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Zach Hensel completed his PhD in Molecular Biophysics at Johns Hopkins University in the laboratory of Dr. Jie Xiao, where he studied single-molecule biophysics problems in gene regulation in E. coli. He then completed postdoctoral work in projects linking single-molecule microscopy and computational biophysics at the Okinawa Institute of Science and Technology (OIST). Since 2017, Dr. Hensel runs the Single Molecule Microbiology lab at ITQB NOVA, within the MOSTMICRO research unit. His lab studies gene regulation and cell division at the single-molecule level in living microbial cells, with a focuses on imaging single mRNA and protein molecules and on investigating structures of protein complexes predicted by deep learning. The lab has built two hybrid commercial/DIY microscope for single-molecule imaging. His interests include advances in rapid and reproducible dissemination of scientific results (i.e. preprints and executable research articles).
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Identification

Personal identification

Full name
Zachary Jay Hensel

Citation names

  • Hensel, Zach
  • Zach Hensel

Author identifiers

Ciência ID
6A11-3CB3-F87F
ORCID iD
0000-0002-4348-6229

Websites

  • https://zach-hensel.github.io/ (Professional)

Languages

Language Speaking Reading Writing Listening Peer-review
English Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
Portuguese Intermediate (B1) Upper intermediate (B2) Intermediate (B1) Intermediate (B1)
Japanese Intermediate (B1) Elementary (A2) Elementary (A2) Intermediate (B1)
Education
Degree Classification
2012/05/24
Concluded
 Molecular Biophysics (Doctor of Philosophy)
Johns Hopkins University School of Medicine, United States
"Single-molecule studies of stochastic gene regulation by the lambda repressor CI in live E. coli cells" (THESIS/DISSERTATION)
 N/A
2005/05
Concluded
 Physics (Bachelor)
University of Illinois at Urbana-Champaign, United States
"Chiral liquid crystals in suspensions of Salmonella flagella" (THESIS/DISSERTATION)
 3.99/4.0
2005
Concluded
 Cinema Studies (Bachelor)
University of Illinois at Urbana-Champaign, United States
"An introduction to lo-fi cinema" (THESIS/DISSERTATION)
 3.99/4.0
Affiliation

Science

Category
Host institution 		Employer
2017/01/03 - Current Auxiliary Researcher (Research) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Others

Category
Host institution 		Employer
2015/04/01 - 2016/12/31 Independent Postdoctoral Researcher, Deans Research Group Advisors: Dr. Ken Peach (04-2015—01-2016), Dr. Gordon Arbuthnott (02-2016—12-2016) Okinawa Kagaku Gijutsu Daigakuin Daigaku, Japan
2012/10/01 - 2015/03/31 Postdoctoral Researcher, Integrative Systems Biology Unit Advisor: Dr. Tatiana Marquez Lago Okinawa Kagaku Gijutsu Daigakuin Daigaku, Japan
Projects

Grant

Designation Funders
2023/04/01 - Current MOSTMICRO-ITQB Exploratory Project
ICA35303
Principal investigator
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
Ongoing
2017/04/01 - 2022/12/31 ITQB-OIST Joint Research Agreement
NA
Principal investigator
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
Concluded
2021/09/16 - 2022/09/15 Prediction of the structure of bacterial cell-division complexes
GCP20210916
Principal investigator
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
 Google Inc
Concluded

Contract

Designation Funders
2023/09/01 - Current Life Sciences for a Healthy and Sustainable Future
LA/P/0087/2020
10.54499/LA/P/0087/2020
Universidade Nova de Lisboa Microbiologia Molecular Estrutural e Celular, Portugal

Instituto Português de Oncologia de Lisboa Francisco Gentil EPE, Portugal

Universidade Nova de Lisboa, Portugal

Instituto Gulbenkian de Ciência, Portugal

Instituto de Biologia Experimental e Tecnológica, Portugal

Universidade de Lisboa Centro de Estudos Comparatistas, Portugal

BioResources 4 Sustainability, Portugal

Universidade de Trás-os-Montes e Alto Douro Centro de Investigação e de Tecnologias Agro-Ambientais e Biologicas, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2019/01/01 - 2019/12/31 Molecular, Structural and Cellular Microbiology
UID/CBQ/04612/2019
Universidade Nova de Lisboa, Portugal

Universidade Nova de Lisboa Microbiologia Molecular Estrutural e Celular, Portugal

Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica António Xavier, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Conference poster
  1. Ruilan Xu; João Ramalheira Ferreira; Hensel, Zach. Corresponding author: Hensel, Zach. "(Flash talk and poster) Fluorescence microscopy in E. coli confirms protein-protein interaction essential in persistent M. tuberculosis infection". Paper presented in 91st Harden Conference: Single Molecule Bacteriology III, 2024.
  2. Ruilan Xu; João Ramalheira Ferreira; Hensel, Zach. Corresponding author: Ruilan Xu. "Mycobacterium tuberculosis FtsB and PerM interact via a C-terminal helix in FtsB to modulate cell division". Paper presented in Single Molecule Localization Microscopy Symposium, 2024.
  3. Sara F. Costa; Margarida A. Pereira; Hensel, Zach. Corresponding author: Hensel, Zach. "Imaging transcription elongation and mRNA localization in E. coli using newly reported fluorescent proteins". Paper presented in Single Molecule Localization Microscopy Symposium, 2024.
  4. Zach Hensel. "Detecting the expression of single messenger RNAs and the protein molecules they encode in living E. coli cells". Paper presented in Spanish & Portuguese Advanced Optical Microscopy Meeting, 2019.
  5. Zach Hensel. "Low-noise expression system for single-molecule mRNA visualization in live E. coli cells". Paper presented in Cutting Edge Developments in RNA Biology for the Control of Gene Expression, 2017.
  6. Zach Hensel. "Single-molecule tracking in living cells reveals disruption of non-specific DNA binding upon translation inhibition". Paper presented in Seeing is Believing EMBO EMBL Symposium, 2017.
  7. Zach Hensel. "Cell-cycle-synchronized oscillations of an autoregulated gene in E. coli: Testing possible biomolecular mechanisms by stochastic simulation". Paper presented in Biochemistry and Molecular Biology Meeting (BMB2015), 2015.
  8. Zach Hensel. "Oscillations in expression of a negatively autoregulated gene in E. coli are synchronized to the cell cycle by gene doubling". Paper presented in Cellular Dynamics and Models Meeting. Cold Spring Harbor Laboratory., 2015.
Journal article
  1. Alexander Crits-Christoph; Joshua I. Levy; Jonathan E. Pekar; Stephen A. Goldstein; Reema Singh; Zach Hensel; Karthik Gangavarapu; et al. "Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic". Cell (2024): http://dx.doi.org/10.1016/j.cell.2024.08.010.
    10.1016/j.cell.2024.08.010
  2. Simon Schäper; António D. Brito; Bruno M. Saraiva; Georgia R. Squyres; Matthew J. Holmes; Ethan C. Garner; Zach Hensel; Ricardo Henriques; Mariana G. Pinho. "Cell constriction requires processive septal peptidoglycan synthase movement independent of FtsZ treadmilling in Staphylococcus aureus". Nature Microbiology (2024): https://doi.org/10.1038/s41564-024-01629-6.
    10.1038/s41564-024-01629-6
  3. Liv Zimmermann; Xiaohan Zhao; Jana Makroczyova; Moritz Wachsmuth-Melm; Vibhu Prasad; Zach Hensel; Ralf Bartenschlager; Petr Chlanda. "SARS-CoV-2 nsp3 and nsp4 are minimal constituents of a pore spanning replication organelle". Nature Communications (2023): https://doi.org/10.1038/s41467-023-43666-5.
    10.1038/s41467-023-43666-5
  4. Brooke M. Britton; Remy A. Yovanno; Sara F. Costa; Joshua McCausland; Albert Y. Lau; Jie Xiao; Zach Hensel. Corresponding author: Zach Hensel. "Conformational changes in the essential E. coli septal cell wall synthesis complex suggest an activation mechanism". Nature Communications (2023): https://doi.org/10.1038/s41467-023-39921-4.
    10.1038/s41467-023-39921-4
  5. Letra-Vilela, Ricardo; Quiteres, Ricardo; Murtinheira, Fernanda; Crevenna, Alvaro; Hensel, Zach; Herrera, Federico. Corresponding author: Hensel, Zach. "New tools for the visualization of glial fibrillary acidic protein in living cells". Experimental Results 1 (2020): https://doi.org/ggnnvq.
    10.1017/exp.2020.1
  6. João P. N. Silva; Soraia Vidigal Lopes; Diogo J. Grilo; Zach Hensel. Corresponding author: Zach Hensel. "Plasmids for Independently Tunable, Low-Noise Expression of Two Genes". mSphere (2019): https://doi.org/gf3vhf.
    10.1128/mSphere.00340-19
  7. Sarvenaz Sarabipour; Humberto J. Debat; Edward Emmott; Steven J. Burgess; Benjamin Schwessinger; Zach Hensel. Corresponding author: Zach Hensel. "On the value of preprints: An early career researcher perspective". PLOS Biology 17 2 (2019): e3000151-e3000151. https://doi.org/gfw8hd.
    10.1371/journal.pbio.3000151
  8. Xiaona Fang; Qiong Liu; Christopher Bohrer; Zach Hensel; Wei Han; Jin Wang; Jie Xiao. "Cell fate potentials and switching kinetics uncovered in a classic bistable genetic switch". Nature Communications 9 1 (2018): https://doi.org/gdwxjt.
    10.1038/s41467-018-05071-1
  9. Hensel, Z.. "A plasmid-based Escherichia coli gene expression system with cell-to-cell variation below the extrinsic noise limit". PLoS ONE 12 10 (2017): https://doi.org/gcg8pf.
    10.1371/journal.pone.0187259
  10. Hensel, Zachary; Marquez-Lago, Tatiana T. "Cell-cycle-synchronized, oscillatory expression of a negatively autoregulated gene in E. coli". arXiv q-bio (2015): https://doi.org/10.48550/arXiv.1506.08596.
  11. Hensel, Z.; Xiao, J.. "Single-molecule methods for studying gene regulation in vivo". Pflugers Archiv European Journal of Physiology 465 3 (2013): 383-395. https://doi.org/gdxw5j.
    10.1007/s00424-013-1243-y
  12. Hensel, Z.; Fang, X.; Xiao, J.. "Single-molecule imaging of gene regulation in vivo using cotranslational activation by cleavage (CoTrAC)". Journal of Visualized Experiments 73 (2013): https://doi.org/gfb8nv.
    10.3791/50042
  13. Hensel, Z.; Weng, X.; Lagda, A.C.; Xiao, J.. "Transcription-Factor-Mediated DNA Looping Probed by High-Resolution, Single-Molecule Imaging in Live E. coli Cells". PLoS Biology 11 6 (2013): https://doi.org/gbdb2z.
    10.1371/journal.pbio.1001591
  14. Hensel, Z.; Feng, H.; Han, B.; Hatem, C.; Wang, J.; Xiao, J.. "Stochastic expression dynamics of a transcription factor revealed by single-molecule noise analysis". Nature Structural and Molecular Biology 19 8 (2012): 797-802. https://doi.org/f358fm.
    10.1038/nsmb.2336
  15. Feng, H.; Hensel, Z.; Xiao, J.; Wang, J.. "Analytical calculation of protein production distributions in models of clustered protein expression". Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 85 3 (2012): https://doi.org/gfb8vm.
    10.1103/PhysRevE.85.031904
  16. Fu, G.; Huang, T.; Buss, J.; Coltharp, C.; Hensel, Z.; Xiao, J.. "In Vivo structure of the E. coli FtsZ-ring revealed by photoactivated localization microscopy (PALM)". PLoS ONE 5 9 (2010): 1-16. https://doi.org/drrw4v.
    10.1371/journal.pone.0012680
  17. Hensel, Z.; Xiao, J.. "A mechanism for stochastic decision making by bacteria". ChemBioChem 10 6 (2009): 974-976. https://doi.org/bzbk92.
    10.1002/cbic.200800824
  18. Barry, E.; Hensel, Z.; Dogic, Z.; Shribak, M.; Oldenbourg, R.. "Entropy-driven formation of a chiral liquid-crystalline phase of helical filaments". Physical Review Letters 96 1 (2006): https://doi.org/b2rbcd.
    10.1103/PhysRevLett.96.018305
Preprint
  1. João Ramalheira Ferreira; Ruilan Xu; Zach Hensel. Corresponding author: Zach Hensel. "Mycobacterium tuberculosis FtsB and PerM interact via a C-terminal helix in FtsB to modulate cell division". 2024. https://doi.org/10.1101/2024.03.11.584518.
    10.1101/2024.03.11.584518
  2. Zach Hensel. Corresponding author: Zach Hensel. "Secondary structure of the SARS-CoV-2 genome is predictive of nucleotide substitution frequency". 2024. https://doi.org/10.1101/2024.02.27.581995.
    10.1101/2024.02.27.581995
  3. F. Débarre; Z. Hensel. Corresponding author: F. Débarre. "A critical reexamination of recovered SARS-CoV-2 sequencing data". 2024. https://doi.org/10.1101/2024.02.15.580500.
    10.1101/2024.02.15.580500
  4. Zach Hensel. "Secondary structure of the SARS-CoV-2 genome is predictive of nucleotide substitution frequency". 2024. https://doi.org/10.7554/eLife.98102.
    10.7554/eLife.98102
  5. Alexander Crits-Christoph; Joshua I. Levy; Jonathan E. Pekar; Stephen A. Goldstein; Reema Singh; Zach Hensel; Karthik Gangavarapu; et al. "Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic". 2023. https://doi.org/10.1101/2023.09.13.557637.
    10.1101/2023.09.13.557637
  6. Simon Schäper; António D. Brito; Bruno M. Saraiva; Georgia Squyres; Matthew J. Holmes; Ethan C. Garner; Zach Hensel; Ricardo Henriques. "Processive movement of Staphylococcus aureus essential septal peptidoglycan synthases is independent of FtsZ treadmilling and drives cell constriction". 2023. http://dx.doi.org/10.1101/2023.06.29.547026.
    10.1101/2023.06.29.547026
  7. Hensel, Zach. "Predicted binding interface between coronavirus nsp3 and nsp4". 2022. http://dx.doi.org/10.1101/2022.03.05.483145.
    10.1101/2022.03.05.483145
  8. Brooke M. Britton; Remy A. Yovanno; Sara F. Costa; Joshua McCausland; Albert Y. Lau; Jie Xiao; Zach Hensel. Corresponding author: Zach Hensel. "Conformational changes in the essential E. coli septal cell wall synthesis complex suggest an activation mechanism". 2022. https://doi.org/10.1101/2022.11.27.518129.
    10.1101/2022.11.27.518129
Website
  1. Hensel, Zach. North America sub-lineages of B.1.617.2 with Spike A222V, V1264L, often N1074S, and sometimes additional Spike mutations (SARS-CoV-2 lineage AY.26 proposal). 2021. https://github.com/cov-lineages/pango-designation/issues/188.
  2. Hensel, Zach; Robinson, Ashley. A new sub-lineage of AY.3 concentrated in Mississippi, USA (SARS-CoV-2 lineage AY.3.1 proposal). 2021. https://github.com/cov-lineages/pango-designation/issues/147.
  3. Hensel, Zach. B.1.617.2 sub-lineage with ORF1a: I3731V (SARS-CoV-2 lineage AY.3 proposal). 2021. https://github.com/cov-lineages/pango-designation/issues/121.

Intellectual property

Patent
  1. Zach Hensel; Dr. Jie Xiao. 2017. "Co-translational activation of a transcription factor by proteolytic cleavage and methods of use". United States.
    Granted/Issued

Other

Other output
  1. Letter: Preprints are good for science and good for the public. Nature 560, 553. 2018. Sarabipour, Sarvenaz; Wissink, Erin M.; Burgess, Steven J.; Hensel, Zach; Debat, Humberto; Emmott, Edward; Akay, Alper; Akdemir, Kadir C.; Schwessinger, Benjamin.
    https://doi.org/gd3xpk
  2. Preprint: Maintaining confidence in the reporting of scientific outputs. 2018. Sarvenaz Sarabipour; Erin M Wissink; Steven J Burgess; Zach Hensel; Humberto Debat; Edward Emmott; Alper Akay; Kadir Akdemir; Benjamin Schwessinger. https://doi.org/hj23.
    10.7287/peerj.preprints.27098v1
Research technique
  1. Plasmids for single-molecule mRNA imaging in E. coli (inducible expression of fluorescent RNA-binding proteins). Distributed freely through AddGene at https://www.addgene.org/Zach_Hensel/. Researcher. Zach Hensel.
    Researcher
  2. Plasmids for low-noise gene expression. Available freely from AddGene at https://www.addgene.org/Zach_Hensel/. Researcher. Zach Hensel.
    Researcher
  3. Plasmid for single-molecule detection of protein expression. Available from AddGene at https://www.addgene.org/47311/. Researcher. Zach Hensel.
    Researcher
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2021/11/24 Live-cell imaging, localization and tracking of single mRNA molecules in E. coli cells Spanish & Portuguese Advanced Optical Microscopy Meeting
Instituto Gulbenkian de Ciência (Remote) (Oeiras, Portugal)
2021/05/21 Immortalization and aggregation in live-cell mRNA imaging in E. coli Invited seminar
Center for Integrative Biology (Remote) (Toulouse, France)
2021/05/04 Single-molecule mRNA FISH in bacteria 2nd DelNAM Summer School "FISHing for Bacteria"
University of Porto (Porto, Portugal)
2020/02/06 Imaging single mRNAs and their encoded proteins in living Escherichia coli Single Molecule Biophysics 2020
(Les Houches, France)
2019/09/05 Progress towards counting single transcription and translation events in living bacteria at the same time Seminar
Dr. Ulf Landegren (Uppsala, Sweden)
2018/09/12 Improved tools for single-molecule mRNA and protein detection in living E. coli Harden Conference: Single-molecule bacteriology
Biochemical Society (Oxford, United Kingdom)
2017/02/02 Microbiology at the nanoscale: Counting and tracking single molecules in living cells Advanced Integrated Microsystems program workshop
(Lisbon, Portugal)
2017/01/10 Single Molecule Microbiology: observing single molecules within living microbial cells for applications in molecular and synthetic biology MOSTMICRO Scientific Advisory Board meeting
(Lisbon, Portugal)
2016/02/19 Cell-cycle-synchronized oscillations of an autoregulated transcription factor in E. coli: single-molecule fluorescence measurements & computational investigations into biomolecular mechanisms Departmental Seminar
Dr. Floyd Reed (Honolulu, United States)
2016/02/15 Exploring oscillatory Cro expression in E. coli by stochastic simulation Winter Q-Bio Meeting
(Honolulu, United States)
2016/01/29 Gene oscillations in E. coli OIST Internal Seminar Series
(Onna-son, Japan)
2012/03/05 Single-molecule studies of stochastic gene regulation by the lambda repressor in live E. coli cells Thesis defense seminar
Johns Hopkins University School of Medicine Department of Biophysics and Biophysical Chemistry (Baltimore, United States)
2010/09/11 A closer look at bacteriophage ¿ lysogeny: Single-molecule studies of gene expression and DNA looping in living cells Institute of Biophysical Research Retreat
Johns Hopkins University (Baltimore, United States)
2010/08/26 Mechanism of transcription autoregulation of the ¿ repressor revealed by single-molecule imaging in live E. coli cells Molecular Genetics of Bacteria and Phages Meeting
Cold Spring Harbor Laboratory (Cold Spring Harbor, United States)
2009/03/02 A single-molecule study of gene regulation in real time Annual meeting
Biophysical Society (Boston, United States)
2007/02/28 Bioindustrial processing of lignocellulose: Structure, catalysis, and remaining challenges Departmental seminar
John Hopkins University School of Medicine Department of Biophysics and Biophysical Chemistry (Baltimore, United States)
2005/01/28 Chiral liquid crystals in suspensions of Salmonella flagella Undergraduate thesis defense presentation
University of Illinois at Urbana Champaign Department of Physics (Urbana, United States)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2023/10/01 - 2024/12/03 Studying Mycobacterium tuberculosis PerM-FtsB interaction under oxidative stress
Supervisor
 Post-graduate program in Practical Research (Scientific initiation)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica António Xavier, Portugal
2024/01/22 - 2024/07/18 Imaging transcription and mRNA localization in E. coli using newly reported fluorescent proteins
Supervisor
Universidade NOVA de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2018/05/25 - 2023/09/15 Understanding the role of gene expression regulation in controlling cell division in Staphylococcus aureus
Co-supervisor of Sara Maria Francisco da Costa
 Biociências Moleculares (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2022/01/12 - 2022/06/24 Quantifying E. coli transcription rate and mRNA localization in changing growth conditions using single-molecule microscopy in living cells
Supervisor of Leonardo Pina
 Cell and Molecular Biology (Scientific initiation)
Universidade NOVA de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2022 - 2022 Characterization on the protein-protein interactions of M. tuberculosis divisome proteins, expressed in E. coli
Supervisor of João Pedro Ramalheira de Araújo Ferreira
 Biological Engineering (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2020/10/06 - 2021/12/13 Improved techniques for single-molecule mRNA detection and tracking in living E. coli cells
Supervisor of Maria Inês Costa de Sousa
 Masters degree in Molecular Biotechnology (Master)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Universidade de Aveiro, Portugal
2019/10/07 - 2021/11/20 Post-graduate research projection: Improved techniques for single-molecule mRNA detection and tracking in living E. coli cells
Supervisor of Cleusia Manuel
 ITQB NOVA Curso de Pós-Graduação (Specialization course)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2018/12/13 - 2019/12/13 The mechanism of the Legionella VipA protein in altering actin dynamics during infection
Co-supervisor of Ana Teresa Carrilho Carvalho
 Bioquímica para a Saúde (Master)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2018/11/25 - 2019/11/26 Developing new molecular tools to study and visualize the intermediate filament GFAP in living cells
Co-supervisor of Ricardo Jorge Pinheiro Quiteres
 Biologia Molecular e Genética (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2019/08/05 - 2019/08/30 New fluorescent protein mutants for improved single-molecule mRNA detection (summer internship)
Supervisor of Inês Neto Silva Rosa Mendes
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2019/08/05 - 2019/08/30 Deep learning for E. coli cell segmentation in timelapse imaging (summer internship)
Supervisor of Joana Luísa Góis Valério
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2018/11/15 - 2018/12/15 Low-noise gene expression system and mRNA tracking (internship)
Supervisor of Diogo Grilo
 1-month undergraduate research internship (Scientific initiation)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2017/11/14 - 2018/11/14 Engineering low-noise gene expression systems for single-molecule experiments
Supervisor of João Pedro Nunes Silva
 Biologia Molecular e Genética (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2017/07/10 - 2017/08/10 Stochastic simulation of bacteriophage infection (summer internship)
Supervisor of João Pedro Ramalheira Ferreira
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2017/07/10 - 2017/08/10 Single-molecule tracking of DNA-binding proteins labeled with synthetic dyes in living E. coli (summer internship)
Supervisor of Pedro Ladino
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2018/07/23 - Current ITQB Summer Science: Week-long course in laboratory skills and career development for undergraduate students looking to enter the workforce. In 2018 and 2019 I hosted one student in my laboratory and also helped organize and co-present a session on career planning/development. (2018/07/23)
Workshop (Member of the Organising Committee)
 Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2020/01/22 - 2020/01/24 ITQB PhD Meeting: Faculty Advisor. In this roll I advised the students on organizing invited speakers and co-coordinated evaluations for student poster and oral presentations. (2020/01/22 - 2020/01/24)
Conference (Member of the Organising Committee)
2017/11/09 - 2018/09/21 ITQB Preprint Journal club: I organized an experimental journal club at ITQB that ran for about one year. We choose articles from the preprint literature to read and discuss, and post collaborative preprint peer reviews online. (2017/11/09 - 2018/09/21)
Other (Co-organisor)
 Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2024/10/17 - Current (Remote) Career development roundtable for students and postdoctoral scholars at the Okinawa Institute of Science and Technology
Round table
 Alumni Stories Mixer
Okinawa Institute of Science and Technology Promotion Corp, Japan
2023/07/23 - Current I helped organize a table at ITQB Open Day 2023 presenting fluorescence and microscopy topics to an audience of local residents who visited our institute to learn about our work and the subjects we work on.
Exhibition
 ITQB Open Day
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2023/07/20 - Current I co-presented a workshop on CV preparation and scientific career paths for students in the one-week SummerScience program. SummerScience 2023
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2014/01/01 - 2016/12/31 Community outreach at the Okinawa Institute of Science and Technology (OIST): Between 2014 and 2016 I contributed to OIST's community education/outreach by (1) presenting my work to students at the elementary and high school levels in public events such as the OIST Children's School of Science and (2) volunteering as a photographer for the OIST Summer Festival.
Exhibition
 Various
Okinawa Institute of Science and Technology Promotion Corp, Japan
2009/07/01 - 2011/07/01 For 3 years I helped organize our lab's presentation for the Fun With Science Summer Camp in which we gave Baltimore-area elementary students hands on experiences with fluorescent proteins.
Festival
 Fun With Science Summer Camp
Johns Hopkins University School of Medicine, United States

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2024/12/17 Opponent for Masters thesis defense in molecular genetics and biomedicine.
(Thesis) Main arguer
 Ana Rita Luazes Sequeira (Master)
Universidade NOVA de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2022/04/12 Bioimage analysis using machine learning
Thesis Member
 Bruno Saraiva (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2018/07/16 Study of the single cell response of Staphylococcus aureaus to cell wall targeting antibiotics
Thesis Member
 Ana Raquel Ramos Pereira (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Ad Hoc journal article review

Journal title (ISSN) Publisher
2017 - Current Invited peer review for iScience, Nature Methods, PLOS Computational Biology, eLife, PLOS ONE, and Nucleic Acids Research

Association member

Society Organization name Role
2017/10/09 - Current ASAPbio In this organization I participate in discussing the evolving publishing ecosystem focusing on preprints and open access
2017/12/08 - 2018/01/15 eLife Early Career Ambassadors My focus in the organization was on preprints; together with other ambassadors I published letters and articles on how preprints affect early career researchers in Nature, PLOS Biology and in preprint

Committee member

Activity description
Role 		Institution / Organization
2023 - Current PhD committee member for Fernando Jorge Neiva Ferreira Nunes (Molecular Biosciences) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2023 - Current PhD committee member for Dominik Alwardt (Molecular Biosciences) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2021/12/15 - Current PhD committee for António Brito
Member
 Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2019/01/18 - Current Thesis committee member for Cristiana Santos
Member
 Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2019 - Current ITQB NOVA Bacterial Imaging Cluster, Scientific Advisor https://www.itqb.unl.pt/bic/team-and-contacts
Advisor / Consultant
 Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2016 - Current OIST Researcher Community (ORC) representative to the OIST Faculty Assembly (elected by peer researchers) Okinawa Institute of Science and Technology Promotion Corp, Japan
2017/08/11 - 2023/04 PhD committee member for Sara Handem
Member
 Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2023/09/20 - Current Fundamentals of light microscopy and image processing (Short Course) Lecture: Basic principles of widefield and widefield Super Resolution microscopy (Outros) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2023/03/20 - 2023/03/24 Mechanisms of Gene Expression (Molecular Biosystems and Plants4Life PhD programs) (Doutoramento) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2021/03/01 - 2021/03/05 Mechanisms of Gene Expression/Gene Expression and Systems Biology (Molecular Biosystems, Plants4Life, and Biology at the Host-Microbe Interface PhD units) (Doutoramento) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2019/02/11 - 2019/02/15 Mechanisms of Gene Expression/Gene Expression and Systems Biology (Molecular Biosystems and Biology at the Host-Microbe Interface PhD units) (Doutoramento) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2018/03/05 - 2018/03/09 Mechanisms of Gene Expression/Gene Expression and Systems Biology (Molecular Biosciences and Biology at the Host-Microbe Interface PhD programs) (Doutoramento) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2017/04/01 - 2017/04/01 "Co-localization and conformation of nucleic acids in vivo: proximity ligation and fluorescence microscopy methods" (Guest Lecture in Plant Cell and Developmental Biology Unit II, ITQB NOVA coordinated by C. Miguel, R. Abranches) (Doutoramento) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2006 - 2006 Teaching assistant (leading discussion sections, grading, test administration) for an undergraduate biophysics course taught by Richard Cone Cellular and Molecular Physiology Johns Hopkins University, United States
2003 - 2005 Teaching assistant positions for 3 courses in the UIUC Physics department in various subjects. Teaching discussion sections of approximately 30 students. Physics X199D (general; continuing education), Thermodynamics and Quantum Mechanics, and Physics 101 (Bachelor) University of Illinois at Urbana-Champaign, United States

Evaluation committee

Activity description
Role 		Institution / Organization Funding entity
2022 - 2023 PhD Program Application Evaluation Committee, Molecular Biosciences
Member
 Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2017 - 2018 PhD Program Application Evaluation Committee, Biology at the Host Microbe Interface
Member
 Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Interview (newspaper / magazine)

Activity description Newspaper / Forum
2024/09/19 Interviewed for article discussing a recent paper I co-authored investigating COVID-19 pandemic origins (Crits-Christoph et al, Cell, 2024). New Scientist
2023/05/24 Interviewed regarding my analysis of correlation in sequencing data from environmental sampling of Huanan Market in Wuhan China. The Atlantic (online article)

Journal scientific committee

Journal title (ISSN) Publisher
2018/04/01 - 2020/01/23 biOverlay

Mentoring / Tutoring

Topic Student name
2017/04/01 - Current Supervision of Masters and PhD Rotation Students Various (11 students)
2023/07/24 - 2023/08/04 NuBioq FCT UNL Undergraduate Research Internship Carolina Nobre
2023/07/17 - 2023/07/21 ITQB SummerScience Internship Ana Mesquita
2023/01 - 2023/02 NuBioq FCT UNL Undergraduate Research Internship Luisa Guerriero

Other jury / evaluation

Activity description Institution / Organization
2022/07/26 - Current Evaluation of final report and oral presentation: Post-graduate Program on Research Practice Level 1 Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
Distinctions

Award

2017 LabArchives Grant Award
2009 Biophysical Society Travel Award
2005 Robert E. Hetrick Outstanding Senior Thesis
2004 Certificate of Teaching Excellence
2003 James Scholar Research Grant

Other distinction

2022 Finalist, Amyris Innovation BIG Impact Award
Amyris Biotechnologies Inc, United States

Universidade Católica Portuguesa, Portugal