Julia Bubis
Julia Bubis
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Protein corona formed on silver nanoparticles in blood plasma is highly selective and resistant to physicochemical changes of the solution
V Gorshkov, JA Bubis, EM Solovyeva, MV Gorshkov, F Kjeldsen
Environmental Science: Nano 6 (4), 1089-1098, 2019
IdentiPy: an extensible search engine for protein identification in shotgun proteomics
LI Levitsky, MV Ivanov, AA Lobas, JA Bubis, IA Tarasova, EM Solovyeva, ...
Journal of proteome research 17 (7), 2249-2255, 2018
Comparative evaluation of label‐free quantification methods for shotgun proteomics
JA Bubis, LI Levitsky, MV Ivanov, IA Tarasova, MV Gorshkov
Rapid Communications in Mass Spectrometry 31 (7), 606-612, 2017
Scavager: a versatile postsearch validation algorithm for shotgun proteomics based on gradient boosting
MV Ivanov, LI Levitsky, JA Bubis, MV Gorshkov
Proteomics 19 (3), 1800280, 2019
DirectMS1: MS/MS-free identification of 1000 proteins of cellular proteomes in 5 minutes
MV Ivanov, JA Bubis, V Gorshkov, IA Tarasova, LI Levitsky, AA Lobas, ...
Analytical chemistry 92 (6), 4326-4333, 2020
Comparative proteomics as a tool for identifying specific alterations within interferon response pathways in human glioblastoma multiforme cells
IA Tarasova, AV Tereshkova, AA Lobas, EM Solovyeva, AS Sidorenko, ...
Oncotarget 9 (2), 1785, 2018
Boosting MS1-only proteomics with machine learning allows 2000 protein identifications in single-shot human proteome analysis using 5 min HPLC gradient
MV Ivanov, JA Bubis, V Gorshkov, DA Abdrakhimov, F Kjeldsen, ...
Journal of proteome research 20 (4), 1864-1873, 2021
MS/MS-free protein identification in complex mixtures using multiple enzymes with complementary specificity
MV Ivanov, IA Tarasova, LI Levitsky, EM Solovyeva, ML Pridatchenko, ...
Journal of Proteome Research 16 (11), 3989-3999, 2017
Cysteine alkylation methods in shotgun proteomics and their possible effects on methionine residues
KG Kuznetsova, LI Levitsky, MA Pyatnitskiy, IY Ilina, JA Bubis, ...
Journal of proteomics 231, 104022, 2021
Multi-omics analysis of glioblastoma cells’ sensitivity to oncolytic viruses
AV Lipatova, AV Soboleva, VA Gorshkov, JA Bubis, EM Solovyeva, ...
Cancers 13 (21), 5268, 2021
Biosaur: An open‐source Python software for liquid chromatography–mass spectrometry peptide feature detection with ion mobility support
DA Abdrakhimov, JA Bubis, V Gorshkov, F Kjeldsen, MV Gorshkov, ...
Rapid Communications in Mass Spectrometry, e9045, 2021
Rpn4 and proteasome-mediated yeast resistance to ethanol includes regulation of autophagy
JA Bubis, DS Spasskaya, VA Gorshkov, F Kjeldsen, AM Kofanova, ...
Applied microbiology and biotechnology 104, 4027-4041, 2020
Validation of peptide identification results in proteomics using amino acid counting
JA Bubis, LI Levitsky, MV Ivanov, MV Gorshkov
Proteomics 18 (23), 1800117, 2018
DirectMS1Quant: ultrafast quantitative proteomics with MS/MS-free mass spectrometry
MV Ivanov, JA Bubis, V Gorshkov, IA Tarasova, LI Levitsky, EM Solovyeva, ...
Analytical chemistry 94 (38), 13068-13075, 2022
Proteomics‐based scoring of cellular response to stimuli for improved characterization of signaling pathway activity
EM Kazakova, EM Solovyeva, LI Levitsky, JA Bubis, DD Emekeeva, ...
Proteomics 23 (5), 2200275, 2023
PhosphoShield: Improving Trypsin Digestion of Phosphoproteins by Shielding the Negatively Charged Phosphate Moiety
JA Bubis, V Gorshkov, MV Gorshkov, F Kjeldsen
Journal of the American Society for Mass Spectrometry 31 (10), 2053-2060, 2020
Massive proteogenomic reanalysis of publicly available proteomic datasets of human tissues in search for protein recoding via adenosine-to-inosine RNA editing
LI Levitsky, MV Ivanov, AO Goncharov, AA Kliuchnikova, JA Bubis, ...
Journal of proteome research, 2023
On the Feasibility of Using an Ultra-Fast DirectMS1 Method of Proteome-Wide Analysis for Searching Drug Targets in Chemical Proteomics
EM Solovyeva, JA Bubis, IA Tarasova, AA Lobas, MV Ivanov, AA Nazarov, ...
Biochemistry (Moscow) 87 (11), 1342-1353, 2022
A comprehensive evaluation of consensus spectrum generation methods in proteomics
X Luo, W Bittremieux, J Griss, EW Deutsch, T Sachsenberg, LI Levitsky, ...
Journal of proteome research 21 (6), 1566-1574, 2022
AA_stat: Intelligent profiling of in vivo and in vitro modifications from open search results
LI Levitsky, JA Bubis, MV Gorshkov, IA Tarasova
Journal of Proteomics 248, 104350, 2021
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