Rickard Sandberg

About me
Publications
Grants
CV
Public outreach and news

About me

Education
- PhD studies, Department of Microbiology, Tumour and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden 2000-2004.
- Postdoctoral training, Massachusetts Institute of Technology (MIT), Cambridge, US 2005-2007.
- Assistant Professor, Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Sweden 2008-2013.
- Associate Professor, Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Sweden 2013-

Academic honours, awards and prizes
- Torsten Söderbergs akademiprofessur i medicin 2022
- Elected Member of EMBO 2019.
- Elected Member of the Nobel Assembly at Karolinska Institutet 2019.
- Anders Jahre's medical prize for young medical researchers (Nordic prize) 2014
- EMBO Young Investigator 2012
- Sven and Ebba-Christina Hagbergs Prize 2012

Research

Using single-cell transcriptomics to investigate gene regulation, cellular heterogeneity and the specification of cell identities. We are studying gene expression and regulation using a combination of genomic technologies. In particular, we are developing and applying single-cell transcriptomics to better understand how cellular identities are specified at the molecular level during differentiation, in pluripotency and to enable studies of the cellular heterogeneity in tumors. Additionally, we believe that analyses of single-cell level gene expression will unravel general aspects of transcription processes and general rules for the composition of transcriptomes.

Selected publications

Article: NATURE BIOTECHNOLOGY. 2020;38(6):708-714
Single-cell RNA counting at allele and isoform resolution using Smart-seq3
Hagemann-Jensen M; Ziegenhain C; Chen P; Ramskold D; Hendriks G-J; Larsson AJM; Faridani OR; Sandberg R
Article: NATURE COMMUNICATIONS. 2019;10(1):3138
NASC-seq monitors RNA synthesis in single cells
Hendriks G-J; Jung LA; Larsson AJM; Lidschreiber M; Forsman OA; Lidschreiber K; Cramer P; Sandberg R
Article: NATURE. 2019;565(7738):251-254
Genomic encoding of transcriptional burst kinetics
Larsson AJM; Johnsson P; Hagemann-Jensen M; Hartmanis L; Faridani OR; Reinius B; Segerstolpe A; Rivera CM; Ren B; Sandberg R
Article: SCIENCE. 2014;343(6167):193-196
Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells
Deng Q; Ramskold D; Reinius B; Sandberg R
Article: NATURE METHODS. 2013;10(11):1096-1098
Smart-seq2 for sensitive full-length transcriptome profiling in single cells
Picelli S; Bjorklund AK; Faridani OR; Sagasser S; Winberg G; Sandberg R

Articles

Article: NATURE CELL BIOLOGY. 2024;26(10):1725-1733
Single-cell new RNA sequencing reveals principles of transcription at the resolution of individual bursts
Ramskold D; Hendriks G-J; Larsson AJM; Mayr JV; Ziegenhain C; Hagemann-Jensen M; Hartmanis L; Sandberg R
Article: NATURE COMMUNICATIONS. 2024;15(1):8373
Introducing synthetic thermostable RNase inhibitors to single-cell RNA-seq.
Noble JC; Lentini A; Hagemann-Jensen M; Sandberg R; Reinius B
Article: GENOME BIOLOGY. 2024;25(1):214
Inferring clonal somatic mutations directed by X chromosome inactivation status in single cells
Demirci I; Larsson AJM; Chen X; Hartman J; Sandberg R; Frisen J
Article: NATURE IMMUNOLOGY. 2024;25(6):1007-1019
Alternative platelet differentiation pathways initiated by nonhierarchically related hematopoietic stem cells
Carrelha J; Mazzi S; Winroth A; Hagemann-Jensen M; Ziegenhain C; Hogstrand K; Seki M; Brennan MS; Lehander M; Wu B; Meng Y; Markljung E; Norfo R; Ishida H; Stralin KB; Grasso F; Karali CS; Aliouat A; Hillen A; Chari E; Siletti K; Thongjuea S; Mead AJ; Linnarsson S; Nerlov C; Sandberg R; Yoshizato T; Woll PS; Jacobsen SEW
Article: ISCIENCE. 2024;27(4):109346
Inflammatory, metabolic, and sex-dependent gene-regulatory dynamics of microglia and macrophages in neonatal hippocampus after hypoxia-ischemia
Di Martino E; Ambikan A; Ramskold D; Umekawa T; Giatrellis S; Vacondio D; Romero AL; Galan MG; Sandberg R; Aden U; Lauschke VM; Neogi U; Blomgren K; Kele J
Article: CELL SYSTEMS. 2024;15(2):149-165.e10
Clonally heritable gene expression imparts a layer of diversity within cell types
Mold JE; Weissman MH; Ratz M; Hagemann-Jensen M; Hard J; Eriksson C-J; Toosi H; Berghenstrahle J; Ziegenhain C; von Berlin L; Martin M; Blom K; Lagergren J; Lundeberg J; Sandberg R; Michaeeurolsson J; Frisen J
Article: CANCER RESEARCH. 2024;84(2):211-225
Erythroid Differentiation Enhances RNA Mis-Splicing in SF3B1-Mutant Myelodysplastic Syndromes with Ring Sideroblasts
Moura PL; Mortera-Blanco T; Hofman IJ; Todisco G; Kretzschmar WW; Bjoerklund A-C; Creignou M; Hagemann-Jensen M; Ziegenhain C; Cabrerizo Granados D; Barbosa I; Walldin G; Jansson M; Ashley N; Mead AJ; Lundin V; Dimitriou M; Yoshizato T; Woll PS; Ogawa S; Sandberg R; Jacobsen SEW; Hellstrom-Lindberg E
Article: GENOME BIOLOGY. 2024;25(1):2
Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network
Hunt G; Vaid R; Pirogov S; Pfab A; Ziegenhain C; Sandberg R; Reimegard J; Mannervik M
Article: NATURE AGING. 2023;3(11):1430-1445
Spatial and single-cell profiling of the metabolome, transcriptome and epigenome of the aging mouse liver
Nikopoulou C; Kleinenkuhnen N; Parekh S; Sandoval T; Ziegenhain C; Schneider F; Giavalisco P; Donahue K-F; Vesting AJ; Kirchner M; Bozukova M; Vossen C; Altmueller J; Wunderlich T; Sandberg R; Kondylis V; Tresch A; Tessarz P
Article: AGING. 2023;15(12):5240-5265
Age prediction from human blood plasma using proteomic and small RNA data: a comparative analysis
Salignon J; Faridani OR; Miliotis T; Janssens GE; Chen P; Zarrouki B; Sandberg R; Davidsson P; Riedel CG
Article: DEVELOPMENTAL CELL. 2023;58(6):450-460.e6
A small noncoding RNA links ribosome recovery and translation control to dedifferentiation during salamander limb regeneration
Subramanian E; Elewa A; Brito G; Kumar A; Segerstolpe A; Karampelias C; Bjorklund A; Sandberg R; Echeverri K; Lui W-O; Andersson O; Simon A
Article: NATURE COMMUNICATIONS. 2023;14(1):982
Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics
Jun S-H; Toosi H; Mold J; Engblom C; Chen X; O'Flanagan C; Hagemann-Jensen M; Sandberg R; Aparicio S; Hartman J; Roth A; Lagergren J
Article: NATURE BIOTECHNOLOGY. 2022;40(10):1452-1457
Scalable single-cell RNA sequencing from full transcripts with Smart-seq3xpress
Hagemann-Jensen M; Ziegenhain C; Sandberg R
Article: NATURE METHODS. 2022;19(5):560-566
Molecular spikes: a gold standard for single-cell RNA counting
Ziegenhain C; Hendriks G-J; Hagemann-Jensen M; Sandberg R
Article: NATURE GENETICS. 2022;54(3):306-317
Transcriptional kinetics and molecular functions of long noncoding RNAs
Johnsson P; Ziegenhain C; Hartmanis L; Hendriks G-J; Hagemann-Jensen M; Reinius B; Sandberg R
Article: NATURE COMMUNICATIONS. 2021;12(1):6216
BAMboozle removes genetic variation from human sequence data for open data sharing
Ziegenhain C; Sandberg R
Article: NATURE. 2021;598(7879):86-102
A multimodal cell census and atlas of the mammalian primary motor cortex
Callaway EM; Dong H-W; Ecker JR; Hawrylycz MJ; Huang ZJ; Lein ES; Ngai J; Osten P; Ren B; Tolias AS; White O; Zeng H; Zhuang X; Ascoli GA; Behrens MM; Chun J; Feng G; Gee JC; Ghosh SS; Halchenko YO; Hertzano R; Lim BK; Martone ME; Ng L; Pachter L; Ropelewski AJ; Tickle TL; Yang XW; Zhang K; Bakken TE; Berens P; Daigle TL; Harris JA; Jorstad NL; Kalmbach BE; Kobak D; Li YE; Liu H; Matho KS; Mukamel EA; Naeemi M; Scala F; Tan P; Ting JT; Xie F; Zhang M; Zhang Z; Zhou J; Zingg B; Bertagnolli D; Casper T; Crichton K; Dee N; Diep D; Ding S-L; Dong W; Dougherty EL; Fong O; Goldman M; Goldy J; Hodge RD; Hu L; Keene CD; Krienen FM; Kroll M; Lake BB; Lathia K; Linnarsson S; Liu CS; Macosko EZ; McCarroll SA; McMillen D; Nadaf NM; Thuc NN; Palmer CR; Thanh P; Plongthongkum N; Reed NM; Regev A; Rimorin C; Romanow WJ; Savoia S; Siletti K; Smith K; Sulc J; Tasic B; Tieu M; Torkelson A; Tung H; van Velthoven CTJ; Vanderburg CR; Yanny AM; Fang R; Hou X; Lucero JD; Osteen JK; Pinto-Duarte A; Poirion O; Preissl S; Wang X; Aldridge AI; Bartlett A; Boggeman L; O'Connor C; Castanon RG; Chen H; Fitzpatrick C; Luo C; Nery JR; Nunn M; Rivkin AC; Tian W; Dominguez B; Ito-Cole T; Jacobs M; Jin X; Lee C-T; Lee K-F; Miyazaki PA; Pang Y; Rashid M; Smith JB; Vu M; Williams E; Armand E; Biancalani T; Booeshaghi AS; Crow M; Dudoit S; Fischer S; Gillis J; Hu Q; Kharchenko PV; Niu S-Y; Ntranos V; Purdom E; Risso D; de Bezieux HR; Somasundaram S; Street K; Svensson V; Vaishnav ED; Van den Berge K; Welch JD; Yao Z; An X; Bateup HS; Bowman I; Chance RK; Foster NN; Galbavy W; Gong H; Gou L; Hatfield JT; Hintiryan H; Hirokawa KE; Kim G; Kramer DJ; Li A; Li X; Luo Q; Munoz-Castaneda R; Stafford DA; Feng Z; Jia X; Jiang S; Jiang T; Kuang X; Larsen R; Lesnar P; Li Y; Li Y; Liu L; Peng H; Qu L; Ren M; Ruan Z; Shen E; Song Y; Wakeman W; Wang P; Wang Y; Wang Y; Yin L; Yuan J; Zhao S; Zhao X; Narasimhan A; Palaniswamy R; Banerjee S; Ding L; Huilgol D; Huo B; Kuo H-C; Laturnus S; Li X; Mitra PP; Mizrachi J; Wang Q; Xie P; Xiong F; Yu Y; Eichhorn SW; Berg J; Bernabucci M; Bernaerts Y; Cadwell CR; Castro JR; Dalley R; Hartmanis L; Horwitz GD; Jiang X; Ko AL; Miranda E; Mulherkar S; Nicovich PR; Owen SF; Sandberg R; Sorensen SA; Tan ZH; Allen S; Hockemeyer D; Lee AY; Veldman MB; Adkins RS; Ament SA; Bravo HC; Carter R; Chatterjee A; Colantuoni C; Crabtree J; Creasy H; Felix V; Giglio M; Herb BR; Kancherla J; Mahurkar A; McCracken C; Nickel L; Olley D; Orvis J; Schor M; Hood G; Dichter B; Grauer M; Helba B; Bandrowski A; Barkas N; Carlin B; D'Orazi FD; Degatano K; Gillespie TH; Khajouei F; Konwar K; Thompson C; Kelly K; Mok S; Sunkin S
Article: NATURE. 2021;598(7879):144-150
Phenotypic variation of transcriptomic cell types in mouse motor cortex
Scala F; Kobak D; Bernabucci M; Bernaerts Y; Cadwell CR; Castro JR; Hartmanis L; Jiang X; Laturnus S; Miranda E; Mulherkar S; Tan ZH; Yao Z; Zeng H; Sandberg R; Berens P; Tolias AS
Article: CELL REPORTS. 2021;35(8):109174
Divergent clonal differentiation trajectories establish CD8⁺ memory T cell heterogeneity during acute viral infections in humans
Mold JE; Modolo L; Hard J; Zamboni M; Larsson AJM; Stenudd M; Eriksson C-J; Durif G; Stahl PL; Borgstrom E; Picelli S; Reinius B; Sandberg R; Reu P; Talavera-Lopez C; Andersson B; Blom K; Sandberg JK; Picard F; Michaelsson J; Frisen J
Article: NATURE COMMUNICATIONS. 2021;12(1):2141
Single-cell RNA sequencing reveals the mesangial identity and species diversity of glomerular cell transcriptomes
He B; Chen P; Zambrano S; Dabaghie D; Hu Y; Moller-Hackbarth K; Unnersjoe-Jess D; Korkut GG; Charrin E; Jeansson M; Bintanel-Morcillo M; Witasp A; Wennberg L; Wernerson A; Schermer B; Benzing T; Ernfors P; Betsholtz C; Lal M; Sandberg R; Patrakka J
Article: PLOS COMPUTATIONAL BIOLOGY. 2021;17(3):e1008772
Transcriptional bursts explain autosomal random monoallelic expression and affect allelic imbalance
Larsson AJM; Ziegenhain C; Hagemann-Jensen M; Reinius B; Jacob T; Dalessandri T; Hendriks G-J; Kasper M; Sandberg R
Article: PLOS ONE. 2021;16(4):e0250282
Understanding interactions between risk factors, and assessing the utility of the additive and multiplicative models through simulations
Diaz-Gallo L-M; Brynedal B; Westerlind H; Sandberg R; Ramskold D
Article: NATURE NANOTECHNOLOGY. 2021;16(1):85-95
A DNA-nanoassembly-based approach to map membrane protein nanoenvironments.
Ambrosetti E; Bernardinelli G; Hoffecker I; Hartmanis L; Kiriako G; de Marco A; Sandberg R; Högberg B; Teixeira AI
Article: GENOME RESEARCH. 2020;30(8):1083-1096
LCM-seq reveals unique transcriptional adaptation mechanisms of resistant neurons and identifies protective pathways in spinal muscular atrophy
Nichterwitz S; Nijssen J; Storvall H; Schweingruber C; Comley LH; Allodi I; van der Lee M; Deng Q; Sandberg R; Hedlund E
Article: NATURE BIOTECHNOLOGY. 2020;38(6):747-755
Benchmarking single-cell RNA-sequencing protocols for cell atlas projects
Mereu E; Lafzi A; Moutinho C; Ziegenhain C; McCarthy DJ; Alvarez-Varela A; Batlle E; Sagar; Gruen D; Lau JK; Boutet SC; Sanada C; Ooi A; Jones RC; Kaihara K; Brampton C; Talaga Y; Sasagawa Y; Tanaka K; Hayashi T; Braeuning C; Fischer C; Sauers S; Trefzer T; Conrad C; Adiconis X; Nguyen LT; Regev A; Levin JZ; Parekh S; Janjic A; Wange LE; Bagnoli JW; Enard W; Gut M; Sandberg R; Nikaido I; Gut I; Stegle O; Heyn H
Article: ELIFE. 2020;9:e52951
Cell type composition and circuit organization of clonally related excitatory neurons in the juvenile mouse neocortex
Cadwell CR; Scala F; Fahey PG; Kobak D; Mulherkar S; Sinz FH; Papadopoulos S; Tan ZH; Johnsson P; Hartmanis L; Li S; Cotton RJ; Tolias KF; Sandberg R; Berens P; Jiang X; Tolias AS
Article: CELL STEM CELL. 2020;26(3):441-457.e7
The Molecular Anatomy of Mouse Skin during Hair Growth and Rest
Joost S; Annusver K; Jacob T; Sun X; Dalessandri T; Sivan U; Sequeira I; Sandberg R; Kasper M
Article: BASIC RESEARCH IN CARDIOLOGY. 2019;115(1):7
Cell shape determines gene expression: cardiomyocyte morphotypic transcriptomes
Esfahani PH; ElBeck Z; Sagasser S; Li X; Hossain MB; Talukdar HA; Sandberg R; Knoll R
Article: NATURE STRUCTURAL & MOLECULAR BIOLOGY. 2019;26(10):963-969
X-chromosome upregulation is driven by increased burst frequency
Larsson AJM; Coucoravas C; Sandberg R; Reinius B
Article: NATURE COMMUNICATIONS. 2019;10(1):4174
Layer 4 of mouse neocortex differs in cell types and circuit organization between sensory areas
Scala F; Kobak D; Shan S; Bernaerts Y; Laturnus S; Cadwell CR; Hartmanis L; Froudarakis E; Castro JR; Tan ZH; Papadopoulos S; Patel SS; Sandberg R; Berens P; Jiang X; Tolias AS
Article: ARTERIOSCLEROSIS, THROMBOSIS, AND VASCULAR BIOLOGY. 2019;39(7):1402-1418
Intussusceptive Vascular Remodeling Precedes Pathological Neovascularization
Ali Z; Mukwaya A; Biesemeier A; Ntzouni M; Ramskold D; Giatrellis S; Mammadzada P; Cao R; Lennikov A; Marass M; Gerri C; Hildesjo C; Taylor M; Deng Q; Peebo B; del Peso L; Kvanta A; Sandberg R; Schraermeyer U; Andre H; Steffensen JF; Lagali N; Cao Y; Kele J; Dahl Jensen L
Article: ARTERIOSCLEROSIS, THROMBOSIS, AND VASCULAR BIOLOGY. 2019;39(7):1432-1447
Disruption of the Extracellular Matrix Progressively Impairs Central Nervous System Vascular Maturation Downstream of β-Catenin Signaling
Jensen LD; Hot B; Ramskold D; Germano RFV; Yokota C; Giatrellis S; Lauschke VM; Hubmacher D; Li MX; Hupe M; Arnold TD; Sandberg R; Frisen J; Trusohamn M; Martowicz A; Wisniewska-Kruk J; Nyqvist D; Adams RH; Apte SS; Vanhollebeke B; Stenman JM; Kele J
Article: EXPERIMENTAL CELL RESEARCH. 2018;371(1):130-138
Exploring parasite heterogeneity using single-cell RNA-seq reveals a gene signature among sexual stage Plasmodium falciparum parasites
Ngara M; Palmkvist M; Sagasser S; Hjelmqvist D; Bjorklund AK; Wahlgren M; Ankarklev J; Sandberg R
Article: NATURE PROTOCOLS. 2018;13(10):2407-2424
Small-seq for single-cell small-RNA sequencing
Hagemann-Jensen M; Abdullayev I; Sandberg R; Faridani OR
Article: NATURE COMMUNICATIONS. 2018;9(1):1873
Parental haplotype-specific single-cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells
Vertesy A; Arindrarto W; Roost MS; Reinius B; Torrens-Juaneda V; Bialecka M; Moustakas I; Ariyurek Y; Kuijk E; Mei H; Sandberg R; van Oudenaarden A; Lopes SMCDS
Article: NATURE METHODS. 2018;15(5):339-342
Identification of spatial expression trends in single-cell gene expression data
Edsgard D; Johnsson P; Sandberg R
Article: GASTROENTEROLOGY. 2018;154(4):1080-1095
Mouse Model of Alagille Syndrome and Mechanisms of Jagged1 Missense Mutations
Andersson ER; Chivukula IV; Hankeova S; Sjoqvist M; Tsoi YL; Ramskold D; Masek J; Elmansuri A; Hoogendoorn A; Vazquez E; Storvall H; Netusilova J; Huch M; Fischler B; Ellis E; Contreras A; Nemeth A; Chien KC; Clevers H; Sandberg R; Bryja V; Lendahl U
Article: NATURE COMMUNICATIONS. 2017;8(1):2286
Reading and editing the Pleurodeles waltl genome reveals novel features of tetrapod regeneration
Elewa A; Wang H; Talavera-Lopez C; Joven A; Brito G; Kumar A; Hameed LS; Penrad-Mobayed M; Yao Z; Zamani N; Abbas Y; Abdullayev I; Sandberg R; Grabherr M; Andersson B; Simon A
Article: NATURE PROTOCOLS. 2017;12(12):2531-2553
Multimodal profiling of single-cell morphology, electrophysiology, and gene expression using Patch-seq
Cadwell CR; Scala F; Li S; Livrizzi G; Shen S; Sandberg R; Jiang X; Tolias AS
Article: EMBO JOURNAL. 2017;36(14):2107-2125
A TRPV1-to-secretagogin regulatory axis controls pancreatic β-cell survival by modulating protein turnover
Malenczyk K; Girach F; Szodorai E; Storm P; Segerstolpe A; Tortoriello G; Schnell R; Mulder J; Romanov RA; Borok E; Piscitelli F; Di Marzo V; Szabo G; Sandberg R; Kubicek S; Lubec G; Hokfelt T; Wagner L; Groop L; Harkany T
Article: NATURE MEDICINE. 2017;23(6):692-702
Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid leukemia
Giustacchini A; Thongjuea S; Barkas N; Woll PS; Povinelli BJ; Booth CAG; Sopp P; Norfo R; Rodriguez-Meira A; Ashley N; Jamieson L; Vyas P; Anderson K; Segerstolpe A; Qian H; Olsson-Stromberg U; Mustjoki S; Sandberg R; Jacobsen SEW; Mead AJ
Article: ELIFE. 2017;6:e22906
Position-and Hippo signaling -dependent plasticity during lineage segregation in the early mouse embryo
Posfai E; Petropoulos S; de Barrosl FRO; Schell JP; Jurisica I; Sandberg R; Lanner F; Rossant J
Article: CELL STEM CELL. 2017;20(1):29-40
Single-Cell Analysis Reveals a Close Relationship between Differentiating Dopamine and Subthalamic Nucleus Neuronal Lineages
Kee N; Volakakis N; Kirkeby A; Dahl L; Storvall H; Nolbrant S; Lahti L; Bjorklund AK; Gillberg L; Joodmardi E; Sandberg R; Parmar M; Perlmann T
Article: NATURE BIOTECHNOLOGY. 2016;34(12):1264-1266
Single-cell sequencing of the small-RNA transcriptome
Faridani OR; Abdullayev I; Hagemann-Jensen M; Schell JP; Lanner F; Sandberg R
Article: NATURE IMMUNOLOGY. 2016;17(12):1424-1435
Initial seeding of the embryonic thymus by immune-restricted lympho-myeloid progenitors
Luis TC; Luc S; Mizukami T; Boukarabila H; Thongjuea S; Woll PS; Azzoni E; Giustacchini A; Lutteropp M; Bouriez-Jones T; Vaidya H; Mead AJ; Atkinson D; Boiers C; Carrelha J; Macaulay IC; Patient R; Geissmann F; Nerlov C; Sandberg R; de Bruijn MFTR; Blackburn CC; Godin I; Jacobsen SEW
Article: NATURE GENETICS. 2016;48(11):1430-1435
Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA-seq
Reinius B; Mold JE; Ramskold D; Deng Q; Johnsson P; Michaelsson J; Frisen J; Sandberg R
Article: CELL METABOLISM. 2016;24(4):593-607
Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes
Segerstolpe A; Palasantza A; Eliasson P; Andersson E-M; Andreasson A-C; Sun X; Picelli S; Sabirsh A; Clausen M; Bjursell MK; Smith DM; Kasper M; Ammala C; Sandberg R
Article: BIOINFORMATICS. 2016;32(19):3038-3040
scphaser: haplotype inference using single-cell RNA-seq data
Edsgard D; Reinius B; Sandberg R
Article: GENOME RESEARCH. 2016;26(10):1342-1354
Single-cell analyses of X Chromosome inactivation dynamics and pluripotency during differentiation
Chen G; Schell JP; Benitez JA; Petropoulos S; Yilmaz M; Reinius B; Alekseenko Z; Shi L; Hedlund E; Lanner F; Sandberg R; Deng Q
Article: NATURE COMMUNICATIONS. 2016;7:12139
Laser capture microscopy coupled with Smart-seq2 for precise spatial transcriptomic profiling
Nichterwitz S; Chen G; Benitez JA; Yilmaz M; Storvall H; Cao M; Sandberg R; Deng Q; Hedlund E
Article: CELL. 2016;165(4):1012-1026
Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos
Petropoulos S; Edsgard D; Reinius B; Deng Q; Panula SP; Codeluppi S; Reyes AP; Linnarsson S; Sandberg R; Lanner F
Article: NATURE IMMUNOLOGY. 2016;17(4):451-460
The heterogeneity of human CD127⁺ innate lymphoid cells revealed by single-cell RNA sequencing
Bjorklund AK; Forkel M; Picelli S; Konya V; Theorell J; Friberg D; Sandberg R; Mjosberg J
Article: NATURE BIOTECHNOLOGY. 2016;34(2):199-203
Electrophysiological, transcriptomic and morphologic profiling of single neurons using Patch-seq
Cadwell CR; Palasantza A; Jiang X; Berens P; Deng Q; Yilmaz M; Reimer J; Shen S; Bethge M; Tolias KF; Sandberg R; Tolias AS
Article: STEM CELLS TRANSLATIONAL MEDICINE. 2015;4(10):1199-1213
In Vivo Effects of Mesenchymal Stromal Cells in Two Patients With Severe Acute Respiratory Distress Syndrome
Simonson OE; Mougiakakos D; Heldring N; Bassi G; Johansson HJ; Dalen M; Jitschin R; Rodin S; Corbascio M; El Andaloussi S; Wiklander OPB; Nordin JZ; Skog J; Romain C; Koestler T; Hellgren-Johansson L; Schiller P; Joachimsson P-O; Haegglund H; Mattsson M; Lentio J; Faridani OR; Sandberg R; Korsgren O; Krampera M; Weiss DJ; Grinnemo K-H; Le Blanc K
Article: BREAST CANCER RESEARCH. 2015;17(1):109
Decoding breast cancer tissue-stroma interactions using species-specific sequencing
Chivukula IV; Ramskold D; Storvall H; Anderberg C; Jin S; Mamaeva V; Sahlgren C; Pietras K; Sandberg R; Lendahl U
Article: GENOME BIOLOGY. 2015;16(1):156
Genome-wide mapping of promoter-anchored interactions with close to single-enhancer resolution
Sahlen P; Abdullayev I; Ramskold D; Matskova L; Rilakovic N; Lotstedt B; Albert TJ; Lundeberg J; Sandberg R
Article: INTERNATIONAL JOURNAL OF CANCER. 2015;136(5):E230-E241
Novel functions and targets of miR-944 in human cervical cancer cells
Xie H; Lee L; Scicluna P; Kavak E; Larsson C; Sandberg R; Lui W-O
Article: GENOME RESEARCH. 2014;24(12):2033-2040
Tn5 transposase and tagmentation procedures for massively scaled sequencing projects
Picelli S; Bjorklund AK; Reinius B; Sagasser S; Winberg G; Sandberg R
Article: CELL STEM CELL. 2014;15(5):619-633
BMP Signaling and Its pSMAD1/5 Target Genes Differentially Regulate Hair Follicle Stem Cell Lineages
Genander M; Cook PJ; Ramskold D; Keyes BE; Mertz AF; Sandberg R; Fuchs E
Article: CANCER CELL. 2014;25(6):794-808
Myelodysplastic Syndromes Are Propagated by Rare and Distinct Human Cancer Stem Cells In Vivo
Woll PS; Kjallquist U; Chowdhury O; Doolittle H; Wedge DC; Thongjuea S; Erlandsson R; Ngara M; Anderson K; Deng Q; Mead AJ; Stenson L; Giustacchini A; Duarte S; Giannoulatou E; Taylor S; Karimi M; Scharenberg C; Mortera-Blanco T; Macaulay IC; Clark S-A; Dybedal I; Josefsen D; Fenaux P; Hokland P; Holm MS; Cazzola M; Malcovati L; Tauro S; Bowen D; Boultwood J; Pellagatti A; Pimanda JE; Unnikrishnan A; Vyas P; Goehring G; Schlegelberger B; Tobiasson M; Kvalheim G; Constantinescu SN; Nerlov C; Nilsson L; Campbell PJ; Sandberg R; Papaemmanuil E; Hellstrom-Lindberg E; Linnarsson S; Jacobsen SEW
Article: CANCER DISCOVERY. 2014;4(4):434-451
RNA Helicase A Is a Downstream Mediator of KIF1Bβ Tumor-Suppressor Function in Neuroblastoma
Chen ZX; Wallis K; Fell SM; Sobrado VR; Hemmer MC; Ramskold D; Hellman U; Sandberg R; Kenchappa RS; Martinson T; Johnsen JI; Kogner P; Schlisio S
Article: NATURE METHODS. 2014;11(1):22-24
Entering the era of single-cell transcriptomics in biology and medicine
Sandberg R
Article: NATURE PROTOCOLS. 2014;9(1):171-181
Full-length RNA-seq from single cells using Smart-seq2
Picelli S; Faridani OR; Bjorklund AK; Winberg G; Sagasser S; Sandberg R
Article: NATURE STRUCTURAL & MOLECULAR BIOLOGY. 2013;20(12):1367-1376
The human cap-binding complex is functionally connected to the nuclear RNA exosome
Andersen PR; Domanski M; Kristiansen MS; Storvall H; Ntini E; Verheggen C; Schein A; Bunkenborg J; Poser I; Hallais M; Sandberg R; Hyman A; LaCava J; Rout MP; Andersen JS; Bertrand E; Jensen TH
Article: CELL STEM CELL. 2013;13(5):535-548
Lymphomyeloid Contribution of an Immune-Restricted Progenitor Emerging Prior to Definitive Hematopoietic Stem Cells
Boiers C; Carrelha J; Lutteropp M; Luc S; Green JCA; Azzoni E; Woll PS; Mead AJ; Hultquist A; Swiers G; Perdiguero EG; Macaulay IC; Melchiori L; Luis TC; Kharazi S; Bouriez-Jones T; Deng Q; Ponten A; Atkinson D; Jensen CT; Sitnicka E; Geissmann F; Godin I; Sandberg R; de Bruijn MFTR; Jacobsen SEW
Article: ONCOGENE. 2013;32(41):4892-4902
Non-canonical Notch signaling activates IL-6/JAK/STAT signaling in breast tumor cells and is controlled by p53 and IKKα/IKKb
Jin S; Mutvei AP; Chivukula IV; Andersson ER; Ramskold D; Sandberg R; Lee KL; Kronqvist P; Mamaeva V; Ostling P; Mpindi J-P; Kallioniemi O; Screpanti I; Poellinger L; Sahlgren C; Lendahl U
Article: EXPERIMENTAL CELL RESEARCH. 2013;319(8):1187-1197
A reference transcriptome and inferred proteome for the salamander Notophthalmus viridescens
Abdullayev I; Kirkham M; Bjorklund AK; Simon A; Sandberg R
Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2013;110(18):7330-7335
SoxB1-driven transcriptional network underlies neural-specific interpretation of morphogen signals
Oosterveen T; Kurdija S; Enstero M; Uhde CW; Bergsland M; Sandberg M; Sandberg R; Muhr J; Ericson J
Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2013;110(6):2360-2365
Transcription factor Nurr1 maintains fiber integrity and nuclear-encoded mitochondrial gene expression in dopamine neurons
Kadkhodaei B; Alvarsson A; Schintu N; Ramskold D; Volakakis N; Joodmardi E; Yoshitake T; Kehr J; Decressac M; Bjorklund A; Sandberg R; Svenningsson P; Perlmann T
Article: PLOS ONE. 2013;8(1):e53822
Efficient and Comprehensive Representation of Uniqueness for Next-Generation Sequencing by Minimum Unique Length Analyses
Storvall H; Ramskold D; Sandberg R
Article: BMC GENOMICS. 2012;13:607
Abundance of female-biased and paucity of male-biased somatically expressed genes on the mouse X-chromosome
Reinius B; Johansson MM; Radomska KJ; Morrow EH; Pandey GK; Kanduri C; Sandberg R; Williams RW; Jazin E
Article: NATURE BIOTECHNOLOGY. 2012;30(8):777-782
Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells
Ramskold D; Luo S; Wang Y-C; Li R; Deng Q; Faridani OR; Daniels GA; Khrebtukova I; Loring JF; Laurent LC; Schroth GP; Sandberg R
Article: METHODS IN MOLECULAR BIOLOGY. 2012;802:259-274
How to analyze gene expression using RNA-sequencing data.
Ramsköld D; Kavak E; Sandberg R
Article: GENES & DEVELOPMENT. 2011;25(23):2453-2464
Sequentially acting Sox transcription factors in neural lineage development
Bergsland M; Ramskold D; Zaouter C; Klum S; Sandberg R; Muhr J
Article: NATURE. 2011;479(7371):74-U99
CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing
Shukla S; Kavak E; Gregory M; Imashimizu M; Shutinoski B; Kashlev M; Oberdoerffer P; Sandberg R; Oberdoerffer S
Article: CELL STEM CELL. 2011;8(6):663-675
Transcription Factor-Induced Lineage Selection of Stem-Cell-Derived Neural Progenitor Cells
Panman L; Andersson E; Alekseenko Z; Hedlund E; Kee N; Mong J; Uhde CW; Deng Q; Sandberg R; Stanton LW; Ericson J; Perlmann T
Article: PLOS COMPUTATIONAL BIOLOGY. 2009;5(12):e1000598
An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data
Ramskold D; Wang ET; Burge CB; Sandberg R
Article: NATURE. 2008;456(7221):470-476
Alternative isoform regulation in human tissue transcriptomes
Wang ET; Sandberg R; Luo S; Khrebtukova I; Zhang L; Mayr C; Kingsmore SF; Schroth GP; Burge CB
Article: SCIENCE. 2008;320(5883):1643-1647
Proliferating cells express mRNAs with shortened 3′ untranslated regions and fewer microRNA target sites
Sandberg R; Neilson JR; Sarma A; Sharp PA; Burge CB
Article: RNA: A PUBLICATION OF THE RNA SOCIETY. 2007;13(11):1894-1910
Determinants of targeting by endogenous and exogenous microRNAs and siRNAs
Nielsen CB; Shomron N; Sandberg R; Hornstein E; Kitzman J; Burge CB
Article: BMC BIOINFORMATICS. 2007;8:48
Improved precision and accuracy for microarrays using updated probe set definitions
Sandberg R; Larsson O
Article: OMICS A JOURNAL OF INTEGRATIVE BIOLOGY. 2006;10(3):381-397
Comparative microarray analysis
Larsson O; Wennmalm K; Sandberg R
Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2005;102(6):2052-2057
Assessment of tumor characteristic gene expression in cell lines using a tissue similarity index (TSI)
Sandberg R; Ernberg I
Article: GENOME BIOLOGY. 2005;6(8):R65
The molecular portrait of in vitro growth by meta-analysis of gene-expression profiles -: art. no. r65
Sandberg R; Ernberg I
Article: GENE. 2003;311:35-42
Quantifying the species-specificity in genomics signatures, synonymous codon choice, amino acid usage and G+C content
Sandberg R; Bränden CI; Ernberg I; Cöster J
Article: GENOME RESEARCH. 2001;11(8):1404-1409
Capturing whole-genome characteristics in short sequences using a naive Bayesian classifier
Sandberg R; Winberg G; Bränden CI; Kaske A; Ernberg I; Cöster J
Article: MICROBIOLOGY (UNITED KINGDOM). 2000;146:2665-2670
Antisense PNA effects in Escherichia coli are limited by the outer-membrane LPS layer
Good L; Sandberg R; Larsson O; Nielsen PE; Wahlestedt C
Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2000;97(20):11038-11043
Regional and strain-specific gene expression mapping in the adult mouse brain
Sandberg R; Yasuda R; Pankratz DG; Carter TA; Del Rio JA; Wodicka L; Mayford M; Lockhart DJ; Barlow C
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All other publications

Letter: CELL RESEARCH. 2023;33(11):883-886
Platelet and myeloid lineage biases of transplanted single perinatal mouse hematopoietic stem cells
Stralin KB; Carrelha J; Winroth A; Ziegenhain C; Hagemann-Jensen M; Kettyle LM; Hillen A; Hogstrand K; Markljung E; Grasso F; Seki M; Mazzi S; Meng Y; Wu B; Chari E; Lehander M; Sandberg R; Woll PS; Jacobsen SEW
Editorial comment: NATURE METHODS. 2022;19(5):530-531
Novel spike-ins for single-cell sequencing enable ground-truth RNA counting
Ziegenhain C; Sandberg R
Corrigendum: NATURE BIOTECHNOLOGY. 2020;38(3):374
Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells (vol 87, pg 123, 2012)
Ramskold D; Luo S; Wang Y-C; Li R; Deng Q; Faridani OR; Daniels GA; Khrebtukova I; Loring JF; Laurent LC; Schroth GP; Sandberg R
Corrigendum: NATURE COMMUNICATIONS. 2019;10(1):5075
Layer 4 of mouse neocortex differs in cell types and circuit organization between sensory areas (vol 10, 4174, 2019)
Scala F; Kobak D; Shan S; Bernaerts Y; Laturnus S; Cadwell CR; Hartmanis L; Froudarakis E; Castro JR; Tan ZH; Papadopoulos S; Patel SS; Sandberg R; Berens P; Jiang X; Tolias AS
Letter: NATURE GENETICS. 2018;50(9):1199-1200
Reply to 'High prevalence of clonal monoallelic expression'
Reinius B; Sandberg R
Letter: NATURE METHODS. 2018;15(5):305-307
Computational correction of index switching in multiplexed sequencing libraries
Larsson AJM; Stanley G; Sinha R; Weissman IL; Sandberg R
Editorial comment: BMC BIOLOGY. 2017;15(1):58
Q&A: using Patch-seq to profile single cells
Cadwell CR; Sandberg R; Jiang X; Tolias AS
Corrigendum: CELL. 2016;167(1):285
Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos (vol 165, pg 1012, 2016)
Petropoulos S; Edsgard D; Reinius B; Deng Q; Panula SP; Codeluppi S; Reyes AP; Linnarsson S; Sandberg R; Lanner F
Corrigendum: NATURE IMMUNOLOGY. 2016;17(6):740
The heterogeneity of human CD127⁺ innate lymphoid cells revealed by single-cell RNA sequencing (vol 17, pg 451, 2016)
Bjorklund AK; Forkel M; Picelli S; Konya V; Theorell J; Friberg D; Sandberg R; Mjosberg J
Editorial comment: OBSTETRICAL AND GYNECOLOGICAL SURVEY. 2016;71(1):29-30
Adult Human and Mouse Ovaries Lack DDX4-Expressing Functional Oogonial Stem Cells EDITORIAL COMMENT
Zhang H; Panula S; Petropoulos S; Edsgard D; Busayavalasa K; Liu L; Li X; Risal S; Shen Y; Shao J; Liu M; Li S; Zhang D; Zhang X; Gerner RR; Sheikhi M; Damdimopoulou P; Sandberg R; Douagi I; Gustafsson J-A; Liu L; Lanner F; Hovatta O; Liu K
Review: NATURE REVIEWS GENETICS. 2015;16(11):653-664
MODES OF TRANSCRIPTIONAL REGULATION Random monoallelic expression of autosomal genes: stochastic transcription and allele-level regulation
Reinius B; Sandberg R
Letter: NATURE MEDICINE. 2015;21(10):1116-1118
Adult human and mouse ovaries lack DDX4-expressing functional oogonial stem cells
Zhang H; Panula S; Petropoulos S; Edsgard D; Busayavalasa K; Liu L; Li X; Risal S; Shen Y; Shao J; Liu M; Li S; Zhang D; Zhang X; Gerner RR; Sheikhi M; Damdimopoulou P; Sandberg R; Douagi I; Gustafsson J-A; Liu L; Lanner F; Hovatta O; Liu K
Editorial comment: NATURE BIOTECHNOLOGY. 2015;33(5):490-491
Putting cells in their place
Faridani OR; Sandberg R
Corrigendum: CANCER CELL. 2015;27(4):603-605
Myelodysplastic Syndromes Are Propagated by Rare and Distinct Human Cancer Stem Cells In Vivo (vol 25, pg 794, 2014)
Woll PS; Kjaellquist U; Chowdhury O; Doolittle H; Wedge DC; Thongjuea S; Erlandsson R; Ngara M; Anderson K; Deng Q; Mead AJ; Stenson L; Giustacchini A; Duarte S; Giannoulatou E; Taylor S; Karimi M; Scharenberg C; Mortera-Blanco T; Macaulay IC; Clark S-A; Dybedal I; Josefsen D; Fenaux P; Hokland P; Holm MS; Cazzola M; Malcovati L; Tauro S; Bowen D; Boultwood J; Pellagatti A; Pimanda JE; Unnikrishnan A; Vyas P; Goehring G; Schlegelberger B; Tobiasson M; Kvalheim G; Constantinescu SN; Nerlov C; Nilsson L; Campbell PJ; Sandberg R; Papaemmanuil E; Hellstroem-Lindberg E; Linnarsson S; Jacobsen SEW
Review: DEVELOPMENT. 2011;138(17):3593-3612
Notch signaling: simplicity in design, versatility in function
Andersson ER; Sandberg R; Lendahl U
Review: EXPERIMENTAL CELL RESEARCH. 2010;316(8):1357-1364
Heterogeneity in mammalian RNA 3′ end formation
Neilson JR; Sandberg R
Letter: NATURE BIOTECHNOLOGY. 2006;24(11):1322-1323
Lack of correct data format and comparability limits future integrative microarray research
Larsson O; Sandberg R
Review: SEMINARS IN CANCER BIOLOGY. 2005;15(5):405-412
Gene expression perturbation in vitro - A growing case for three-dimensional (3D) culture systems
Birgersdotter A; Sandberg R; Ernberg I
Thesis / dissertation: 2004
Analyses of genomic and gene expression signatures
Sandberg, Rickard
Editorial comment: GENOME RESEARCH. 2003;13(11):2377-2380
Systems biology is taking off
Ehrenberg M; Elf J; Aurell E; Sandberg R; Tegnér J

Grants

Sandberg, Rickard – Large-scale identification of direct transcriptional effects of anti-cancer drugs
Swedish Cancer Society
1 January 2022
Understand gene regulation through massively parallel single-cell genomics
Swedish Research Council
1 January 2018 - 31 December 2027
Deciphering the building blocks of hippocampal circuits
National Institute of Mental Health
1 September 2017 - 30 June 2024
Elucidating the principles of allelic expression and regulation using single-cell genomics
Knut and Alice Wallenberg Foundation
1 January 2017 - 1 January 2022
Single-Cell Gene Regulation in Differentiation and Pluripotency
Swedish Research Council
1 January 2013 - 31 December 2017

Employments

Professor, Department of Cell and Molecular Biology, Karolinska Institutet, 2015-

Degrees and Education

Docent, Karolinska Institutet, 2013
Doctor Of Philosophy, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 2004
Licentiate Degree, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 2002
Master Of Medical Science, Karolinska Institutet, 2000

About me

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