This page is no longer updated! Please find the new version of my resume on https://sebastian.proost.science/.

Experience

Senior PostDoc, KULeuven | VIB, Leuven, Belgium

PostDoc, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany

Junior PostDoc/Bioinformatics Expert, Universität Potsdam | Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany

PhD Student, Universiteit Gent | VIB-PSB, Ghent, Belgium

Education

Doctor in Science : Biotechnology, Universiteit Gent (Doctoral Schools), Gent, Belgium

Master in Biotechnology, Universiteit Gent, Gent, Belgium

Graduated Cum Laude
Option: Bioinformatics, Genetic Manipulation of Model Organisms and Genome Biology
Master thesis: Genomewide prediction of protein-protein interactions in Arabidopsis thaliana
Promoter: Prof. Dr. Yves Van de Peer, Supervisor: Dr. Stefanie De Bodt

Bachelor in Biology, Universiteit Hasselt, Hasselt, Belgium

Graduated Cum Laude
Option: Philosophy of Biology

Software

CoNekT : Co-Expression Network Toolkit url

PhytoNet : Comparative co-expression network analyses across phytoplankton and land plants url

LSTrAP : Large-Scale Transcriptomics Analysis Pipeline url

Plasmid DB : Lab Management software url

PLAZA : Online comparative genomics platform url

Trapid : Online transcript annotation and phylogeny tool url

i-ADHoRe : Software to detect genomic homology url

Publications (Show more...)

33 publications, 5434 citations. H-index: 22 ( Google Scholar, 30/10/2020 )

T. Naake, H. A. Maeda, S. Proost, T. Takayuki, A. R. Fernie, Kingdom-wide analysis of the evolution of the plant type III polyketide synthase superfamily, bioRxiv (2020)
S. Vieira-Silva, G. Falony, E. Belda, T. Nielsen, J. Aron-Wisnewsky, R. Chakaroun, S. K. Forslund, K. Assmann, M. Valles-Colomer, T. T. D. Nguyen, S. Proost, ... , K. Clément and J. Raes, Statin therapy is associated with lower prevalence of gut microbiota dysbiosis, Nature (2020) pubmed
N. Sujeeth, N. Mehterov, S. Gupta, M. K. Qureshi, A. Fischer, S. Proost, M. A. Omidbakhshfard, T. Obata, M. Benina, N. Staykov, S. Balazadeh, D. Walther, A. R. Fernie, B. Mueller-Roeber, J. Hille, T. S. Gechev, A novel seed plants gene regulates oxidative stress tolerance in Arabidopsis thaliana, Cellular and Molecular Life Sciences (2019) pubmed
L. Rosado-Souza, S. Proost, M. Moulin, S. Bergmann, S. Bocobza, A. Aharoni, T. B. Fitzpatrick, M. Mutwil, A. R. Fernie, T. Obata, Appropriate thiamin pyrophosphate levels are required for acclimation to changes in photoperiod, Plant physiology (2019) pubmed
C. Ferrari, S. Proost, M. Janowski, J. Becker, Z. Nikoloski, D. Bhattacharya, D. Price, T. Tohge, A. Bar-Even, A. Fernie, M. Stitt, M. Mutwil, Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida, Nature communications (2019) pubmed
M. Flores-Tornero, S. Proost, M. Mutwil, C. P. Scutt, T. Dresselhaus, S. Sprunck, Transcriptomics of manually isolated Amborella trichopoda egg apparatus cells, Plant reproduction (2019) pubmed
L. Perez de Souza, F. Scossa, S. Proost, E. Bitocchi, R Papa, T. Tohge, A. R. Fernie, Multi‐tissue integration of transcriptomic and specialized metabolite profiling provides tools for assessing the common bean (Phaseolus vulgaris) metabolome, The Plant Journal (2018) pubmed
S. Proost, M. Mutwil, CoNekT: an open-source framework for comparative genomic and transcriptomic network analyses, Nucleic acids research (2018) pubmed
C. Ferrari, S. Proost, C. Ruprecht, M. Mutwil, PhytoNet: Comparative co-expression network analyses across phytoplankton and land plants, Nucleic acids research (2018) pubmed
M. Janowski, R. Zoschke, L Scharff, S. Martinez Jaime, C. Ferrari, S. Proost, N. Omranian, M. Musialak-Lange, Z. Nikoloski, A. Graf, M. A. Schottler, A. Sampathkumar, N. Vaid, M. Mutwil, AtRsgA from Arabidopsis thaliana controls maturation of the small subunit of the chloroplast ribosome, The Plant Journal (2018) pubmed
S. Proost, A. Krawczyk, M. Mutwil, LSTrAP: efficiently combining RNA sequencing data into co-expression networks, BMC Bioinformatics (2017) pubmed
R. Sibout, S. Proost, B. Hansen, N. Vaid, F. Giorgi, S. Ho-Yue-Kuang, F. Legée, L. Cezart, O. Bouchabké-Coussa, C. Soulhat, N. Provart, A. Pasha, P. Le Bris, E. Jamet, D. Roujol, H. Hoefte, C. Lapierre, S. Persson, M. Mutwil, Expression atlas and comparative co-expression network analyses reveal important genes involved in the formation of lignified cell wall in Brachypodium distachyon, New Phytologist (2017) pubmed
C. Ruprecht, S. Proost, M. Hernandez-Coronado, C. Ortiz-Ramirez, D. Lang, S. A. Rensing, J. D. Becker, K. Vandepoele, M. Mutwil, Phylogenomic analysis of gene co-expression networks reveals evolution of functional modules, The Plant Journal (2017) pubmed
C. Ruprecht, N. Vaid, S. Proost, S. Persson, M. Mutwil, Beyond genomics: studying evolution with gene networks, Trends in Plant Science (2017) pubmed
S. Proost, M.Mutwil, PlaNet: Comparative Co-Expression Network Analyses for Plants, Plant Genomics Databases (Book Chapter) (2017) pubmed
M. Swiadek*, S. Proost*, D. Sieh, J. Yu, M. Todesco, C. Jorzig, A. E. Rodriguez Cubillos, B. Ploetner, Z. Nikoloski, E. Chae, P. Giavalisco, A. Fischer, F. Schroeder, S.-T. Kim, D. Weigel, R.A.E. Laitinen, Novel allelic variants in ACD6 cause hybrid necrosis in local collection of Arabidopsis thaliana, New Phytologist (2017) pubmed
S. Proost, M.Mutwil, Tools of the trade: studying molecular networks in plants, Current Opinion in Plant Biology (2016) pubmed
M. A. Omidbakhshfard, S. Proost, U. Fujikura, B. Mueller-Roeber, Growth-regulating factors (GRFs): a small transcription factor family with important functions in plant biology, Molecular plant (2015) pubmed
J. Cai*, X. Liu*, K. Vanneste*, S. Proost*, W.-C. Tsai*, K.-W. Liu*, ..., Y. Van de Peer, and Z.-J. Liu, The genome sequence of the orchid Phalaenopsis equestris, Nature genetics (2015) pubmed
S. Proost*, M. Van Bel*, D. Vaneechoutte, Y. Van de Peer, D. Inzé, B. Mueller-Roeber, and K. Vandepoele, PLAZA 3.0: an access point for plant comparative genomics, Nucleic acids research (2014) pubmed
S. Balazadeh, J. Schildhauer, W. L. Araújo, S. Munné-Bosch, A. R Fernie, S. Proost, K. Humbeck, and B. Mueller-Roeber, Reversal of senescence by N resupply to N-starved Arabidopsis thaliana: transcriptomic and metabolomic consequences, Journal of experimental botany (2014) pubmed
M. Van Bel, S. Proost, C. Van Neste, D. Deforce, Y. Van de Peer, and K. Vandepoele, TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes, Genome biology (2013) pubmed
P. Ruelens, R. A. de Maagd, S. Proost, G. Theißen, K. Geuten, and K. Kaufmann, FLOWERING LOCUS C in monocots and the tandem origin of angiosperm-specific MADS-box genes, Nature Communications (2013) pubmed
D. Vekemans*, S. Proost*, K. Vanneste, H. Coenen, T. Viaene, P. Ruelens, S. Maere, Y. Van de Peer, and K. Geuten., Gamma paleohexaploidy in the stem lineage of core eudicots: significance for MADS-Box gene and species diversification, Molecular biology and evolution (2012) pubmed
M. Van Bel*, S. Proost*, E. Wischnitzki, S. Mohavedi, C. Scheerlinck, Y. Van de Peer, and K. Vandepoele., Dissecting plant genomes with the PLAZA comparative genomics platform, Plant Physiology (2012) pubmed
S. Proost*, J. Fostier*, D. De Witte, B. Dhoedt, P. Demeester, Y. Van de Peer, and K. Vandepoele., i-ADHoRe 3.0 - fast and sensitive detection of genomic homology in extremely large data sets, Nucleic Acids Research (2012) pubmed
N. D. Young, F. Debelle, G. Oldroyd, R. Geurts, S. B. Cannon, M. K. Udvardi,V. A. Benedito, K. F. X. Mayer, J. Gouzy, H. Schoof, Y. Van de Peer, S. Proost, D. R. Cook, ..., D. C. Schwartz, J. Rogers, F. Quetier, C. D. Town, and B. A. Roe., The Medicago genome provides insight into the evolution of rhizobial symbioses, Nature (2011) pubmed
S. Proost, P. Pattyn, T. Gerats, and Y. Van de Peer., Journey through the past: 150 million years of plant genome evolution, The Plant Journal (2011) pubmed
J. Fostier*, S. Proost*, B. Dhoedt, Y. Saeys, P. Demeester, Y. Van de Peer, and K. Vandepoele., A greedy, graph-based algorithm for the alignment of multiple homologous gene lists, Bioinformatics (2011) pubmed
R. Velasco, A. Zharkikh, J. Affourtit, A. Dhingra, A. Cestaro, A. Kalyanaraman, P. Fontana, S. K. Bhatnagar, M. Troggio, D. Pruss, ..., J. A. Fawcett, S. Proost, P. Rouze, L. Sterck, S. Toppo, B. Lazzari, R. P. Hellens, C. E. Durel, A. Gutin, R. E. Bumgarner, S. E. Gardiner, M. Skolnick, M. Egholm, Y. Van de Peer, F. Salamini, and R. Viola., The genome of the domesticated apple (Malus x domestica Borkh.), Nature genetics (2010) pubmed
Y. Van de Peer, J. A. Fawcett, S. Proost, L. Sterck, and K. Vandepoele., The flowering world: a tale of duplications, Trends in plant science (2009) pubmed
S. Proost*, M. Van Bel*, L. Sterck, K. Billiau, T. Van Parys, Y. Van de Peer, and K. Vandepoele., PLAZA: a comparative genomics resource to study gene and genome evolution in plants, The Plant Cell (2009) pubmed
S. De Bodt, S. Proost, K. Vandepoele, P. Rouze, and Y. Van de Peer., Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression, BMC genomics (2009) pubmed

Media

Pint of Science: Bytes & Bacteria
Streamed presentation for Pint of Science
Talk Python To Me: A gut feeling about Python
I was a guest on the podcast "Talk Python To Me"
Biotech Glashelder door EOS: Bytes & Bacteriën
Ten minute presentation suited for a broad audience (in Dutch)
Wetenschap uitgedokterd: Bytes & Bacteriën
Two minute pitch about my work (in Dutch, English subtitles)
Fokus jongeren: Ad Biotechdag
Advertisement for Biotechdag 2019

Training (Show more...)

Screencasting from A to Z (by LIMEL - KU Leuven), 2nd Semester, 2019. Leuven, Belgium
Science Figured Out (by The Floor is Yours (Toon Verlinden)), June 11, 2019. Leuven, Belgium
Scientists on Stage (by The Floor is Yours (Hans Van de Water)), March 15 & April 1, 2019. Leuven/Gent, Belgium
Enabling Innovation (by Max Planck Innovation and Atrineo AG), November 13, 2017. Potsdam-Golm, Germany
Proposal Writing (by Dr. Brain Cusack & Dr. Babette Regierer), October 17-18, 2016. Potsdam-Golm, Germany
Team Dynamics and Leadership (by Betty Boden), May 23-24, 2016. Potsdam-Golm, Germany
Fundamentals of image processing with Adobe Photoshop (by Dr. Katja Toepfer), April 29-30, 2015. Potsdam-Golm, Germany
Intercultural Communication (by Alexia Petersen), January 20-21, 2014. Potsdam-Golm, Germany
Team Dynamics (by Betty Boden), November 11-12, 2013. Potsdam-Golm, Germany
Basic Assistant Training (by Liesje Liagre), May 10-11, 2012. Ghent, Belgium
Unix Systems for Bioinformatics (by Dr. Lieven Sterck), 2nd Semester, 2011. Ghent, Belgium
Creative Thinking (by Karl Raats), April 20-22, 2011. Ghent, Belgium
Project Management (by Tom Jacobs), March 2,9,16, 2011. Ghent, Belgium
Effective Oral Presentations (by Dr. Jean-Luc Doumont), February 1,7,10,21, 2011. Ghent, Belgium
Effective Writing for Life Sciences (by Dr. Jane Fraser), October 19-20, 2010. Ghent, Belgium
Ensembl Workshop (by Bert Overduin), September 20, 2007. Ghent, Belgium

Conferences (Show more...)

Nanyang Technological University Singapore Guest Scientist, January, 2018. NTU, Singapore. Guest Scientist.
EVOREPRO PlaNet 2.0 Workshop, March 8, 2017. IGC Oeiras, Portugal. Trainer.
Plant Biology Europe EPSO/FESPB 2016, June 26-30, 2016. Prague, Czech Republic. Poster presentation.
EMBO workshop - New model systems for early land plant evolution, June 22-24, 2016. GMI, Vienna, Austria. Poster presentation.
IMPRS Course - Linux and Scripting For Biologists, April, 2015. MPI-MP, Potsdam-Golm, Germany. Teacher.
IMPRS - Comparative Genomics Workshop, November 24, 2014. MPI-MP, Potsdam-Golm, Germany. Trainer.
PSB PLAZA 3.0 Workshop, September 29, 2014. PSB/VIB Ghent, Belgium. Trainer.
Vibes 2014 - 4th International VIB PhD Symposium, September 17-19, 2014. Antwerpen, Belgium. No active contribution.
AllBio Tutorial: New methods in genome annotation, July 10-11, 2014. Berlin, Germany. Trainer.
AllBio Tutorial: Comparative genome annotation methods, April 29-30, 2014. Potsdam, Germany. Trainer.
PSB/VIB Guest Scientist, November 15 - December 23, 2013. PSB/VIB Ghent, Belgium. Guest Scientist.
Black Forest Summer School, September 10-13, 2013. Herzogenhorn, Germany. Trainer.
Plants & People, June 18-19, 2013. MPI-MP,Potsdam-Golm, Germany. Poster presentation.
IMPRS - PLAZA Workshop, April 22 ,25, 2013. MPI-MP, Potsdam-Golm, Germany. Trainer.
Bioinformatics Affinity Seminar, March 6, 2013. MPI-MP, Potsdam-Golm, Germany. Guest Speaker.
AllBio Course on Data Resources and Tools for Plant-Omics, February 18-22, 2013. EBI-Hinxton, Cambridgeshire, United Kingdom. Trainer.
FU Berlin - PLAZA Workshop, March 4, 2013. FU Berlin, Berlin, Germany. Trainer.
Vibes 2012 - 3th International VIB PhD Symposium, September 5-7, 2012. Gent, Belgium. Organizing committee.
VIB Seminar, PhD Student Day, April 18, 2012. Blankenberge, Belgium. Chair Bioinformatics & Systems Biology Session.
Bioinformatics Affinity Seminar, February 8, 2012. MPI-MP, Potsdam-Golm, Germany. Guest Speaker.
Plant Genome Evolution, September 4-6, 2011. Amsterdam, The Netherlands. Poster presentation and software demonstration.
GMPF Summer School 2011: Introduction to Bioinformatics, June 28 - July 1, 2011. IASMA, San Michele all'Adige, Italy. Invited speaker.
Comparative & Regulatory Genomics in Plants - Workshop, April 13-15, 2011. UGent, Gent, Belgium. Organizing committee, lecturer.
Comparative & Regulatory Genomics in Plants - Conference, April 11-12, 2011. PSB/VIB, Gent, Belgium. Organizing committee, oral presentation and poster presentation.
BioMaGNet's Annual Meeting, March 21, 2011. ULB Campus Plaine, Brussels, Belgium. Poster presentation.
Vibes 2010 - 2nd International VIB PhD Symposium, October 14-15, 2010. Leuven, Belgium. No active contribution.
9th European Conference on Computational Biology (ECCB2010), September 26-29, 2010. Ghent, Belgium. Poster presentation.
First European Student Council Symposium (ESCS1), September 26, 2010. Ghent, Belgium. Poster presentation.
Brassicacea Map Alignment Project - 2nd BMAP meeting, March 22, 2010. Max Planck Institute, Tuebingen, Germany. Oral presentation.
BioMaGNet's Annual Meeting, October 22, 2009. VIB-Ghent University, Ghent, Belgium. Oral presentation and poster presentation.
6th Annual RECOMB Satellite Meeting on Comparative Genomics, October 13-15, 2008. Ecole Normale Superieure, Paris, France. Poster presentation.
Benelux Bioinformatics Conference 2007, November 12-13, 2007. Leuven, Belgium. No active contribution.

Educational support

Systems Biology (by Prof. Dr. Alisdair Fernie), Potsdam, Germany, Guest Lecture: Functional Annotation using Comparative Genomics and Transcriptomics

Agnieszka Krawczyk, Engineer in Biotechnology , specialization: Molecular Biotechnology and Technical Biochemistry. International Faculty of Engineering, Lodz University of Technology, Development of a transcriptome analysis pipeline

Functional Plant Genomics (by Dr. Pierre Hilson), Ghent, Belgium, Guest Lecture: Introduction: Comparative Genomics Using the PLAZA Platform

Christopher Scheerlinck, Master in Industrial Engineering: Informatics, HoGent, Integration and visualization of evolutionary genomics data within an online comparative genomics platform

Steven Timmermans, 1st Master in Biochemistry and Biotechnology, UGent, Homology identification through sequence similarity clustering of multidomain proteins

Comparative Genomics (by Prof. Dr. Klaas Vandepoele), Ghent, Belgium, Assisted practical courses

Marieke Dubois, 1st Master in Biochemistry and Biotechnology, UGent, Analysis of pseudogenes in Arabidopsis thaliana

Grants and Awards

VIB Scientists on Stage - Best Presentation

IWT Personal Fellowship, Funding from Flemish government to support doctoral research

WELEK Robotics Competition - Fourth Place Autonomous Sumo Robot

WELEK Robotics Competition - Fourth Place Light Finder

IWT Personal Fellowship, Funding from Flemish government to support doctoral research

Speculaas van de Maand - Award from the city council of Hasselt

International Biology Olympiad - Bronze Medal Minsk, Belarus

Flemish Biology Olympiad - First Place

Skills (hover over for more info)

Programming: Python

Check out my GitHub repository for examples!

, R

Used for metabolite analysis in Swiadek et al.

, PHP

The CakePHP framework was used for PLAZA.
PlasmidDB is based on CodeIgniter.

, JavaScript

Used in PLAZA and extensively for CoNekT.

ReactJS was used for smaller projects in my GitHub repository : MemoBoard and Pomodoro Timer

, LaTeX, HTML & CSS

System Administration: MySQL

Used extensively for PLAZA and for CoNekT.

, Linux

All web-tools and scientific software I've worked on is designed to run on Linux

I've taught the Linux for Biologists course for a Doctoral School type program.

, Cluster/Cloud computing

Required to generate data for PLAZA, testing and developing i-ADHoRe 3.0.
Also check out LSTrAP

Languages

Dutch, Mothertongue

English, Fluent

German, intermediate (CEFR level: B2/1)

French, intermediate

Sebastian Proost, PhD

Bioinformatician, data scientist and web developer