Jens Lagergren

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Guest Editors' Foreword

Peter Bro Miltersen, Jens Lagergren, 1999, Nord. J. Comput..

Recognizable Sets of Graphs of Bounded Tree-Width

Bruno Courcelle, Jens Lagergren, B. Courcelle, 1993, Dagstuhl Seminar on Graph Transformations in Computer Science.

Computational Cancer Biology: An Evolutionary Perspective

Niko Beerenwinkel, Jens Lagergren, Chris D. Greenman, 2016, PLoS Comput. Biol..

Genome-wide probabilistic reconciliation analysis across vertebrates

Joel Sjöstrand, Bengt Sennblad, Jens Lagergren, 2013, BMC Bioinformatics.

primetv: a viewer for reconciled trees

Bengt Sennblad, Lars Arvestad, Jens Lagergren, 2006, BMC Bioinformatics.

Hunting for Functionally Analogous Genes

Michael T. Hallett, Jens Lagergren, J. Lagergren, 2000, FSTTCS.

A Structural EM Algorithm for Learning Oncogenetic Networks by Reducing to MILP

Jens Lagergren, Hossein Shahrabi Farahani, 2013 .

The gene evolution model and computing its associated probabilities

Bengt Sennblad, Lars Arvestad, Jens Lagergren, 2009, JACM.

GenPhyloData: realistic simulation of gene family evolution

Joel Sjöstrand, Bengt Sennblad, Lars Arvestad, 2013, BMC Bioinformatics.

Compatibility of unrooted phylogenetic trees is FPT

David Bryant, Jens Lagergren, J. Lagergren, 2006, Theor. Comput. Sci..

Motif Yggdrasil: Sampling from a Tree Mixture Model

Jens Lagergren, Samuel A. Andersson, J. Lagergren, 2006, RECOMB.

Probabilistic inference of lateral gene transfer events

Lars Arvestad, Jens Lagergren, Ikram Ullah, 2016, BMC Bioinformatics.

Scuphr: A probabilistic framework for cell lineage tree reconstruction

Jens Lagergren, Hazal Koptagel, Seong-Hwan Jun, 2018, bioRxiv.

The Size of an Interwine

Jens Lagergren, J. Lagergren, 1994, ICALP.

Problems Easy for Tree-Decomposable Graphs (Extended Abstract)

Stefan Arnborg, Jens Lagergren, Detlef Seese, 1988, ICALP.

A structural EM algorithm for learning hidden variable oncogenetic networks

Jens Lagergren, Hossein Shahrabi Farahani, 2013 .

Towards Identifying Lateral Gene Transfer Events

Michael T. Hallett, Jens Lagergren, Louigi Addario-Berry, 2002, Pacific Symposium on Biocomputing.

An upper bound on the size of an obstruction

Jens Lagergren, 1991, Graph Structure Theory.

Combining polynomial running time and fast convergence for the disk-covering method

Jens Lagergren, 2002, J. Comput. Syst. Sci..

Learning oncogenetic networks by reducing to MILP

Jens Lagergren, Hossein Shahrabi Farahani, 2013 .

Upper Bounds on the Size of Obstructions and Intertwines

Jens Lagergren, J. Lagergren, 1998, J. Comb. Theory, Ser. B.

Bayesian gene/species tree reconciliation and orthology analysis using MCMC

Bengt Sennblad, Lars Arvestad, Jens Lagergren, 2003, ISMB.

Simultaneous Identification of Duplications and Lateral Gene Transfers

Michael T. Hallett, Jens Lagergren, Ali Tofigh, 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Problems Easy for Tree-Decomposable Graphs (Extended Abstract)

Detlef Seese, Stefan Arnborg, Jens Lagergren, 1988, ICALP.

Fast neighbor joining

Jens Lagergren, Isaac Elias, 2009, Theor. Comput. Sci..

Learning Bounded Tree-width Bayesian Networks using Integer Linear Programming

Jens Lagergren, Hossein Shahrabi Farahani, Pekka Parviainen, 2014, AISTATS.

On the Approximability of the Steiner Tree Problem in Phylogeny

David Fernández-Baca, Jens Lagergren, 1996, ISAAC.

A Polynomial-Time Algorithm for Near-Perfect Phylogeny

David Fernández-Baca, Jens Lagergren, 1996, ICALP.

Simultaneous identification of duplications and lateral transfers

Michael T. Hallett, Jens Lagergren, Ali Tofigh, 2004, RECOMB.

Hypothesis Testing in Perfect Phylogeny for a Bounded Number of Characters

Jens Lagergren, 1996, STACS.

Fastphylo: Fast tools for phylogenetics

Kristina Nylander, Lars Arvestad, Roman Valls Guimera, 2013, BMC Bioinformatics.

MSCAN: identification of functional clusters of transcription factor binding sites

Wyeth W. Wasserman, Jens Lagergren, Wynand Alkema, 2004, Nucleic Acids Res..

Approximate Max k-Cut with Subgraph Guarantee

Alessandro Panconesi, Jens Lagergren, Viggo Kann, 1998, Inf. Process. Lett..

Easy Problems for Tree-Decomposable Graphs

Detlef Seese, Stefan Arnborg, Jens Lagergren, 1991, J. Algorithms.

Viewpoint and Topic Modeling of Current Events pdf

Cheng Zhang, Jussi Karlgren, Jens Lagergren, 2016, ArXiv.

A Global Structural EM Algorithm for a Model of Cancer Progression

Erik Sjölund, Jens Lagergren, Mattias Höglund, 2011, NIPS.

Fitting points on the real line and its application to RH mapping

Johan Håstad, Jens Lagergren, Lars Ivansson, 2003, J. Algorithms.

Motif Yggdrasil: Sampling Sequence Motifs from a Tree Mixture Model

Jens Lagergren, Samuel A. Andersson, J. Lagergren, 2007, J. Comput. Biol..

Fast neighbor joining

Jens Lagergren, Isaac Elias, J. Lagergren, 2005, Theor. Comput. Sci..

Genome-Wide Survey for Biologically Functional Pseudogenes

Lars Arvestad, Jens Lagergren, Örjan Svensson, 2006, PLoS Comput. Biol..

Fast and general tests of genetic interaction for genome-wide association studies

Bengt Sennblad, Jens Lagergren, Rona J. Strawbridge, 2017, PLoS Comput. Biol..

Algorithms in Bioinformatics, 8th International Workshop, WABI 2008, Karlsruhe, Germany, September 15-19, 2008. Proceedings

Jens Lagergren, Keith A. Crandall, K. Crandall, 2008, WABI.

On the Approximability of the Steiner Tree Problem in Phylogeny

David Fernández-Baca, Jens Lagergren, J. Lagergren, 1996, Discret. Appl. Math..

Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution

Bengt Sennblad, Lars Arvestad, Jens Lagergren, 2004, RECOMB.

A Polynomial-Time Algorithm for Near-Perfect Phylogeny

David Fernández-Baca, Jens Lagergren, J. Lagergren, 1996, SIAM J. Comput..

The Nonexistence of Reduction Rules Giving an Embedding into a K-tree

Jens Lagergren, J. Lagergren, 1994, Discret. Appl. Math..

Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm

Wyeth W. Wasserman, Jens Lagergren, Wynand Alkema, 2003, ISMB.

New algorithms for the duplication-loss model

Jens Lagergren, M. T. Hallett, 1999 .

Ancestral Maximum Likelihood of Evolutionary Trees Is Hard

Alessandro Panconesi, Michael T. Hallett, Todd Wareham, 2004, J. Bioinform. Comput. Biol..

Efficient Parallel Algorithms for Graphs of Bounded Tree-Width

Jens Lagergren, J. Lagergren, 1996, J. Algorithms.

New Probabilistic Network Models and Algorithms for Oncogenesis

Jens Lagergren, Mattias Höglund, Marcus Hjelm, 2006, J. Comput. Biol..

Efficient algorithms for lateral gene transfer problems

Michael T. Hallett, Jens Lagergren, J. Lagergren, 2001, RECOMB.

A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins

Terrence S. Furey, Bei Wang, Jens Lagergren, 2010, BMC Bioinformatics.

Algorithms for RH Mapping: New Ideas and Improved Analysis

Jens Lagergren, Lars Ivansson, 2004, SIAM J. Comput..

On the Hardness of Approximating Max k-Cut and its Dual

Sanjeev Khanna, Alessandro Panconesi, Jens Lagergren, 1997, Chic. J. Theor. Comput. Sci..

Approximability of Maximum Splitting of k-Sets and Some Other Apx-Complete Problems

Alessandro Panconesi, Jens Lagergren, Viggo Kann, 1996, Inf. Process. Lett..

Fitting Points on the Real Line and Its Application to RH Mapping

Johan Håstad, Jens Lagergren, Lars Ivansson, 1998, ESA.

Equivalent definitions of recognizability for sets of graphs of bounded tree-width

Bruno Courcelle, Jens Lagergren, B. Courcelle, 1996, Mathematical Structures in Computer Science.

Proceedings of the 8th international workshop on Algorithms in Bioinformatics

Jens Lagergren, Keith A. Crandall, 2008 .

New algorithms for the duplication-loss model

Michael T. Hallett, Jens Lagergren, J. Lagergren, 2000, RECOMB '00.

The Klarna Product Page Dataset: A Realistic Benchmark for Web Representation Learning pdf

Riccardo Sven Risuleo, Jens Lagergren, Aref Moradi, 2021, ArXiv.

Integrating Sequence Evolution into Probabilistic Orthology Analysis.

Joel Sjöstrand, Bengt Sennblad, Jens Lagergren, 2015, Systematic biology.

Species Tree Inference Using a Mixture Model.

Jens Lagergren, Pekka Parviainen, J. Lagergren, 2015, Molecular biology and evolution.

Birth-death prior on phylogeny and speed dating

Bengt Sennblad, Jens Lagergren, Örjan Åkerborg, 2008, BMC Evolutionary Biology.

A Bayesian method for analyzing lateral gene transfer.

Joel Sjöstrand, Bengt Sennblad, Lars Arvestad, 2014, Systematic biology.

Detecting LGTs using a novel probabilistic modelintegrating duplications, LGTs, losses, rate variation,and sequence evolution

Joel Sjöstrand, Bengt Sennblad, Jens Lagergren, 2009 .

Hunting for functionally analogous genes

Jens Lagergren, Michael Hallett, 1999 .

Species tree-aware simultaneous reconstruction of gene and domain evolution

Bengt Sennblad, Jens Lagergren, Sayyed Auwn Muhammad, 2018, bioRxiv.

RNA editing of non-coding RNA and its role in gene regulation.

Jens Lagergren, Marie Öhman, J. Lagergren, 2015, Biochimie.

A-to-I editing of microRNAs in the mammalian brain increases during development

Jens Lagergren, Hossein Shahrabi Farahani, Marie Öhman, 2012, Genome research.

Comparative Genomics: RECOMB 2004 International Workshop, RCG 2004, Bertinoro, Italy, October 16-19, 2004, Revised Selected Papers (Lecture Notes in Computer Science / Lecture Notes in Bioinformatics)

Jens Lagergren, 2005, RECOMB 2005.

ADARs and editing: The role of A-to-I RNA modification in cancer progression.

Jens Lagergren, Marie Öhman, J. Lagergren, 2017, Seminars in cell & developmental biology.