19;10:1141. Epub 2019 Nov 19.

Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany.

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http://dx.doi.org/10.3389/fgene.2019.01141DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6878726PMC
November 2019

Predicting novel disease mutations in the cardiac sodium channel.

Biochem Biophys Res Commun 2020 01 31;521(3):603-611. Epub 2019 Oct 31.

Almazov National Medical Research Centre, St. Petersburg, 197341, Russia; Department of Bioinformatics, Peter the Great Polytechnic University, St. Petersburg, 195251, Russia; Department of Bioinformatics, Technical University of Munich, Wissenschaftszentrum Weihenstephan, Maximus-von-Imhof Forum 3, 85354, Freising, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.bbrc.2019.10.142DOI Listing
January 2020

Kinetics of hepatitis B surface antigen quasispecies during REP 2139-Ca therapy in HBeAg-positive chronic HBV infection.

J Viral Hepat 2019 12 13;26(12):1454-1464. Epub 2019 Aug 13.

Institute of Virology, Technische Universität München, Munich, Germany.

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http://dx.doi.org/10.1111/jvh.13180DOI Listing
December 2019

Switching the Post-translational Modification of Translation Elongation Factor EF-P.

Front Microbiol 2019 24;10:1148. Epub 2019 May 24.

Center for Integrated Protein Science Munich, Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany.

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http://dx.doi.org/10.3389/fmicb.2019.01148DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6544042PMC
May 2019

Conserved Secondary Structures in Viral mRNAs.

Viruses 2019 04 29;11(5). Epub 2019 Apr 29.

Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, D-85354 Freising, Germany.

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https://www.mdpi.com/1999-4915/11/5/401
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http://dx.doi.org/10.3390/v11050401DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6563262PMC
April 2019

Residue co-evolution helps predict interaction sites in α-helical membrane proteins.

J Struct Biol 2019 05 2;206(2):156-169. Epub 2019 Mar 2.

Department of Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, Maximus-von-Imhof Forum 3, 85354 Freising, Germany; Laboratory of Bioinformatics, RASA Research Center, St Petersburg State Polytechnical University, St Petersburg, 195251, Russia. Electronic address:

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http://dx.doi.org/10.1016/j.jsb.2019.02.009DOI Listing
May 2019

Genetic diversity of hepatitis D virus genotype-1 in Europe allows classification into subtypes.

J Viral Hepat 2019 07 15;26(7):900-910. Epub 2019 Mar 15.

Institute of Virology, Technische Universität München, Munich, Germany.

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http://dx.doi.org/10.1111/jvh.13086DOI Listing
July 2019

Statistical analysis of disease-causing and neutral mutations in human membrane proteins.

Proteins 2019 06 25;87(6):452-466. Epub 2019 Feb 25.

Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India.

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http://doi.wiley.com/10.1002/prot.25667
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http://dx.doi.org/10.1002/prot.25667DOI Listing
June 2019

Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.

Genome Biol Evol 2018 03;10(3):928-938

Department of Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, Freising, Germany.

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http://dx.doi.org/10.1093/gbe/evy049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5952966PMC
March 2018

SCOTCH: subtype A coreceptor tropism classification in HIV-1.

Bioinformatics 2018 08;34(15):2575-2580

Department of Mathematics and Computer Science, Philipps-University of Marburg, Marburg, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bty170DOI Listing
August 2018

MutHTP: mutations in human transmembrane proteins.

Bioinformatics 2018 07;34(13):2325-2326

Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, Indian Institute of Technology Madras, Chennai, Tamilnadu, India.

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http://dx.doi.org/10.1093/bioinformatics/bty054DOI Listing
July 2018

Evolutionary analysis of polyproline motifs in Escherichia coli reveals their regulatory role in translation.

PLoS Comput Biol 2018 02 1;14(2):e1005987. Epub 2018 Feb 1.

Department of Bioinformatics, Wissenschaftzentrum Weihenstephan, Technische Universität München, Freising, Germany.

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http://dx.doi.org/10.1371/journal.pcbi.1005987DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5811046PMC
February 2018

Expitope 2.0: a tool to assess immunotherapeutic antigens for their potential cross-reactivity against naturally expressed proteins in human tissues.

BMC Cancer 2017 12 28;17(1):892. Epub 2017 Dec 28.

Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, 85354, Germany.

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http://dx.doi.org/10.1186/s12885-017-3854-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5745885PMC
December 2017

Conserved RNA structures in the intergenic regions of ambisense viruses.

Sci Rep 2017 11 30;7(1):16625. Epub 2017 Nov 30.

Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, D-85354, Freising, Germany.

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http://dx.doi.org/10.1038/s41598-017-16875-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5709424PMC
November 2017

Structural consequences of mutations associated with idiopathic restrictive cardiomyopathy.

Amino Acids 2017 Nov 22;49(11):1815-1829. Epub 2017 Aug 22.

Department of Bioinformatics, Peter the Great Saint Petersburg Polytechnic University, St. Petersburg, 195251, Russian Federation.

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http://dx.doi.org/10.1007/s00726-017-2480-8DOI Listing
November 2017

Annotation of the Domestic Pig Genome by Quantitative Proteogenomics.

J Proteome Res 2017 08 29;16(8):2887-2898. Epub 2017 Jun 29.

Center for Integrated Protein Science Munich , Munich, Germany.

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http://dx.doi.org/10.1021/acs.jproteome.7b00184DOI Listing
August 2017

Genome-wide analysis of somatic copy number alterations and chromosomal breakages in osteosarcoma.

Int J Cancer 2017 08 25;141(4):816-828. Epub 2017 May 25.

Clinical Cooperation Group Osteosarcoma, Helmholtz Zentrum Munich - German Research Center for Environmental Health, Neuherberg, Germany.

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http://dx.doi.org/10.1002/ijc.30778DOI Listing
August 2017

Melting temperature highlights functionally important RNA structure and sequence elements in yeast mRNA coding regions.

Nucleic Acids Res 2017 Jun;45(10):6109-6118

Department of Bioinformatics, Technische Universität München, Wissenschaftzentrum Weihenstephan, Maximus-von-Imhof-Forum 3, D-85354 Freising, Germany.

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http://dx.doi.org/10.1093/nar/gkx161DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5449622PMC
June 2017

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

Bioinformatics 2017 01 10;33(1):104-111. Epub 2016 Sep 10.

Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising 85354, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btw567DOI Listing
January 2017

Sequence- and Structure-Based Analysis of Tissue-Specific Phosphorylation Sites.

PLoS One 2016 22;11(6):e0157896. Epub 2016 Jun 22.

Department of Genome Oriented Bioinformatics, Technische Universität München, Freising, Germany.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0157896PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4917084PMC
July 2017

Accurate prediction of helix interactions and residue contacts in membrane proteins.

J Struct Biol 2016 Apr 3;194(1):112-23. Epub 2016 Feb 3.

Department of Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, Maximus-von-Imhof Forum 3, 85354 Freising, Germany; Helmholtz Zentrum Munich, German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, 85764 Neuherberg, Germany; Laboratory of Bioinformatics, RASA Research Center, St Petersburg State Polytechnical University, St Petersburg 195251, Russia. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10478477163002
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http://dx.doi.org/10.1016/j.jsb.2016.02.005DOI Listing
April 2016

Genomic determinants of somatic copy number alterations across human cancers.

Hum Mol Genet 2016 Mar 4;25(5):1019-30. Epub 2016 Jan 4.

Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany, Helmholtz Center Munich - German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Ingolstädter Landstrasse 1, D-85764 Neuherberg, Germany and St Petersburg State Polytechnic University, St Petersburg 195251, Russia

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http://dx.doi.org/10.1093/hmg/ddv623DOI Listing
March 2016

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

BMC Bioinformatics 2015 Nov 10;16:380. Epub 2015 Nov 10.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.

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http://dx.doi.org/10.1186/s12859-015-0817-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4641393PMC
November 2015

Differential expression analysis of human endogenous retroviruses based on ENCODE RNA-seq data.

BMC Med Genomics 2015 Nov 3;8:71. Epub 2015 Nov 3.

Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, TU München, Maximus-von-Imhof-Forum 3, Freising, 85354, Germany.

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http://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12
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http://dx.doi.org/10.1186/s12920-015-0146-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4632268PMC
November 2015

Identification of novel hereditary cancer genes by whole exome sequencing.

Cancer Lett 2015 Dec 30;369(2):274-88. Epub 2015 Sep 30.

Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia; Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia; Department of Oncology, I.I. Mechnikov North-Western Medical University, St.-Petersburg 191015, Russia; Department of Oncology, St.-Petersburg State University, St.-Petersburg 199034, Russia. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S03043835150060
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http://dx.doi.org/10.1016/j.canlet.2015.09.014DOI Listing
December 2015

Tissue-specific sequence and structural environments of lysine acetylation sites.

J Struct Biol 2015 Jul 3;191(1):39-48. Epub 2015 Jun 3.

Department of Genome Oriented Bioinformatics, Technische Universität München, 85354 Freising, Germany; Helmholtz Zentrum Munich, German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, 85764, Neuherberg, Germany; St Petersburg State Polytechnical University, St Petersburg 195251, Russia. Electronic address:

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http://dx.doi.org/10.1016/j.jsb.2015.06.001DOI Listing
July 2015

Inter-chromosomal contact networks provide insights into Mammalian chromatin organization.

PLoS One 2015 11;10(5):e0126125. Epub 2015 May 11.

Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, Freising, Germany; Institute for Bioinformatics and Systems Biology, HMGU German Research Center for Environmental Health, Neuherberg, Germany; Department of Bioinformatics, St Petersburg State Polytechnical University, St Petersburg, Russia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0126125PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4427453PMC
February 2016

Expitope: a web server for epitope expression.

Bioinformatics 2015 Jun 1;31(11):1854-6. Epub 2015 Feb 1.

Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 85354 Freising, Germany, Immune Monitoring Group, Helmholtz Zentrum Munich, Institute of Molecular Immunology, 81377 München, Germany, Medigene Immunotherapies GmbH a Subsidiary of Medigene AG, 82152 Planegg, Germany, Helmholtz Zentrum Munich, Institute of Bioinformatics and Systems Biology, 85764 Neuherberg, Germany and St Petersburg State Polytechnical University, St Petersburg, 195251, Russia Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 85354 Freising, Germany, Immune Monitoring Group, Helmholtz Zentrum Munich, Institute of Molecular Immunology, 81377 München, Germany, Medigene Immunotherapies GmbH a Subsidiary of Medigene AG, 82152 Planegg, Germany, Helmholtz Zentrum Munich, Institute of Bioinformatics and Systems Biology, 85764 Neuherberg, Germany and St Petersburg State Polytechnical University, St Petersburg, 195251, Russia Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 85354 Freising, Germany, Immune Monitoring Group, Helmholtz Zentrum Munich, Institute of Molecular Immunology, 81377 München, Germany, Medigene Immunotherapies GmbH a Subsidiary of Medigene AG, 82152 Planegg, Germany, Helmholtz Zentrum Munich, Institute of Bioinformatics and Systems Biology, 85764 Neuherberg, Germany and St Petersburg State Polytechnical University, St Petersburg, 195251, Russia.

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http://bioinformatics.oxfordjournals.org/content/early/2015/
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http://bioinformatics.oxfordjournals.org/content/early/2015/
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/btv068DOI Listing
June 2015

Analysis of micro-rearrangements in 25 eukaryotic species pairs by SyntenyMapper.

PLoS One 2014 6;9(11):e112341. Epub 2014 Nov 6.

Department of Genome Oriented Bioinformatics, Technische Universität München, Freising, Bavaria, Germany; Institute of Bioinformatics and Systems Biology, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany; Department of Bioinformatics, St Petersburg State Polytechnical University, St Petersburg, Russia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0112341PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4223023PMC
December 2015

Genetic variability within the Polish tomato torrado virus Kra isolate caused by deletions in the 3'-untranslated region of genomic RNA1.

Virus Res 2014 Jun 19;185:47-52. Epub 2014 Mar 19.

Interdepartmental Laboratory of Molecular Biology, Institute of Plant Protection - National Research Institute, W. Wegorka 20, 60-318 Poznań, Poland. Electronic address:

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http://dx.doi.org/10.1016/j.virusres.2014.03.008DOI Listing
June 2014

Challenges in RNA virus bioinformatics.

Bioinformatics 2014 Jul 3;30(13):1793-9. Epub 2014 Mar 3.

Friedrich-Schiller-University Jena, Faculty of Mathematics und Computer Science, Leutragraben 1, 07743 Jena, Germany, Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, SIB Swiss Institute of Bioinformatics, CH-4058 Basel, Switzerland, Universitätsklinikum Bonn, Institut für Virologie, Sigmund-Freud-Str. 25, 53127 Bonn, Technische Universität Muenchen, Wissenschaftszentrum Weihenstephan, Am Forum 1, 85354 Freising, Helmholtz Center Munich-German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany, Moscow Institute of Physics and Technology, Institutskii Per. 9, Moscow Region, Dolgoprudny 141700, Russia, Institut für theoretische Chemie, Universität Wien, Währingerstraße 17, A-1090 Wien, Austria, Institute of Virology, Technical University of Munich, Trogerstr. 30, 81675 München, Germany, University of Leipzig, Faculty of Mathematics and Computer Science, Institute for Computer Science, Augustusplatz 10, 04109 Leipzig, Germany, Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, Universität Wien, Althanstraße 14, 1090 Wien, Austria, Department of Computer Science and Interdisciplinary Center of Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany and The Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USAFriedrich-Schiller-University Jena, Faculty of Mathematics und Computer Science, Leutragraben 1, 07743 Jena, Germany, Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, SIB Swiss Institute of Bioinformatics, CH-4058 Basel, Switzerland, Universitätsklinikum Bonn, Institut für Virologie, Sigmund-Freud-Str. 25, 53127 Bonn, Technische Universität Muenchen, Wissenschaftszentrum Weihenstephan, Am Forum 1, 85354 Freising, Helmholtz

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http://dx.doi.org/10.1093/bioinformatics/btu105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7110044PMC
July 2014

Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis.

Nucleic Acids Res 2014 Jan 8;42(Database issue):D396-400. Epub 2013 Nov 8.

Institute for Bioinformatics and Systems Biology/MIPS, HMGU - German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany, Clueda AG, Elsenheimerstraße 59, 80687 Munich, Germany and Department of Genome Oriented Bioinformatics, Technische Universitaet Muenchen Wissenschaftszentrum Weihenstephan, 85350 Freising, Germany.

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http://dx.doi.org/10.1093/nar/gkt1079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965096PMC
January 2014

Classification of α-helical membrane proteins using predicted helix architectures.

PLoS One 2013 25;8(10):e77491. Epub 2013 Oct 25.

Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, Freising, Germany.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0077491PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3808409PMC
August 2014

Conservation of mRNA secondary structures may filter out mutations in Escherichia coli evolution.

Nucleic Acids Res 2013 Sep 19;41(16):7854-60. Epub 2013 Jun 19.

Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftzentrum Weihenstephan, Maximus-von-Imhof-Forum 3, D-85354, Freising, Germany, Helmholtz Center Munich-German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany and Cure Lab, Inc., 43 Rybury Hillway, Needham, MA 02492, USA.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkt507DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3763529PMC
September 2013

RNAtips: Analysis of temperature-induced changes of RNA secondary structure.

Nucleic Acids Res 2013 Jul 12;41(Web Server issue):W486-91. Epub 2013 Jun 12.

Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftzentrum Weihenstephan, Maximus-von-Imhof-Forum 3, D-85354 Freising, Germany.

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http://academic.oup.com/nar/article/41/W1/W486/1110364/RNAti
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http://dx.doi.org/10.1093/nar/gkt486DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692058PMC
July 2013

QARIP: a web server for quantitative proteomic analysis of regulated intramembrane proteolysis.

Nucleic Acids Res 2013 Jul 31;41(Web Server issue):W459-64. Epub 2013 May 31.

Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, Maximus-von-Imhof Forum 3, 85354 Freising, Germany.

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http://dx.doi.org/10.1093/nar/gkt436DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692105PMC
July 2013

How many signal peptides are there in bacteria?

Environ Microbiol 2013 Apr;15(4):983-90

Technische Universität München, Department of Genome-Oriented Bioinformatics, 85354, Freising, Germany.

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http://dx.doi.org/10.1111/1462-2920.12105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3621014PMC
April 2013

Phosphorylation variation during the cell cycle scales with structural propensities of proteins.

PLoS Comput Biol 2013 10;9(1):e1002842. Epub 2013 Jan 10.

Genome-Oriented Bioinformatics Department, Technische Universität München, Freising, Germany.

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http://dx.plos.org/10.1371/journal.pcbi.1002842
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http://dx.doi.org/10.1371/journal.pcbi.1002842DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3542066PMC
June 2013

Unexpected diversity of signal peptides in prokaryotes.

mBio 2012 Nov 20;3(6). Epub 2012 Nov 20.

Division of Biological Sciences, Pacific Northwest National Laboratory, Richland, Washington, USA.

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http://dx.doi.org/10.1128/mBio.00339-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3509430PMC
November 2012

PROSO II--a new method for protein solubility prediction.

FEBS J 2012 Jun 21;279(12):2192-200. Epub 2012 May 21.

Department of Genome Oriented Bioinformatics, Technische Universität Muenchen, Freising, Germany.

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http://dx.doi.org/10.1111/j.1742-4658.2012.08603.xDOI Listing
June 2012

Camps 2.0: exploring the sequence and structure space of prokaryotic, eukaryotic, and viral membrane proteins.

Proteins 2012 Mar 28;80(3):839-57. Epub 2011 Dec 28.

Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, 85354 Freising, Germany.

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http://dx.doi.org/10.1002/prot.23242DOI Listing
March 2012

Sequence-structure relationships in yeast mRNAs.

Nucleic Acids Res 2012 Feb 27;40(3):956-62. Epub 2011 Sep 27.

Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftzentrum Weihenstephan, Maximus-von-Imhof-Forum 3, D-85354, Freising, Germany.

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http://dx.doi.org/10.1093/nar/gkr790DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3273797PMC
February 2012

Testis-specific glyceraldehyde-3-phosphate dehydrogenase: origin and evolution.

BMC Evol Biol 2011 Jun 10;11:160. Epub 2011 Jun 10.

Faculty of Bioengineering and Bioinformatics, MV Lomonosov Moscow State University, Moscow, Russian Federation.

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http://dx.doi.org/10.1186/1471-2148-11-160DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3224139PMC
June 2011

Complex principal component and correlation structure of 16 yeast genomic variables.

Mol Biol Evol 2011 Sep 28;28(9):2501-12. Epub 2011 Mar 28.

Helmholtz Center Munich-German Research Center for Environmental Health, Institute of Bioinformatics and Systems Biology, Ingolstädter Landstraße 1, Neuherberg, Germany.

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http://dx.doi.org/10.1093/molbev/msr077DOI Listing
September 2011

MIPS: curated databases and comprehensive secondary data resources in 2010.

Nucleic Acids Res 2011 Jan 24;39(Database issue):D220-4. Epub 2010 Nov 24.

Institute for Bioinformatics and Systems Biology, MIPS, Helmholtz Center F Health and Environment, Ingolstädter Landstr 1, D-85764 Neuherberg, Germany.

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http://dx.doi.org/10.1093/nar/gkq1157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013725PMC
January 2011

DIMA 3.0: Domain Interaction Map.

Nucleic Acids Res 2011 Jan 19;39(Database issue):D724-9. Epub 2010 Nov 19.

Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, 85350 Freising, Germany.

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http://dx.doi.org/10.1093/nar/gkq1200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013740PMC
January 2011

Coevolution predicts direct interactions between mtDNA-encoded and nDNA-encoded subunits of oxidative phosphorylation complex i.

J Mol Biol 2010 Nov 22;404(1):158-71. Epub 2010 Sep 22.

Department of Life Sciences and the Nation Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.

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http://dx.doi.org/10.1016/j.jmb.2010.09.029DOI Listing
November 2010

Correlated mutations: a hallmark of phenotypic amino acid substitutions.

PLoS Comput Biol 2010 Sep 16;6(9). Epub 2010 Sep 16.

Lehrstuhl für Genomorientierte Bioinformatik, Technische Universität München, Wissenschaftszentrum Weihenstephan, Freising, Germany.

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http://dx.doi.org/10.1371/journal.pcbi.1000923DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2940720PMC
September 2010

Structural comparison and classification of alpha-helical transmembrane domains based on helix interaction patterns.

Proteins 2010 Sep;78(12):2587-99

Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, Freising 85354, Germany.

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http://dx.doi.org/10.1002/prot.22768DOI Listing
September 2010

TargetSpy: a supervised machine learning approach for microRNA target prediction.

BMC Bioinformatics 2010 May 28;11:292. Epub 2010 May 28.

Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany.

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http://dx.doi.org/10.1186/1471-2105-11-292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889937PMC
May 2010

Protein crystallizability.

Methods Mol Biol 2010 ;609:385-400

MIPS & Helmholz Institute München, Martinsried, Germany.

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http://dx.doi.org/10.1007/978-1-60327-241-4_22DOI Listing
May 2010

Current status of membrane protein structure classification.

Proteins 2010 May;78(7):1760-73

Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, D-85354 Freising, Germany.

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http://dx.doi.org/10.1002/prot.22692DOI Listing
May 2010

Ionic interactions promote transmembrane helix-helix association depending on sequence context.

J Mol Biol 2010 Feb 1;396(2):452-61. Epub 2009 Dec 1.

Lehrstuhl für Chemie der Biopolymere, Department für biowissenschaftliche Grundlagen, Technische Universität München, Freising, Germany.

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http://dx.doi.org/10.1016/j.jmb.2009.11.054DOI Listing
February 2010

The Negatome database: a reference set of non-interacting protein pairs.

Nucleic Acids Res 2010 Jan 17;38(Database issue):D540-4. Epub 2009 Nov 17.

Institute for Bioinformatics and Systems Biology/MIPS, HMGU-German Research Center for Environmental Health Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany.

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http://dx.doi.org/10.1093/nar/gkp1026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808923PMC
January 2010

Pitfalls of supervised feature selection.

Bioinformatics 2010 Feb 29;26(3):440-3. Epub 2009 Oct 29.

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http://dx.doi.org/10.1093/bioinformatics/btp621DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2815655PMC
February 2010

Protein function annotation by homology-based inference.

Genome Biol 2009 Feb 2;10(2):207. Epub 2009 Feb 2.

Department of Biological Chemistry, The Hebrew University of Jerusalem, Sudarsky Center, Jerusalem 91904, Israel.

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http://dx.doi.org/10.1186/gb-2009-10-2-207DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688287PMC
February 2009

An evolutionary and structural characterization of mammalian protein complex organization.

BMC Genomics 2008 Dec 23;9:629. Epub 2008 Dec 23.

Helmholtz Center Munich-German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Ingolstädter Landstrasse 1, Neuherberg, Germany.

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http://dx.doi.org/10.1186/1471-2164-9-629DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2645396PMC
December 2008

Complex patterns of histidine, hydroxylated amino acids and the GxxxG motif mediate high-affinity transmembrane domain interactions.

J Mol Biol 2009 Jan 30;385(3):912-23. Epub 2008 Oct 30.

Lehrstuhl für Chemie der Biopolymere, Department für biowissenschaftliche Grundlagen, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany.

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http://linkinghub.elsevier.com/retrieve/pii/S002228360801359
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January 2009

PEDANT covers all complete RefSeq genomes.

Nucleic Acids Res 2009 Jan 21;37(Database issue):D408-11. Epub 2008 Oct 21.

Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.

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http://dx.doi.org/10.1093/nar/gkn749DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686588PMC
January 2009

Prediction of helix-helix contacts and interacting helices in polytopic membrane proteins using neural networks.

Proteins 2009 Mar;74(4):857-71

Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, 85354 Freising, Germany.

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http://doi.wiley.com/10.1002/prot.22194
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March 2009

Prediction of beta-turns and beta-turn types by a novel bidirectional Elman-type recurrent neural network with multiple output layers (MOLEBRNN).

Gene 2008 Oct 10;422(1-2):22-9. Epub 2008 Jun 10.

Department of Genome Oriented Bioinformatics, Technische Universität München, Weihenstephan, Germany.

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http://dx.doi.org/10.1016/j.gene.2008.06.008DOI Listing
October 2008

Designability and disease.

Methods Mol Biol 2008 ;484:491-504

Institute for Bioinformatics, GSF-National Research Center for Environment and Health, Neuherberg, Germany.

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http://link.springer.com/10.1007/978-1-59745-398-1_29
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February 2009

Assignment of isochores for all completely sequenced vertebrate genomes using a consensus.

Genome Biol 2008 30;9(6):R104. Epub 2008 Jun 30.

Department of Genome-Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, D-85350 Freising, Germany.

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http://dx.doi.org/10.1186/gb-2008-9-6-r104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2481423PMC
August 2008

Protein abundance profiling of the Escherichia coli cytosol.

BMC Genomics 2008 Feb 27;9:102. Epub 2008 Feb 27.

Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan.

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http://dx.doi.org/10.1186/1471-2164-9-102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2292177PMC
February 2008

Cellulose as an extracellular matrix component present in Enterobacter sakazakii biofilms.

J Food Prot 2008 Jan;71(1):13-8

Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, CH-8057 Zurich, Switzerland.

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http://dx.doi.org/10.4315/0362-028x-71.1.13DOI Listing
January 2008

Co-evolving residues in membrane proteins.

Bioinformatics 2007 Dec;23(24):3312-9

Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, 85350 Freising, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btm515DOI Listing
December 2007

DIMA 2.0--predicted and known domain interactions.

Nucleic Acids Res 2008 Jan 13;36(Database issue):D651-5. Epub 2007 Nov 13.

Lehrstuhl für Genomorientierte Bioinformatik, Wissenschaftszentrum Weihenstephan, Technische Universität München, Am Forum 1, D-85350 Freising, Germany.

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http://dx.doi.org/10.1093/nar/gkm996DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238836PMC
January 2008

Phenylalanine promotes interaction of transmembrane domains via GxxxG motifs.

J Mol Biol 2007 Nov 26;374(3):705-18. Epub 2007 Sep 26.

Technische Universität München, Lehrstuhl für Chemie der Biopolymere, Weihenstephaner Berg 3, D-85354 Freising-Weihenstephan, and Munich Center For Integrated Protein Science (CIPS(M)), Germany.

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http://dx.doi.org/10.1016/j.jmb.2007.09.056DOI Listing
November 2007

Predicting experimental properties of integral membrane proteins by a naive Bayes approach.

Proteins 2008 Mar;70(4):1243-56

Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenchaftszentrum Weihenstephan, 85350 Freising, Germany.

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http://doi.wiley.com/10.1002/prot.21605
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March 2008

Applying negative rule mining to improve genome annotation.

BMC Bioinformatics 2007 Jul 21;8:261. Epub 2007 Jul 21.

Institute for Bioinformatics, GSF-National Research Center for Environment and Health, Neuherberg, Germany.

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http://dx.doi.org/10.1186/1471-2105-8-261DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1940032PMC
July 2007

Protein annotation at genomic scale: the current status.

Authors:
Dmitrij Frishman

Chem Rev 2007 Aug 21;107(8):3448-66. Epub 2007 Jul 21.

Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenchaftszentrum Weihenstephan, 85350 Freising, Germany.

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http://dx.doi.org/10.1021/cr068303kDOI Listing
August 2007

Predicting experimental properties of proteins from sequence by machine learning techniques.

Curr Protein Pept Sci 2007 Apr;8(2):121-33

Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, 85350 Freising, Germany.

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http://dx.doi.org/10.2174/138920307780363398DOI Listing
April 2007

Protein solubility: sequence based prediction and experimental verification.

Bioinformatics 2007 Oct 6;23(19):2536-42. Epub 2006 Dec 6.

Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, 85350 Freising, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btl623DOI Listing
October 2007

PEDANT genome database: 10 years online.

Nucleic Acids Res 2007 Jan 5;35(Database issue):D354-7. Epub 2006 Dec 5.

Institute for Bioinformatics, GSF-National Research Center for Health and Environment, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.

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http://dx.doi.org/10.1093/nar/gkl1005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1761421PMC
January 2007

Cloning and characterization of Enterobacter sakazakii pigment genes and in situ spectroscopic analysis of the pigment.

FEMS Microbiol Lett 2006 Dec 27;265(2):244-8. Epub 2006 Oct 27.

Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.

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https://academic.oup.com/femsle/article-lookup/doi/10.1111/j
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http://dx.doi.org/10.1111/j.1574-6968.2006.00500.xDOI Listing
December 2006

PROMPT: a protein mapping and comparison tool.

BMC Bioinformatics 2006 Jul 4;7:331. Epub 2006 Jul 4.

Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, 85350 Freising, Germany.

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http://dx.doi.org/10.1186/1471-2105-7-331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1569443PMC
July 2006