Author

B. Budnik

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

Click to filter author papers

Biochemistry· 4 Bioengineering· 2 Biophysics· 1 Cell Biology· 1 Microbiology· 1 Physiology· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Approach:experimental assay· 7 Organism:human· 7 Research Focus:cell type annotation· 5 Assay:proteomics· 5 Research Focus:protein folding & dynamics· 4 Assay:bulk RNA-seq· 2 Research Focus:cell signaling & trafficking· 2 Research Focus:differential expression· 2

Frequent Co-Authors

S. A. Trauger· 3 shared D. E. Ingber· 2 shared E. I. Shakhnovich· 2 shared E. Serebryany· 2 shared S. Shahriar· 2 shared V. Horvath· 2 shared A. Alvarez-Buylla· 1 shared A. B. Roland· 1 shared

Activity by Year

2018-2024 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 15 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

3 shared papersBiophysics

S. A. Trauger

Mutual co-authors in cluster

Author profile →

10 papers

Recent·Most cited

Control of Molecular Biochemistry and Cell Injury Responses through Highly Ordered Supramolecular Assembly of Flavonoids

C. B. Reilly, S. G. Bernier, S. Shahriar, V. Horvath, M. Lewandowski, E. Javorsky, B. Budnik, D. E. Ingber

Molecular dynamic simulations reveal flavonoids self-assemble into ordered structures that interact with proteins, modulate enzyme activity, and protect cells from UV-induced injury.

bioRxiv · Apr 3, 2024 · PreprintBiochemistry

Mucus production, host-microbiome interactions, hormone sensitivity, and innate immune responses modeled in human cervix chips

Z. Izadifar, J. Cotton, C. Chen, N. A. Bustos, V. Horvath, A. Stejskalova, C. Wu, A. Gulati, N. T. LoGrande, B. Budnik, S. Shahriar, E. Doherty, T. To, S. E. Gilpin, A. M. Sesay, , D. E. Ingber

This paper develops human cervical Organ Chip models to study mucus production, host-microbiome interactions, and immune responses, showing they mimic in vivo conditions and respond to microbiome changes.

bioRxiv · Feb 22, 2023 · PreprintBioengineering

Improved Isolation of Extracellular Vesicles by Removal of Both Free Proteins and Lipoproteins

D. Ter-Ovanesyan, T. Gilboa, B. Budnik, A. Nikitina, S. Whiteman, R. Lazarovits, W. Trieu, D. Kalish, G. M. Church, D. R. Walt

The paper develops a method to improve EV isolation by quantitatively measuring and removing free proteins and lipoproteins using Simoa assays and chromatography.

bioRxiv · Jan 20, 2023Bioengineering

A Proximity Biotinylation Assay with a Host Protein Bait Reveals Multiple Factors Modulating Enterovirus Replication

S. Moghimi, E. Viktorova, S. Gabaglio, A. Zimina, B. Budnik, B. G. Wynn, E. Sztul, G. Belov

This study uses a proximity biotinylation assay to identify host and viral proteins associated with poliovirus replication organelles, revealing new factors and mechanisms involved in enterovirus replication.

bioRxiv · May 24, 2022Microbiology

Systematic conformation-to-phenotype mapping via limited deep-sequencing of proteins

E. Serebryany, V. Y. Zhao, K. Park, A. Bitran, S. A. Trauger, B. Budnik, E. I. Shakhnovich

The paper develops a method to map protein conformations to phenotypes by systematically analyzing disulfide bonds in proteins.

bioRxiv · Apr 12, 2022Biophysics

Development of photo-lenalidomide for cellular target identification

Z. Lin, Y. Amako, F. Kabir, H. A. Flaxman, B. Budnik, C. M. Woo

This paper develops photo-lenalidomide, a modified lenalidomide probe, to identify cellular targets using chemical proteomics, revealing new targets like eIF3i.

bioRxiv · Jul 12, 2021 · PreprintBiochemistry

In-depth analysis of proteomic and genomic fluctuations during the time course of human embryonic stem cells directed differentiation into beta cells.

B. Budnik, J. Straubhaar, J. M. Neveu, D. Shvartsman

The paper analyzes proteomic and genomic changes during human embryonic stem cell differentiation into beta cells, identifying new phosphorylation events and proteoform profiles.

bioRxiv · Oct 5, 2020Cell Biology

Molecular physiology of chemical defenses in a poison frog

S. N. Caty, A. Alvarez-Buylla, G. D. Byrd, C. Vidoudez, A. B. Roland, E. E. Tapia, B. Budnik, S. A. Trauger, L. A. Coloma, L. A. O'Connell

The paper investigates how alkaloid sequestration affects gene expression and protein abundance in poison frogs, identifying transport proteins and saxiphilin as potential mediators of toxin accumulation.

bioRxiv · May 3, 2019Physiology

6-Phosphogluconate Dehydrogenase Links Cytosolic Carbohydrate Metabolism to Protein Secretion

H. Li, M. Ericsson, B. Rabasha, B. Budnik, B. Wagner, L. Garraway, S. Schreiber

This study identifies 6-phosphogluconate dehydrogenase (PGD) as essential for ER structural integrity and protein secretion, linking cytosolic carbohydrate metabolism to ECM secretion processes.

bioRxiv · Nov 26, 2018Biochemistry

Catalysis of cataract-associated human γD crystallin aggregation via dynamic disulfide exchange

E. Serebryany, S. Yu, S. A. Trauger, B. Budnik, E. I. Shakhnovich

The paper shows wild-type human γD crystallin catalyzes aggregation of its W42Q variant through disulfide bond transfer, revealing a redox mechanism relevant to protein aggregation in oxidizing environments.

bioRxiv · Apr 12, 2018Biochemistry