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1

A comparison of single-cell trajectory inference methods

Saelens, Wouter, Cannoodt, Robrecht, Todorov, Helena, Saeys, Yvan

Journal:

Nature Biotechnology

Year:

2019

Language:

english

File:

PDF, 5.64 MB

english, 2019

2

Computational flow cytometry: helping to make sense of high-dimensional immunology data

Saeys, Yvan, Gassen, Sofie Van, Lambrecht, Bart N.

Journal:

Nature Reviews Immunology

Year:

2016

Language:

english

File:

PDF, 1.51 MB

english, 2016

3

A review of estimation of distribution algorithms in bioinformatics

Rubén Armañanzas, Iñaki Inza, Roberto Santana, Yvan Saeys, Jose Luis Flores, Jose Antonio Lozano, Van de Yves Peer, Rosa Blanco, Víctor Robles, Concha Bielza, Pedro Larrañaga

Journal:

Year:

2008

Language:

english

File:

PDF, 457 KB

english, 2008

4

Validating module network learning algorithms using simulated data

Tom Michoel, Steven Maere, Eric Bonnet, Anagha Joshi, Yvan Saeys, Tim Van den Bulcke, Koenraad Van Leemput, Piet van Remortel, Martin Kuiper, Kathleen Marchal, Yves Van de Peer

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 631 KB

english, 2007

5

FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

Van Gassen, Sofie, Callebaut, Britt, Van Helden, Mary J., Lambrecht, Bart N., Demeester, Piet, Dhaene, Tom, Saeys, Yvan

Journal:

Cytometry Part A

Year:

2015

Language:

english

File:

PDF, 1009 KB

english, 2015

6

Fuzzy rough classifiers for class imbalanced multi-instance data

Vluymans, Sarah, Sánchez Tarragó, Dánel, Saeys, Yvan, Cornelis, Chris, Herrera, Francisco

Journal:

Pattern Recognition

Year:

2015

Language:

english

File:

PDF, 1.27 MB

english, 2015

7

Applications of Fuzzy Rough Set Theory in Machine Learning: a Survey

Vluymans, Sarah, D’eer, Lynn, Saeys, Yvan, Cornelis, Chris, Cornelis, Chris, Nguyen, Hung Son, Pal, Sankar K., Skowron, Andrzej, Wu, Wei-Zhi

Journal:

Fundamenta Informaticae

Year:

2015

Language:

english

File:

PDF, 330 KB

english, 2015

8

Dynamic affinity-based classification of multi-class imbalanced data with one-versus-one decomposition: a fuzzy rough set approach

Vluymans, Sarah, Fernández, Alberto, Saeys, Yvan, Cornelis, Chris, Herrera, Francisco

Journal:

Knowledge and Information Systems

Year:

2017

Language:

english

File:

PDF, 1.40 MB

english, 2017

9

[IEEE 2019 IEEE International Congress on Big Data (BigData Congress) - Milan, Italy (2019.7.8-2019.7.13)] 2019 IEEE International Congress on Big Data (BigDataCongress) - Distributed, Numerically Stable Distance and Covariance Computation with MPI for Extremely Large Datasets

Peralta, Daniel, Saeys, Yvan

Year:

2019

Language:

english

File:

PDF, 175 KB

english, 2019

10

TinGa: fast and flexible trajectory inference with Growing Neural Gas

Todorov, Helena, Cannoodt, Robrecht, Saelens, Wouter, Saeys, Yvan

Journal:

Year:

2020

File:

PDF, 2.18 MB

2020

11

HIGH-PRECISION BIO-MOLECULAR EVENT EXTRACTION FROM TEXT USING PARALLEL BINARY CLASSIFIERS

Sofie Van Landeghem, Bernard De Baets, Yves Van de Peer, Yvan Saeys

Journal:

Computational Intelligence

Year:

2011

Language:

english

File:

PDF, 2.39 MB

english, 2011

12

Investigating ancient duplication events in the Arabidopsis genome

Jeroen Raes, Klaas Vandepoele, Cedric Simillion, Yvan Saeys, Yves Van de Peer

Journal:

Journal of Structural and Functional Genomics

Year:

2003

Language:

english

File:

PDF, 194 KB

english, 2003

13

Highlights of the BioTM 2010 workshop on advances in bio text mining

Thomas Abeel, Sofie Van Landeghem, Roser Morante, Vincent Van Asch, Yves Van de Peer, Walter Daelemans, Yvan Saeys

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 170 KB

english, 2010

14

Feature selection for splice site prediction: A new method using EDA-based feature ranking

Yvan Saeys, Sven Degroeve, Dirk Aeyels, Pierre Rouzé, Yves Van de Peer

Journal:

BMC Bioinformatics

Year:

2004

Language:

english

File:

PDF, 409 KB

english, 2004

15

Robust calibrations on reduced sample sets for API content prediction in tablets: Definition of a cost-effective NIR model development strategy

Pieters, Sigrid, Saeys, Wouter, Van den Kerkhof, Tom, Goodarzi, Mohammad, Hellings, Mario, De Beer, Thomas, Heyden, Yvan Vander

Journal:

Analytica Chimica Acta

Year:

2013

Language:

english

File:

PDF, 993 KB

english, 2013

16

[Lecture Notes in Computer Science] Knowledge Discovery and Emergent Complexity in Bioinformatics Volume 4366 || The NetGenerator Algorithm: Reconstruction of Gene Regulatory Networks

Tuyls, Karl, Westra, Ronald, Saeys, Yvan, Nowé, Ann

Year:

2007

Language:

english

File:

PDF, 457 KB

english, 2007

17

The function of Fcγ receptors in dendritic cells and macrophages

Guilliams, Martin, Bruhns, Pierre, Saeys, Yvan, Hammad, Hamida, Lambrecht, Bart N.

Journal:

Nature Reviews Immunology

Year:

2014

Language:

english

File:

PDF, 1.54 MB

english, 2014

18

Binary classification of chalcone derivatives with LDA or KNN based on their antileishmanial activity and molecular descriptors selected using the Successive Projections Algorithm feature-selection technique

Goodarzi, Mohammad, Saeys, Wouter, de Araujo, Mario Cesar Ugulino, Galvão, Roberto Kawakami Harrop, Vander Heyden, Yvan

Journal:

European Journal of Pharmaceutical Sciences

Year:

2014

Language:

english

File:

PDF, 328 KB

english, 2014

19

The unfolded-protein-response sensor IRE-1α regulates the function of CD8α+ dendritic cells

Osorio, Fabiola, Tavernier, Simon J, Hoffmann, Eik, Saeys, Yvan, Martens, Liesbet, Vetters, Jessica, Delrue, Iris, De Rycke, Riet, Parthoens, Eef, Pouliot, Philippe, Iwawaki, Takao, Janssens, Sophie,

Journal:

Nature Immunology

Year:

2014

Language:

english

File:

PDF, 1.56 MB

english, 2014

20

Particle swarm optimization and genetic algorithm as feature selection techniques for the QSAR modeling of imidazo[1,5-a]pyrido[3,2-e]pyrazines, inhibitors of phosphodiesterase 10A

Goodarzi, Mohammad, Saeys, Wouter, Deeb, Omar, Pieters, Sigrid, Vander Heyden, Yvan

Journal:

Chemical Biology & Drug Design

Year:

2013

Language:

english

File:

PDF, 835 KB

english, 2013

21

[IEEE 2011 Winter Simulation Conference - (WSC 2011) - Phoenix, AZ, USA (2011.12.11-2011.12.14)] Proceedings of the 2011 Winter Simulation Conference (WSC) - An alternative approach to avoid overfitting for surrogate models

Nguyen, Huu Minh, Couckuyt, Ivo, Knockaert, Luc, Dhaene, Tom, Gorissen, Dirk, Saeys, Yvan

Year:

2011

Language:

english

File:

PDF, 1.10 MB

english, 2011

22

[Lecture Notes in Computer Science] Knowledge Discovery and Emergent Complexity in Bioinformatics Volume 4366 || Boolean Algebraic Structures of the Genetic Code: Possibilities of Applications

Tuyls, Karl, Westra, Ronald, Saeys, Yvan, Nowé, Ann

Year:

2007

Language:

english

File:

PDF, 386 KB

english, 2007

23

CATCh, an Ensemble Classifier for Chimera Detection in 16S rRNA Sequencing Studies

Mysara, Mohamed, Saeys, Yvan, Leys, Natalie, Raes, Jeroen, Monsieurs, Pieter, Wommack, K. E.

Journal:

Applied and Environmental Microbiology

Year:

2015

Language:

english

File:

PDF, 1.62 MB

english, 2015

24

Characterization of genome-wide ordered sequence-tagged Mycobacterium mutant libraries by Cartesian Pooling-Coordinate Sequencing

Vandewalle, Kristof, Festjens, Nele, Plets, Evelyn, Vuylsteke, Marnik, Saeys, Yvan, Callewaert, Nico

Journal:

Nature Communications

Year:

2015

Language:

english

File:

PDF, 1.10 MB

english, 2015

25

[ACM Press the 1st international conference - Hong Kong (2006.05.30-2006.06.01)] Proceedings of the 1st international conference on Scalable information systems - InfoScale '06 - Scalable hardware accelerator for comparing DNA and protein sequences

Faes, Philippe, Minnaert, Bram, Christiaens, Mark, Bonnet, Eric, Saeys, Yvan, Stroobandt, Dirk, Van de Peer, Yves

Year:

2006

Language:

english

File:

PDF, 121 KB

english, 2006

26

The function of Fcγ receptors in dendritic cells and macrophages

Guilliams, Martin, Bruhns, Pierre, Saeys, Yvan, Hammad, Hamida, Lambrecht, Bart N.

Journal:

Nature Reviews Immunology

Year:

2014

File:

PDF, 532 KB

2014

27

Fuzzy Multi-Instance Classifiers

Vluymans, Sarah, Sanchez Tarrago, Danel, Saeys, Yvan, Cornelis, Chris, Herrera, Francisco

Journal:

IEEE Transactions on Fuzzy Systems

Year:

2016

Language:

english

File:

PDF, 2.26 MB

english, 2016

28

[IEEE 2015 Annual Conference of the North American Fuzzy Information Processing Society (NAFIPS) held jointly with 2015 5th World Conference on Soft Computing (WConSC) - Redmond, WA, USA (2015.8.17-2015.8.19)] 2015 Annual Conference of the North American Fuzzy Information Processing Society (NAFIPS) held jointly with 2015 5th World Conference on Soft Computing (WConSC) - Distributed fuzzy rough prototype selection for Big Data regression

Vluymans, Sarah, Asfoor, Hasan, Saeys, Yvan, Cornelis, Chris, Tolentino, Matthew, Teredesai, Ankur, De Cock, Martine

Year:

2015

Language:

english

File:

PDF, 689 KB

english, 2015

29

Bone marrow-derived monocytes give rise to self-renewing and fully differentiated Kupffer cells

Scott, Charlotte L., Zheng, Fang, De Baetselier, Patrick, Martens, Liesbet, Saeys, Yvan, De Prijck, Sofie, Lippens, Saskia, Abels, Chloé, Schoonooghe, Steve, Raes, Geert, Devoogdt, Nick, Lambrecht, Ba

Journal:

Nature Communications

Year:

2016

Language:

english

File:

PDF, 2.51 MB

english, 2016

30

Yolk Sac Macrophages, Fetal Liver, and Adult Monocytes Can Colonize an Empty Niche and Develop into Functional Tissue-Resident Macrophages

van de Laar, Lianne, Saelens, Wouter, De Prijck, Sofie, Martens, Liesbet, Scott, Charlotte L., Van Isterdael, Gert, Hoffmann, Eik, Beyaert, Rudi, Saeys, Yvan, Lambrecht, Bart N., Guilliams, Martin

Journal:

Year:

2016

Language:

english

File:

PDF, 5.61 MB

english, 2016

31

[IEEE 2015 IEEE International Conference on Fuzzy Systems (FUZZ-IEEE) - Istanbul, Turkey (2015.8.2-2015.8.5)] 2015 IEEE International Conference on Fuzzy Systems (FUZZ-IEEE) - Fuzzy Rough Set Prototype Selection for Regression

Vluymans, Sarah, Saeys, Yvan, Cornelis, Chris, Teredesai, Ankur, De Cock, Martine

Year:

2015

Language:

english

File:

PDF, 230 KB

english, 2015

32

Improving nearest neighbor classification using Ensembles of Evolutionary Generated Prototype Subsets

Verbiest, Nele, Vluymans, Sarah, Cornelis, Chris, García-Pedrajas, Nicolás, Saeys, Yvan

Journal:

Applied Soft Computing

Year:

2016

Language:

english

File:

PDF, 1.78 MB

english, 2016

33

Efficient analysis of mouse genome sequences reveal many nonsense variants

Steeland, Sophie, Timmermans, Steven, Van Ryckeghem, Sara, Hulpiau, Paco, Saeys, Yvan, Van Montagu, Marc, Vandenbroucke, Roosmarijn E., Libert, Claude

Journal:

Proceedings of the National Academy of Sciences

Year:

2016

Language:

english

File:

PDF, 986 KB

english, 2016

34

The transcription factor Zeb2 regulates development of conventional and plasmacytoid DCs by repressing Id2

Scott, Charlotte L., Soen, Bieke, Martens, Liesbet, Skrypek, Nicolas, Saelens, Wouter, Taminau, Joachim, Blancke, Gillian, Van Isterdael, Gert, Huylebroeck, Danny, Haigh, Jody, Saeys, Yvan, Guilliams,

Journal:

Journal of Experimental Medicine

Year:

2016

Language:

english

File:

PDF, 3.19 MB

english, 2016

35

Netter: re-ranking gene network inference predictions using structural network properties

Ruyssinck, Joeri, Demeester, Piet, Dhaene, Tom, Saeys, Yvan

Journal:

BMC Bioinformatics

Year:

2016

Language:

english

File:

PDF, 954 KB

english, 2016

36

Mining the Enriched Subgraphs for Specific Vertices in a Biological Graph

Meysman, Pieter, Saeys, Yvan, Sabaghian, Ehsan, Bittremieux, Wout, van de Peer, Yves, Goethals, Bart, Laukens, Kris

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2016

Language:

english

File:

PDF, 494 KB

english, 2016

37

An evolutionary perspective on the necroptotic pathway

Dondelinger, Yves, Hulpiau, Paco, Saeys, Yvan, Bertrand, Mathieu J.M., Vandenabeele, Peter

Journal:

Trends in Cell Biology

Year:

2016

Language:

english

File:

PDF, 1.81 MB

english, 2016

38

FloReMi: Flow density survival regression using minimal feature redundancy

Van Gassen, Sofie, Vens, Celine, Dhaene, Tom, Lambrecht, Bart N., Saeys, Yvan

Journal:

Cytometry Part A

Year:

2016

Language:

english

File:

PDF, 321 KB

english, 2016

39

A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes

Aghaeepour, Nima, Chattopadhyay, Pratip, Chikina, Maria, Dhaene, Tom, Van Gassen, Sofie, Kursa, Miron, Lambrecht, Bart N., Malek, Mehrnoush, McLachlan, G. J., Qian, Yu, Qiu, Peng, Saeys, Yvan, Stanton

Journal:

Cytometry Part A

Year:

2016

Language:

english

File:

PDF, 169 KB

english, 2016

40

Metazoan evolution of the armadillo repeat superfamily

Gul, Ismail Sahin, Hulpiau, Paco, Saeys, Yvan, van Roy, Frans

Journal:

Cellular and Molecular Life Sciences

Year:

2017

Language:

english

File:

PDF, 2.25 MB

english, 2017

41

EPRENNID: An evolutionary prototype reduction based ensemble for nearest neighbor classification of imbalanced data

Vluymans, Sarah, Triguero, Isaac, Cornelis, Chris, Saeys, Yvan

Journal:

Year:

2016

Language:

english

File:

PDF, 977 KB

english, 2016

42

Computational methods for trajectory inference from single-cell transcriptomics

Cannoodt, Robrecht, Saelens, Wouter, Yvan, Saey

Journal:

European Journal of Immunology

Year:

2016

Language:

english

File:

PDF, 2.11 MB

english, 2016

43

Differential expression of lncRNAs during the HIV replication cycle: an underestimated layer in the HIV-host interplay

Trypsteen, Wim, Mohammadi, Pejman, Van Hecke, Clarissa, Mestdagh, Pieter, Lefever, Steve, Saeys, Yvan, De Bleser, Pieter, Vandesompele, Jo, Ciuffi, Angela, Vandekerckhove, Linos, De Spiegelaere, Ward

Journal:

Scientific Reports

Year:

2016

Language:

english

File:

PDF, 1.81 MB

english, 2016

44

[IEEE 2016 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) - Orlando, FL, USA (2016.8.16-2016.8.20)] 2016 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) - Bayesian deconvolution of scanning electron microscopy images using point-spread function estimation and non-local regularization

Roels, Joris, Aelterman, Jan, De Vylder, Jonas, Luong, Hiep, Saeys, Yvan, Philips, Wilfried

Year:

2016

Language:

english

File:

PDF, 1.23 MB

english, 2016

45

[IEEE 2016 IEEE International Conference on Fuzzy Systems (FUZZ-IEEE) - Vancouver, BC, Canada (2016.7.24-2016.7.29)] 2016 IEEE International Conference on Fuzzy Systems (FUZZ-IEEE) - Fuzzy rough sets for self-labelling: An exploratory analysis

Vluymans, Sarah, Parthalain, Neil Mac, Cornelis, Chris, Saeys, Yvan

Year:

2016

Language:

english

File:

PDF, 318 KB

english, 2016

46

Evolution and diversity of cadherins and catenins

Gul, Ismail Sahin, Hulpiau, Paco, Saeys, Yvan, van Roy, Frans

Journal:

Experimental Cell Research

Year:

2017

Language:

english

File:

PDF, 582 KB

english, 2017

47

Distributed incremental fingerprint identification with reduced database penetration rate using a hierarchical classification based on feature fusion and selection

Peralta, Daniel, Triguero, Isaac, García, Salvador, Saeys, Yvan, Benitez, Jose M., Herrera, Francisco

Journal:

Knowledge-Based Systems

Year:

2017

Language:

english

File:

PDF, 1.43 MB

english, 2017

48

Myocardial Infarction Primes Autoreactive T Cells through Activation of Dendritic Cells

Van der Borght, Katrien, Scott, Charlotte L., Nindl, Veronika, Bouché, Ann, Martens, Liesbet, Sichien, Dorine, Van Moorleghem, Justine, Vanheerswynghels, Manon, De Prijck, Sofie, Saeys, Yvan, Ludewig,

Journal:

Year:

2017

Language:

english

File:

PDF, 5.86 MB

english, 2017

49

A Murine Intestinal Intraepithelial NKp46-Negative Innate Lymphoid Cell Population Characterized by Group 1 Properties

Van Acker, Aline, Gronke, Konrad, Biswas, Aindrila, Martens, Liesbet, Saeys, Yvan, Filtjens, Jessica, Taveirne, Sylvie, Van Ammel, Els, Kerre, Tessa, Matthys, Patrick, Taghon, Tom, Vandekerckhove, Bar

Journal:

Year:

2017

Language:

english

File:

PDF, 4.32 MB

english, 2017

50

Radiation-induced alternative transcription and splicing events and their applicability to practical biodosimetry

Macaeva, Ellina, Saeys, Yvan, Tabury, Kevin, Janssen, Ann, Michaux, Arlette, Benotmane, Mohammed A., De Vos, Winnok H., Baatout, Sarah, Quintens, Roel

Journal:

Scientific Reports

Year:

2016

Language:

english

File:

PDF, 1.86 MB

english, 2016