Laboratory of Multi-omic Integrative Bioinformatics

Research

Spatial multi-omics

A human body comprises approximately 100 trillion cells. As most of our organ functions are executed by the concerted action of those individual cells in a spatially organised context, it is paramount to research these individual cells in their native spatial context. This is not only important to understand normal organ development and function, but also to investigate how cells are perturbed in diseased conditions. Technological developments in the last few years allow us to assay the expression of hundreds to thousands of genes at single-cell resolution while retaining the complete morphological and spatial information.

At LMIB, we are at the fore-front of the development of these technologies by working together with technologists and biologists, as part of the Leuven Single-Cell Institute, to create the next generation of spatial multi-omic technologies. We aim to develop novel data fusion strategies which integrate information gained from conventional microscopy with sub-cellular resolution multi-omics information by leveraging state-of-the-art deep neural network architectures.

Variant Prioritization

Genome sequencing studies reveal thousands to millions of genetic variants in any typical individual. These genetic variants are often benign, but a small subset can give rise to disease. However, the fundamental challenge of distinguishing between neutral and pathogenic variants is often non-trivial, and follow-up investigation of variants is often time and cost-prohibitive. Therefore, variant prioritization tools are needed which rank the most likely candidates based on available information on the nature of the respective variants, the genes wherein they reside, the tissues wherein these genes are expressed and the patient’s phenotypic presentation.

At LMIB we aim to develop variant prioritization tools leveraging the latest publicly available data and state-of-the-art machine learning algorithms and apply these tools in large-scale genetic studies in order to further understand the genetic etiology of human diseases and to provide improved genetic diagnostic outputs for patients.

Highlighted

A multi-omics genome-and-transcriptome single-cell atlas of human preimplantation embryogenesis reveals the cellular and molecular impact of chromosome instability
A multi-omics genome-and-transcriptome single-cell atlas of human preimplantation embryogenesis reveals the cellular and molecular impact of chromosome instability
Elia Fernandez Gallardo, Alejandro Sifrim, Joel Chappell, Jonas Demeulemeester, Jennifer Clara Herrmann, ..., Joris Robert Vermeesch, Karen Peeraer, Sophie Debrock, Vincent Pasque, Thierry Voet
Cold Spring Harbor Laboratory   ·   10 Mar 2023   ·   doi:10.1101/2023.03.08.530586

All

2024

Single cell transcriptomics reveal mast cell heterogeneity in the human gut
Single cell transcriptomics reveal mast cell heterogeneity in the human gut
Hind Hussein, Elodie Modave, Nathalie Stakenborg, Marcello Delfini, Katy Vandereyken, Alejandro Sifrim, Thierry Voet, Guy E Boeckxstaens
Cold Spring Harbor Laboratory   ·   03 Dec 2024   ·   doi:10.1101/2024.11.29.626054

2023

Assessing the contribution of rare variants to congenital heart disease through a large-scale case-control exome study
Assessing the contribution of rare variants to congenital heart disease through a large-scale case-control exome study
Enrique Audain, Anna Wilsdon, Gregor Dombrowsky, Alejandro Sifrim, Jeroen Breckpot, ..., Hans-Heiner Kramer, Vivek Iyer, Lars Allan Larsen, J David Brook, Marc-Phillip Hitz
Cold Spring Harbor Laboratory   ·   28 Dec 2023   ·   doi:10.1101/2023.12.23.23300495
A multi-omics genome-and-transcriptome single-cell atlas of human preimplantation embryogenesis reveals the cellular and molecular impact of chromosome instability
A multi-omics genome-and-transcriptome single-cell atlas of human preimplantation embryogenesis reveals the cellular and molecular impact of chromosome instability
Elia Fernandez Gallardo, Alejandro Sifrim, Joel Chappell, Jonas Demeulemeester, Jennifer Clara Herrmann, ..., Joris Robert Vermeesch, Karen Peeraer, Sophie Debrock, Vincent Pasque, Thierry Voet
Cold Spring Harbor Laboratory   ·   10 Mar 2023   ·   doi:10.1101/2023.03.08.530586

2021

Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease
Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease
Enrique Audain, Anna Wilsdon, Jeroen Breckpot, Jose M. G. Izarzugaza, Tomas W. Fitzgerald, ..., Gregor Andelfinger, Matthew E. Hurles, Bernard Thienpont, Lars Allan Larsen, Marc-Phillip Hitz
PLOS Genetics   ·   29 Jul 2021   ·   doi:10.1371/journal.pgen.1009679

2020

Detecting cryptic clinically-relevant structural variation in exome sequencing data increases diagnostic yield for developmental disorders
Detecting cryptic clinically-relevant structural variation in exome sequencing data increases diagnostic yield for developmental disorders
Eugene J. Gardner, Alejandro Sifrim, Sarah J. Lindsay, Elena Prigmore, Diana Rajan, ..., Hilary C. Martin, Caroline F. Wright, David R. FitzPatrick, Helen V. Firth, Matthew E. Hurles
Cold Spring Harbor Laboratory   ·   02 Oct 2020   ·   doi:10.1101/2020.10.02.20194241
Systems genetics analysis identifies calcium-signaling defects as novel cause of congenital heart disease
Systems genetics analysis identifies calcium-signaling defects as novel cause of congenital heart disease
Jose M. G. Izarzugaza, Sabrina G. Ellesøe, Canan Doganli, Natasja Spring Ehlers, Marlene D. Dalgaard, ..., Sabine Klaassen, J. David Brook, Marc-Phillip Hitz, Lars A. Larsen, Søren Brunak
Genome Medicine   ·   28 Aug 2020   ·   doi:10.1186/s13073-020-00772-z
Heterotypic cell–cell communication regulates glandular stem cell multipotency
Heterotypic cell–cell communication regulates glandular stem cell multipotency
Alessia Centonze, Shuheng Lin, Elisavet Tika, Alejandro Sifrim, Marco Fioramonti, ..., Viviane de Maertelaer, Christian W. Siebel, Alexandra Van Keymeulen, Thierry Voet, Cédric Blanpain
Nature   ·   26 Aug 2020   ·   doi:10.1038/s41586-020-2632-y
Mechanisms of stretch-mediated skin expansion at single-cell resolution
Mechanisms of stretch-mediated skin expansion at single-cell resolution
Mariaceleste Aragona, Alejandro Sifrim, Milan Malfait, Yura Song, Jens Van Herck, ..., Seungmin Han, Fadel Tissir, Thierry Voet, Benjamin D. Simons, Cédric Blanpain
Nature   ·   29 Jul 2020   ·   doi:10.1038/s41586-020-2555-7
Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease
Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease
E Audain, A Wilsdon, J Breckpot, JMG Izarzugaza, TW Fitzgerald, ..., G Andelfinger, ME Hurles, B Thienpont, LA Larsen, MP Hitz
Cold Spring Harbor Laboratory   ·   25 Jun 2020   ·   doi:10.1101/2020.06.25.169573
Interstitial Cell Remodeling Promotes Aberrant Adipogenesis in Dystrophic Muscles
Interstitial Cell Remodeling Promotes Aberrant Adipogenesis in Dystrophic Muscles
Jordi Camps, Natacha Breuls, Alejandro Sifrim, Nefele Giarratana, Marlies Corvelyn, ..., Rik Gijsbers, Giulio Cossu, Yvan Torrente, Thierry Voet, Maurilio Sampaolesi
Cell Reports   ·   01 May 2020   ·   doi:10.1016/j.celrep.2020.107597
Defining the Design Principles of Skin Epidermis Postnatal Growth
Defining the Design Principles of Skin Epidermis Postnatal Growth
Sophie Dekoninck, Edouard Hannezo, Alejandro Sifrim, Yekaterina A. Miroshnikova, Mariaceleste Aragona, ..., Christine Dubois, Thierry Voet, Sara A. Wickström, Benjamin D. Simons, Cédric Blanpain
Cell   ·   01 Apr 2020   ·   doi:10.1016/j.cell.2020.03.015
The contribution of X-linked coding variation to severe developmental disorders
The contribution of X-linked coding variation to severe developmental disorders
Hilary C. Martin, Eugene J. Gardner, Kaitlin E. Samocha, Joanna Kaplanis, Nadia Akawi, ..., Jeremy McRae, Caroline F. Wright, David R. FitzPatrick, Helen V. Firth, Matthew E. Hurles
Cold Spring Harbor Laboratory   ·   23 Mar 2020   ·   doi:10.1101/2020.03.18.20037960

2019

Systems genetics analysis identify calcium signalling defects as novel cause of congenital heart disease
Systems genetics analysis identify calcium signalling defects as novel cause of congenital heart disease
Jose M.G. Izarzugaza, Sabrina G. Ellesøe, Canan Doganli, Natasja Spring Ehlers, Marlene D. Dalgaard, ..., Marc Gewillig, J. David Brook, Marc-Phillip Hitz, Lars A. Larsen, Søren Brunak
Cold Spring Harbor Laboratory   ·   12 Dec 2019   ·   doi:10.1101/2019.12.11.872424
Finding Diagnostically Useful Patterns in Quantitative Phenotypic Data
Finding Diagnostically Useful Patterns in Quantitative Phenotypic Data
Stuart Aitken, Helen V. Firth, Jeremy McRae, Mihail Halachev, Usha Kini, ..., H.V. Firth, D.R. FitzPatrick, C.F. Wright, J.C. Barrett, M.E. Hurles
The American Journal of Human Genetics   ·   01 Nov 2019   ·   doi:10.1016/j.ajhg.2019.09.015
Contribution of retrotransposition to developmental disorders
Contribution of retrotransposition to developmental disorders
Eugene J. Gardner, Elena Prigmore, Giuseppe Gallone, Petr Danecek, Kaitlin E. Samocha, ..., Katrina Prescott, Elisabeth Rosser, David R. FitzPatrick, Helen V. Firth, Matthew E. Hurles
Nature Communications   ·   11 Oct 2019   ·   doi:10.1038/s41467-019-12520-y
Heterozygous Variants in KMT2E Cause a Spectrum of Neurodevelopmental Disorders and Epilepsy
Heterozygous Variants in KMT2E Cause a Spectrum of Neurodevelopmental Disorders and Epilepsy
Anne H. O’Donnell-Luria, Lynn S. Pais, Víctor Faundes, Jordan C. Wood, Abigail Sveden, ..., Helen V. Firth, Caroline F. Wright, David R. FitzPatrick, Jeffrey C. Barrett, Matthew E. Hurles
The American Journal of Human Genetics   ·   01 Jun 2019   ·   doi:10.1016/j.ajhg.2019.03.021
Bi-allelic Loss-of-Function CACNA1B Mutations in Progressive Epilepsy-Dyskinesia
Bi-allelic Loss-of-Function CACNA1B Mutations in Progressive Epilepsy-Dyskinesia
Kathleen M. Gorman, Esther Meyer, Detelina Grozeva, Egidio Spinelli, Amy McTague, ..., John Wort, Nigel Yeatman, Patrick Yong, Tim Young, Ping Yu
The American Journal of Human Genetics   ·   01 May 2019   ·   doi:10.1016/j.ajhg.2019.03.005
HiVA: an integrative wet- and dry-lab platform for haplotype and copy number analysis of single-cell genomes
HiVA: an integrative wet- and dry-lab platform for haplotype and copy number analysis of single-cell genomes
Masoud Zamani Esteki, Amin Ardeshirdavani, Daniel Alcaide, Heleen Masset, Jia Ding, ..., Eftychia Dimitriadou, Jan Aerts, Thierry Voet, Yves Moreau, Joris Robert Vermeesch
Cold Spring Harbor Laboratory   ·   07 Mar 2019   ·   doi:10.1101/564914

2018

Contribution of Retrotransposition to Developmental Disorders
Contribution of Retrotransposition to Developmental Disorders
Eugene J. Gardner, Elena Prigmore, Giuseppe Gallone, Petr Danecek, Kaitlin E. Samocha, ..., Katrina Prescott, Elisabeth Rosser, David R. FitzPatrick, Helen V. Firth, Matthew E. Hurles
Cold Spring Harbor Laboratory   ·   16 Nov 2018   ·   doi:10.1101/471375
CHD3 helicase domain mutations cause a neurodevelopmental syndrome with macrocephaly and impaired speech and language
CHD3 helicase domain mutations cause a neurodevelopmental syndrome with macrocephaly and impaired speech and language
Lot Snijders Blok, Justine Rousseau, Joanna Twist, Sophie Ehresmann, Motoki Takaku, ..., Tjitske Kleefstra, Han G. Brunner, Paul A. Wade, Simon E. Fisher, Philippe M. Campeau
Nature Communications   ·   05 Nov 2018   ·   doi:10.1038/s41467-018-06014-6
Making new genetic diagnoses with old data: iterative reanalysis and reporting from genome-wide data in 1,133 families with developmental disorders
Making new genetic diagnoses with old data: iterative reanalysis and reporting from genome-wide data in 1,133 families with developmental disorders
Caroline F. Wright, Jeremy F. McRae, Stephen Clayton, Giuseppe Gallone, Stuart Aitken, ..., Michael J. Parker, Jeffrey C. Barrett, Matthew E. Hurles, David R. FitzPatrick, Helen V. Firth
Genetics in Medicine   ·   01 Oct 2018   ·   doi:10.1038/gim.2017.246
Early lineage segregation of multipotent embryonic mammary gland progenitors
Early lineage segregation of multipotent embryonic mammary gland progenitors
Aline Wuidart, Alejandro Sifrim, Marco Fioramonti, Shigeru Matsumura, Audrey Brisebarre, ..., Anne Dannau, Christine Dubois, Alexandra Van Keymeulen, Thierry Voet, Cédric Blanpain
Nature Cell Biology   ·   21 May 2018   ·   doi:10.1038/s41556-018-0095-2
Identification of the tumour transition states occurring during EMT
Identification of the tumour transition states occurring during EMT
Ievgenia Pastushenko, Audrey Brisebarre, Alejandro Sifrim, Marco Fioramonti, Tatiana Revenco, ..., Isabelle Salmon, Jean-Christophe Marine, Thierry Voet, Panagiota A. Sotiropoulou, Cédric Blanpain
Nature   ·   01 Apr 2018   ·   doi:10.1038/s41586-018-0040-3
De novo mutations in regulatory elements in neurodevelopmental disorders
De novo mutations in regulatory elements in neurodevelopmental disorders
Patrick J. Short, Jeremy F. McRae, Giuseppe Gallone, Alejandro Sifrim, Hyejung Won, ..., Caroline F. Wright, Helen V. Firth, David R. FitzPatrick, Jeffrey C. Barrett, Matthew E. Hurles
Nature   ·   01 Mar 2018   ·   doi:10.1038/nature25983
Histone Lysine Methylases and Demethylases in the Landscape of Human Developmental Disorders
Histone Lysine Methylases and Demethylases in the Landscape of Human Developmental Disorders
Víctor Faundes, William G. Newman, Laura Bernardini, Natalie Canham, Jill Clayton-Smith, ..., Helen V. Firth, Caroline F. Wright, David R. FitzPatrick, Jeffrey C. Barrett, Matthew E. . Hurles
The American Journal of Human Genetics   ·   01 Jan 2018   ·   doi:10.1016/j.ajhg.2017.11.013

2017

Not all
            <i>SCN1A</i>
            epileptic encephalopathies are Dravet syndrome
Not all SCN1A epileptic encephalopathies are Dravet syndrome
Lynette G. Sadleir, Emily I. Mountier, Deepak Gill, Suzanne Davis, Charuta Joshi, ..., Wayne Lam, Wendy D. Jones, Yanick Crow, Zara Skitt, Zosia Miedzybrodzka
Neurology   ·   05 Sep 2017   ·   doi:10.1212/wnl.0000000000004331
Detection of structural mosaicism from targeted and whole-genome sequencing data
Detection of structural mosaicism from targeted and whole-genome sequencing data
Daniel A. King, Alejandro Sifrim, Tomas W. Fitzgerald, Raheleh Rahbari, Emma Hobson, ..., Sarju G. Mehta, Mohammed Shehla, Susan E. Tomkins, Pradeep C. Vasudevan, Matthew E. Hurles
Genome Research   ·   30 Aug 2017   ·   doi:10.1101/gr.212373.116
Clinical and molecular consequences of disease-associated de novo mutations in SATB2
Clinical and molecular consequences of disease-associated de novo mutations in SATB2
Hemant Bengani, Mark Handley, Mohsan Alvi, Rita Ibitoye, Melissa Lees, ..., Helen V. Firth, F. Lucy Raymond, Usha Kini, Christoffer Nellåker, David R. FitzPatrick
Genetics in Medicine   ·   01 Aug 2017   ·   doi:10.1038/gim.2016.211
Recent advances in congenital heart disease genomics
Recent advances in congenital heart disease genomics
Anna Wilsdon, Alejandro Sifrim, Marc-Phillip Hitz, Matthew Hurles, J. David Brook
F1000Research   ·   12 Jun 2017   ·   doi:10.12688/f1000research.10113.1
<i>De novo</i>mutations in regulatory elements cause neurodevelopmental disorders
De novomutations in regulatory elements cause neurodevelopmental disorders
Patrick J. Short, Jeremy F. McRae, Giuseppe Gallone, Alejandro Sifrim, Hyejung Won, ..., Caroline F. Wright, Helen V. Firth, David R. FitzPatrick, Jeffrey C. Barrett, Matthew E. Hurles
Cold Spring Harbor Laboratory   ·   13 Mar 2017   ·   doi:10.1101/112896
Prevalence and architecture of de novo mutations in developmental disorders
Prevalence and architecture of de novo mutations in developmental disorders
[no author info]
Nature   ·   25 Jan 2017   ·   doi:10.1038/nature21062

2016

Distinct genetic architectures for syndromic and nonsyndromic congenital heart defects identified by exome sequencing
Distinct genetic architectures for syndromic and nonsyndromic congenital heart defects identified by exome sequencing
Alejandro Sifrim, Marc-Phillip Hitz, Anna Wilsdon, Jeroen Breckpot, Saeed H Al Turki, ..., Jeffrey C Barrett, Koenraad Devriendt, David R FitzPatrick, J David Brook, Matthew E Hurles
Nature Genetics   ·   01 Aug 2016   ·   doi:10.1038/ng.3627
Comparison of aggregation methods for multiphenotype exomic variant prioritization
Comparison of aggregation methods for multiphenotype exomic variant prioritization
Alejandro Sifrim, Dusan Popovic, Joris R. Vermeesch, Jan Aerts, Bart De Moor, Yves Moreau
Cold Spring Harbor Laboratory   ·   20 Jul 2016   ·   doi:10.1101/064899
Detection of structural mosaicism from targeted and whole-genome sequencing data
Detection of structural mosaicism from targeted and whole-genome sequencing data
Daniel A. King, Alejandro Sifrim, Tomas W. Fitzgerald, Raheleh Rahbari, Emma Hobson, ..., Sarju G. Mehta, Mohammed Shehla, Susan E. Tomkins, Pradeep C. Vasudevan, Matthew E. Hurles
Cold Spring Harbor Laboratory   ·   07 Jul 2016   ·   doi:10.1101/062620
Prevalence, phenotype and architecture of developmental disorders caused by<i>de novo</i>mutation: The Deciphering Developmental Disorders Study
Prevalence, phenotype and architecture of developmental disorders caused byde novomutation: The Deciphering Developmental Disorders Study
Jeremy F McRae, Stephen Clayton, Tomas W Fitzgerald, Joanna Kaplanis, Elena Prigmore, ..., Helen V Firth, Caroline F Wright, David R FitzPatrick, Jeffrey C Barrett, Matthew E Hurles
Cold Spring Harbor Laboratory   ·   20 Apr 2016   ·   doi:10.1101/049056

2015

Mutations in Either TUBB or MAPRE2 Cause Circumferential Skin Creases Kunze Type
Mutations in Either TUBB or MAPRE2 Cause Circumferential Skin Creases Kunze Type
Mala Isrie, Martin Breuss, Guoling Tian, Andi Harley Hansen, Francesca Cristofoli, ..., Joris Robert Vermeesch, Erica E. Davis, Nicholas J. Cowan, David Anthony Keays, Hilde Van Esch
The American Journal of Human Genetics   ·   01 Dec 2015   ·   doi:10.1016/j.ajhg.2015.10.014
A Note on the Evaluation of Mutation Prioritization Algorithms
A Note on the Evaluation of Mutation Prioritization Algorithms
Dusan Popovic, Jesse Davis, Alejandro Sifrim, Bart De Moor
2015 IEEE Symposium Series on Computational Intelligence   ·   01 Dec 2015   ·   doi:10.1109/ssci.2015.193
Mutations in NONO lead to syndromic intellectual disability and inhibitory synaptic defects
Mutations in NONO lead to syndromic intellectual disability and inhibitory synaptic defects
Dennis Mircsof, Maéva Langouët, Marlène Rio, Sébastien Moutton, Karine Siquier-Pernet, ..., Arnold Munnich, Jeanne Amiel, Steven A Brown, Shiva K Tyagarajan, Laurence Colleaux
Nature Neuroscience   ·   16 Nov 2015   ·   doi:10.1038/nn.4169
Discovery of four recessive developmental disorders using probabilistic genotype and phenotype matching among 4,125 families
Discovery of four recessive developmental disorders using probabilistic genotype and phenotype matching among 4,125 families
Nadia Akawi, Jeremy McRae, Morad Ansari, Meena Balasubramanian, Moira Blyth, ..., Helen V Firth, Jeffrey C Barrett, Cecilia W Lo, David R FitzPatrick, Matthew E Hurles
Nature Genetics   ·   05 Oct 2015   ·   doi:10.1038/ng.3410
<i>Beegle:</i>from literature mining to disease-gene discovery
Beegle:from literature mining to disease-gene discovery
Sarah ElShal, Léon-Charles Tranchevent, Alejandro Sifrim, Amin Ardeshirdavani, Jesse Davis, Yves Moreau
Nucleic Acids Research   ·   17 Sep 2015   ·   doi:10.1093/nar/gkv905
Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data
Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data
Caroline F Wright, Tomas W Fitzgerald, Wendy D Jones, Stephen Clayton, Jeremy F McRae, ..., Nigel P Carter, Jeffrey C Barrett, Matthew E Hurles, David R FitzPatrick, Helen V Firth
The Lancet   ·   01 Apr 2015   ·   doi:10.1016/s0140-6736(14)61705-0
Problems with the nested granularity of feature domains in bioinformatics: the eXtasy case
Problems with the nested granularity of feature domains in bioinformatics: the eXtasy case
Dusan Popovic, Alejandro Sifrim, Jesse Davis, Yves Moreau, Bart De Moor
BMC Bioinformatics   ·   23 Feb 2015   ·   doi:10.1186/1471-2105-16-s4-s2

2014

Large-scale discovery of novel genetic causes of developmental disorders
Large-scale discovery of novel genetic causes of developmental disorders
[no author info]
Nature   ·   24 Dec 2014   ·   doi:10.1038/nature14135
Synaptic, transcriptional and chromatin genes disrupted in autism
Synaptic, transcriptional and chromatin genes disrupted in autism
Silvia De Rubeis, Xin He, Arthur P. Goldberg, Christopher S. Poultney, Kaitlin Samocha, ..., David J. Cutler, Kathryn Roeder, Bernie Devlin, Mark J. Daly, Joseph D. Buxbaum
Nature   ·   29 Oct 2014   ·   doi:10.1038/nature13772
A Self-Tuning Genetic Algorithm with Applications in Biomarker Discovery
A Self-Tuning Genetic Algorithm with Applications in Biomarker Discovery
Dusan Popovic, Charalampos Moschopoulos, Ryo Sakai, Alejandro Sifrim, Jan Aerts, Yves Moreau, Bart De Moor
2014 IEEE 27th International Symposium on Computer-Based Medical Systems   ·   01 May 2014   ·   doi:10.1109/cbms.2014.10

2013

eXtasy simplified-towards opening the black box
eXtasy simplified-towards opening the black box
Dusan Popovic, Alejandro Sifrim, Yves Moreau, Bart De Moor
2013 IEEE International Conference on Bioinformatics and Biomedicine   ·   01 Dec 2013   ·   doi:10.1109/bibm.2013.6732713
eXtasy: variant prioritization by genomic data fusion
eXtasy: variant prioritization by genomic data fusion
Alejandro Sifrim, Dusan Popovic, Leon-Charles Tranchevent, Amin Ardeshirdavani, Ryo Sakai, Peter Konings, Joris R Vermeesch, Jan Aerts, Bart De Moor, Yves Moreau
Nature Methods   ·   29 Sep 2013   ·   doi:10.1038/nmeth.2656
Unraveling genomic variation from next generation sequencing data
Unraveling genomic variation from next generation sequencing data
Georgios A Pavlopoulos, Anastasis Oulas, Ernesto Iacucci, Alejandro Sifrim, Yves Moreau, Reinhard Schneider, Jan Aerts, Ioannis Iliopoulos
BioData Mining   ·   25 Jul 2013   ·   doi:10.1186/1756-0381-6-13
TrioVis: a visualization approach for filtering genomic variants of parent–child trios
TrioVis: a visualization approach for filtering genomic variants of parent–child trios
Ryo Sakai, Alejandro Sifrim, Andrew Vande Moere, Jan Aerts
Bioinformatics   ·   08 May 2013   ·   doi:10.1093/bioinformatics/btt267
Meander: visually exploring the structural variome using space-filling curves
Meander: visually exploring the structural variome using space-filling curves
G. A. Pavlopoulos, P. Kumar, A. Sifrim, R. Sakai, M. L. Lin, T. Voet, Y. Moreau, J. Aerts
Nucleic Acids Research   ·   19 Apr 2013   ·   doi:10.1093/nar/gkt254
A Hybrid Approach to Feature Ranking for Microarray Data Classification
A Hybrid Approach to Feature Ranking for Microarray Data Classification
Dusan Popovic, Alejandro Sifrim, Charalampos Moschopoulos, Yves Moreau, Bart De Moor
Communications in Computer and Information Science   ·   01 Jan 2013   ·   doi:10.1007/978-3-642-41016-1_26
A Genetic Algorithm for Pancreatic Cancer Diagnosis
A Genetic Algorithm for Pancreatic Cancer Diagnosis
Charalampos Moschopoulos, Dusan Popovic, Alejandro Sifrim, Grigorios Beligiannis, Bart De Moor, Yves Moreau
Communications in Computer and Information Science   ·   01 Jan 2013   ·   doi:10.1007/978-3-642-41016-1_24

2012

Heterozygous missense mutations in SMARCA2 cause Nicolaides-Baraitser syndrome
Heterozygous missense mutations in SMARCA2 cause Nicolaides-Baraitser syndrome
Jeroen K J Van Houdt, Beata Anna Nowakowska, Sérgio B Sousa, Barbera D C van Schaik, Eve Seuntjens, ..., Orsetta Zuffardi, Antoine H C van Kampen, Koenraad Devriendt, Raoul Hennekam, Joris Robert Vermeesch
Nature Genetics   ·   26 Feb 2012   ·   doi:10.1038/ng.1105
Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease
Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease
Alejandro Sifrim, Jeroen KJ Van Houdt, Leon-Charles Tranchevent, Beata Nowakowska, Ryo Sakai, Georgios A Pavlopoulos, Koen Devriendt, Joris R Vermeesch, Yves Moreau, Jan Aerts
Genome Medicine   ·   01 Jan 2012   ·   doi:10.1186/gm374
A Simple Genetic Algorithm for Biomarker Mining
A Simple Genetic Algorithm for Biomarker Mining
Dusan Popovic, Alejandro Sifrim, Georgios A. Pavlopoulos, Yves Moreau, Bart De Moor
Lecture Notes in Computer Science   ·   01 Jan 2012   ·   doi:10.1007/978-3-642-34123-6_20

2011

Medusa: A tool for exploring and clustering biological networks
Medusa: A tool for exploring and clustering biological networks
Georgios A Pavlopoulos, Sean D Hooper, Alejandro Sifrim, Reinhard Schneider, Jan Aerts
BMC Research Notes   ·   06 Oct 2011   ·   doi:10.1186/1756-0500-4-384

2010

Alternative Experimental Design with an Applied Normalization Scheme Can Improve Statistical Power in 2D-DIGE Experiments
Alternative Experimental Design with an Applied Normalization Scheme Can Improve Statistical Power in 2D-DIGE Experiments
Kristof Engelen, Alejandro Sifrim, Babs Van de Plas, Kris Laukens, Lutgarde Arckens, Kathleen Marchal
Journal of Proteome Research   ·   24 Aug 2010   ·   doi:10.1021/pr100010u