Julia A. Bubis

发表

Boosting the MS1-only proteomics with machine learning allows 2000 protein identifications in 5-minute proteome analysis

Mark V. Ivanov, Julia A. Bubis, Vladimir Gorshkov, 2020, bioRxiv.

Cysteine alkylation methods in shotgun proteomics and their possible effects on methionine residues.

Julia A. Bubis, M. Pyatnitskiy, E. Solovyeva, 2020, Journal of proteomics.

AA_stat enables extensive characterization of artefact and post-translational modifications in bottom-up proteomics

Julia A. Bubis, M. Gorshkov, L. Levitsky, 2020, bioRxiv.

Comparative proteomics as a tool for identifying specific alterations within interferon response pathways in human glioblastoma multiforme cells

Julia A. Bubis, M. V. Ivanov, P. Chumakov, 2017, Oncotarget.

DirectMS1Quant: ultrafast quantitative proteomics with MS/MS-free mass spectrometry

Julia A. Bubis, M. V. Ivanov, E. Solovyeva, 2022, bioRxiv.

MS/MS-Free Protein Identification in Complex Mixtures Using Multiple Enzymes with Complementary Specificity.

Julia A. Bubis, M. V. Ivanov, A. Lobas, 2017, Journal of proteome research.

Rpn4 and proteasome-mediated yeast resistance to ethanol includes regulation of autophagy

Julia A. Bubis, D. Karpov, M. Gorshkov, 2020, Applied Microbiology and Biotechnology.

On the Feasibility of Using an Ultra-Fast DirectMS1 Method of Proteome-Wide Analysis for Searching Drug Targets in Chemical Proteomics

Julia A. Bubis, M. V. Ivanov, A. Lobas, 2022, Biochemistry (Moscow).

Massive proteogenomic reanalysis of publicly available proteomic datasets of human tissues in search for protein recoding via adenosine-to-inosine RNA editing

Julia A. Bubis, M. V. Ivanov, M. Pyatnitskiy, 2022, bioRxiv.

Comparative evaluation of label-free quantification methods for shotgun proteomics.

Julia A. Bubis, Lev I Levitsky, Mark V Ivanov, 2017, Rapid communications in mass spectrometry : RCM.

Multi-Omics Analysis of Glioblastoma Cells’ Sensitivity to Oncolytic Viruses

Julia A. Bubis, P. Chumakov, G. Krasnov, 2021, Cancers.

Biosaur: An open-source Python software for LC/MS1 peptide feature detection with ion-mobility support.

Julia A. Bubis, Daniil A. Abdrakhimov, M. V. Ivanov, 2020, Rapid communications in mass spectrometry : RCM.

Scavager: A Versatile Postsearch Validation Algorithm for Shotgun Proteomics Based on Gradient Boosting

Julia A. Bubis, Lev I Levitsky, Mark V Ivanov, 2019, Proteomics.

Proteomics‐based scoring of cellular response to stimuli for improved characterization of signaling pathway activity

Julia A. Bubis, E. Solovyeva, M. Gorshkov, 2022, Proteomics.

HUMOS: How to Understand My Orbitrap Spectrum? - An interactive web-based tool to teach the basics of mass spectrometry-based proteomics.

Julia A. Bubis, Frank Kjeldsen, Julia A Bubis, 2020, Journal of proteome research.

Yeast Ribonucleotide Reductase Is a Direct Target of the Proteasome and Provides Hyper Resistance to the Carcinogen 4-NQO

Julia A. Bubis, D. Karpov, F. Kjeldsen, 2023, Journal of fungi.

AA_stat: Intelligent profiling of in vivo and in vitro modifications from open search results.

Julia A. Bubis, M. Gorshkov, L. Levitsky, 2021, Journal of proteomics.

Boosting MS1-only Proteomics with Machine Learning Allows 2000 Protein Identifications in Single-Shot Human Proteome Analysis Using 5 min HPLC Gradient.

Julia A. Bubis, Vladimir Gorshkov, Daniil A. Abdrakhimov, 2021, Journal of proteome research.

PhosphoShield: Improving Trypsin Digestion of Phosphoproteins by Shielding the Negatively Charged Phosphate Moiety.

Julia A. Bubis, M. Gorshkov, F. Kjeldsen, 2020, Journal of the American Society for Mass Spectrometry.

IQMMA: an efficient MS1 intensity extraction using multiple feature detection algorithms for DDA proteomics

Julia A. Bubis, M. V. Ivanov, M. Gorshkov, 2023, bioRxiv.

Validation of Peptide Identification Results in Proteomics Using Amino Acid Counting

Julia A. Bubis, Lev I Levitsky, Mark V Ivanov, 2018, Proteomics.

A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics

Julia A. Bubis, M. V. Ivanov, E. Deutsch, 2022, bioRxiv.

DirectMS1: MS/MS-free identification of 1000 proteins of cellular proteomes in 5 minutes

Julia A. Bubis, M. V. Ivanov, A. Lobas, 2019, bioRxiv.

IdentiPy: An Extensible Search Engine for Protein Identification in Shotgun Proteomics.

Julia A. Bubis, Lev I Levitsky, Mark V Ivanov, 2018, Journal of proteome research.

Rpn4 and proteasome-mediated yeast resistance to ethanol includes regulation of autophagy

Julia A. Bubis, D. Karpov, M. Gorshkov, 2020, Applied Microbiology and Biotechnology.

Quantitative assessment of strain isolates and microbiomes using fast MS/MS-free metaproteomics

Julia A. Bubis, V. Gorshkov, Y. Delegan, 2024, bioRxiv.

Protein corona formed on silver nanoparticles in blood plasma is highly selective and resistant to physicochemical changes of the solution

Julia A. Bubis, E. Solovyeva, M. Gorshkov, 2019, Environmental science. Nano.