Rickard Sandberg

Rickard Sandberg

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Rickard Sandberg

Rickard Sandberg

Publications by authors named "Rickard Sandberg"

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X-chromosome upregulation is driven by increased burst frequency.

Nat Struct Mol Biol 2019 Oct 3;26(10):963-969. Epub 2019 Oct 3.

Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.

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http://dx.doi.org/10.1038/s41594-019-0306-yDOI Listing
October 2019

NASC-seq monitors RNA synthesis in single cells.

Nat Commun 2019 Jul 17;10(1):3138. Epub 2019 Jul 17.

Department of Cell and Molecular Biology, Karolinska Instiutet, Biomedicum, Solnavägen 9, 171 65, Solna, Sweden.

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http://dx.doi.org/10.1038/s41467-019-11028-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6637240PMC
July 2019

Genomic encoding of transcriptional burst kinetics.

Nature 2019 01 2;565(7738):251-254. Epub 2019 Jan 2.

Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.

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http://www.nature.com/articles/s41586-018-0836-1
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http://dx.doi.org/10.1038/s41586-018-0836-1DOI Listing
January 2019

Exploring parasite heterogeneity using single-cell RNA-seq reveals a gene signature among sexual stage Plasmodium falciparum parasites.

Exp Cell Res 2018 10 8;371(1):130-138. Epub 2018 Aug 8.

Ludwig Institute for Cancer Research, Karolinska Institutet, Box 240, SE-171 77 Stockholm, Sweden; Dept. of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 1, Box 285, SE-171 77 Stockholm, Sweden. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00144827183064
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http://dx.doi.org/10.1016/j.yexcr.2018.08.003DOI Listing
October 2018

Small-seq for single-cell small-RNA sequencing.

Nat Protoc 2018 10;13(10):2407-2424

Ludwig Institute for Cancer Research, Stockholm, Sweden.

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http://dx.doi.org/10.1038/s41596-018-0049-yDOI Listing
October 2018

Reply to 'High prevalence of clonal monoallelic expression'.

Nat Genet 2018 09;50(9):1199-1200

Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.

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http://dx.doi.org/10.1038/s41588-018-0189-6DOI Listing
September 2018

Identification of spatial expression trends in single-cell gene expression data.

Nat Methods 2018 05 19;15(5):339-342. Epub 2018 Mar 19.

Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.

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http://dx.doi.org/10.1038/nmeth.4634DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6314435PMC
May 2018

Computational correction of index switching in multiplexed sequencing libraries.

Nat Methods 2018 04;15(5):305-307

Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.

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http://dx.doi.org/10.1038/nmeth.4666DOI Listing
April 2018

Q&A: using Patch-seq to profile single cells.

BMC Biol 2017 07 6;15(1):58. Epub 2017 Jul 6.

Department of Neuroscience, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, 77030, USA.

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http://dx.doi.org/10.1186/s12915-017-0396-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499043PMC
July 2017

Single-Cell Analysis Reveals a Close Relationship between Differentiating Dopamine and Subthalamic Nucleus Neuronal Lineages.

Cell Stem Cell 2017 01 27;20(1):29-40. Epub 2016 Oct 27.

Ludwig Institute for Cancer Research, Box 240, 171 77 Stockholm, Sweden; Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2016.10.003DOI Listing
January 2017

Single-cell sequencing of the small-RNA transcriptome.

Nat Biotechnol 2016 Dec 31;34(12):1264-1266. Epub 2016 Oct 31.

Ludwig Institute for Cancer Research, Stockholm, Sweden.

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http://dx.doi.org/10.1038/nbt.3701DOI Listing
December 2016

Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA-seq.

Nat Genet 2016 11 26;48(11):1430-1435. Epub 2016 Sep 26.

Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.

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http://dx.doi.org/10.1038/ng.3678DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5117254PMC
November 2016

scphaser: haplotype inference using single-cell RNA-seq data.

Bioinformatics 2016 10 6;32(19):3038-40. Epub 2016 Aug 6.

Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden Ludwig Institute for Cancer Research, Box 240, 171 77 Stockholm, Sweden.

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http://dx.doi.org/10.1093/bioinformatics/btw484DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5039928PMC
October 2016

Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes.

Cell Metab 2016 10 22;24(4):593-607. Epub 2016 Sep 22.

Department of Cell and Molecular Biology (CMB), Karolinska Institutet, 171 77 Stockholm, Sweden; Integrated Cardio Metabolic Center (ICMC), Karolinska Institutet, 141 57 Huddinge, Sweden; Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden. Electronic address:

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http://dx.doi.org/10.1016/j.cmet.2016.08.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5069352PMC
October 2016

Laser capture microscopy coupled with Smart-seq2 for precise spatial transcriptomic profiling.

Nat Commun 2016 07 8;7:12139. Epub 2016 Jul 8.

Department of Neuroscience, Karolinska Institutet, Retzius v. 8, 171 77 Stockholm, Sweden.

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http://dx.doi.org/10.1038/ncomms12139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4941116PMC
July 2016

Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos.

Cell 2016 May 7;165(4):1012-26. Epub 2016 Apr 7.

Department of Clinical Science, Intervention and Technology, Karolinska Institutet, and Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, 141 86 Stockholm, Sweden. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.03.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4868821PMC
May 2016

The heterogeneity of human CD127(+) innate lymphoid cells revealed by single-cell RNA sequencing.

Nat Immunol 2016 Apr 15;17(4):451-60. Epub 2016 Feb 15.

Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Sweden.

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http://dx.doi.org/10.1038/ni.3368DOI Listing
April 2016

Random monoallelic expression of autosomal genes: stochastic transcription and allele-level regulation.

Nat Rev Genet 2015 Nov 7;16(11):653-64. Epub 2015 Oct 7.

Ludwig Institute for Cancer Research, Box 240, and the Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.

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http://dx.doi.org/10.1038/nrg3888DOI Listing
November 2015

In Vivo Effects of Mesenchymal Stromal Cells in Two Patients With Severe Acute Respiratory Distress Syndrome.

Stem Cells Transl Med 2015 Oct 18;4(10):1199-213. Epub 2015 Aug 18.

Departments of Molecular Medicine and Surgery, Cardiothoracic Surgery and Anesthesia, and Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Department of Internal Medicine, Hematology and Oncology, University of Erlangen-Nuremberg, Erlangen, Germany; Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy; Cancer Proteomics Mass Spectrometry, Science for Life Laboratory, Department of Oncology-Pathology, Department of Medical Biochemistry and Biophysics, and Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Center for Diseases of Aging, Vaccine and Gene Therapy Institute Florida, Port St. Lucie, Florida, USA; Exosome Diagnostics Inc., New York, New York, USA; Departments of Cardiothoracic Surgery, Hematology, and Immunology, Genetics and Pathology, Uppsala University Hospital, Uppsala, Sweden; Ludwig Institute for Cancer Research, Stockholm, Sweden; Health Sciences Research Facility, Department of Medicine, University of Vermont, Burlington, Vermont, USA

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http://dx.doi.org/10.5966/sctm.2015-0021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4572899PMC
October 2015

Decoding breast cancer tissue-stroma interactions using species-specific sequencing.

Breast Cancer Res 2015 Aug 13;17:109. Epub 2015 Aug 13.

Department of Cell and Molecular Biology, Karolinska Institutet, von Eulers väg 3, SE-17177, Stockholm, Sweden.

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http://dx.doi.org/10.1186/s13058-015-0616-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4534116PMC
August 2015

Putting cells in their place.

Nat Biotechnol 2015 May;33(5):490-1

Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.

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http://dx.doi.org/10.1038/nbt.3219DOI Listing
May 2015

Novel functions and targets of miR-944 in human cervical cancer cells.

Int J Cancer 2015 Mar 4;136(5):E230-41. Epub 2014 Sep 4.

Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden; Cancer Center Karolinska, Karolinska University Hospital, Stockholm, Sweden.

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http://doi.wiley.com/10.1002/ijc.29160
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http://dx.doi.org/10.1002/ijc.29160DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4277326PMC
March 2015

Tn5 transposase and tagmentation procedures for massively scaled sequencing projects.

Genome Res 2014 Dec 30;24(12):2033-40. Epub 2014 Jul 30.

Ludwig Institute for Cancer Research, 171 77 Stockholm, Sweden; Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden

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http://dx.doi.org/10.1101/gr.177881.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4248319PMC
December 2014

BMP signaling and its pSMAD1/5 target genes differentially regulate hair follicle stem cell lineages.

Cell Stem Cell 2014 Nov 9;15(5):619-33. Epub 2014 Oct 9.

Howard Hughes Medical Institute, Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2014.09.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4276600PMC
November 2014

Myelodysplastic syndromes are propagated by rare and distinct human cancer stem cells in vivo.

Cancer Cell 2014 Jun 15;25(6):794-808. Epub 2014 May 15.

Haematopoietic Stem Cell Biology Laboratory, MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Departments of Cell and Molecular Biology, Medicine Huddinge, and Laboratory Medicine, Huddinge, Karolinska Institutet and Center for Hematology and Regenerative Medicine, Karolinska University Hospital Huddinge, 141 86 Stockholm, Sweden. Electronic address:

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http://dx.doi.org/10.1016/j.ccr.2014.03.036DOI Listing
June 2014

RNA helicase A is a downstream mediator of KIF1Bβ tumor-suppressor function in neuroblastoma.

Cancer Discov 2014 Apr 27;4(4):434-51. Epub 2014 Jan 27.

1Ludwig Institute for Cancer Research Ltd.; 2Department of Cell and Molecular Biology, Karolinska Institutet; 3Department of Women's and Children's Health, Karolinska University Hospital, Stockholm; 4Ludwig Institute for Cancer Research Ltd., Biomedical Center, Uppsala; 5Department of Clinical Genetics, Institute of Biomedicine, University of Gothenburg, Sahlgrenska University Hospital, Göteborg, Sweden; and 6Moffitt Cancer Center, Neuro-Oncology Program, Tampa, Florida.

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http://cancerdiscovery.aacrjournals.org/content/early/2014/0
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http://cancerdiscovery.aacrjournals.org/cgi/doi/10.1158/2159
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http://dx.doi.org/10.1158/2159-8290.CD-13-0362DOI Listing
April 2014

Full-length RNA-seq from single cells using Smart-seq2.

Nat Protoc 2014 Jan 2;9(1):171-81. Epub 2014 Jan 2.

1] Ludwig Institute for Cancer Research, Stockholm, Sweden. [2] Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.

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http://www.nature.com/articles/nprot.2014.006
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http://dx.doi.org/10.1038/nprot.2014.006DOI Listing
January 2014

Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells.

Science 2014 Jan;343(6167):193-6

Ludwig Institute for Cancer Research, Box 240, 171 77 Stockholm, Sweden.

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http://dx.doi.org/10.1126/science.1245316DOI Listing
January 2014

Entering the era of single-cell transcriptomics in biology and medicine.

Authors:
Rickard Sandberg

Nat Methods 2014 Jan;11(1):22-4

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January 2014

Smart-seq2 for sensitive full-length transcriptome profiling in single cells.

Nat Methods 2013 Nov 22;10(11):1096-8. Epub 2013 Sep 22.

Ludwig Institute for Cancer Research, Stockholm, Sweden.

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http://www.nature.com/articles/nmeth.2639
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http://dx.doi.org/10.1038/nmeth.2639DOI Listing
November 2013

A reference transcriptome and inferred proteome for the salamander Notophthalmus viridescens.

Exp Cell Res 2013 May 28;319(8):1187-97. Epub 2013 Feb 28.

Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.

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http://dx.doi.org/10.1016/j.yexcr.2013.02.013DOI Listing
May 2013

How to analyze gene expression using RNA-sequencing data.

Methods Mol Biol 2012 ;802:259-74

Department of Cell and Molecular Biology, Karolinska Institutet and Ludwig Institute for Cancer Research, Stockholm, Sweden.

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http://dx.doi.org/10.1007/978-1-61779-400-1_17DOI Listing
April 2012

Sequentially acting Sox transcription factors in neural lineage development.

Genes Dev 2011 Dec 15;25(23):2453-64. Epub 2011 Nov 15.

Ludwig Institute for Cancer Research, Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden.

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http://dx.doi.org/10.1101/gad.176008.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3243056PMC
December 2011

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing.

Nature 2011 Nov;479(7371):74-9

Center for Cancer Research, Mouse Cancer Genetics Program, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA.

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http://dx.doi.org/10.1038/nature10442DOI Listing
November 2011

Notch signaling: simplicity in design, versatility in function.

Development 2011 Sep;138(17):3593-612

Department of Cell and Molecular Biology, Karolinska Institute, SE-171 77 Stockholm, Sweden.

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http://dx.doi.org/10.1242/dev.063610DOI Listing
September 2011

Heterogeneity in mammalian RNA 3' end formation.

Exp Cell Res 2010 May 6;316(8):1357-64. Epub 2010 Mar 6.

Department of Molecular Physiology and Biophysics and Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1016/j.yexcr.2010.02.040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2866830PMC
May 2010

An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data.

PLoS Comput Biol 2009 Dec 11;5(12):e1000598. Epub 2009 Dec 11.

Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.

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http://dx.doi.org/10.1371/journal.pcbi.1000598DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2781110PMC
December 2009

Alternative isoform regulation in human tissue transcriptomes.

Nature 2008 Nov;456(7221):470-6

Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1038/nature07509DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2593745PMC
November 2008

Proliferating cells express mRNAs with shortened 3' untranslated regions and fewer microRNA target sites.

Science 2008 Jun;320(5883):1643-7

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1126/science.1155390DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2587246PMC
June 2008

Improved precision and accuracy for microarrays using updated probe set definitions.

BMC Bioinformatics 2007 Feb 8;8:48. Epub 2007 Feb 8.

Massachusetts Institute of Technology, Department of biology, 68-211, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1186/1471-2105-8-48DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1805763PMC
February 2007

Comparative microarray analysis.

OMICS 2006 ;10(3):381-97

Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA.

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http://dx.doi.org/10.1089/omi.2006.10.381DOI Listing
December 2006

The molecular portrait of in vitro growth by meta-analysis of gene-expression profiles.

Genome Biol 2005 27;6(8):R65. Epub 2005 Jul 27.

Microbiology and Tumor Biology Center (MTC), Karolinska Institutet, S-171 77 Stockholm, Sweden.

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http://dx.doi.org/10.1186/gb-2005-6-8-r65DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1273632PMC
July 2006

Gene expression perturbation in vitro--a growing case for three-dimensional (3D) culture systems.

Semin Cancer Biol 2005 Oct;15(5):405-12

Microbiology and Tumor Biology Center, MTC, Karolinska Institutet, Box 280, 171 77 Stockholm, Sweden.

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http://linkinghub.elsevier.com/retrieve/pii/S1044579X0500041
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http://dx.doi.org/10.1016/j.semcancer.2005.06.009DOI Listing
October 2005

Assessment of tumor characteristic gene expression in cell lines using a tissue similarity index (TSI).

Proc Natl Acad Sci U S A 2005 Feb 25;102(6):2052-7. Epub 2005 Jan 25.

Microbiology and Tumor Biology Center, Karolinska Institutet, S-171 77 Stockholm, Sweden.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0408105102
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http://dx.doi.org/10.1073/pnas.0408105102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC548538PMC
February 2005

Systems biology is taking off.

Genome Res 2003 Nov;13(11):2377-80

Department of Cell and Molecular Biology, Uppsala University, BMC, 751-24 Uppsala, Sweden.

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http://dx.doi.org/10.1101/gr.1763203DOI Listing
November 2003

Quantifying the species-specificity in genomic signatures, synonymous codon choice, amino acid usage and G+C content.

Gene 2003 Jun;311:35-42

Microbiology and Tumor Biology Center, Karolinska Institute, S-171 77 Stockholm, Sweden.

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http://dx.doi.org/10.1016/s0378-1119(03)00581-xDOI Listing
June 2003