Publications 2011

191 publications

Cdc6 expression represses E-cadherin transcription and activates adjacent replication origins.
Sideridou M, Zakopoulou R, Evangelou K, ..., Moustakas A, Gorgoulis VG
J. Cell Biol. 195 (7) 1123-1140 [2011-12-26; online 2011-12-28]
Affiliated researcher
Multiple polymorphisms affect expression and function of the neuropeptide S receptor (NPSR1).
Anedda F, Zucchelli M, Schepis D, ..., Kere J, D'Amato M
PLoS ONE 6 (12) e29523 [2011-12-21; online 2011-12-21]
Affiliated researcher
Assessing recent smoking status by measuring exhaled carbon monoxide levels.
Sandberg A, Sköld CM, Grunewald J, Eklund A, Wheelock ÅM
PLoS ONE 6 (12) e28864 [2011-12-16; online 2011-12-16]
Affiliated researcher
A disposable and multifunctional capsule for easy operation of microfluidic elastomer systems
Thorslund S, Nguyen H, Läräng T, Barkefors I, Kreuger J
J. Micromech. Microeng. 21 (12) 127001 [2011-12-01; online 2011-11-24]
Affiliated researcher
The Conserved Foot Domain of RNA Pol II Associates with Proteins Involved in Transcriptional Initiation and/or Early Elongation
García-López MC, Pelechano V, Mirón-García MC, ..., Pérez-Ortín JE, Navarro F
Genetics 189 (4) 1235-1248 [2011-12-00; online 2011-09-27]
SciLifeLab Fellow Vicent Pelechano
Postpartum depressive symptoms and the BDNF Val66Met functional polymorphism: effect of season of delivery.
Comasco E, Sylvén SM, Papadopoulos FC, ..., Sundström-Poromaa I, Skalkidou A
Arch Womens Ment Health 14 (6) 453-463 [2011-12-00; online 2011-10-14]
Erika Comasco SciLifeLab Fellow
High nuclear RBM3 expression is associated with an improved prognosis in colorectal cancer.
Hjelm B, Brennan DJ, Zendehrokh N, ..., Jirström K, Uhlen M
Proteomics Clin Appl 5 (11-12) 624-635 [2011-12-00; online 2011-10-01]
Affiliated researcher
Autoregulation of the nonsense-mediated mRNA decay pathway in human cells.
Yepiskoposyan H, Aeschimann F, Nilsson D, Okoniewski M, Mühlemann O
RNA 17 (12) 2108-2118 [2011-12-00; online 2011-10-25]
Affiliated researcher
Counting absolute numbers of molecules using unique molecular identifiers.
Kivioja T, Vähärautio A, Karlsson K, ..., Linnarsson S, Taipale J
Nat. Methods 9 (1) 72-74 [2011-11-20; online 2011-11-20]
Affiliated researcher
Genome sequencing reveals a phage in Helicobacter pylori.
Lehours P, Vale FF, Bjursell MK, ..., Engstrand L, Andersson AF
MBio 2 (6) - [2011-11-15; online 2011-11-15]
Affiliated researcher
A lateral flow protein microarray for rapid and sensitive antibody assays.
Gantelius J, Bass T, Sjöberg R, Nilsson P, Andersson-Svahn H
Int J Mol Sci 12 (11) 7748-7759 [2011-11-09; online 2011-11-09]
Affiliated researcher
Archaic human ancestry in East Asia.
Skoglund P, Jakobsson M
Proc. Natl. Acad. Sci. U.S.A. 108 (45) 18301-18306 [2011-11-08; online 2011-10-31]
Affiliated researcher
Plasma profiling reveals human fibulin-1 as candidate marker for renal impairment.
Neiman M, Hedberg JJ, Dönnes PR, ..., Schwenk JM, Nilsson P
J. Proteome Res. 10 (11) 4925-4934 [2011-11-04; online 2011-09-29]
Affiliated researcher
Hypothalamic mitochondrial dysfunction associated with anorexia in the anx/anx mouse.
Lindfors C, Nilsson IA, Garcia-Roves PM, ..., Schalling M, Johansen JE
Proc. Natl. Acad. Sci. U.S.A. 108 (44) 18108-18113 [2011-11-01; online 2011-10-24]
Affiliated researcher
Western blotting via proximity ligation for high performance protein analysis.
Liu Y, Gu J, Hagner-McWhirter Å, ..., Ivansson D, Landegren U
Mol. Cell Proteomics 10 (11) O111.011031 [2011-11-00; online 2011-08-02]
Affiliated researcher
The Human Protein Atlas as a proteomic resource for biomarker discovery.
Pontén F, Schwenk JM, Asplund A, Edqvist PH
J. Intern. Med. 270 (5) 428-446 [2011-11-00; online 2011-08-03]
Affiliated researcher
Oncolytic viruses for the treatment of neuroendocrine tumors.
Essand M, Leja J, Giandomenico V, Oberg KE
Horm. Metab. Res. 43 (12) 877-883 [2011-11-00; online 2011-05-30]
Affiliated researcher
Ligand discovery from a dopamine D3 receptor homology model and crystal structure
Carlsson J, Coleman RG, Setola V, ..., Roth BL, Shoichet BK
Nat Chem Biol 7 (11) 769-778 [2011-11-00; online 2011-09-18]
Jens Carlsson SciLifeLab Fellow
Generation of monospecific antibodies based on affinity capture of polyclonal antibodies.
Hjelm B, Forsström B, Igel U, ..., Johansson C, Uhlén M
Protein Sci. 20 (11) 1824-1835 [2011-11-00; online 2011-10-12]
Affiliated researcher
Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity.
Rasmussen M, Sundström M, Göransson Kultima H, ..., Glimelius B, Isaksson A
Genome Biol. 12 (10) R108 [2011-10-24; online 2011-10-24]
Affiliated researcher
Increased throughput of proteomics analysis by multiplexing high-resolution tandem mass spectra.
Ledvina AR, Savitski MM, Zubarev AR, ..., Coon JJ, Zubarev RA
Anal. Chem. 83 (20) 7651-7656 [2011-10-15; online 2011-09-28]
Affiliated researcher
MED12, the mediator complex subunit 12 gene, is mutated at high frequency in uterine leiomyomas.
Mäkinen N, Mehine M, Tolvanen J, ..., Vahteristo P, Aaltonen LA
Science 334 (6053) 252-255 [2011-10-14; online 2011-08-25]
Affiliated researcher
A high-resolution map of human evolutionary constraint using 29 mammals.
Lindblad-Toh K, Garber M, Zuk O, ..., Lander ES, Kellis M
Nature 478 (7370) 476-482 [2011-10-12; online 2011-10-12]
Affiliated researcher
Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea.
Herlemann DP, Labrenz M, Jürgens K, ..., Waniek JJ, Andersson AF
ISME J 5 (10) 1571-1579 [2011-10-00; online 2011-04-07]
Affiliated researcher
Impact of CYP3A5*3 and CYP2C8-HapC on paclitaxel/carboplatin-induced myelosuppression in patients with ovarian cancer.
Gréen H, Khan MS, Jakobsen-Falk I, Åvall-Lundqvist E, Peterson C
J Pharm Sci 100 (10) 4205-4209 [2011-10-00; online 2011-06-23]
Affiliated researcher
Heme binding in gas-phase holo-myoglobin cations: distal becomes proximal?
Enyenihi AA, Yang H, Ytterberg AJ, Lyutvinskiy Y, Zubarev RA
J. Am. Soc. Mass Spectrom. 22 (10) 1763-1770 [2011-10-00; online 2011-07-19]
Affiliated researcher
Fibroblast growth factor 10 haploinsufficiency causes chronic obstructive pulmonary disease.
Klar J, Blomstrand P, Brunmark C, ..., Bergendal B, Dahl N
J. Med. Genet. 48 (10) 705-709 [2011-10-00; online 2011-07-08]
Affiliated researcher
Diffraction-unlimited all-optical imaging and writing with a photochromic GFP
Grotjohann T, Testa I, Leutenegger M, ..., Jakobs S, Hell SW
Nature 478 (7368) 204-208 [2011-10-00; online 2011-09-11]
Ilaria Testa SciLifeLab Fellow
ProteinSeq: high-performance proteomic analyses by proximity ligation and next generation sequencing.
Darmanis S, Nong RY, Vänelid J, ..., Kamali-Moghaddam M, Landegren U
PLoS ONE 6 (9) e25583 [2011-09-29; online 2011-09-29]
Affiliated researcher
Genomic determinants of protein evolution and polymorphism in Arabidopsis.
Slotte T, Bataillon T, Hansen TT, ..., Wright SI, Schierup MH
Genome Biol Evol 3 (-) 1210-1219 [2011-09-16; online 2011-09-16]
SciLifeLab Fellow Tanja Slotte
Molecular Characteristics of ERCC1-Negative versus ERCC1-Positive Tumors in Resected NSCLC.
Friboulet L, Barrios-Gonzales D, Commo F, ..., André F, Soria JC
Clin. Cancer Res. 17 (17) 5562-5572 [2011-09-01; online 2011-07-12]
Affiliated researcher
Inactivation of Pmel alters melanosome shape but has only a subtle effect on visible pigmentation.
Hellström AR, Watt B, Fard SS, ..., Marks MS, Andersson L
PLoS Genet 7 (9) e1002285 [2011-09-00; online 2011-09-15]
Affiliated researcher
Deciphering the rules governing assembly order of mammalian septin complexes
Sellin ME, Sandblad L, Stenmark S, Gullberg M
MBoC 22 (17) 3152-3164 [2011-09-00; online 2011-09-00]
Mikael Sellin SciLifeLab Fellow
The genome of the green anole lizard and a comparative analysis with birds and mammals.
Alföldi J, Di Palma F, Grabherr M, ..., Ponting CP, Lindblad-Toh K
Nature 477 (7366) 587-591 [2011-08-31; online 2011-08-31]
Affiliated researcher
Short-time repeat high-risk HPV testing by self-sampling for screening of cervical cancer.
Gyllensten U, Sanner K, Gustavsson I, ..., Wikström I, Wilander E
Br. J. Cancer 105 (5) 694-697 [2011-08-23; online 2011-08-02]
Affiliated researcher
Overexpression of podocalyxin-like protein is an independent factor of poor prognosis in colorectal cancer.
Larsson A, Johansson ME, Wangefjord S, ..., Uhlén M, Jirström K
Br. J. Cancer 105 (5) 666-672 [2011-08-23; online 2011-08-09]
Affiliated researcher
Three periods of regulatory innovation during vertebrate evolution.
Lowe CB, Kellis M, Siepel A, ..., Lindblad-Toh K, Haussler D
Science 333 (6045) 1019-1024 [2011-08-19; online 2011-08-20]
Affiliated researcher
Titration-free 454 sequencing using Y adapters.
Zheng Z, Advani A, Melefors Ö, ..., Engstrand L, Andersson AF
Nat Protoc 6 (9) 1367-1376 [2011-08-18; online 2011-08-18]
Affiliated researcher
Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.
International Multiple Sclerosis Genetics Consortium , Wellcome Trust Case Control Consortium 2 , Sawcer S, ..., Donnelly P, Compston A
Nature 476 (7359) 214-219 [2011-08-10; online 2011-08-10]
Affiliated researcher
Mapping the subcellular protein distribution in three human cell lines.
Fagerberg L, Stadler C, Skogs M, ..., Uhlén M, Lundberg E
J. Proteome Res. 10 (8) 3766-3777 [2011-08-05; online 2011-06-29]
Affiliated researcher
Domain architecture conservation in orthologs.
Forslund K, Pekkari I, Sonnhammer EL
BMC Bioinformatics 12 (-) 326 [2011-08-05; online 2011-08-05]
Affiliated researcher
Influence of the COMT genotype on working memory and brain activity changes during development.
Dumontheil I, Roggeman C, Ziermans T, ..., Kere J, Klingberg T
Biol. Psychiatry 70 (3) 222-229 [2011-08-01; online 2011-04-22]
Affiliated researcher
The short non-coding transcriptome of the protozoan parasite Trypanosoma cruzi.
Franzén O, Arner E, Ferella M, ..., Andersson B, Daub CO
PLoS Negl Trop Dis 5 (8) e1283 [2011-08-00; online 2011-08-30]
Affiliated researcher
A screening method for phosphohistidine phosphatase 1 activity.
Beckman-Sundh U, Ek B, Zetterqvist O, Ek P
Ups. J. Med. Sci. 116 (3) 161-168 [2011-08-00; online 2011-06-17]
Affiliated researcher
A genomic view of mRNA turnover in yeast
Pérez-Ortín JE, Jordán-Pla A, Pelechano V
Comptes Rendus Biologies 334 (8-9) 647-654 [2011-08-00; online 2011-08-00]
SciLifeLab Fellow Vicent Pelechano
FAAST: Flow-space Assisted Alignment Search Tool.
Lysholm F, Andersson B, Persson B
BMC Bioinformatics 12 (-) 293 [2011-07-19; online 2011-07-19]
Affiliated researcher
Scalable transcriptome preparation for massive parallel sequencing.
Stranneheim H, Werne B, Sherwood E, Lundeberg J
PLoS ONE 6 (7) e21910 [2011-07-07; online 2011-07-07]
Affiliated researcher
Thrombospondin-1: an islet endothelial cell signal of importance for β-cell function.
Olerud J, Mokhtari D, Johansson M, ..., Welsh N, Carlsson PO
Diabetes 60 (7) 1946-1954 [2011-07-00; online 2011-05-26]
Gustaf Christoffersson SciLifeLab Fellow
Sequence scrambling in shotgun proteomics is negligible.
Goloborodko AA, Gorshkov MV, Good DM, Zubarev RA
J. Am. Soc. Mass Spectrom. 22 (7) 1121-1124 [2011-07-00; online 2011-04-15]
Affiliated researcher
LGI2 truncation causes a remitting focal epilepsy in dogs.
Seppälä EH, Jokinen TS, Fukata M, ..., Minassian BA, Lohi H
PLoS Genet 7 (7) e1002194 [2011-07-00; online 2011-07-28]
Affiliated researcher
Isolated oligodontia associated with mutations in EDARADD, AXIN2, MSX1, and PAX9 genes.
Bergendal B, Klar J, Stecksén-Blicks C, Norderyd J, Dahl N
Am. J. Med. Genet. A 155A (7) 1616-1622 [2011-07-00; online 2011-05-27]
Affiliated researcher
Functional consequences of bidirectional promoters
Wei W, Pelechano V, Järvelin AI, Steinmetz LM
Trends in Genetics 27 (7) 267-276 [2011-07-00; online 2011-07-00]
SciLifeLab Fellow Vicent Pelechano
CoMet--a web server for comparative functional profiling of metagenomes.
Lingner T, Asshauer KP, Schreiber F, Meinicke P
Nucleic Acids Res. 39 (Web Server issue) W518-W523 [2011-07-00; online 2011-05-26]
Affiliated researcher
Genome wide association study identifies KCNMA1 contributing to human obesity.
Jiao H, Arner P, Hoffstedt J, ..., Clement K, Dahlman I
BMC Med Genomics 4 (-) 51 [2011-06-28; online 2011-06-28]
Affiliated researcher
The asthma candidate gene NPSR1 mediates isoform specific downstream signalling.
Pietras CO, Vendelin J, Anedda F, ..., Söderhäll C, Kere J
BMC Pulm Med 11 (-) 39 [2011-06-27; online 2011-06-27]
Affiliated researcher
Genetic variation near IRS1 associates with reduced adiposity and an impaired metabolic profile.
Kilpeläinen TO, Zillikens MC, Stančákova A, ..., Laakso M, Loos RJ
Nat. Genet. 43 (8) 753-760 [2011-06-26; online 2011-06-26]
Affiliated researcher
Mutations in Frizzled 6 cause isolated autosomal-recessive nail dysplasia.
Fröjmark AS, Schuster J, Sobol M, ..., Klar J, Dahl N
Am. J. Hum. Genet. 88 (6) 852-860 [2011-06-10; online 2011-06-15]
Affiliated researcher
Nanosilver on nanostructured silica: Antibacterial activity and Ag surface area.
Sotiriou GA, Teleki A, Camenzind A, ..., Panke S, Pratsinis SE
Chem Eng J 170 (2-3) 547-554 [2011-06-01; online 2011-06-01]
Alexandra Teleki SciLifeLab Fellow
Endolithic chlorophyll d-containing phototrophs.
Behrendt L, Larkum AW, Norman A, ..., Trampe E, Kühl M
ISME J 5 (6) 1072-1076 [2011-06-00; online 2010-12-16]
Lars Behrendt SciLifeLab Fellow
Association of the HLA-G gene +3142C>G polymorphism with systemic lupus erythematosus.
Consiglio CR, Veit TD, Monticielo OA, ..., Brenol JC, Chies JA
Tissue Antigens 77 (6) 540-545 [2011-06-00; online 2011-03-14]
Camila Consiglio DDLS Fellow
The zebrafish transcriptome during early development.
Vesterlund L, Jiao H, Unneberg P, Hovatta O, Kere J
BMC Dev. Biol. 11 (-) 30 [2011-05-24; online 2011-05-24]
Affiliated researcher
Multiple recognition assay reveals prostasomes as promising plasma biomarkers for prostate cancer.
Tavoosidana G, Ronquist G, Darmanis S, ..., Landegren UD, Kamali-Moghaddam M
Proc. Natl. Acad. Sci. U.S.A. 108 (21) 8809-8814 [2011-05-24; online 2011-05-09]
Affiliated researcher
Rapid screening of complex DNA samples by single-molecule amplification and sequencing.
Huang J, Zheng Z, Andersson AF, Engstrand L, Ye W
PLoS ONE 6 (5) e19723 [2011-05-19; online 2011-05-19]
Affiliated researcher
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Grabherr MG, Haas BJ, Yassour M, ..., Friedman N, Regev A
Nat. Biotechnol. 29 (7) 644-652 [2011-05-15; online 2011-05-15]
Affiliated researcher
Nitrogenase gene amplicons from global marine surface waters are dominated by genes of non-cyanobacteria.
Farnelid H, Andersson AF, Bertilsson S, ..., Hagström Å, Riemann L
PLoS ONE 6 (4) e19223 [2011-04-29; online 2011-04-29]
Affiliated researcher
Large scale library generation for high throughput sequencing.
Borgström E, Lundin S, Lundeberg J
PLoS ONE 6 (4) e19119 [2011-04-27; online 2011-04-27]
Affiliated researcher
Hybrid, silica-coated, Janus-like plasmonic-magnetic nanoparticles.
Sotiriou GA, Hirt AM, Lozach PY, ..., Krumeich F, Pratsinis SE
Chem Mater 23 (7) 1985-1992 [2011-04-12; online 2011-04-12]
Alexandra Teleki SciLifeLab Fellow
Systematic analysis of native membrane protein complexes in Escherichia coli.
Maddalo G, Stenberg-Bruzell F, Götzke H, ..., Ilag LL, Daley DO
J. Proteome Res. 10 (4) 1848-1859 [2011-04-01; online 2011-02-18]
Affiliated researcher
TIM23-mediated insertion of transmembrane α-helices into the mitochondrial inner membrane.
Botelho SC, Osterberg M, Reichert AS, ..., von Heijne G, Kim H
EMBO J. 30 (6) 1003-1011 [2011-03-16; online 2011-02-15]
Affiliated researcher
Decoding a substantial set of samples in parallel by massive sequencing.
Neiman M, Lundin S, Savolainen P, Ahmadian A
PLoS ONE 6 (3) e17785 [2011-03-09; online 2011-03-09]
Affiliated researcher
Ultra-deep sequencing of mouse mitochondrial DNA: mutational patterns and their origins.
Ameur A, Stewart JB, Freyer C, ..., Larsson NG, Gyllensten U
PLoS Genet 7 (3) e1002028 [2011-03-00; online 2011-03-24]
Affiliated researcher
Systematic antibody and antigen-based proteomic profiling with microarrays.
Ayoglu B, Häggmark A, Neiman M, ..., Schwenk JM, Nilsson P
Expert Rev. Mol. Diagn. 11 (2) 219-234 [2011-03-00; online 2011-03-17]
Affiliated researcher
CUBN is a gene locus for albuminuria.
Böger CA, Chen MH, Tin A, ..., Fox CS, Kao WH
J. Am. Soc. Nephrol. 22 (3) 555-570 [2011-03-00; online 2011-03-01]
Affiliated researcher
TGFbeta activates mitogen- and stress-activated protein kinase-1 (MSK1) to attenuate cell death.
van der Heide LP, van Dinther M, Moustakas A, ten Dijke P
J. Biol. Chem. 286 (7) 5003-5011 [2011-02-18; online 2010-11-24]
Affiliated researcher
Improved predictions by using multiple templates.
Larsson P, Skwark MJ, Wallner B, Elofsson A
Bioinformatics 27 (3) 426-427 [2011-02-01; online 2010-12-11]
Affiliated researcher
miR-182-mediated downregulation of BRCA1 impacts DNA repair and sensitivity to PARP inhibitors.
Moskwa P, Buffa FM, Pan Y, ..., Helleday T, Chowdhury D
Mol. Cell 41 (2) 210-220 [2011-01-21; online 2010-12-30]
Affiliated researcher
Contributions of the EMERALD project to assessing and improving microarray data quality.
Beisvåg V, Kauffmann A, Malone J, ..., Sandvik AK, Kuiper M
BioTechniques 50 (1) 27-31 [2011-01-00; online 2011-01-15]
Affiliated researcher

Publications 9.5.0