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Prof Dr Olga Kalinina

About

Olga Kalinina received a M.Sc. degree with distinction in mathematics from the Moscow State University in 2003 and a Ph.D. from the Engelhardt Institute for Molecular Biology of the Russian Academy of Sciences in 2007. She continued her research in bioinformatics as a postdoctoral fellow at the European Laboratory for Molecular Biology, for which she was awarded an EMBO Long Term Fellowship from the European Molecular Biology Organization, and later at the University of Heidelberg, working with Prof. Dr. Robert B. Russell (2007-2011). In 2012, she established her independent junior group at the Max Planck Institute for Informatics in the Department for Computational Biology and Applied Algorithmics lead by Prof. Dr. Dr. Thomas Lengauer, where she was researching resistance mechanisms in human viruses until 2018.


2020

A hydrogel-based in vitro assay for the fast prediction of antibiotic accumulation in Gram-negative bacteria

Richter R, Kamal M, García-Rivera M, Kaspar J, Junk M, Elgaher W, Srikakulam S, Gress A, Beckmann A, Grißmer A, …, Schneider-Daum N, Lehr C (2020)

Materials today. Bio 8DOI: 10.1016/j.mtbio.2020.100084

An extended catalogue of tandem alternative splice sites in human tissue transcriptomes

Mironov A, Denisov S, Gress A, Kalinina O, Pervouchine D (2020)

BookDOI: 10.1101/2020.09.11.292722

The bottromycin epimerase BotH defines a group of atypical α/β-hydrolase-fold enzymes

Sikandar A, Franz L, Adam S, Santos-Aberturas J, Horbal L, Luzhetskyy A, Truman A, Kalinina O, Koehnke J (2020)

Nat Chem Biol 16 (9): 1013-1018DOI: 10.1038/s41589-020-0569-y

DIGGER: exploring the functional role of alternative splicing in protein interactions

Louadi Z, Yuan K, Gress A, Tsoy O, Kalinina O, Baumbach J, Kacprowski T, List M (2020)

Nucleic Acids ResDOI: 10.1093/nar/gkaa768

Frequent subgraph mining for biologically meaningful structural motifs

Keller S, Miettinen P, Kalinina O (2020)

BookDOI: 10.1101/2020.05.14.095695

SphereCon-a method for precise estimation of residue relative solvent accessible area from limited structural information

Gress A, Kalinina O (2020)

Bioinformatics (Oxford, England) 36 (11): 3372-3378DOI: 10.1093/bioinformatics/btaa159

Resistance-associated substitutions in patients with chronic hepatitis C virus genotype 4 infection

Dietz J, Kalinina O, Vermehren J, Peiffer K, Matschenz K, Buggisch P, Niederau C, Schattenberg J, Müllhaupt B, Yerly S, …, Welsch C, Sarrazin C (2020)

J. Viral Hepat.DOI: 10.1111/jvh.13322.

Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors

Bastys T, Gapsys V, Walter H, Heger E, Doncheva N, Kaiser R, Groot B, Kalinina O (2020)

Retrovirology 17 (1)DOI: 10.1186/s12977-020-00520-6

A shift of dynamic equilibrium between the KIT active and inactive states causes drug resistance

Srikakulam S, Bastys T, Kalinina O (2020)

ProteinsDOI: 10.1002/prot.25963

2019

Relative Principal Components Analysis: Application to Analyzing Biomolecular Conformational Changes

Ahmad M, Helms V, Kalinina O, Lengauer T (2019)

Journal of chemical theory and computation 15 (4): 2166-2178DOI: 10.1021/acs.jctc.8b01074

Adenosine-to-Inosine RNA Editing in Mouse and Human Brain Proteomes

Levitsky L, Kliuchnikova A, Kuznetsova K, Karpov D, Ivanov M, Pyatnitskiy M, Kalinina O, Gorshkov M, Moshkovskii S (2019)

Proteomics 19 (23)DOI: 10.1002/pmic.201900195.

Targeting actin inhibits repair of doxorubicin-induced DNA damage: a novel therapeutic approach for combination therapy

Pfitzer L, Moser C, Gegenfurtner F, Arner A, Foerster F, Atzberger C, Zisis T, Kubisch-Dohmen R, Busse J, Smith R, …, Vollmar A, Zahler S (2019)

Cell Death Dis. 10 (4)DOI: 10.1038/s41419-019-1546-9

2018

Epistatic Interactions in NS5A of Hepatitis C Virus Suggest Drug Resistance Mechanisms

Knops E, Sierra S, Kalaghatgi P, Heger E, Kaiser R, Kalinina O (2018)

Genes 9 (7)DOI: 10.3390/genes9070343

Consistent Prediction of Mutation Effect on Drug Binding in HIV-1 Protease Using Alchemical Calculations

Bastys T, Gapsys V, Doncheva N, Kaiser R, Groot B, Kalinina O (2018)

Journal of chemical theory and computation 14 (7): 3397-3408DOI: 10.1021/acs.jctc.7b01109

Adaptation of a Bacterial Multidrug Resistance System Revealed by the Structure and Function of AlbA

Sikandar A, Cirnski K, Testolin G, Volz C, Brönstrup M, Kalinina O, Müller R, Koehnke J (2018)

J. Am. Chem. Soc. 140 (48): 16641-16649DOI: 10.1021/jacs.8b08895

2017

Spatial distribution of disease-associated variants in three-dimensional structures of protein complexes

Gress A, Ramensky V, Kalinina O (2017)

Oncogenesis 6 (9)DOI: 10.1038/oncsis.2017.79.

2016

Patterns of amino acid conservation in human and animal immunodeficiency viruses

Voitenko O, Dhroso A, Feldmann A, Korkin D, Kalinina O (2016)

Bioinformatics (Oxford, England) 32 (17): 685-DOI: 10.1093/bioinformatics/btw441

StructMAn: annotation of single-nucleotide polymorphisms in the structural context

Gress A, Ramensky V, Büch J, Keller A, Kalinina O (2016)

Nucleic Acids Res 44 (W1): 463-8DOI: 10.1093/nar/gkw364

BALL-SNPgp-from genetic variants toward computational diagnostics

Mueller S, Backes C, Gress A, Baumgarten N, Kalinina O, Moll A, Kohlbacher O, Meese E, Keller A (2016)

Bioinformatics (Oxford, England) 32 (12): 1888-90DOI: 10.1093/bioinformatics/btw084