Joakim Lundeberg

发表

SpatialCPie: an R/Bioconductor package for spatial transcriptomics cluster evaluation

Joseph Bergenstråhle, Ludvig Bergenstråhle, Joakim Lundeberg, 2020, BMC Bioinformatics.

BESST - Efficient scaffolding of large fragmented assemblies

Lars Arvestad, Kristoffer Sahlin, Francesco Vezzi, 2014, BMC Bioinformatics.

Spatially Resolved Transcriptomes—Next Generation Tools for Tissue Exploration

Joseph Bergenstråhle, Joakim Lundeberg, Michaela Asp, 2020, BioEssays : news and reviews in molecular, cellular and developmental biology.

Spatial mapping of cell types by integration of transcriptomics data

Joseph Bergenstråhle, Ludvig Bergenstråhle, Joakim Lundeberg, 2019 .

Classification of DNA sequences using Bloom filters

Björn Andersson, Lars Arvestad, Joakim Lundeberg, 2010, Bioinform..

Improved gap size estimation for scaffolding algorithms

Lars Arvestad, Kristoffer Sahlin, Joakim Lundeberg, 2012, Bioinform..

ST Pipeline: an automated pipeline for spatial mapping of unique transcripts

Joel Sjöstrand, Joakim Lundeberg, José Fernández Navarro, 2017, Bioinform..

Increased Throughput by Parallelization of Library Preparation for Massive Sequencing

Joakim Lundeberg, Erik Pettersson, Henrik Stranneheim, 2010, PloS one.

ST viewer: a tool for analysis and visualization of spatial transcriptomics datasets

Joakim Lundeberg, José Fernández Navarro, Patrik L. Ståhl, 2018, Bioinform..

Quality Matters: 2016 Annual Conference of the National Infrastructures for Biobanking.

Jan-Eric Litton, Andres Metspalu, Helen M Moore, 2017, Biopreservation and biobanking.

ST Spot Detector: a web-based application for automatic spot and tissue detection for spatial Transcriptomics image datasets

Ludvig Bergenstråhle, Joakim Lundeberg, Kim Wong, 2018, Bioinform..

Super-resolved spatial transcriptomics by deep data fusion

Joseph Bergenstråhle, Ludvig Bergenstråhle, Joakim Lundeberg, 2020, Nature Biotechnology.

Splotch: Robust estimation of aligned spatial temporal gene expression data

Richard Bonneau, Joakim Lundeberg, Tarmo Äijö, 2019, bioRxiv.

Gene expression analysis in tissue sections

Joakim Lundeberg, 2012 .

sepal: identifying transcript profiles with spatial patterns by diffusion-based modeling

Joakim Lundeberg, Alma Andersson, J. Lundeberg, 2021, Bioinform..

Integrated molecular portrait of non-small cell lung cancers

Pierre Validire, Philippe Dessen, Joakim Lundeberg, 2013, BMC Medical Genomics.

TagGD: Fast and Accurate Software for DNA Tag Generation and Demultiplexing

Joakim Lundeberg, Pelin Akan, P. Costea, 2013, PloS one.

SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes

Masahiro Yoshida, Fabian J. Theis, Oliver Eickelberg, 2020, Nature Medicine.

High-density spatial transcriptomics arrays for in situ tissue profiling

Richard Bonneau, Aviv Regev, Ludvig Bergenstråhle, 2019, bioRxiv.

Viral and microbial genotyping by a combination of multiplex competitive hybridization and specific extension followed by hybridization to generic tag arrays.

Joakim Lundeberg, Mathias Uhlén, Max Käller, 2003, Nucleic acids research.

Expression profiling of adrenocortical neoplasms suggests a molecular signature of malignancy.

Joakim Lundeberg, Peter Nilsson, Bertil Hamberger, 2005, Surgery.

High-definition spatial transcriptomics for in situ tissue profiling

Richard Bonneau, Aviv Regev, Ludvig Bergenstråhle, 2019, Nature Methods.

Activated paper surfaces for the rapid hybridization of DNA through capillary transport.

Joakim Lundeberg, Harry Brumer, Patrik L. Ståhl, 2012, Analytical chemistry.

Molecular atlas of the adult mouse brain

Joakim Lundeberg, Antje Märtin, Konstantinos Meletis, 2019, Science Advances.

Large Scale Library Generation for High Throughput Sequencing

Joakim Lundeberg, Erik Borgström, Sverker Lundin, 2011, PloS one.

Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis

Markus S. Schröder, Joakim Lundeberg, Yafeng Zhu, 2017, Nucleic acids research.

High-Density Microwell Chip for Culture and Analysis of Stem Cells

Helene Andersson-Svahn, Joakim Lundeberg, Sara Lindström, 2009, PloS one.

Massive and parallel expression profiling using microarrayed single-cell sequencing

Joakim Lundeberg, Jakub Orzechowski Westholm, Jonas Frisén, 2016, Nature Communications.

Visual detection of DNA on paper chips.

Joakim Lundeberg, Harry Brumer, Patrik L. Ståhl, 2014, Analytical chemistry.

Using Whole-Exome Sequencing to Identify Genetic Markers for Carboplatin and Gemcitabine-Induced Toxicities

Joakim Lundeberg, Henrik Gréen, Andrea Lindgren, 2015, Clinical Cancer Research.

The biotin‐streptavidin interaction can be reversibly broken using water at elevated temperatures

Joakim Lundeberg, Mathias Uhlén, M. Uhlén, 2005, Electrophoresis.

Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications.

Thomas Altmann, Yves Moreau, Hans Lehrach, 2004, Genome research.

A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart

Joakim Lundeberg, Daniel Fürth, Christer Sylvén, 2019, Cell.

Stepping stones in DNA sequencing

Joakim Lundeberg, Henrik Stranneheim, J. Lundeberg, 2012, Biotechnology journal.

Efficient de novo assembly of large and complex genomes by massively parallel sequencing of Fosmid pools

Andrey Alexeyenko, Bjarne Knudsen, Francesco Vezzi, 2013, BMC Genomics.

Tag-array based HPV genotyping by competitive hybridization and extension.

Joakim Lundeberg, Max Käller, Afshin Ahmadian, 2005, Journal of virological methods.

Multidimensional transcriptomics provides detailed information about immune cell distribution and identity in HER2+ breast tumors

Joakim Lundeberg, Jari Häkkinen, Johan Vallon-Christersson, 2018, bioRxiv.

The genome sequence of Mycoplasma mycoides subsp. mycoides SC type strain PG1T, the causative agent of contagious bovine pleuropneumonia (CBPP).

Bertil Pettersson, Alexander Goesmann, Joakim Lundeberg, 2004, Genome research.

Analysis of stranded information using an automated procedure for strand specific RNA sequencing

Joakim Lundeberg, Olof Emanuelsson, O. Emanuelsson, 2014, BMC Genomics.

Arrayed identification of DNA signatures

Joakim Lundeberg, Max Käller, Afshin Ahmadian, 2007, Expert review of molecular diagnostics.

Serum Microarrays for Large Scale Screening of Protein Levels *S

Joakim Lundeberg, Peter Nilsson, M. Uhlén, 2005, Molecular & Cellular Proteomics.

Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer’s Disease

Joakim Lundeberg, Sebastian Munck, Malte Kühnemund, 2020, Cell.

Rapid flow-sorting to simultaneously resolve multiplex massively parallel sequencing products

Joakim Lundeberg, J. Lundeberg, M. Dessing, 2011, Scientific reports.

In-Depth Transcriptome Analysis Reveals Novel TARs and Prevalent Antisense Transcription in Human Cell Lines

Joakim Lundeberg, Daniel Klevebring, Olof Emanuelsson, 2010, PloS one.

Generations of sequencing technologies.

Joakim Lundeberg, Afshin Ahmadian, J. Lundeberg, 2009, Genomics.

Competitive enzymatic reaction to control allele-specific extensions

Joakim Lundeberg, Max Käller, Afshin Ahmadian, 2005, Nucleic acids research.

Global gene expression analysis in time series following N-acetyl L-cysteine induced epithelial differentiation of human normal and cancer cells in vitro

Joakim Lundeberg, Thomas Lundeberg, J. Lundeberg, 2005, BMC Cancer.

Sequencing Degraded RNA Addressed by 3' Tag Counting

Joakim Lundeberg, Olof Emanuelsson, O. Emanuelsson, 2014, PloS one.

Forensic evidence based on mtDNA from dog and wolf hairs.

Joakim Lundeberg, Peter Savolainen, 1999 .

Assessment of Whole Genome Amplification for Sequence Capture and Massively Parallel Sequencing

Pierre Validire, Joakim Lundeberg, Mikael Huss, 2014, PloS one.

Integrating spatial gene expression and breast tumour morphology via deep learning

Ludvig Bergenstråhle, Joakim Lundeberg, Abubakar Abid, 2020, Nature Biomedical Engineering.

Effect of infliximab on mRNA expression profiles in synovial tissue of rheumatoid arthritis patients

Joakim Lundeberg, Peter Nilsson, P. Nilsson, 2006, Arthritis research & therapy.

Spatially resolved transcriptome profiling in model plant species

Andrey Alexeyenko, Chanaka Mannapperuma, Joakim Lundeberg, 2017, Nature Plants.

The Human Cell Atlas

Roland Eils, Alexander van Oudenaarden, Hans Clevers, 2017, bioRxiv.

Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis

Aaron Watters, Richard Bonneau, Joakim Lundeberg, 2018, Science.

Monitoring Resistance to Human Immunodeficiency Virus Type 1 Protease Inhibitors by Pyrosequencing

Joakim Lundeberg, Jan Albert, J. Lundeberg, 2001, Journal of Clinical Microbiology.