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1

Networks: expanding evolutionary thinking

Bapteste, Eric, van Iersel, Leo, Janke, Axel, Kelchner, Scot, Kelk, Steven, McInerney, James O., Morrison, David A., Nakhleh, Luay, Steel, Mike, Stougie, Leen, Whitfield, James

Journal:

Trends in Genetics

Year:

2013

Language:

english

File:

PDF, 127 KB

english, 2013

2

Constructing the Simplest Possible Phylogenetic Network from Triplets

Leo van Iersel, Steven Kelk

Journal:

Year:

2011

Language:

english

File:

PDF, 946 KB

english, 2011

3

Deciding the existence of a cherry-picking sequence is hard on two trees

Döcker, Janosch, van Iersel, Leo, Kelk, Steven, Linz, Simone

Journal:

Discrete Applied Mathematics

Year:

2019

Language:

english

File:

PDF, 495 KB

english, 2019

4

Reconstructing Tree-Child Networks from Reticulate-Edge-Deleted Subnetworks

Murakami, Yukihiro, van Iersel, Leo, Janssen, Remie, Jones, Mark, Moulton, Vincent

Journal:

Bulletin of Mathematical Biology

Year:

2019

Language:

english

File:

PDF, 1.36 MB

english, 2019

5

Locating a tree in a phylogenetic network

Leo van Iersel, Charles Semple, Mike Steel

Journal:

Information Processing Letters

Year:

2010

Language:

english

File:

PDF, 199 KB

english, 2010

6

When two trees go to war

Leo van Iersel, Steven Kelk

Journal:

Journal of Theoretical Biology

Year:

2011

Language:

english

File:

PDF, 426 KB

english, 2011

7

The Complexity of the Single Individual SNP Haplotyping Problem

Rudi Cilibrasi, Leo van Iersel, Steven Kelk, John Tromp

Journal:

Year:

2007

Language:

english

File:

PDF, 234 KB

english, 2007

8

Quantifying the Extent of Lateral Gene Transfer Required to

Leo van Iersel, Charles Semple, Mike Steel

Journal:

Bulletin of Mathematical Biology

Year:

2010

Language:

english

File:

PDF, 437 KB

english, 2010

9

Every ternary permutation constraint satisfaction problem parameterized above average has a kernel with a quadratic number of variables

Gregory Gutin, Leo van Iersel, Matthias Mnich, Anders Yeo

Journal:

Journal of Computer and System Sciences

Year:

2012

Language:

english

File:

PDF, 272 KB

english, 2012

10

Cycle Killer...Qu'est-ce que c'est? On the Comparative Approximability of Hybridization Number and Directed Feedback Vertex Set

Kelk, Steven, van Iersel, Leo, Lekić, Nela, Linz, Simone, Scornavacca, Celine, Stougie, Leen

Journal:

SIAM Journal on Discrete Mathematics

Year:

2012

Language:

english

File:

PDF, 409 KB

english, 2012

11

Trinets encode tree-child and level-2 phylogenetic networks

Leo van Iersel, Vincent Moulton

Journal:

Journal of Mathematical Biology

Year:

2014

Language:

english

File:

PDF, 557 KB

english, 2014

12

A Practical Algorithm for Reconstructing Level-1 Phylogenetic Networks

Huber, Katharina T, van Iersel, Leo, Kelk, Steven, Suchecki, R

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2011

Language:

english

File:

PDF, 993 KB

english, 2011

13

A quadratic kernel for computing the hybridization number of multiple trees

van Iersel, Leo, Linz, Simone

Journal:

Information Processing Letters

Year:

2013

Language:

english

File:

PDF, 173 KB

english, 2013

14

On the Elusiveness of Clusters

Kelk, Steven, Scornavacca, Celine, van Iersel, Leo

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2012

Language:

english

File:

PDF, 1.26 MB

english, 2012

15

Prefix Reversals on Binary and Ternary Strings

Hurkens, Cor, van Iersel, Leo, Keijsper, Judith, Kelk, Steven, Stougie, Leen, Tromp, John

Journal:

SIAM Journal on Discrete Mathematics

Year:

2007

Language:

english

File:

PDF, 250 KB

english, 2007

16

Approximation Algorithms for Nonbinary Agreement Forests

van Iersel, Leo, Kelk, Steven, Lekić, Nela, Stougie, Leen

Journal:

SIAM Journal on Discrete Mathematics

Year:

2014

Language:

english

File:

PDF, 285 KB

english, 2014

17

W hats H ap : Weighted Haplotype Assembly for Future-Generation Sequencing Reads

Patterson, Murray, Marschall, Tobias, Pisanti, Nadia, van Iersel, Leo, Stougie, Leen, Klau, Gunnar W., Schönhuth, Alexander

Journal:

Journal of Computational Biology

Year:

2015

Language:

english

File:

PDF, 280 KB

english, 2015

18

TriLoNet: Piecing together small networks to reconstruct reticulate evolutionary histories

Oldman, James, Wu, Taoyang, van Iersel, Leo, Moulton, Vincent

Journal:

Molecular Biology and Evolution

Year:

2016

Language:

english

File:

PDF, 502 KB

english, 2016

19

Satisfying ternary permutation constraints by multiple linear orders or phylogenetic trees

van Iersel, Leo, Kelk, Steven, Lekić, Nela, Linz, Simone

Journal:

Theoretical Computer Science

Year:

2016

Language:

english

File:

PDF, 662 KB

english, 2016

20

Kernelizations for the hybridization number problem on multiple nonbinary trees

van Iersel, Leo, Kelk, Steven, Scornavacca, Celine

Journal:

Journal of Computer and System Sciences

Year:

2016

Language:

english

File:

PDF, 965 KB

english, 2016

21

Reconstructing Phylogenetic Level-1 Networks from Nondense Binet and Trinet Sets

Huber, Katharina T., van Iersel, Leo, Moulton, Vincent, Scornavacca, Celine, Wu, Taoyang

Journal:

Year:

2017

Language:

english

File:

PDF, 1007 KB

english, 2017

22

UNIQUENESS, INTRACTABILITY AND EXACT ALGORITHMS: REFLECTIONS ON LEVEL-K PHYLOGENETIC NETWORKS

VAN IERSEL, LEO, KELK, STEVEN, MNICH, MATTHIAS

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2009

Language:

english

File:

PDF, 657 KB

english, 2009

23

On Computing the Maximum Parsimony Score of a Phylogenetic Network

Fischer, Mareike, van Iersel, Leo, Kelk, Steven, Scornavacca, Celine

Journal:

SIAM Journal on Discrete Mathematics

Year:

2015

Language:

english

File:

PDF, 420 KB

english, 2015

24

Do Branch Lengths Help to Locate a Tree in a Phylogenetic Network?

Gambette, Philippe, van Iersel, Leo, Kelk, Steven, Pardi, Fabio, Scornavacca, Celine

Journal:

Bulletin of Mathematical Biology

Year:

2016

Language:

english

File:

PDF, 912 KB

english, 2016

25

Nonbinary tree-based phylogenetic networks

Jetten, Laura, van Iersel, Leo

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2016

Language:

english

File:

PDF, 352 KB

english, 2016

26

Binets: Fundamental Building Blocks for Phylogenetic Networks

Leo van Iersel,Vincent Moulton,Eveline de Swart…

Journal:

Bulletin of Mathematical Biology

Year:

2017

Language:

english

File:

PDF, 743 KB

english, 2017

27

Hybridization Number on Three Rooted Binary Trees is EPT

van Iersel, Leo, Kelk, Steven, Lekić, Nela, Whidden, Chris, Zeh, Norbert

Journal:

SIAM Journal on Discrete Mathematics

Year:

2016

Language:

english

File:

PDF, 628 KB

english, 2016

28

Improved maximum parsimony models for phylogenetic networks

van Iersel, Leo, Jones, Mark, Scornavacca, Celine

Journal:

Systematic Biology

Year:

2017

Language:

english

File:

PDF, 800 KB

english, 2017

29

On Unrooted and Root-Uncertain Variants of Several Well-Known Phylogenetic Network Problems

van Iersel, Leo, Kelk, Steven, Stamoulis, Georgios, Stougie, Leen, Boes, Olivier

Journal:

Year:

2017

Language:

english

File:

PDF, 786 KB

english, 2017

30

Rearrangement moves on rooted phylogenetic networks

Gambette, Philippe, van Iersel, Leo, Jones, Mark, Lafond, Manuel, Pardi, Fabio, Scornavacca, Celine, Matsen, Frederick A

Journal:

PLoS Computational Biology

Year:

2017

Language:

english

File:

PDF, 1.68 MB

english, 2017

31

Ancient Dispersal of the Human Fungal Pathogen Cryptococcus gattii from the Amazon Rainforest

Hagen, Ferry, Ceresini, Paulo C., Polacheck, Itzhack, Ma, Hansong, Nieuwerburgh, Filip van, Gabaldón, Toni, Kagan, Sarah, Pursall, E. Rhiannon, Hoogveld, Hans L., van Iersel, Leo J. J., Klau, Gunnar W

Journal:

Year:

2013

Language:

english

File:

PDF, 1.33 MB

english, 2013

32

Exploring the Tiers of Rooted Phylogenetic Network Space Using Tail Moves

Janssen, Remie, Jones, Mark, Erdős, Péter L., van Iersel, Leo, Scornavacca, Celine

Journal:

Bulletin of Mathematical Biology

Year:

2018

Language:

english

File:

PDF, 1.27 MB

english, 2018

33

A priori TSP in the scenario model

van Ee, Martijn, van Iersel, Leo, Janssen, Teun, Sitters, René

Journal:

Discrete Applied Mathematics

Year:

2018

Language:

english

File:

PDF, 384 KB

english, 2018

34

Finding a most parsimonious or likely tree in a network with respect to an alignment

Kelk, Steven, Pardi, Fabio, Scornavacca, Celine, van Iersel, Leo

Journal:

Journal of Mathematical Biology

Year:

2018

Language:

english

File:

PDF, 635 KB

english, 2018

35

Not all phylogenetic networks are leaf-reconstructible

Erdős, Péter L., van Iersel, Leo, Jones, Mark

Journal:

Journal of Mathematical Biology

Year:

2019

Language:

english

File:

PDF, 567 KB

english, 2019

36

Polynomial-Time Algorithms for Phylogenetic Inference Problems involving duplication and reticulation

Van Iersel, Leo, Janssen, Remie, Jones, Mark, Murakami, Yukihiro, Zeh, Norbert

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2019

Language:

english

File:

PDF, 1.03 MB

english, 2019

37

Reconstructibility of unrooted level-k phylogenetic networks from distances

van Iersel, Leo, Moulton, Vincent, Murakami, Yukihiro

Journal:

Advances in Applied Mathematics

Year:

2020

File:

PDF, 551 KB

2020

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