Curriculum Vitae & Industry Portfolio

Education

• Ph.D. in Structural Biology, Weizmann Institute of Science
  Direct Accelerated Track from M.Sc.
  Adviser: Nobel Laureate Ada Yonath
  Honors: Adams Ph.D. Fellowship of the Israel Academy of Sciences and Humanities, 2008 – 2016.
• B.Sc. in Chemistry, Bar-Ilan University
  Graduated Magna Cum Laude
  Dean’s Honors List (2006), 2005 – 2008.

Honors, Fellowships & National Recognition

• Leading Edge Fellow (2025): Selected for the premier national fellowship program honoring outstanding women and non-binary postdocs transitioning to scientific independence.
• Compass Scholar (2025): Washington University in St. Louis School of Medicine.
• New England Future Faculty Fellow (2025): Regional recognition for emerging leaders in biomedical sciences.
• NSF Award, RNA 2021 (2021): The RNA Society Annual Meeting.
• Clinical Research Fellowship Award (2016): Cincinnati Children’s Hospital Medical Center.
• Best Lecture Award (2015): Genetics, Genomics and Evolution Conference, Tel Aviv University.
• Vallee Lindau Fellow (2013): Competitive award to attend the 63rd Lindau Nobel Laureate Meeting, Germany.
• Adams Ph.D. Fellowship (2012 – 2016): Prestigious national doctoral award of the Israel Academy of Sciences and Humanities ($100,000+ plus tuition).
• Schächter Summer Research Scholar (2007): Bar-Ilan University.
• Dean’s Honors List (2006): Bar-Ilan University.

Computational Software Suites & Open-Source Platforms

• FoldCheck-RNA ↗: Automated nucleic acid structural validation suite evaluating generative predictions (AlphaFold 3) against empirical Cryo-EM and crystallographic ground truth. Implements coarse-grained phosphorus (P) backbone superimposition and an extensible 30+ non-canonical nucleotide modification registry (Python, BioPython, SciPy, PyTest).
• FoldCheck-Pro ↗: High-throughput validation pipeline for protein assemblies leveraging the Hungarian matching algorithm (scipy.optimize.linear_sum_assignment) to resolve asymmetric heterodimer subunit pairing (HIV-1 RTase p66/p51) and automated dynamic pLDDT/RASA surface classification (Python, NumPy, SciPy, REST APIs).

Research Appointments & Leadership

Postdoctoral Fellow / Research Scientist | Stanford University

Department of Structural Biology | Advisers: Prof. Joseph D. Puglisi and Dr. Elisabetta Viani Puglisi
2019 – Present

• Program Leadership (Viral RNA Architecture): Direct empirical structural investigations decoding the dynamic multi-scale architecture of full-length HIV-1 genomic RNA (>9,000 nt) and associated viral ribonucleoprotein complexes.
• Platform Innovation for Large RNA: Engineered a proprietary large-scale RNA stabilization protocol eliminating solution precipitation for highly structured transcripts (>9,000 nt), enabling in situ cryo-ET ultrastructure characterization and single-molecule fluorescence tracking (yielding 2 manuscripts in preparation).
• Modular VLP Encapsidation Platform: Built a modular synthetic packaging engine encapsidating full-length viral RNAs into Virus-Like Particles (VLPs); validated encapsidation efficiency and viral mechanics via in situ cryo-ET and single-molecule microscopy.
• Resolving Genetic Code Bottlenecks (NAR Cover Paper, 2022): Spearheaded Cryo-EM structural determination of ribosome-bound synthetic tRNA complexes; identified core steric clashes during A-to-P translocation and executed structure-guided rational point mutations to restore kinetics (Nucleic Acids Res, Journal Cover).
• Automated Pipeline & Generative AI Architecture: Architected automated Python and MATLAB data pipelines integrating custom image analysis and kinetic fitting routines, eliminating manual bottlenecks across multi-gigabyte Cryo-EM and single-molecule datasets.
• Consortium Milestone Leadership (NIH CHEETAH): Serve as technical milestone lead and primary scientific speaker within the Capsid & Core Architecture subgroups of the NIH-funded CHEETAH consortium; supervised 3 graduate researchers across structural workflows (yielding 3 publications).

Postdoctoral Research Associate | Massachusetts Institute of Technology (MIT)

Department of Biological Engineering | Adviser: Prof. Katharina Ribbeck
2017 – 2019

• Biomimetic Hydrogels & Microfluidics: Designed and fabricated microfluidic devices and biophysical assays to quantify barrier permeability and establish physicochemical baselines for drug delivery across reconstituted mucin hydrogels (Biomacromolecules 2023, co-first author; Gates Foundation Global Health Initiative); supervised 4 students and interns across 3 publications.
• Clinical Specimen Governance: Directed end-to-end clinical biospecimen procurement and hospital biobanking workflows under strict IRB, CITI, and HIPAA regulatory protocols.
• Consortium Governance: Managed multi-institutional research milestones within a Gates Foundation initiative, synthesizing complex biophysical and microbiological data into structured monthly executive briefings.

Doctoral Researcher | Weizmann Institute of Science

Department of Structural Biology | Adviser: Prof. Ada Yonath (Nobel Laureate in Chemistry)
2008 – 2017

• Direct Ph.D. Dissertation: The origin of the ribosome and its paralysis by antibiotics.
• M.Sc. Thesis: Towards the determination of the structure of Mycobacterium smegmatis ribosome.
• Ribosome Structural Elucidation & SBDD: Determined atomic-resolution crystal structures of bacterial ribosomes complexed with novel orthosomycin, macrolide, and pleuromutilin therapeutics in active co-development with Pfizer and Nabriva Therapeutics; mapped drug-binding pockets and allosteric resistance pathways across 8 peer-reviewed papers.
• Prebiotic RNA Machine Engineering: Directed cross-functional teams in synthesizing, modeling, and biochemically validating prebiotic dimeric RNA machines capable of spontaneous peptide-bond formation (supervised 16 students and interns across sub-teams of 4; yielded 4 papers).
• Synchrotron Campaign Operations: Directed continuous 24-hour synchrotron diffraction campaigns across European storage rings (ESRF France, SLS Switzerland, Diamond UK) with zero instrument downtime.

Curriculum Architecture, Teaching & Outreach

• Course Director & Lead Instructor | Introduction to Medicine, Stanford University (2026): Designed and directed an intensive 10-module STEM curriculum introducing foundational biomedical sciences, translational medicine, and molecular mechanisms. Delivered core coursework spanning bacterial and viral pathogenesis, antibiotic pharmacology, genetics, and CRISPR gene editing; recruited and hosted 6 clinical and industry guest lecturers (MDs, research scientists, and a clinical pharmacist) to connect basic science with therapeutic translation.
• Founder & Program Director | Atomic Architecture Outreach Initiative (2026): Architected and instructed a 10-module community outreach program (“Atom Structure”) translating fundamental physical chemistry into accessible STEM modules for young learners. Engineered tactile modeling workshops using structural clay media to teach 3D atomic geometry, periodic properties, and chemical bonding across diverse educational backgrounds.
• Co-Founder & Director | MIT GlycoBioClub, Massachusetts Institute of Technology (2018 – 2019): Co-founded and organized an interdepartmental seminar series; established monthly literature curricula, recruited faculty and trainee speakers, and moderated cross-disciplinary discussions spanning glycobiology, chemical biology, and biophysics.
• Curriculum Developer & Instructor | Polymer Structure & Function, MIT (2017 – 2018): Designed and instructed a modular science workshop pairing a 1-hour conceptual lecture with interactive polymer synthesis laboratories, presented at the Boston Museum of Science and on MIT Polymer Day.
• Course Director & Lecturer | The Ribosome Structure and Function, Weizmann Institute (2009 – 2017): Designed and instructed a foundational structural biology workshop combining lectures with an interactive 3D virtual-reality theater demonstration, presented regularly at the Davidson Institute of Science Education.
• Workshop Director | Gender Balance in Chemical Sciences, Weizmann Institute (2015): Architected and delivered an institutional workshop for the Faculty of Chemistry; recruited keynote panelists and moderated discussions addressing retention and systemic equity in academic chemistry.
• Workshop Director | Graduate Rotation Placement Seminar, Weizmann Institute (2013): Developed and delivered an institutional seminar advising incoming graduate students on laboratory rotation strategies, research alignment, and advisor selection architectures.

Academic Governance, Service & Editorial Leadership

• Editorial Boards:
  • Handling Editor & Board Member, BMC Research Notes (2022 – Present)
  • Guest Editor & Reviewer Board Member, Antibiotics (2020 – Present)
• Ad-Hoc Peer Reviewer (16+ Manuscripts): Antibiotics, Viruses, International Journal of Molecular Sciences (IJMS), BMC Structural Biology.
• Symposium Organization & Scientific Operations:
  • Co-Organizer & Moderator: Bay Area RNA Club (BARC 2020, 2023). Managed scientific curation, abstract evaluation committees, poster competitions, and operational budget.
  • Co-Organizer: MIT-Harvard Microbiome Symposium (2018 – 2019).
  • Co-Organizer & Moderator: Frontiers in Chemical Sciences Symposium, Weizmann Institute (2015).
• Institutional Governance & Community Building:
  • Founder & Curator, The International Postdoc Club (Postdociot) (2020 – Present): Built a global peer network providing mutual mentorship, career architectures, and scientific seminars during COVID-19.
  • Leadership Teams: MIT Postdoctoral Organization for Women Engaged in Research (POWER) & MIT Microbiome Club (2018 – 2019).
  • Student Council Chair, Weizmann Institute of Science (2013): Managed an institutional operating budget, led executive policy negotiations with administration, and spearheaded student access and community initiatives.

Invited Talks (Selected)

• Structural Dynamics of Viral RNA
  • Bay Area RNA Conference, UCSF, 2026.
  • Inter-Lab Structural Biology Symposium, Chan Zuckerberg Biohub, poster, 2025.
  • HIV Structural Biology Meeting, NIH, Invited Talk, 2025.
  • CHEETAH Seminar Series, NIH, Consortium Presentation,2022, 2024.
  • SLAC National Accelerator Laboratory, Invited Panelist, 2022.
• Mucosal Barrier Biophysics
  • Frontiers of Biophysics (17th Course), Erice, Italy, flash Talk, 2019.
  • Department of Structural Biology, Stanford School of Medicine, Seminar, 2019.
  • Department of Biochemistry & Biophysics, UCSF, Seminar, 2019.
  • Department of Chemistry, University of Utah, Seminar, 2019.
• Ribosomal Antibiotics
  • Simons Electron Microscopy Center, NYSBC, Seminar, 2017.
  • Department of Biological Engineering, MIT, Seminar, 2016.
  • Cincinnati Children’s Hospital Medical Center, Seminar, 2016.
  • Ribosome Structure and Function EMBO Conference, Strasbourg, Poster, 2016.
• Proto-ribosome
  • Genetics, Genomics and Evolution Conference, Tel Aviv, Best Lecture Award, 2015.

Specialized Structural Biology & Biophysics Training

• High-Resolution Cryo-EM & Cryo-ET (Titan Krios 300 kV, Glacios 200 kV): Stanford University, SLAC National Accelerator Laboratory (S2C2), NIH, EMBL (2019 – Present).
• Microfluidics & Single-Molecule Biophysics (TIRF & ZMW Instrumentation): MIT, Stanford University (2017 – Present).
• Macromolecular X-ray Crystallography & Synchrotron Campaigns: Weizmann Institute, Oxford University (2009 – 2017).
  • Synchrotron Storage Ring Operations: ESRF (France), SLS (Switzerland), Diamond Light Source (UK).
• Microbiology, Biosafety & Clinical Biobanking (BSL-2, CITI, HIPAA): Weizmann Institute, MIT, Stanford University, Cold Spring Harbor Laboratory (CSHL) (2009 – Present).

Publications

Full citation record on PubMed. ^*Denotes equal contribution.

1. Krupkin M, OhAinle M, Sundquist W, Puglisi JD, Puglisi EV. Packaging a synthetic full-length HIV viral RNA into functional virions. (In final preparation, manuscript available upon request).
2. Dugan AE, …, Krupkin M, Ribbeck K, Xavier R, Bevins C, Kiessling L. Intelectin-2 is a broad-spectrum antimicrobial lectin. Nature Communications (2026). Link.
3. Yapici I, Dao H, Yokoi S, Krupkin M, Puglisi EV, Puglisi JD, Wakatsuki S, DeMirci H. 4D Crystallography Captures Transient IF1-Ribosome Dynamics in Translation Initiation. (Submitted to EMBO J).
4. Christensen D, …, Krupkin M, …, Sundquist W. Efficient HIV-1 Endogenous Reverse Transcription and Integration in a Cell-Free System. (Submitted).
5. Diehl RC, Chorghade JS, Keys AM, Alam MM, Early SA, Dugan AE, Krupkin M, Ribbeck K, Kulik HJ, Kiessling LL. A CH-π Interaction Is Required for Human Galectin-3 Function. JACS Au (2024). Link.
6. Wagner CE*, Krupkin M*, Smith-Dupont KB*, Wu CM, Bustos NA, Witten J, Ribbeck K. Comparison of Physicochemical Properties of Native Mucus and Reconstituted Mucin Gels. Biomacromolecules (2023). Link.
7. Nouhin J, Tzou PL, Rhee SY, Sahoo MK, Pinsky BA, Krupkin M, Puglisi JD, Puglisi EV, Shafer RW. Human immunodeficiency virus 1 5’-leader mutations in plasma viruses before and after the development of reverse transcriptase inhibitor-resistance mutations. J Gen Virol (2023). Link.
8. Prabhakar A*, Krahn N*, Zhang J*, Vargas-Rodriguez O, Krupkin M, Fu Z, Acosta-Reyes FJ, Ge X, Choi J, Crnkovic A, Ehrenberg M, Puglisi EV, Söll D, Puglisi JD. Uncovering translation roadblocks during the development of a synthetic tRNA. Nucleic Acids Res (2022). Journal Cover. Link.
9. Bose T, Fridkin G, Davidovich C, Krupkin M, Dinger N, Falkovich AH, Peleg Y, Agmon I, Bashan A, Yonath A. Origin of life: proto ribosome forms peptide bonds and links RNA and protein dominated worlds. Nucleic Acids Res (2022). Link. Featured in Nature News.
10. Krupkin M*, Jackson LN*, Ha B*, Puglisi EV. Advances in understanding the initiation of HIV-1 reverse transcription. Curr Opin Struct Biol (2020). Link.
11. Matzov D*, Eyal Z*, Benhamou RI, Shalev-Benami M, Halfon Y, Krupkin M, Zimmerman E, Rozenberg H, Bashan A, Fridman M, Yonath A. Structural insights of lincosamides targeting the ribosome of Staphylococcus aureus. Nucleic Acids Res (2017). Link.
12. Wekselman I, Zimmerman E, Davidovich C, Belousoff M, Matzov D, Krupkin M, Rozenberg H, Bashan A, Friedlander G, Kjeldgaard J, Ingmer H, Lindahl L, Zengel JM, Yonath A. The Ribosomal Protein uL22 Modulates the Shape of the Protein Exit Tunnel. Structure (2017). Link.
13. Krupkin M*, Wekselman I*, Matzov D, Eyal Z, Diskin Posner Y, Rozenberg H, Zimmerman E, Bashan A, Yonath A. Avilamycin and evernimicin induce structural changes in rProteins uL16 and CTC that enhance the inhibition of A-site tRNA binding. Proc Natl Acad Sci USA (2016). Link.
14. Eyal Z*, Matzov D*, Krupkin M, Paukner S, Riedl R, Rozenberg H, Zimmerman E, Bashan A, Yonath A. A novel pleuromutilin antibacterial compound, its binding mode and selectivity mechanism. Sci Rep (2016). Link.
15. Auerbach-Nevo T, Baram D, Bashan A, Belousoff M, Breiner E, Davidovich C, Cimicata G, Eyal Z, Halfon Y, Krupkin M, …, Yonath A. Ribosomal antibiotics: Contemporary challenges. Antibiotics (Basel) (2016). Link.
16. Eyal Z*, Matzov D*, Krupkin M, Wekselman I, Paukner S, Zimmerman E, Rozenberg H, Bashan A, Yonath A. Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus. Proc Natl Acad Sci USA (2015). Link.
17. Sun L, Xiong Y, Bashan A, Zimmerman E, Shulman Daube S, Peleg Y, Albeck S, Unger T, Yonath H, Krupkin M, Matzov D, Yonath A. A recombinant collagen–mRNA platform for controllable protein synthesis. Chembiochem (2015). Link.
18. Krupkin M, Bashan A, Yonath A. Glimpse into the Origin of Life: What was First, the Genetic Code or its Products, the Proteins? Why does Evolution Matter? The Importance of Understanding Evolution, Cambridge Scholars Publishing, p. 87-100 (2014). Link.
19. Huang L, Krupkin M, Bashan A, Yonath A, Massa L. Protoribosome by quantum kernel energy method. Proc Natl Acad Sci USA (2013). Link.
20. Krupkin M, Matzov D, Tang H, Metz M, Kalaora R, Belousoff MJ, Zimmerman E, Bashan A, Yonath A. A vestige of a prebiotic bonding machine is functioning within the contemporary ribosome. Phil Trans R Soc B Biol Sci (2011). Link.
21. Bashan A, Zimmerman E, Belousoff MJ, Rozenberg H, Davidovich C, Wekselman I, Shapira T, Krupkin M, Yonath A. The ribosome as drug target: lessons from 3D structures. Isr Chem Soc (2010). Journal Cover.
22. Davidovich C, Belousoff M, Wekselman I, Shapira T, Krupkin M, Zimmerman E, Bashan A, Yonath A. The proto-ribosome: An ancient nano-machine for peptide bond formation. Isr J Chem (2010). Journal Cover.