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Rafael Najmanovich
Curriculum Vitae & List of Publications
(Updated 30.03.2015)
PERSONAL DETAILS
Name: Rafael Najmanovich
Born: October 13, 1972 in Tel Aviv, Israel; Canadian permanent resident.
E-mail: [email protected]
EDUCATION & WORK EXPERIENCE
06/2014-Present: Associate Professor, Department of Biochemistry, Faculty of Medicine and
Health Sciences, Université de Sherbrooke (UdeS). Cross appointment
Department of Computer Sciences (UdeS).
04/2009-05/2014: Assistant Professor, Department of Biochemistry, Faculty of Medicine and
Health Sciences, Université de Sherbrooke (UdeS). Cross appointment
Department of Computer Sciences (UdeS).
01/2009-03/2009: Postdoctoral Fellow associated to the Structural Genomics Consortium
(SGC) Toronto, Canada.
01/2005-12/2008: Staff Scientist at the European Bioinformatics Institute (EMBL-EBI),
Cambridge, UK.
06/2003-12/2004:
Postdoc at the European Bioinformatics Institute (EMBL-EBI),
Cambridge, UK.
04/1998-05/2003:
PhD in Physics and Biology at the departments of Plant Sciences &
Physics of Complex Systems, Weizmann Institute of Sciences, Rehovot,
Israel, under Supervision of Prof. Meir Edelman. Thesis title: “Protein
Flexibility upon Ligand Binding: Docking Predictions and Statistical
Analysis”.
10/1996-03/1998: Visiting student at the department of Physics of Complex Systems,
Weizmann Institute of Sciences, Rehovot, Israel.
1994-1996:
MSc in Physics – University of Sao Paulo (USP), São Paulo, Brazil,
Statistical Mechanics group, General Physics Department under supervision
of Prof. Vera Henriques. Title: “The Collapse Transition in the HP model”.
1990-1994:
Undergraduate Studies – Molecular Sciences, University of Sao Paulo (USP),
São Paulo, Brazil.
1989-1992:
Experimental work on DNA repair mechanisms in S. cerevisiae.
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COMMITTEES
Invited external member of the committee evaluating the undergraduate bioinformatics
program offered at Laval University, Quebec (October 2015).
PhD thesis committee member for Maryah Safi (U. Toronto), Robert Fieldhouse (U.
Guelph), Abdellali Kelil (U. Sherbrooke)
Member of the 2011 FRSQ evaluating committee for PhD fellowships (FF2-4D: biologie
cellulaire, biochimie, protéomique et ingénierie tissulaire).
Member of the Scientific committee of the Institut de Pharmacologie de Sherbrooke (IPS).
Member of the Board of Directors (2010-2012) of Proteo, the Québec network for research
on protein function, structure and engineering.
Member of the organizing committee of the yearly ISMB satellite meeting “3DSIG:
Structural bioinformatics and computational biophysics” from 2006-current (largest
meeting in the field with around 200 participants per year)
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• Member of the International Society for Computational Biology (ISCB) council on
Communities of Special Interests (COSIs).
MEMBERSHIPS
Life member of the International Society for Computational Biology (ISCB).
Member of the American Chemical Society (ACS).
Faculty member of the Faculty of 1000 Genomics and Bioinformatics section.
PROTEO (the Québec network for research on protein function, structure and
engineering).
• GRASP (Groupe de Recherche Axé sur la Structure des Protéines).
• Institute of Pharmacology of Sherbrooke
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REVIEWING WORK
Academic editor for PLOS Computational Biology, PLOS One, PeerJ and F1000Research.
Reviewer Discovery program grants Natural Sciences and Engineering Research Council
(NSERC), 2009.
Reviewer operating grants Israeli Science Foundation (ISF) 2008.
Reviewer US National Science Foundation (NSF) 2007, 2014.
Review of papers for the following journals (partial list): Bioinformatics (over 20),
Proteins (around 10), FEBS letters (1), Nucleic Acids Research (numerous), BioEssays (1),
PLoS Computational Biology (2), Protein Science (numerous), Cellular and Molecular
Biology Letters (1), Algorithms (1), IEEE/ACM Transactions on Computational Biology
and Bioinformatics (1), BMC Bioinformatics (1), Journal of Molecular Biology (2), PLoS
ONE (1) and Nature Chemical Biology (1).
Review of papers for the Pacific Symposium on Biocomputing (PSB), 2007.
SCIENTIFIC MEETINGS AND WORKSHOPS (PARTIAL LIST)
Organizing committee, Structural Bioinformatics Symposium, part of the 97th Canadian
Chemistry Conference and Exhibition, Ottawa, June 13-17, 2015.
Organizing committee, Proteo Summer School on computational methods in
biochemistry. Concordia University, August 14-15, 2014. 150+ attendees.
Organizing committee member, “3DSig: Structural Bioinformatics and computational
biophysics” satellite meetings. Annual meeting since 2006. 200+ attendees yearly.
Organising committee member “New Perspectives on Anticancer Drug Development”
session on the 2nd Middle East Frontiers of Science and Engineering (FOSE) 2007, 19-21
of March 2007, Seville, Spain.
PHD STUDENTS (FINISH DATE)
1. Francis Gaudreault (2015, expected)
2. Vincent Frappier (2016, expected)
3. Matthieu Chartier (2016, expected)
4. Thierry Chénard (2017, expected)
5. Louis-Philippe Morency (2017, expected)
MSC STUDENTS (FINISH DATE)
1. Mathieu Larocque (2017/01, expected)
2. Dominic Dûchene (2014, expected)
3. Ingrid Um Nlend (2014/08) – Completed.
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UNDERGRADUATE STUDENT INTERNSHIPS
1. Sara Laurin-Lactôt (Biology, May 2009)
2. Dany Gilbert (Chemistry, May 2009)
3. Olivier Blanchette (Physics, May 2009)
4. Thierry Chénard (Biotechnology, May 2009, Jan 2010, Sept 2011, May 2012)
5. Thomas Goudreaut (Chemistry, Sept 2009)
5. Eugene Morin (Computer engineering, Aug 2010)
6. Samuel Larrivée (Pharmacology, Sept. 2011)
7. Olivier Martel (Biochemistry, May 2012, Jan 2013)
8. Maxime Gagnon (Biochemistry, May 2012, Jan 2013)
10. Jean-Philippe Croisetiere (Biochemistry, May 2012)
11. Mathieu Larocque (Biology, Sept 2013, May 2014)
12. Olivier Mailhot (Biochemistry, May 2014, May 2015)
FUNDING
PI
Status
Year
Source
Amount
2015
CIHR
696,577$
R. Najmanovich
R
2014
NSERC
175,000$
R. Najmanovich
G
2013
CIHR
740,325$
R. Leduc
G
2013
NSERC
147,201$
E. Marsault
G
2012
FRQ-NT
200,000$
E. Marsault
G
2012
MITACS
200,000$
E. Marsault
G
2012
MDEIE
750,000$
D. Lafontaine
G
2012
MSBi
200,000$
D. Lafontaine
G
2011
CQDM
299,920$
R. Najmanovich
G
2011
RQRM
124,800$
E. Marsault
G
2010
NSERC
107,176$
JP Perreault
G
2010
FRQ-S
246,321$
R. Najmanovich
G
2010
FRQ-S
45,000$
R. Najmanovich
G
3
Title
A combined computational and
experimental approach to study
biased signalling in class A GPCRs
Dynamics in molecular recognition
Role of matriptase and TMPRSS6 in
health and disease
An institutional LC-MS platform for
research in pharmacology and
medicinal chemistry
le riborégulateur guanine comme
nouvelle cible antibiotique contre les
infections au C. difficile
le riborégulateur guanine comme
nouvelle cible antibiotique contre les
infections au C. difficile
Nouvelles classes d'antibiotiques
ciblant le riborégulateur guanine
pour le traitement des infections à C.
difficile
le riborégulateur guanine comme
nouvelle cible antibiotique contre les
infections au C. difficile
Detection of molecular interaction
field similarities and its application
in the rational drug design of
selective multi-functional inhibitors
Exploring privileged structures to
identify new GPCR ligands
Development of department- wide
bioinformatics solutions
Chercheur-Boursier Junior 1
Déterminants structuraux pour la
liaison des cofacteurs et la sélectivité
2009
NSERC
90,000$
R. Najmanovich
G
des substrats chez la famille
protéique des sulfotransférases
Structural
causes,
control
mechanisms and consequences of
small- molecule binding promiscuity
G=Granted, R=Requested.
DISTINCTIONS
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FRQ-S Chercheur Bursier Junior 1 fellowship (2010-2014)
INVITED TALKS (ONLY THE MOST RELEVANT RECENT SHOWN)
31. Leloir Institute, Buenos Aires, Argentine. March 20, 2015 (keynote).
30. 98th Canadian Chemistry Conference and Exhibition, Ottawa, June 13-17, 2015 (keynote).
29. Protein Engineering Canada Conference. Ottawa, June 20, 2014.
28. Boehringen-Ingelheim. Ridgefield, Connecticut, June 16, 2014.
27. BioMOLAR Invited speaker, Dept. of Chemistry, University of Ottawa, April 21, 2014.
26. 96th Canadian Chemistry Conference and Exhibition, Quebec City, May 26-30, 2013
(keynote).
25. American Chemical Society Spring 2012 Annual Meeting, San Diego, March 25-29, 2012
(keynote).
21. 94th Canadian Chemistry Conference and Exhibition, Montreal, June 5-9, 2011 (keynote).
ARTICLES UNDERGOING REVIEW
40. Chartier, M. & Najmanovich, R.J. (2015) Detection of binding-site Molecular interaction
field similarities.. Journal of Chemical Information and Modelling.
39. Gaudreault, F., & Najmanovich, R.J. (2015) FlexAID: Revisiting docking on non nativecomplex structures. Journal of Chemical Information and Modelling. (BioRxiv preprint
DOI: 10.1101/011791)
ACCEPTED OR PUBLISHED ARTICLES
2015
38. Frappier, V., Chartier, M. & Najmanovich, R.J. The ENCoM server for the prediction of
the effect of mutations on thermostability and dynamics. Nucleic Acid Research (2015
Web-server issue, accepted).
37. Frappier, V. & Najmanovich, R.J. (2015) Applications of Normal Mode Analysis
methods on Computational Protein Design. Methods in Molecular Biology (accepted).
36. Gaudreault F, Morency L-P, Najmanovich R.J. (2015) NRGsuite: A PyMOL plugin to
perform docking simulations in real-time using FlexAID. Bioinformatics (accepted,
revision requested).
35. Samish, I., Bourne, P.E. & Najmanovich, R. J. (2015). Achievements and challenges in
Structural Bioinformatics and computational biophysics. Invited perspective for the
International Society for Computational Biology (ISCB), Bioinformatics 31(1): 146-150.
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34. Frappier, V. & Najmanovich, R. J. (2015) Vibrational entropy differences between
mesophile and thermophile proteins and their use in protein engineering. Protein Science.
24(4): 474-483. DOI: 10.1002/pro.2592
2014
33. Duchene, D., Colombo, E., Boudreault, P.-L., Desilets, A., Leduc, R., Marsault, E. &
Najmanovich, R.J. (2014). Analysis of subpocket druggability and the detection of
potent selective inhibitors for matriptase and matriptase-2. Journal of Medicinal
Chemistry. 57(23): 10198-10204. DOI: 10.1021/jm5015633.
32. Larocque, M., Chénard, T., & Najmanovich, R. J. (2014) A curated C. difficile strain 630
metabolic network: prediction of essential targets and inhibitors. BMC Systems Biology 8:
117. DOI: 10.1186/s12918-014-0117-z
31. Frappier, V., & Najmanovich, R. J. (2014). A coarse-grained elastic network atom
contact model and its use in the simulation of protein dynamics and the prediction of the
effect of mutations. PLoS Computational Biology, 10(4), e1003569.
30. Glouzon, J.-P. S., Bolduc, F., Wang, S., Najmanovich*, R. J., & Perreault*, J.-P. (2014).
Deep-sequencing of the peach latent mosaic viroid reveals new aspects of population
heterogeneity. PLoS ONE, 9(1), e87297. * co-corresponding authors
2013
29. Chartier, M., Chénard, T., Barker, J., & Najmanovich, R. (2013). Kinome Render: a
stand-alone and web-accessible tool to annotate the human protein kinome tree. PeerJ,
1(3), e126. doi:10.7717/peerj.126
28. Leonardo Astolfi Rosado, Igor Bordin Vasconcelos, Mário Sérgio Palma, Vincent
Frappier, Rafael Josef Najmanovich, Diógenes Santiago Santos mail, Luiz Augusto
Basso (2013). The Mode of Action of Recombinant Mycobacterium tuberculosis
Shikimate Kinase: Kinetics and Thermodynamics Analyses. PLoS ONE 8(5): e61918.
27. Kurbatova, N., Chartier, M., Zylber, M. I., & Najmanovich, R. (2013). IsoCleft Finder - a
web-based tool for the detection and analysis of protein binding-site geometric and
chemical similarities. F1000Research, 2, 117.
2012
26. Letourneau D, Lorin A, Lefebvre A, Frappier V, Gaudreault F, Najmanovich R, Lavigne
P, Lehoux JG (2012). Star-related lipid transfer domain protein 5 (STARD5) binds
primary bile acids. Journal of Lipid Research 53(12):2677-89.
25. Gaudreault, F., Chartier, M. & Najmanovich, R. Side-chain rotamer changes upon ligand
binding: Common, crucial, correlate with entropy and rearrange hydrogen bonding.
Bioinformatics Bioinformatics (2012) 28(18):i423-i430.
24. Chartier, M., Gaudreault, F. & Najmanovich, R. Large scale analysis of conserved rare
codon clusters suggests an involvement in co-translational molecular recognition
events. Bioinformatics (2012) 28(11):1438-45
23. Colombo, E., Désilets, A., Duchêne, D., Chagnon, F., Najmanovich, R., Leduc, R., &
Marsault, E. (2012). Design and synthesis of potent, selective inhibitors of matriptase.
ACS Medicinal Chemistry Letters, 3(7), 530–534.
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2011
22. Campagna-Slater, V., Mok, M. W., Nguyen, K., Feher, M.; Najmanovich, R., Schapira,
M. (2011) “Structural Chemistry of the Histone Methyltransferases Cofactor Binding
Site. Journal of Chemical Information and Modeling”. Journal of Chemical Information
and Modeling 51(3):612-623.
2010
21. Lavigne, P., Najmanivich, R. & Lehoux, J.-G. Mammalian StAR-related lipid transfer
(START) domains with specificity for cholesterol: structural conservation and
mechanism of reversible binding. Subcell Biochem 51, 425–437 (2010).
20. Han, G. W., Bakolitsa, C., Miller, M. D., Kumar, A., Carlton, D., Najmanovich, R. J., et
al. (2010). Structures of the first representatives of Pfam family PF06938 (DUF1285)
reveal a new fold with repeated structural motifs and possible involvement in signal
transduction. Acta Crystallographica Section F, Structural Biology and Crystallization
Communications, 66(Pt 10), 1218–1225.
19. Bakolitsa, C., Kumar, A., McMullan, D., Krishna, S. S., Miller, M. D., Carlton, D.,
Najmanovich, R. et al. (2010). The structure of the first representative of Pfam family
PF06475 reveals a new fold with possible involvement in glycolipid metabolism. Acta
Crystallographica Section F, Structural Biology and Crystallization Communications,
66(Pt 10), 1211–1217.
2009
18. Andreini, C., Bertini, I., Cavallaro, G., Najmanovich, R.J. and Thornton, J.M. (2009).
“Structural analysis of metal sites in proteins: non-heme iron sites as a case study”.
Journal of Molecular Biology 388(2):356-380.
17. Herrera, J.L., Fernandez-Montesinos, R., Quintana, F.J., Najmanovich, R., GonzalezRey, E., Pozo, D. (2009) “Toll-like receptor stimulation differentially regulates
vasoactive intestinal peptide type 2 receptor in macrophages“.Journal of Cellular and
Molecular Medicine,13(2):1-9.
2008
16. Rafael Najmanovich, Kurbatova, N. & Thornton, J. (2008) “Detection of 3D atomic
similarities and their use in the discrimination of small-molecule protein binding sites”
Bionformatics 24(16):i105-111.
15. Jeyanthy Eswaran, A. Bernad, Jose M. Ligos, Barbara Guinea, Judit E. Debreczeni,
Rafael Najmanovich, Benjamin E. Turk and Stefan Knapp (2008). "Structure of the
human protein Kinase MPSK1 Reveals a Novel Activation Loop Architecture".
Structure 16(1): 115-124.
2007
14. Abdellah Allali-Hassani*, Patricia W. Pan*, Ludmila Dombrovski*, Rafael Najmanovich*,
Wolfram Tempel, Aiping Dong, Peter Loppnau, Fernando Martin, Janet Thornton,
Aled M. Edwards, Alexey Bochkarev, Alexander N. Plotnikov*, Masoud Vedadi*,
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Cheryl H. Arrowsmith (2007). “Structural and Chemical Profiling of the Human
Cytosolic Sulfotransferases“ PloS Biology, 5(5):e97. * equal contributing authors.
13. Rafael J. Najmanovich, Abdellah Allali-Hassani, Richard J. Morris, Ludmila
Dombrovsky, Patricia W. Pan, Masoud Vedadi, Alexander N. Plotnikov, Aled
Edwards, Cheryl Arrowsmith & Janet M. Thornton (2007). "Analysis of binding site
similarity, small molecule similarity and experimental binding profiles in the human
cytosolic sulfotransferase family" Bioinformatics, 23(2):e104-109.
2006
12. Glaser, F., Morris, R. J., Najmanovich, R. J. and J.M. Thornton. (2006). "A Method for
Localizing Ligand Binding Pockets in Protein Structures." Proteins 62(2):479-88.
2005
11. Najmanovich, R. J., Torrance, J.W. and J.M. Thornton. (2005). "Prediction of protein
function from structure: Insights from methods for the detection of local structural
similarities." BioTechniques 38(6):847-851.
10. Morris, R. J., R. J. Najmanovich, A. Kahraman and J. M. Thornton (2005). "Real
spherical harmonic expansion coefficients as 3D shape descriptors for protein binding
pocket and ligand comparisons." Bioinformatics 21(10): 2347-2355.
9. Funkhouser, T., Glaser, F., Laskowski, R., Morris, R., Najmanovich, R., Stockwell, G., &
Thornton, J. (2005). "Shape-based classification of bound ligands". Quantitative
Biology, Shape Analysis, and Wavelets. pp. 39-42, Edited by S. Barber, P. D. Baxter,
K. V. Mardia, R. E. Wells. Leeds. Leeds University Press.
8. Morris, R. J.,Kahraman, A., Funkhouser, T., Najmanovich, R. J., Stockwell, G.,
Laskowski, R., and J.M. Thornton. (2005). "Binding pocket shape analysis for protein
function prediction". Quantitative Biology, Shape Analysis, and Wavelets. pp. 91-94,
Edited by S. Barber, P. D. Baxter, K. V. Mardia, R. E. Wells. Leeds. Leeds University
Press.
2004
7. Eyal, E., R. Najmanovich, B. J. McConkey, M. Edelman and V. Sobolev (2004).
"Importance of solvent accessibility and contact surfaces in modeling side-chain
conformations in proteins." Journal of Computational Chemistry 25(5): 712-24.
2003
6. Eyal, E., R. Najmanovich, M. Edelman and V. Sobolev (2003). "Protein side-chain
rearrangement in regions of point mutations." Proteins 50(2): 272-82.
2001
5. Eyal, E., R. Najmanovich, V. Sobolev and M. Edelman (2001). "MutaProt: a web interface
for structural analysis of point mutations." Bioinformatics 17(4): 381-382.
2000
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4. Najmanovich, R., J. Kuttner, V. Sobolev and M. Edelman (2000). "Side-chain flexibility in
proteins upon ligand binding." Proteins-Structure Function and Genetics 39(3): 261268.
3. Vendruscolo, M., R. Najmanovich and E. Domany (2000). "Can a pairwise contact
potential stabilize native protein folds against decoys obtained by threading?"
Proteins-Structure Function and Genetics 38(2): 134-148.
1999
2. Vendruscolo, M., R. Najmanovich and E. Domany (1999). "Protein folding in contact map
space." Physical Review Letters 82(3): 656-659.
1998
1. Najmanovich, R. J., J. L. deLyra and V. B. Henriques (1998). "The collapse transition in
the HP model." Physica A 249(1-4): 374-379.
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