Scalable single-cell RNA sequencing from full transcripts with Smart-seq3xpress
Michael Hagemann-Jensen, Christoph Ziegenhain & Rickard Sandberg
Nat Biotechnology (2022). https://doi.org/10.1038/s41587-022-01311-4
Molecular spikes: a gold standard for single-cell RNA counting
Christoph Ziegenhain , Gert-Jan Hendriks, Michael Hagemann-Jensen and Rickard Sandberg
Nature Methods (2022) https://doi.org/10.1038/s41592-022-01446-x
Transcriptional kinetics and molecular functions of long noncoding RNAs
Per Johnsson, Christoph Ziegenhain, Leonard Hartmanis, Gert-Jan Hendriks, Michael Hagemann-Jensen, Bjorn Reinius and Rickard Sandberg
Nature Genetics (2022). https://doi.org/10.1038/s41588-022-01014-1
BAMboozle removes genetic variation from human sequence data for open data sharing
Christoph Ziegenhain and Rickard Sandberg
Nature Communications 12, 6216 (2021).
Transcriptional bursts explain autosomal random monoallelic expression and affect allelic imbalance
Anton JM Larsson, Christoph Ziegenhain, Michael Hagemann-Jensen, Björn Reinius, Tina Jacob, Tim Dalessandri, Gert-Jan Hendriks, Maria Kasper, Rickard Sandberg
PLoS Computational Biology (2021) https://doi.org/10.1371/journal.pcbi.1008772
A DNA-nanoassembly-based approach to map membrane protein nanoenvironments
Elena Ambrosetti, Giulio Bernardinelli, Ian Hoffecker, Leonard Hartmanis, Georges Kiriako, Ario De Marco, Rickard Sandberg, Björn Högberg, Ana I Teixeira
Nature Nanotechnology 16, 85–95 (2021).
Phenotypic variation of transcriptomic cell types in mouse motor cortex
Federico Scala, Dmitry Kobak, Matteo Bernabucci, Yves Bernaerts, Cathryn René Cadwell, Jesus Ramon Castro, Leonard Hartmanis, Xiaolong Jiang, Sophie Laturnus, Elanine Miranda, Shalaka Mulherkar, Zheng Huan Tan, Zizhen Yao, Hongkui Zeng, Rickard Sandberg, Philipp Berens, Andreas S Tolias
Nature (2020). https://doi.org/10.1038/s41586-020-2907-3
Single-cell RNA counting at allele and isoform resolution using Smart-seq3
Michael Hagemann-Jensen, Christoph Ziegenhain, Ping Chen, Daniel Ramsköld, Gert-Jan Hendriks, Anton J. M. Larsson, Omid R. Faridani & Rickard Sandberg
Nature Biotechnology 2020. https://doi.org/10.1038/s41587-020-0497-0
Benchmarking single-cell RNA-sequencing protocols for cell atlas projects
Elisabetta Mereu, Atefeh Lafzi, Catia Moutinho, Christoph Ziegenhain, Davis J McCarthy, Adrián Álvarez-Varela, Eduard Batlle, Dominic Grün, Julia K Lau, Stéphane C Boutet, Chad Sanada, Aik Ooi, Robert C Jones, Kelly Kaihara, Chris Brampton, Yasha Talaga, Yohei Sasagawa, Kaori Tanaka, Tetsutaro Hayashi, Caroline Braeuning, Cornelius Fischer, Sascha Sauer, Timo Trefzer, Christian Conrad, Xian Adiconis, Lan T Nguyen, Aviv Regev, Joshua Z Levin, Swati Parekh, Aleksandar Janjic, Lucas E Wange, Johannes W Bagnoli, Wolfgang Enard, Marta Gut, Rickard Sandberg, Itoshi Nikaido, Ivo Gut, Oliver Stegle, Holger Heyn
Nature Biotechnology 2020. https://doi.org/10.1038/s41587-020-0469-4
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
eLife, 2020
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
Cell stem cell, 2020, 441-457.e7.
Cell shape determines gene expression: cardiomyocyte morphotypic transcriptomes
Haftbaradaran Esfahani, P; ElBeck, Z; Sagasser, S; Li, X; Hossain, MB; Talukdar, HA; Sandberg, R; Knöll, R
Basic research in cardiology, 2019, 7-.
Disruption of the Extracellular Matrix Progressively Impairs Central Nervous System Vascular Maturation Downstream of β-Catenin Signaling
Jensen, LD; Hot, B; Ramsköld, D; Germano, RFV; Yokota, C; Giatrellis, S; Lauschke, VM; Hubmacher, D; Li, MX; Hupe, M; Arnold, TD; Sandberg, R; Frisén, J; Trusohamn, M; Martowicz, A; Wisniewska-Kruk, J; Nyqvist, D; Adams, RH; Apte, SS; Vanhollebeke, B; Stenman, JM; Kele, J
Arteriosclerosis, thrombosis, and vascular biology, 2019, 1432-1447.
Genomic encoding of transcriptional burst kinetics
Larsson, AJM; Johnsson, P; Hagemann-Jensen, M; Hartmanis, L; Faridani, OR; Reinius, B; Segerstolpe, Å; Rivera, CM; Ren, B; Sandberg, R
Nature, 2019, 251-254.
Intussusceptive Vascular Remodeling Precedes Pathological Neovascularization
Ali, Z; Mukwaya, A; Biesemeier, A; Ntzouni, M; Ramsköld, D; Giatrellis, S; Mammadzada, P; Cao, R; Lennikov, A; Marass, M; Gerri, C; Hildesjö, 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; Jensen, LD
Arteriosclerosis, thrombosis, and vascular biology, 2019, 1402-1418.
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, XL; Tolias, AS
Nature Communications, 2019, 4174-.
NASC-seq monitors RNA synthesis in single cells
Hendriks, GJ; Jung, LA; Larsson, AJM; Lidschreiber, M; Andersson Forsman, O; Lidschreiber, K; Cramer, P; Sandberg, R
Nature communications, 2019, 3138-.
X-chromosome upregulation is driven by increased burst frequency
Larsson, AJM; Coucoravas, C; Sandberg, R; Reinius, B
Nature Structural & Molecular Biology, 2019, 963-969.
Computational correction of index switching in multiplexed sequencing libraries
Larsson, AJM; Stanley, G; Sinha, R; Weissman, IL; Sandberg, R
Nature methods, 2018, 305-307.
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; Björklund, ÅK; Wahlgren, M; Ankarklev, J; Sandberg, R
Experimental cell research, 2018, 130-138.
Identification of spatial expression trends in single-cell gene expression data
Edsgärd, D; Johnsson, P; Sandberg, R
Nature methods, 2018, 339-342.
Mouse Model of Alagille Syndrome and Mechanisms of Jagged1 Missense Mutations
Andersson, ER; Chivukula, IV; Hankeova, S; Sjöqvist, M; Tsoi, YL; Ramsköld, D; Masek, J; Elmansuri, A; Hoogendoorn, A; Vazquez, E; Storvall, H; Netušilová, J; Huch, M; Fischler, B; Ellis, E; Contreras, A; Nemeth, A; Chien, KC; Clevers, H; Sandberg, R; Bryja, V; Lendahl, U
Gastroenterology, 2018, 1080-1095.
Parental haplotype-specific single-cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells
Vértesy, Á; Arindrarto, W; Roost, MS; Reinius, B; Torrens-Juaneda, V; Bialecka, M; Moustakas, I; Ariyurek, Y; Kuijk, E; Mei, H; Sandberg, R; van Oudenaarden, A; Chuva de Sousa Lopes, SM
Nature communications, 2018, 1873-.
Reply to 'High prevalence of clonal monoallelic expression'
Reinius, B; Sandberg, R
Nature genetics, 2018, 1199-1200.
Small-seq for single-cell small-RNA sequencing
Hagemann-Jensen, M; Abdullayev, I; Sandberg, R; Faridani, OR
Nature protocols, 2018, 2407-2424.
A TRPV1-to-secretagogin regulatory axis controls pancreatic β-cell survival by modulating protein turnover
Malenczyk, K; Girach, F; Szodorai, E; Storm, P; Segerstolpe, Å; Tortoriello, G; Schnell, R; Mulder, J; Romanov, RA; Borók, E; Piscitelli, F; Di Marzo, V; Szabó, G; Sandberg, R; Kubicek, S; Lubec, G; Hökfelt, T; Wagner, L; Groop, L; Harkany, T
The EMBO journal, 2017, 2107-2125.
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
Nature protocols, 2017, 2531-2553.
Position- and Hippo signaling-dependent plasticity during lineage segregation in the early mouse embryo
Posfai, E; Petropoulos, S; de Barros, FRO; Schell, JP; Jurisica, I; Sandberg, R; Lanner, F; Rossant, J
eLife, 2017
Q&A: using Patch-seq to profile single cells
Cadwell, CR; Sandberg, R; Jiang, X; Tolias, AS
BMC biology, 2017, 58-.
Reading and editing the Pleurodeles waltl genome reveals novel features of tetrapod regeneration
Elewa, A; Wang, H; Talavera-López, 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
Nature communications, 2017, 2286-.
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; Björklund, ÅK; Gillberg, L; Joodmardi, E; Sandberg, R; Parmar, M; Perlmann, T
Cell stem cell, 2017, 29-40.
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, Å; Qian, H; Olsson-Strömberg, U; Mustjoki, S; Sandberg, R; Jacobsen, SEW; Mead, AJ
Nature medicine, 2017, 692-702.
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, JC; Liu, M; Li, SS; Zhang, DD; Zhang, XX; Gerner, RR; Sheikhi, M; Damdimopoulou, P; Sandberg, R; Douagi, I; Gustafsson, JA; Liu, L; Lanner, F; Hovatta, O; Liu, K
OBSTETRICAL & GYNECOLOGICAL SURVEY, 2016, 29-30.
Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA-seq
Reinius, B; Mold, JE; Ramsköld, D; Deng, Q; Johnsson, P; Michaëlsson, J; Frisén, J; Sandberg, R
Nature genetics, 2016, 1430-1435.
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*
Nature biotechnology, 2016, 199-203.
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; Böiers, C; Carrelha, J; Macaulay, IC; Patient, R; Geissmann, F; Nerlov, C; Sandberg, R; de Bruijn, MFTR; Blackburn, CC; Godin, I; Jacobsen, SEW
Nature immunology, 2016, 1424-1435.
Laser capture microscopy coupled with Smart-seq2 for precise spatial transcriptomic profiling
Nichterwitz, S; Chen, G; Aguila Benitez, J; Yilmaz, M; Storvall, H; Cao, M; Sandberg, R; Deng, Q; Hedlund, E
Nature communications, 2016, 12139-.
scphaser: haplotype inference using single-cell RNA-seq data
Edsgärd, D; Reinius, B; Sandberg, R
Bioinformatics (Oxford, England), 2016, 3038-40.
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
Genome research, 2016, 1342-1354.
Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos
Petropoulos, S; Edsgärd, D; Reinius, B; Deng, Q; Panula, SP; Codeluppi, S; Plaza Reyes, A; Linnarsson, S; Sandberg, R*; Lanner, F*
Cell, 2016, 1012-26.
Single-cell sequencing of the small-RNA transcriptome
Faridani, OR; Abdullayev, I; Hagemann-Jensen, M; Schell, JP; Lanner, F; Sandberg, R
Nature biotechnology, 2016, 1264-1266.
Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes
Segerstolpe, Å; Palasantza, A; Eliasson, P; Andersson, EM; Andréasson, AC; Sun, X; Picelli, S; Sabirsh, A; Clausen, M; Bjursell, MK; Smith, DM; Kasper, M; Ämmälä, C; Sandberg, R
Cell metabolism, 2016, 593-607.
The heterogeneity of human CD127(+) innate lymphoid cells revealed by single-cell RNA sequencing
Björklund, ÅK; Forkel, M; Picelli, S; Konya, V; Theorell, J; Friberg, D; Sandberg, R; Mjösberg, J
Nature immunology, 2016, 451-60.
Adult human and mouse ovaries lack DDX4-expressing functional oogonial stem cells
Zhang, H; Panula, S; Petropoulos, S; Edsgärd, 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, JÅ; Liu, L; Lanner, F; Hovatta, O; Liu, K
Nature medicine, 2015, 1116-8.
Decoding breast cancer tissue-stroma interactions using species-specific sequencing
Chivukula, IV; Ramsköld, D; Storvall, H; Anderberg, C; Jin, S; Mamaeva, V; Sahlgren, C; Pietras, K; Sandberg, R; Lendahl, U
Breast cancer research : BCR, 2015, 109-.
Genome-wide mapping of promoter-anchored interactions with close to single-enhancer resolution
Sahlén, P; Abdullayev, I; Ramsköld, D; Matskova, L; Rilakovic, N; Lötstedt, B; Albert, TJ; Lundeberg, J; Sandberg, R
Genome biology, 2015, 156-.
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; Dalén, M; Jitschin, R; Rodin, S; Corbascio, M; El Andaloussi, S; Wiklander, OP; Nordin, JZ; Skog, J; Romain, C; Koestler, T; Hellgren-Johansson, L; Schiller, P; Joachimsson, PO; Hägglund, H; Mattsson, M; Lehtiö, J; Faridani, OR; Sandberg, R; Korsgren, O; Krampera, M; Weiss, DJ; Grinnemo, KH; Le Blanc, K
Stem cells translational medicine, 2015, 1199-213.
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, WO
INTERNATIONAL JOURNAL OF CANCER, 2015, E230-41.
Putting cells in their place
Faridani, OR; Sandberg, R
Nature biotechnology, 2015, 490-1.
Random monoallelic expression of autosomal genes: stochastic transcription and allele-level regulation
Reinius, B; Sandberg, R
Nature reviews. Genetics, 2015, 653-64.
BMP signaling and its pSMAD1/5 target genes differentially regulate hair follicle stem cell lineages
Genander, M; Cook, PJ; Ramsköld, D; Keyes, BE; Mertz, AF; Sandberg, R; Fuchs, E
Cell stem cell, 2014, 619-33.
Entering the era of single-cell transcriptomics in biology and medicine
Sandberg, R
Nature Methods, 2014, 22-4.
Full-length RNA-seq from single cells using Smart-seq2
Picelli, S; Faridani, OR; Björklund, AK; Winberg, G; Sagasser, S; Sandberg, R
Nature protocols, 2014, 171-81.
Myelodysplastic syndromes are propagated by rare and distinct human cancer stem cells in vivo
Woll, PS; Kjällquist, 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, SA; 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; Göhring, G; Schlegelberger, B; Tobiasson, M; Kvalheim, G; Constantinescu, SN; Nerlov, C; Nilsson, L; Campbell, PJ; Sandberg, R; Papaemmanuil, E; Hellström-Lindberg, E; Linnarsson, S; Jacobsen, SE
Cancer cell, 2014, 794-808.
RNA helicase A is a downstream mediator of KIF1Bβ tumor-suppressor function in neuroblastoma
Chen, ZX; Wallis, K; Fell, SM; Sobrado, VR; Hemmer, MC; Ramsköld, D; Hellman, U; Sandberg, R; Kenchappa, RS; Martinson, T; Johnsen, JI; Kogner, P; Schlisio, S
Cancer discovery, 2014, 434-51.
Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells
Deng, Q; Ramsköld, D; Reinius, B; Sandberg, R
Science (New York, N.Y.), 2014, 193-6.
Tn5 transposase and tagmentation procedures for massively scaled sequencing projects
Picelli, S; Björklund, AK; Reinius, B; Sagasser, S; Winberg, G; Sandberg, R
Genome research, 2014, 2033-40.
A reference transcriptome and inferred proteome for the salamander Notophthalmus viridescens
Abdullayev, I; Kirkham, M; Björklund, ÅK; Simon, A; Sandberg, R
Experimental cell research, 2013, 1187-97.
Efficient and comprehensive representation of uniqueness for next-generation sequencing by minimum unique length analyses
Storvall, H; Ramsköld, D; Sandberg, R
PloS one, 2013, e53822-.
Lymphomyeloid contribution of an immune-restricted progenitor emerging prior to definitive hematopoietic stem cells
Böiers, C; Carrelha, J; Lutteropp, M; Luc, S; Green, JC; 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; Pontén, A; Atkinson, D; Jensen, CT; Sitnicka, E; Geissmann, F; Godin, I; Sandberg, R; de Bruijn, MF; Jacobsen, SE
Cell stem cell, 2013, 535-48.
Non-canonical Notch signaling activates IL-6/JAK/STAT signaling in breast tumor cells and is controlled by p53 and IKKα/IKKβ
Jin, S; Mutvei, AP; Chivukula, IV; Andersson, ER; Ramsköld, D; Sandberg, R; Lee, KL; Kronqvist, P; Mamaeva, V; Ostling, P; Mpindi, JP; Kallioniemi, O; Screpanti, I; Poellinger, L; Sahlgren, C; Lendahl, U
Oncogene, 2013, 4892-902.
Smart-seq2 for sensitive full-length transcriptome profiling in single cells
Picelli, S; Björklund, ÅK; Faridani, OR; Sagasser, S; Winberg, G; Sandberg, R
Nature methods, 2013, 1096-8.
SoxB1-driven transcriptional network underlies neural-specific interpretation of morphogen signals
Oosterveen, T; Kurdija, S; Ensterö, M; Uhde, CW; Bergsland, M; Sandberg, M; Sandberg, R; Muhr, J; Ericson, J
Proceedings of the National Academy of Sciences of the United States of America, 2013, 7330-5.
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
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 2013, 1367-76.
Transcription factor Nurr1 maintains fiber integrity and nuclear-encoded mitochondrial gene expression in dopamine neurons
Kadkhodaei, B; Alvarsson, A; Schintu, N; Ramsköld, D; Volakakis, N; Joodmardi, E; Yoshitake, T; Kehr, J; Decressac, M; Björklund, A; Sandberg, R; Svenningsson, P; Perlmann, T
Proceedings of the National Academy of Sciences of the United States of America, 2013, 2360-5.
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
BMC genomics, 2012, 607-.
Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells
Ramsköld, D; Luo, S; Wang, YC; Li, R; Deng, Q; Faridani, OR; Daniels, GA; Khrebtukova, I; Loring, JF; Laurent, LC; Schroth, GP; Sandberg, R
Nature biotechnology, 2012, 777-82.
How to analyze gene expression using RNA-sequencing data
Ramsköld, D; Kavak, E; Sandberg, R
Methods in molecular biology (Clifton, N.J.), 2012, 259-74.
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
Nature, 2011, 74-9.
Notch signaling: simplicity in design, versatility in function
Andersson, ER; Sandberg, R; Lendahl, U
Development, 2011, 3593-612.
Sequentially acting Sox transcription factors in neural lineage development
Bergsland, M; Ramskold, D; Zaouter, C; Klum, S; Sandberg, R; Muhr, J
Genes & Development, 2011, 2453-64.
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, QL; Sandberg, R; Stanton, LW; Ericson, J; Perlmann, T
Cell Stem Cell, 2011, 663-75.
Heterogeneity in mammalian RNA 3 ' end formation
Neilson, JR; Sandberg, R
Experimental Cell Research, 2010, 1357-64.
An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data
Ramskold, D; Wang, ET; Burge, CB; Sandberg, R
PLOS Computational Biology, 2009, e1000598-.
Alternative isoform regulation in human tissue transcriptomes
Wang, ET; Sandberg, R; Luo, SJ; Khrebtukova, I; Zhang, L; Mayr, C; Kingsmore, SF; Schroth, GP; Burge, CB
Nature, 2008, 470-6.
Proliferating cells express mRNAs with shortened 3 ' untranslated regions and fewer microRNA target sites
Sandberg, R; Neilson, JR; Sarma, A; Sharp, PA; Burge, CB
Science, 2008, 1643-7.
Determinants of targeting by endogenous and exogenous microRNAs and siRNAs
Nielsen, CB; Shomron, N; Sandberg, R; Hornstein, E; Kitzman, J; Burge, CB
RNA, 2007, 1894-910.
Improved precision and accuracy for microarrays using updated probe set definitions
Sandberg, R; Larsson, O
BMC Bioinformatics, 2007, 48-.
Comparative microarray analysis
Larsson, O; Wennmalm, K; Sandberg, R
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, 2006, 381-97.
Lack of correct data format and comparability limits future integrative microarray research
Larsson, O; Sandberg, R
Nature Biotechnology, 2006, 1322-3.
Assessment of tumor characteristic gene expression in cell lines using a tissue similarity index (TSI)
Sandberg, R; Ernberg, I
PNAS, 2005, 2052-7.
Gene expression perturbation in vitro - A growing case for three-dimensional (3D) culture systems
Birgersdotter, A; Sandberg, R; Ernberg, I
SEMINARS IN CANCER BIOLOGY, 2005, 405-12.
The molecular portrait of in vitro growth by meta-analysis of gene-expression profiles
Sandberg, R; Ernberg, I
Genome Biology, 2005, R65-.
Quantifying the species-specificity in genomics signatures, synonymous codon choice, amino acid usage and G+C content
Sandberg, R; Branden, CI; Ernberg, I; Coster, J
Gene, 2003, 35-42.
Systems biology is taking off
Ehrenberg, M; Elf, J; Aurell, E; Sandberg, R; Tegner, J
Genome Research, 2003, 2377-80.
Capturing whole-genome characteristics in short sequences using a naive Bayesian classifier
Sandberg, R; Winberg, G; Branden, CI; Kaske, A; Ernberg, I; Coster, J
Genome Research, 2001, 1404-9.
Antisense PNA effects in Escherichia coli are limited by the outer-membrane LPS layer
Good, L; Sandberg, R; Larsson, O; Nielsen, PE; Wahlestedt, C
Microbiology-SGM, 2000, 2665-2670.
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
PNAS, 2000, 11038-43.
© 2022 Sandberg lab at Karolinska Institutet, Stockholm, Sweden.