Problems Easy for Tree-Decomposable Graphs (Extended Abstract). - Stefan Arnborg; Jens Lagergren; Detlef Seese (ICALP, 1988)

Efficient Parallel Algorithms for Tree-Decomposition and Related Problems - Jens Lagergren (FOCS, 1990)

An upper bound on the size of an obstruction. - Jens Lagergren (Graph Structure Theory, 1991)

Finding Minimal Forbidden Minors Using a Finite Congruence. - Jens Lagergren; Stefan Arnborg (ICALP, 1991)

Easy Problems for Tree-Decomposable Graphs. - Stefan Arnborg; Jens Lagergren; Detlef Seese (J. Algorithms, 1991)

Recognizable Sets of Graphs of Bounded Tree-Width. - Bruno Courcelle; Jens Lagergren (Dagstuhl Seminar on Graph Transformations in Computer Science, 1993)

The Size of an Interwine. - Jens Lagergren (ICALP, 1994)

The Nonexistence of Reduction Rules Giving an Embedding into a K-tree. - Jens Lagergren (Discret. Appl. Math., 1994)

Hypothesis Testing in Perfect Phylogeny for a Bounded Number of Characters. - Jens Lagergren (STACS, 1996)

Approximability of Maximum Splitting of k-Sets and Some Other Apx-Complete Problems. - Viggo Kann; Jens Lagergren; Alessandro Panconesi (Inf. Process. Lett., 1996)

Efficient Parallel Algorithms for Graphs of Bounded Tree-Width. - Jens Lagergren (J. Algorithms, 1996)

Equivalent Definitions of Recognizability for Sets of Graphs of Bounded Tree-Width. - Bruno Courcelle; Jens Lagergren (Math. Struct. Comput. Sci., 1996)

On the Hardness of Approximating Max k-Cut and its Dual. - Viggo Kann; Sanjeev Khanna; Jens Lagergren; Alessandro Panconesi (Chic. J. Theor. Comput. Sci., 1997)

On the Approximability of the Steiner Tree Problem in Phylogeny. - David Fernández-Baca; Jens Lagergren (Discret. Appl. Math., 1998)

Approximate Max k-Cut with Subgraph Guarantee. - Viggo Kann; Jens Lagergren; Alessandro Panconesi (Inf. Process. Lett., 1998)

Upper Bounds on the Size of Obstructions and Intertwines. - Jens Lagergren (J. Comb. Theory B, 1998)

Guest Editors' Foreword. - Jens Lagergren; Peter Bro Miltersen (Nord. J. Comput., 1999)

Hunting for Functionally Analogous Genes. - Michael T. Hallett; Jens Lagergren (FSTTCS, 2000)

New algorithms for the duplication-loss model. - Michael T. Hallett; Jens Lagergren (RECOMB, 2000)

Efficient algorithms for lateral gene transfer problems. - Michael T. Hallett; Jens Lagergren (RECOMB, 2001)

Combining polynomial running time and fast convergence for the disk-covering method. - Jens Lagergren (J. Comput. Syst. Sci., 2002)

Bayesian gene/species tree reconciliation and orthology analysis using MCMC. - Lars Arvestad; Ann-Charlotte Berglund; Jens Lagergren; Bengt Sennblad (ISMB (Supplement of Bioinformatics), 2003)

Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm. - Öjvind Johansson; Wynand Alkema; Wyeth W. Wasserman; Jens Lagergren (ISMB (Supplement of Bioinformatics), 2003)

Towards Identifying Lateral Gene Transfer Events. - Louigi Addario-Berry; Michael T. Hallett; Jens Lagergren (Pacific Symposium on Biocomputing, 2003)

Fitting points on the real line and its application to RH mapping. - Johan Håstad; Lars Ivansson; Jens Lagergren (J. Algorithms, 2003)

A Polynomial-Time Algorithm for Near-Perfect Phylogeny. - David Fernández-Baca; Jens Lagergren (SIAM J. Comput., 2003)

Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution. - Lars Arvestad; Ann-Charlotte Berglund; Jens Lagergren; Bengt Sennblad (RECOMB, 2004)

Simultaneous identification of duplications and lateral transfers. - Michael T. Hallett; Jens Lagergren; Ali Tofigh (RECOMB, 2004)

Ancestral Maximum Likelihood of Evolutionary Trees Is Hard. - Louigi Addario-Berry; Benny Chor; Michael T. Hallett; Jens Lagergren; Alessandro Panconesi; Todd Wareham (J. Bioinform. Comput. Biol., 2004)

MSCAN: identification of functional clusters of transcription factor binding sites. - Wynand Alkema; Öjvind Johansson; Jens Lagergren; Wyeth W. Wasserman (Nucleic Acids Res., 2004)

Algorithms for RH Mapping: New Ideas and Improved Analysis. - Lars Ivansson; Jens Lagergren (SIAM J. Comput., 2004)

Motif Yggdrasil: Sampling from a Tree Mixture Model. - Samuel A. Andersson; Jens Lagergren (RECOMB, 2006)

New Probabilistic Network Models and Algorithms for Oncogenesis. - Marcus Hjelm; Mattias Höglund; Jens Lagergren (J. Comput. Biol., 2006)

Genome-Wide Survey for Biologically Functional Pseudogenes. - Örjan Svensson; Lars Arvestad; Jens Lagergren (PLoS Comput. Biol., 2006)

Compatibility of unrooted phylogenetic trees is FPT. - David Bryant; Jens Lagergren (Theor. Comput. Sci., 2006)

Fast computation of distance estimators. - Isaac Elias; Jens Lagergren (BMC Bioinform., 2007)

primetv: a viewer for reconciled trees. - Bengt Sennblad; Eva Schreil; Ann-Charlotte Berglund Sonnhammer; Jens Lagergren; Lars Arvestad (BMC Bioinform., 2007)

Motif Yggdrasil: Sampling Sequence Motifs from a Tree Mixture Model. - Samuel A. Andersson; Jens Lagergren (J. Comput. Biol., 2007)

The gene evolution model and computing its associated probabilities. - Lars Arvestad; Jens Lagergren; Bengt Sennblad (J. ACM, 2009)

Fast neighbor joining. - Isaac Elias; Jens Lagergren (Theor. Comput. Sci., 2009)

A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins. - Mats Ensterö; Örjan Åkerborg; Daniel Lundin; Bei Wang 001; Terrence S. Furey; Marie Öhman; Jens Lagergren (BMC Bioinform., 2010)

A Global Structural EM Algorithm for a Model of Cancer Progression. - Ali Tofigh; Erik Sjölund; Mattias Höglund; Jens Lagergren (NIPS, 2011)

Simultaneous Identification of Duplications and Lateral Gene Transfers. - Ali Tofigh; Michael T. Hallett; Jens Lagergren (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

DLRS: gene tree evolution in light of a species tree. - Joel Sjöstrand; Bengt Sennblad; Lars Arvestad; Jens Lagergren (Bioinform., 2012)

fastphylo: Fast tools for phylogenetics. - Mehmood Alam Khan; Isaac Elias; Erik Sjölund; Kristina Nylander; Roman Valls Guimera; Richard Schobesberger; Peter Schmitzberger; Jens Lagergren; Lars Arvestad (BMC Bioinform., 2013)

Genome-wide probabilistic reconciliation analysis across vertebrates. - Owais Mahmudi; Joel Sjöstrand; Bengt Sennblad; Jens Lagergren (BMC Bioinform., 2013)

GenPhyloData: realistic simulation of gene family evolution. - Joel Sjöstrand; Lars Arvestad; Jens Lagergren; Bengt Sennblad (BMC Bioinform., 2013)

Learning Bounded Tree-width Bayesian Networks using Integer Linear Programming. - Pekka Parviainen; Hossein Shahrabi Farahani; Jens Lagergren (AISTATS, 2014)

Probabilistic inference of lateral gene transfer events. - Mehmood Alam Khan; Owais Mahmudi; Ikram Ullah 004; Lars Arvestad; Jens Lagergren (BMC Bioinform., 2016)

Viewpoint and Topic Modeling of Current Events. - Kerry Zhang; Jussi Karlgren; Cheng Zhang; Jens Lagergren (CoRR, 2016)

Computational Cancer Biology: An Evolutionary Perspective. - Niko Beerenwinkel; Chris D. Greenman; Jens Lagergren (PLoS Comput. Biol., 2016)

Fast and general tests of genetic interaction for genome-wide association studies. - Mattias Frånberg; Rona J. Strawbridge; Anders Hamsten; PROCARDIS Consortium; Ulf de Faire; Jens Lagergren; Bengt Sennblad (PLoS Comput. Biol., 2017)

Orthogonal Mixture of Hidden Markov Models. - Negar Safinianaini; Camila P. E. de Souza; Henrik Boström; Jens Lagergren (ECML/PKDD (1), 2020)

Inferring tumor progression in large datasets. - Mohammadreza Mohaghegh Neyshabouri; Seong-Hwan Jun; Jens Lagergren (PLoS Comput. Biol., 2020)

The Klarna Product Page Dataset: A Realistic Benchmark for Web Representation Learning. - Alexandra Hotti; Riccardo Sven Risuleo; Stefan Magureanu; Aref Moradi; Jens Lagergren (CoRR, 2021)

Multiple Importance Sampling ELBO and Deep Ensembles of Variational Approximations. - Oskar Kviman; Harald Melin; Hazal Koptagel; Victor Elvira; Jens Lagergren (AISTATS, 2022)

VaiPhy: a Variational Inference Based Algorithm for Phylogeny. - Hazal Koptagel; Oskar Kviman; Harald Melin; Negar Safinianaini; Jens Lagergren (NeurIPS, 2022)

DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data. - José Bonet 001; Mandi Chen; Marc Dabad; Simon Heath; Abel Gonzalez-Perez; Núria López-Bigas; Jens Lagergren (Bioinform., 2022)

Learning with MISELBO: The Mixture Cookbook. - Oskar Kviman; Ricky Molén; Alexandra Hotti; Semih Kurt; Víctor Elvira; Jens Lagergren (CoRR, 2022)

Statistical Distance Based Deterministic Offspring Selection in SMC Methods. - Oskar Kviman; Hazal Koptagel; Harald Melin; Jens Lagergren (CoRR, 2022)

ToMExO: A probabilistic tree-structured model for cancer progression. - Mohammadreza Mohaghegh Neyshabouri; Jens Lagergren (PLoS Comput. Biol., 2022)

Cooperation in the Latent Space: The Benefits of Adding Mixture Components in Variational Autoencoders. - Oskar Kviman; Ricky Molén; Alexandra Hotti; Semih Kurt; Víctor Elvira; Jens Lagergren (ICML, 2023)

Learning Stationary Markov Processes with Contrastive Adjustment. - Ludvig Bergenstråhle; Jens Lagergren; Joakim Lundeberg (CoRR, 2023)

Benefits of Non-Linear Scale Parameterizations in Black Box Variational Inference through Smoothness Results and Gradient Variance Bounds. - Alexandra Maria Hotti; Lennart Alexander Van der Goten; Jens Lagergren (AISTATS, 2024)

Variational Resampling. - Oskar Kviman; Nicola Branchini; Víctor Elvira; Jens Lagergren (AISTATS, 2024)

Efficient Mixture Learning in Black-Box Variational Inference. - Alexandra Hotti; Oskar Kviman; Ricky Molén; Víctor Elvira; Jens Lagergren (ICML, 2024)

Indirectly Parameterized Concrete Autoencoders. - Alfred Nilsson; Klas Wijk; Sai Bharath Chandra Gutha; Erik Englesson; Alexandra Hotti; Carlo Saccardi; Oskar Kviman; Jens Lagergren; Ricardo Vinuesa; Hossein Azizpour (ICML, 2024)

VICTree - A Variational Inference Method for Clonal Tree Reconstruction. - Harald Melin; Vittorio Zampinetti; Andrew McPherson 003; Jens Lagergren (RECOMB, 2024)

CopyMix: Mixture model based single-cell clustering and copy number profiling using variational inference. - Negar Safinianaini; Camila P. E. de Souza; Andrew Roth; Hazal Koptagel; Hosein Toosi; Jens Lagergren (Comput. Biol. Chem., 2024)

Scuphr: A probabilistic framework for cell lineage tree reconstruction. - Hazal Koptagel; Seong-Hwan Jun; Joanna Hård; Jens Lagergren (PLoS Comput. Biol., 2024)

The Klarna Product Page Dataset: Web Element Nomination with Graph Neural Networks and Large Language Models. - Alexandra Hotti; Riccardo Sven Risuleo; Stefan Magureanu; Aref Moradi; Jens Lagergren (Trans. Mach. Learn. Res., 2024)

Improved Variational Bayesian Phylogenetic Inference using Mixtures. - Ricky Molén; Oskar Kviman; Jens Lagergren (Trans. Mach. Learn. Res., 2024)