Peer-reviewed papers
33. MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations
Tiemann JKS#, Szczuka M, Bouarroudj L, Oussaren M, Garcia S, Howard RJ, Delemotte L,
Lindahl E, Baaden M, Lindorff-Larsen K, Chavent M#, Poulain P#
eLife, (2023) [Open Access]
DOI 10.1093/bib/bbad375
# These authors contributed equally to this work. Corresponding authors.
MDverse data explorer web app
Source code:
32. 3D models of fungal chromosomes to enhance visual integration of omics data
Poinsignon T, Gallopin M, Grognet P, Malagnac F, Lelandais G#, Poulain P#
NAR Genomics & Bioinformatics, (2023) [Open Access]
DOI 10.1093/nargab/lqad104
# These authors contributed equally to this work. Corresponding authors.
Source code: 3D genome builder (3DGB)
31. The five pillars of computational reproducibility: bioinformatics and beyond
Ziemann M, Poulain P, Bora A
Briefings in Bioformatics, (2023)
DOI 10.1093/bib/bbad375
30. A field guide for implementing a flipped classroom
Poulain P#, Bertrand M, Dufour H, Taly A,
Biochemistry and Molecular Biology Education, (2023) [Open Access]
DOI 10.1002/bmb.21737
29. AutoClassWeb: a simple web interface for Bayesian clustering of omics data
Poulain P#, Camadro JM,
BMC Research Notes, (2022). [Open Access]
local PDF -
DOI 10.1186/s13104-022-06129-6
# Corresponding author.
AutoClassWeb is available on GitHub and archived on Software Heritage.
28. Additional insights into the organization of transcriptional regulatory modules based on a 3D model of the Saccharomyces cerevisiae genome
Poinsignon T, Gallopin M, Camadro, JM, Poulain P#, Lelandais G#,
BMC Research Notes, (2022). [Open Access]
local PDF -
DOI 10.1186/s13104-022-05940-5
# These authors contributed equally to this work. Corresponding authors.
3d-scere is available on GitHub and archived on Software Heritage.
27. buildH: Build hydrogen atoms from united-atom molecular dynamics of lipids and calculate the order parameters
Santuz H, Bacle A, Poulain P, Fuchs PFJ,
The Journal of Open Source Software, (2021). [Open Access]
local PDF -
DOI 10.21105/joss.03521
The review for this paper was fully open.
buildH is available on GitHub and archived on Zenodo and Software Heritage.
26. Novel Insights into Quantitative Proteomics from an Innovative Bottom-Up Simple Light Isotope Metabolic (bSLIM) Labeling Data Processing Strategy
Sénécaut N, Alves G, Weisser H, Lignières L, Terrier S, Yang-Crosson L, Poulain P, Lelandais G, Yu YK, Camadro JM,
Journal of Proteome Research, (2021). [Open Access]
local PDF -
DOI 10.1021/acs.jproteome.0c00478 -
PMID 33573382
25. AutoClassWrapper: a Python wrapper for AutoClass C classification
Camadro JM, Poulain P,
The Journal of Open Source Software, (2019). [Open Access]
local PDF -
DOI 10.21105/joss.01390
The review for this paper was fully open.
AutoClassWrapper is available on GitHub and archived on Zenodo.
24. Pixel: a content management platform for quantitative omics data
Denecker T$, Durand W$, Maupetit J$, Hébert C, Camadro JM, Poulain P#, Lelandais G#,
PeerJ, (2019). [Open Access]
local PDF -
DOI 10.7717/peerj.6623 -
PMID 30944779
$ These authors contributed equally to this work.
# These authors contributed equally to this work.
Pixel is available on GitHub and archived on Zenodo.
23. Meet-U: Educating through research immersion
Abdollahi, Albani, Anthony, Baud, Cardon, Clerc, Czernecki, Conte, David, Delaune, Djerroud, Fourgoux, Guiglielmoni, Laurentie, Lehmann, Lochard, Montagne, Myrodia, Opuu, Parey, Polit, Privé, Quignot, Ruiz-Cuevas, Sissoko, Sompairac, Vallerix, Verrecchia, Delarue, Guérois, Ponty, Sacquin-Mora, Carbone, Froidevaux, Le Crom, Lespinet, Weigt, Abboud, Bernardes, Bouvier, Bouvier, Ferré, Fuchs, Lelandais, Poulain, Richard, Schweke, Laine, Lopes,
PLOS Computational Biology, (2018). [Open Access]
local PDF -
DOI 10.1371/journal.pcbi.1005992 -
PMID 29543809
22. PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks
Barnoud J$, Santuz H$, Craveur P, Joseph AP, Jallu V, de Brevern AG#, Poulain P#,
PeerJ, (2017). [Open Access]
local PDF -
DOI 10.7717/peerj.4013 -
PMID 29177113
$ These authors contributed equally to this work.
# These authors contributed equally to this work.
PBxplore is available on GitHub and archived on Zenodo.
21. Plasmodium falciparum infection in febrile Congolese children: prevalence of clinical malaria 10 years after introduction of artemisinin-combination therapies
Etoka-Beka MK, Ntoumi F, Kombo M, Deibert J, Poulain P, Vouvoungui C, Kobawila SC, Koukouikila-Koussounda F,
Tropical Medicine & International Health, 21: 1496-1503 (2016).
local PDF -
DOI 10.1111/tmi.12786 -
PMID 27671736
Data used in this study are available on Zenodo.
20. HIV-1 Genetic Diversity in the Republic of Congo: Seventeen Years in Review
Ghoma Linguissi LS, Ndembi N, Nkenfou CN, Poulain P#, Ntoumi F#,
JSM Microbiology, 3: 1025 (2015). [Open Access]
local PDF -
web site
# These authors contributed equally to this work.
19. Diagnosis of smear-negative pulmonary tuberculosis based on clinical signs in the Republic of Congo
Ghoma Linguissi LS, Vouvoungui JC, Poulain P, Bango Essassa G, Kwedi S, Ntoumi F,
BMC Research Notes, 8: 804 (2015). [Open Access]
local PDF -
DOI 10.1186/s13104-015-1774-8
18. Factors influencing acceptability of voluntary HIV testing among pregnant women in Gamboma, Republic of Congo
Ghoma Linguissi LS, Ebourombi DF, Sidibe A, Kivouele TS, Vouvoungui JC, Poulain P, Ntoumi F,
BMC Research Notes, 8: 652 (2015). [Open Access]
local PDF -
DOI 10.1186/s13104-015-1651-5 -
PMID 26545975
17. Prevention of Mother-to-Child HIV Transmission (PMTCT) in the Republic of Congo: Challenges to Implementation
Ghoma Linguissi LS, Bisseye C, Poulain P, Ntoumi F, Simpore J,
Journal of AIDS & Clinical Research, 6: 503 (2015). [Open Access]
local PDF -
DOI 10.4172/2155-6113.1000503
16. Protein flexibility in the light of structural alphabets
Craveur P, Joseph AP, Esque J, Narwani TJ, Noël F, Shinada N, Goguet M, Leonard S, Poulain P, Bertrand O, Faure G, Rebehmed J, Ghozlane A, Swapna LS, Bhaskara RM, Barnoud J, Téletchéa S, Jallu V, Cerny J, Schneider B, Etchebest C, Srinivasan N, Gelly J-C, de Brevern AG,
Frontiers in Molecular Biosciences, 2: 20 (2015). [Open Access]
local PDF -
DOI 10.3389/fmolb.2015.00020 -
PMID 26075209
15. An Integrative Approach to the Study of Filamentous Oligomeric Assemblies, with Application to RecA
Boyer B, Ezelin J, Poulain P, Saladin A, Zacharias M, Robert CH, Prévost C,
PLoS ONE, 10: e0116414 (2015). [Open Access]
local PDF -
supplementary data -
DOI 10.1371/journal.pone.0116414 -
PMID 25785454
14. Modeling and molecular dynamics simulations of the V33 variant of the integrin subunit β3: Structural comparison with the L33 (HPA-1a) and P33 (HPA-1b) variants
Jallu V#, Poulain P#, Fuchs PFJ, Kaplan C, de Brevern AG,
Biochimie, 105: 84-80 (2014).
local PDF -
supplementary data -
DOI 10.1016/j.biochi.2014.06.017 -
PMID 24994675
# These authors contributed equally to this work.
13. Cis–trans isomerization of omega dihedrals in proteins
Craveur P, Joseph AP, Poulain P, de Brevern AG, Rebehmed J,
Amino Acids, 45: 279-289 (2013).
local PDF -
DOI 10.1007/s00726-013-1511-3 -
PMID 23728840
12. The αIIb p.Leu841Met (Cab3a+) Polymorphism Results in a New Human Platelet Alloantigen Involved in Neonatal Alloimmune Thrombocytopenia
Jallu V, Bertrand G, Bianchi F, Chenet C, Poulain P, Kaplan C,
Transfusion, 53:554-563 (2013).
local PDF -
DOI 10.1111/j.1537-2995.2012.03762.x -
PMID 22738334
11. Modeling and Molecular Dynamics of HPA-1a and -1b Polymorphisms: Effects on the Structure of the β3 Subunit of the αIIbβ3 Integrin
Jallu V#, Poulain P#, Fuchs PFJ, Kaplan C, de Brevern AG,
PLoS ONE, 7: e47304 (2012). [Open Access]
local PDF -
DOI 10.1371/journal.pone.0047304 -
PMID 23155369
# These authors contributed equally to this work.
The model of the β3 subunit of integrin αIIbβ3 and the molecular dynamics protocol (Gromacs 4.0.7) used in this paper are available on figshare.
10. Ten Simple Rules for Getting Help from Online Scientific Communities
Dall'Olio GM, Marino J, Schubert M, Keys KL, Stefan MI, Gillespie CS, Poulain P, Shameer K, Sugar R, Invergo BM, Jensen LJ, Bertranpetit J, Laayouni H,
PLoS Computational Biology, 7: e1002202 (2011). [Open Access]
local PDF -
DOI 10.1371/journal.pcbi.1002202 -
PMID 21980280 -
HAL
9. Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments
Saladin A, Amourda C, Poulain P, Férey N, Baaden M, Zacharias M, Delalande O, Prévost C,
Nucleic Acids Research, 38: 6313-6323 (2010). [Open Access]
local PDF -
DOI 10.1093/nar/gkq459 -
PMID 20507912 -
HAL
8. Detection and Architecture of Small Heat Shock Protein Monomers
Poulain P, Gelly J-C, Flatters D,
PLoS ONE 5: e9990 (2010). [Open Access]
local PDF -
DOI 10.1371/journal.pone.0009990 -
PMID 20383329 -
HAL
7. PTools: an opensource molecular docking library
Saladin A, Fiorucci S, Poulain P, Prévost C, Zacharias M,
BMC Structural Biology 9: 27 (2009). [Open Access]
local PDF -
DOI 10.1186/1472-6807-9-27 -
PMID 19409097 -
HAL
6. Transitions between secondary structures in isolated polyalanines
Calvo F, Poulain P,
The European Physical Journal D 51: 15-23 (2009).
local PDF -
DOI 10.1140/epjd/e2008-00096-0 -
HAL
5. Insights on protein-DNA recognition by coarse grain modelling
Poulain P, Saladin A, Hartmann B, Prévost C,
Journal of Computational Chemistry 29: 2582-2592 (2008).
local PDF -
DOI 10.1002/jcc.21014 -
PMID 18478582 -
HAL
4. Competition between secondary structures in gas phase polyalanines
Poulain P, Calvo F, Antoine R, Broyer M, Dugourd P,
Europhysics Letters 79:66003 (2007).
local PDF -
DOI 10.1209/0295-5075/79/66003
3. Performances of Wang-Landau algorithms for continuous systems
Poulain P, Calvo F, Dugourd P, Antoine R, Broyer M,
Physical Review E 73: 056704 (2006).
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DOI 10.1103/PhysRevE.73.056704 -
PMID 16803071
2. Comparison of the fragmentation pattern induced by collisions, laser excitation and electron capture. Influence of the initial excitation
Antoine R, Broyer M, Chamot-Rooke J, Dedonder C, Desfrancois C, Dugourd P, Gregoire G, Jouvet C, Onidas D, Poulain P, Tabarin T, van der Rest G,
Rapid Communications in Mass Spectrometry 20: 1-5 (2006).
local PDF -
DOI 10.1002/rcm.2489 -
PMID 16637002
1. Monte Carlo simulations of flexible molecules in a static electric field: electric dipole and conformation
Poulain P, Antoine R, Broyer M, Dugourd P,
Chemical Physics Letters 400: 1-6 (2005).
local PDF -
DOI 10.1016/j.cplett.2004.11.025
Book chapters
2. Working with omics data, an interdisciplinary challenge at the crossroads of biology and computer science
Poinsignon T, Poulain P, Gallopin M, Lelandais G,
Machine Learning for Brain Disorders, in press (2022).
1. Quantitative proteomics in yeast: from bSLIM and Proteome Discoverer outputs to graphical assessment of the significance of protein quantification scores
Sénécaut N, Poulain P, Lignières L, Terrier S, Legros V, Chevreux G, Lelandais G, Camadro JM,
Yeast Functional Genomics, 2nd edition, Methods in Molecular Biology, vol 2477: 275-292 (2022). [Open Access]
local PDF -
DOI 10.1007/978-1-0716-2257-5_16
Non peer-reviewed papers
3D protein structure modeling: A tool to provide insight into the platelet alloimmune response
Jallu V, Poulain P, Kaplan C, de Brevern AG,
Transfusion Today 86: 10-11 (2011).
local PDF
PhD thesis (in French, 2006)
Structure et dynamique de protéines isolées : approches statistiques
download from local PDF or from the CNRS TEL multidisciplinary thesis server.
