J. Lagergren

发表

Finding Minimal Forbidden Minors Using a Finite Congruence

S. Arnborg, J. Lagergren, 1991, ICALP.

Charting Tissue Expression Anatomy by Spatial Transcriptome Deconvolution

J. Maaskola, J. Lagergren, J. Lundeberg, 2018 .

Simultaneous Bayesian gene tree reconstruction and reconciliation analysis

J. Lagergren, B. Sennblad, O. Akerborg, 2009, Proceedings of the National Academy of Sciences.

Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity

Patrik L. Ståhl, E. Sonnhammer, J. Maaskola, 2018, Nature Communications.

Learning Oncogenetic Networks by Reducing to Mixed Integer Linear Programming

J. Lagergren, Hossein Shahrabi Farahani, 2013, PloS one.

A Neural Network Approach to Arbitrary Symbol Recognition on Modern Smartphones

J. Lagergren, 2014 .

Computational Cancer Biology: An Evolutionary Perspective

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

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

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

A Hidden Markov Model for Cancer Progression

J. Lagergren, L. Almeida, M. A. Dias, 2010 .

Probabilistic Inference of Evolutionary Gene Branching Events

J. Lagergren, 2010 .

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 .

Inferring Duplications and Lateral Gene Transfers : An Algorithm for Parametric Tree Reconciliation

J. Lagergren, A. Tofigh, 2009 .

Bayesian Estimation and Inference of Large-Scale Duplications

J. Lagergren, 2010 .

Discovering Genetic Interactions in Large-Scale Association Studies by Stage-wise Likelihood Ratio Tests

J. Lagergren, A. Hamsten, K. Gertow, 2015, PLoS genetics.

Learning Bounded Tree-width Bayesian Networks using Integer Linear Programming

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

Qualitative Comparison of Normalization Approaches in MALDI-MS

S. Arnborg, J. Lagergren, M. Pernemalm, 2008 .

Fastphylo: Fast tools for phylogenetics

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

Gene-pseudogene evolution: a probabilistic approach

J. Lagergren, B. Sennblad, Katja Nowick, 2015, BMC Genomics.

An Observational Study of the Characteristics of Taxi Floating Car Data Compared to Radar Sensor Data

J. Lagergren, 2012 .

Functional Network Identification in Human Resting-state fMRI using Hierarchical Clustering by Time-Lagged Correlations

A. Lansner, J. Lagergren, 2011 .

Protein Level Probabilities for Shotgun Proteomics Experiments

L. Käll, J. Lagergren, 2013 .

Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data

L. Kaczmarek, J. Lagergren, D. Nowis, 2022, bioRxiv.

Purine deoxyribonucleosides counteract effects of hydroxyurea on deoxyribonucleoside triphosphate pools and DNA synthesis.

J. Lagergren, P. Reichard, Jesper Lagergren, 1987, Biochemical pharmacology.

Hunting for Functionally Analogous

J. Lagergren, GenesM. T. Hallett, 2000 .

Tumoroscope: a probabilistic model for mapping cancer clones in tumor tissues

Jeff E. Mold, J. Hartman, J. Lagergren, 2022, bioRxiv.

Determining expertise from indirect evidence

J. Lagergren, Johan Boye, 2013 .

Combined Chromatin and Expression Analysis Reveals Specific Regulatory Mechanisms within Cytokine Genes in the Macrophage Early Immune Response

O. Emanuelsson, J. Odeberg, J. Lagergren, 2012, PloS one.

VaiPhy: a Variational Inference Based Algorithm for Phylogeny

J. Lagergren, Hazal Koptagel, Oskar Kviman, 2022, ArXiv.

ToMExO: A probabilistic tree-structured model for cancer progression

J. Lagergren, M. Neyshabouri, Mohammadreza Mohaghegh Neyshabouri, 2022, PLoS Comput. Biol..

C-ToMExO: Learning Cancer Progression Dynamics from Clonal Composition of Tumors

J. Lagergren, M. Neyshabouri, Smaragda Dimitrakopoulou, 2022, bioRxiv.

Stock market forecasting: investigation of a relationship between GDP per capita and stock market volatility

J. Lagergren, Jacqueline Eriksson, Mitra Strandberg, 2016 .

GenPhyloData: realistic simulation of gene family evolution

J. Lagergren, B. Sennblad, Lars Arvestad, 2013, BMC Bioinformatics.

Statistical Distance Based Deterministic Offspring Selection in SMC Methods

J. Lagergren, Hazal Koptagel, Oskar Kviman, 2022, ArXiv.

The gene evolution model and computing its associated probabilities

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

CopyMix: Mixture Model Based Single-Cell Clustering and Copy Number Profiling using Variational Inference

Jens Lagergren, Negar Safinianaini, Camila P. E. de Souza, 2020, bioRxiv.

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

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

Probabilistic orthology analysis.

J. Lagergren, B. Sennblad, BENGT SENNBLAD, 2009, Systematic biology.

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.

DLRS: gene tree evolution in light of a species tree

Joel Sjöstrand, Bengt Sennblad, Lars Arvestad, 2012, Bioinform..

Birth-death prior on phylogeny and speed dating

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

Fast computation of distance estimators

Jens Lagergren, Isaac Elias, J. Lagergren, 2007, BMC Bioinformatics.

Fast neighbor joining

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

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

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

Scuphr: A probabilistic framework for cell lineage tree reconstruction

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

Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity

Patrik L. Ståhl, E. Sonnhammer, J. Maaskola, 2018, Nature Communications.

Gene-pseudogene evolution: a probabilistic approach

J. Lagergren, B. Sennblad, Katja Nowick, 2015, BMC Genomics.

Clonally heritable gene expression imparts a layer of diversity within cell types

Jeff E. Mold, R. Sandberg, J. Lagergren, 2022, bioRxiv.

New Probabilistic Network Models and Algorithms for Oncogenesis

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

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.

Inferring tumor progression in large datasets

Jens Lagergren, Seong-Hwan Jun, Mohammadreza Mohaghegh Neyshabouri, 2020, bioRxiv.

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

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

Genome-wide probabilistic reconciliation analysis across vertebrates

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

Simultaneous Identification of Duplications and Lateral Gene Transfers

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

MSCAN: identification of functional clusters of transcription factor binding sites

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

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

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

Compatibility of unrooted phylogenetic trees is FPT

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

Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics

Jeff E. Mold, R. Sandberg, J. Hartman, 2023, Nature Communications.

PhylEx: Accurate reconstruction of clonal structure via integrated analysis of bulk DNA-seq and single cell RNA-seq data

Jeff E. Mold, R. Sandberg, J. Hartman, 2021, bioRxiv.

Genome-Wide Survey for Biologically Functional Pseudogenes

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

Simultaneous identification of duplications and lateral transfers

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

Bayesian gene/species tree reconciliation and orthology analysis using MCMC

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

Efficient algorithms for lateral gene transfer problems

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

Probabilistic inference of lateral gene transfer events

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

SUMOylation Mediates the Nuclear Translocation and Signaling of the IGF-1 Receptor

O. Larsson, J. Lagergren, A. Tofigh, 2010, Science Signaling.

Evolutionary history of metastatic breast cancer reveals minimal seeding from axillary lymph nodes

Gustav Stålhammar, J. Bergh, J. Hartman, 2018, The Journal of clinical investigation.

Towards Identifying Lateral Gene Transfer Events

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

Spatial transcriptomics of T and B cell receptors uncovers lymphocyte clonal dynamics in human tissue

Jeff E. Mold, J. Hartman, J. Lagergren, 2022, bioRxiv.

Hunting for Functionally Analogous Genes

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

New algorithms for the duplication-loss model

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

Species Tree Inference Using a Mixture Model.

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

DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data

S. Heath, A. Gonzalez-Perez, N. López-Bigas, 2021, bioRxiv.

A Polynomial-Time Algorithm for Near-Perfect Phylogeny

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

VaiPhy: a Variational Inference Based Algorithm for Phylogeny

J. Lagergren, Hazal Koptagel, Oskar Kviman, 2022, NeurIPS.

Supporting information S 1 Text for Modeling genetic interactions using generalized linear models

J. Lagergren, A. Hamsten, R. Strawbridge, 2016 .

Correction: Combined Chromatin and Expression Analysis Reveals Specific Regulatory Mechanisms within Cytokine Genes in the Macrophage Early Immune Response

O. Emanuelsson, J. Odeberg, J. Lagergren, 2012, PLoS ONE.

Problems Easy for Tree-Decomposable Graphs (Extended Abstract)

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

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

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

Efficient Parallel Algorithms for Graphs of Bounded Tree-Width

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

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

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

Learning Stationary Markov Processes with Contrastive Adjustment

J. Lagergren, J. Lundeberg, L. Bergenstråhle, 2023, ArXiv.

Species tree-aware simultaneous reconstruction of gene and domain evolution

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

Multiple Importance Sampling ELBO and Deep Ensembles of Variational Approximations

J. Lagergren, V. Elvira, Hazal Koptagel, 2022, AISTATS.

Ancestral Maximum Likelihood of Evolutionary Trees Is Hard

Alessandro Panconesi, Michael T. Hallett, Todd Wareham, 2003, WABI.

On the Approximability of the Steiner Tree Problem in Phylogeny

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

Motif Yggdrasil: Sampling Sequence Motifs from a Tree Mixture Model

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

Motif Yggdrasil: Sampling from a Tree Mixture Model

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

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

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

Easy Problems for Tree-Decomposable Graphs

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

Upper Bounds on the Size of Obstructions and Intertwines

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

An upper bound on the size of an obstruction

J. Lagergren, 1991, Graph Structure Theory.

The Size of an Interwine

Jens Lagergren, J. Lagergren, 1994, ICALP.

Breast cancer patient-derived whole-tumor cell culture model for efficient drug profiling and treatment response prediction

S. Robertson, J. Bergh, J. Hartman, 2022, Proceedings of the National Academy of Sciences of the United States of America.

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

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

Cooperation in the Latent Space: The Benefits of Adding Mixture Components in Variational Autoencoders

J. Lagergren, V. Elvira, Semih Kurt, 2022, ICML.

Learning with MISELBO: The Mixture Cookbook

J. Lagergren, V. Elvira, Semih Kurt, 2022, ArXiv.

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

Riccardo Sven Risuleo, Stefan Magureanu, J. Lagergren, 2021, ArXiv.

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

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

Recognizable Sets of Graphs of Bounded Tree-Width

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

Problems Easy for Tree-Decomposable Graphs (Extended Abstract)

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

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

J. Lagergren, Chammiran Daniel, Marie Öhman, 2015, Biochimie.

Graph Neural Networks for Nomination and Representation Learning of Web Elements

Riccardo Sven Risuleo, Stefan Magureanu, J. Lagergren, 2021, 2111.02168.

GenPhyloData: realistic simulation of gene family evolution

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

Spatial transcriptomics of B cell and T cell receptors reveals lymphocyte clonal dynamics

Jeff E. Mold, J. Lagergren, J. Lundeberg, 2023, Science.