SciLifeLab Stockholm's Publications List

Sun-induced nonsynonymous p53 mutations are extensively accumulated and tolerated in normal appearing human skin.

2011-05-09T20:48:50Z

Here we demonstrate that intermittently sun-exposed human skin contains an extensive number of phenotypically intact cell compartments bearing missense and nonsense mutations in the p53 tumor suppressor gene. Deep sequencing of sun-exposed and shielded microdissected skin from mid-life individuals revealed that persistent p53 mutations had accumulated in 14% of all epidermal cells, with no apparen...

Patrik L Ståhl, Henrik Stranneheim, Anna Asplund, Lisa Berglund, Fredrik Pontén, Joakim Lundeberg (2011) J Invest Dermatol 131: 2 504-508

Improved predictions by Pcons.net using multiple templates.

2011-05-09T20:35:37Z

Multiple templates can often be used to build more accurate homology models than models built from a single template. Here we introduce PconsM, an automated protocol that uses multiple templates to build protein models. PconsM has been among the top-performing methods in the recent CASP experiments and consistently perform better than the single template models used in Pcons.net. In particular for...

Per Larsson, Marcin J Skwark, Björn Wallner, Arne Elofsson (2011) Bioinformatics 27: 3 426-427

Systematic antibody and antigen-based proteomic profiling with microarrays.

2011-05-09T20:51:21Z

Current approaches within affinity-based proteomics are driven both by the accessibility and availability of antigens and capture reagents, and by suitable multiplexed technologies onto which these are implemented. By combining planar microarrays and other multiparallel systems with sets of reagents, possibilities to discover new and unpredicted protein-disease associations, either via directed hy...

Burcu Ayoglu, Anna Häggmark, Maja Neiman, Ulrika Igel, Mathias Uhlén, Jochen M Schwenk, Peter Nilsson (2011) Expert Rev Mol Diagn 11: 2 219-234

Antibody suspension bead arrays.

2011-05-09T20:51:21Z

Alongside the increasing availability of affinity reagents, antibody microarrays have been developed to become a powerful tool to screen for target proteins in complex samples. Besides multiplexed sandwich immunoassays, the application of directly applying labeled sample onto arrays with immobilized capture reagents offers an approach to facilitate a systematic, high-throughput analysis of body fl...

Jochen M Schwenk, Peter Nilsson (2011) Methods Mol Biol 723: 29-36

Shotgun sequencing analysis of Trypanosoma cruzi I Sylvio X10/1 and comparison with T. cruzi VI CL Brener.

2011-05-09T20:35:37Z

Trypanosoma cruzi is the causative agent of Chagas disease, which affects more than 9 million people in Latin America. We have generated a draft genome sequence of the TcI strain Sylvio X10/1 and compared it to the TcVI reference strain CL Brener to identify lineage-specific features. We found virtually no differences in the core gene content of CL Brener and Sylvio X10/1 by presence/absence analy...

Oscar Franzén, Stephen Ochaya, Ellen Sherwood, Michael D Lewis, Martin S Llewellyn, Michael A Miles, Björn Andersson (2011) PLoS Negl Trop Dis 5: 3

Introduction into the analysis of high-throughput-sequencing based epigenome data.

2011-05-09T20:35:37Z

Sequencing-based approaches now allow high-resolution, genome-scale investigation of cellular epigenetic landscapes. For example, mapping of open chromatin regions, post-translational histone modifications and DNA methylation across a whole genome is now feasible, and new non-coding regulatory RNAs can be sensitively identified via RNA sequencing. The resulting large-scale data sets promise to con...

Mikael Huss (2010) Brief Bioinform 11: 5 512-523

Toward next generation plasma profiling via heat-induced epitope retrieval and array-based assays.

2011-05-09T20:35:37Z

There is a need for high throughput methods for screening patient samples in the quest for potential biomarkers for diagnostics and patient care. Here, we used a combination of undirected target selection, antibody suspension bead arrays, and heat-induced epitope retrieval to allow for protein profiling of human plasma in a novel and systematic manner. Several antibodies were found to reveal alter...

Jochen M Schwenk, Ulrika Igel, Maja Neiman, Hanno Langen, Charlotte Becker, Anders Bjartell, Fredrik Ponten, Fredrik Wiklund, Henrik Grönberg, Peter Nilsson, Mathias Uhlen (2010) Mol Cell Proteomics 9: 11 2497-2507

International network of cancer genome projects.

2011-05-09T20:42:30Z

The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover tr...

Thomas J Hudson, Warwick Anderson, Axel Artez, Anna D Barker, Cindy Bell, Rosa R Bernabé, M K Bhan, Fabien Calvo, Iiro Eerola, Daniela S Gerhard, Alan Guttmacher, Mark Guyer, Fiona M Hemsley, Jennifer L Jennings, David Kerr, Peter Klatt, Patrik Kolar, Jun Kusada, David P Lane, Frank Laplace, Lu Youyong, Gerd Nettekoven, Brad Ozenberger, Jane Peterson, T S Rao, Jacques Remacle, Alan J Schafer, Tatsuhiro Shibata, Michael R Stratton, Joseph G Vockley, Koichi Watanabe, Huanming Yang, Matthew M F Yuen, Bartha M Knoppers, Martin Bobrow, Anne Cambon-Thomsen, Lynn G Dressler, Stephanie O M Dyke, Yann Joly, Kazuto Kato, Karen L Kennedy, Pilar Nicolás, Michael J Parker, Emmanuelle Rial-Sebbag, Carlos M Romeo-Casabona, Kenna M Shaw, Susan Wallace, Georgia L Wiesner, Nikolajs Zeps, Peter Lichter, Andrew V Biankin, Christian Chabannon, Lynda Chin, Bruno Clément, Enrique de Alava, Françoise Degos, Martin L Ferguson, Peter Geary, D Neil Hayes, Amber L Johns, Arek Kasprzyk, Hidewaki Nakagawa, Robert Penny, Miguel A Piris, Rajiv Sarin, Aldo Scarpa, Marc van de Vijver, P Andrew Futreal, Hiroyuki Aburatani, Mónica Bayés, David D L Botwell, Peter J Campbell, Xavier Estivill, Sean M Grimmond, Ivo Gut, Martin Hirst, Carlos López-Otín, Partha Majumder, Marco Marra, John D McPherson, Zemin Ning, Xose S Puente, Yijun Ruan, Hendrik G Stunnenberg, Harold Swerdlow, Victor E Velculescu, Richard K Wilson, Hong H Xue, Liu Yang, Paul T Spellman, Gary D Bader, Paul C Boutros, Paul Flicek, Gad Getz, Roderic Guigó, Guangwu Guo, David Haussler, Simon Heath, Tim J Hubbard, Tao Jiang, Steven M Jones, Qibin Li, Nuria López-Bigas, Ruibang Luo, Lakshmi Muthuswamy, B F Francis Ouellette, John V Pearson, Victor Quesada, Benjamin J Raphael, Chris Sander, Terence P Speed, Lincoln D Stein, Joshua M Stuart, Jon W Teague, Yasushi Totoki, Tatsuhiko Tsunoda, Alfonso Valencia, David A Wheeler, Honglong Wu, Shancen Zhao, Guangyu Zhou, Mark Lathrop, Gilles Thomas, Teruhiko Yoshida, Myles Axton, Chris Gunter, Linda J Miller, Junjun Zhang, Syed A Haider, Jianxin Wang, Christina K Yung, Anthony Cross, Yong Liang, Saravanamuttu Gnaneshan, Jonathan Guberman, Jack Hsu, Don R C Chalmers, Karl W Hasel, Terry S H Kaan, William W Lowrance, Tohru Masui, Laura Lyman Rodriguez, Catherine Vergely, David D L Bowtell, Nicole Cloonan, Anna deFazio, James R Eshleman, Dariush Etemadmoghadam, Brooke A Gardiner, James G Kench, Robert L Sutherland, Margaret A Tempero, Nicola J Waddell, Peter J Wilson, Steve Gallinger, Ming-Sound Tsao, Patricia A Shaw, Gloria M Petersen, Debabrata Mukhopadhyay, Ronald A DePinho, Sarah Thayer, Kamran Shazand, Timothy Beck, Michelle Sam, Lee Timms, Vanessa Ballin, Youyong Lu, Jiafu Ji, Xiuqing Zhang, Feng Chen, Xueda Hu, Qi Yang, Geng Tian, Lianhai Zhang, Xiaofang Xing, Xianghong Li, Zhenggang Zhu, Yingyan Yu, Jun Yu, Jörg Tost, Paul Brennan, Ivana Holcatova, David Zaridze, Alvis Brazma, Lars Egevard, Egor Prokhortchouk, Rosamonde Elizabeth Banks, Mathias Uhlén, Juris Viksna, Fredrik Ponten, Konstantin Skryabin, Ewan Birney, Ake Borg, Anne-Lise Børresen-Dale, Carlos Caldas, John A Foekens, Sancha Martin, Jorge S Reis-Filho, Andrea L Richardson, Christos Sotiriou, Giles Thoms, Laura van't Veer, Daniel Birnbaum, Hélène Blanche, Pascal Boucher, Sandrine Boyault, Jocelyne D Masson-Jacquemier, Iris Pauporté, Xavier Pivot, Anne Vincent-Salomon, Eric Tabone, Charles Theillet, Isabelle Treilleux, Paulette Bioulac-Sage, Thomas Decaens, Dominique Franco, Marta Gut, Didier Samuel, Jessica Zucman-Rossi, Roland Eils, Benedikt Brors, Jan O Korbel, Andrey Korshunov, Pablo Landgraf, Hans Lehrach, Stefan Pfister, Bernhard Radlwimmer, Guido Reifenberger, Michael D Taylor, Christof von Kalle, Partha P Majumder, Paolo Pederzoli, Rita A Lawlor, Massimo Delledonne, Alberto Bardelli, Thomas Gress, David Klimstra, Giuseppe Zamboni, Yusuke Nakamura, Satoru Miyano, Akihiro Fujimoto, Elias Campo, Silvia de Sanjosé, Emili Montserrat, Marcos González-Díaz, Pedro Jares, Heinz Himmelbaue, Silvia Bea, Samuel Aparicio, Douglas F Easton, Francis S Collins, Carolyn C Compton, Eric S Lander, Wylie Burke, Anthony R Green, Stanley R Hamilton, Olli P Kallioniemi, Timothy J Ley, Edison T Liu, Brandon J Wainwright (2010) Nature 464: 7291 993-998

Control of membrane protein topology by a single C-terminal residue.

2011-05-09T20:47:00Z

The mechanism by which multispanning helix-bundle membrane proteins are inserted into their target membrane remains unclear. In both prokaryotic and eukaryotic cells, membrane proteins are inserted cotranslationally into the lipid bilayer. Positively charged residues flanking the transmembrane helices are important topological determinants, but it is not known whether they act strictly locally, af...

Susanna Seppälä, Joanna S Slusky, Pilar Lloris-Garcerá, Mikaela Rapp, Gunnar von Heijne (2010) Science 328: 5986 1698-1700

Defining the transcriptome and proteome in three functionally different human cell lines.

2011-05-09T20:58:58Z

An essential question in human biology is how cells and tissues differ in gene and protein expression and how these differences delineate specific biological function. Here, we have performed a global analysis of both mRNA and protein levels based on sequence-based transcriptome analysis (RNA-seq), SILAC-based mass spectrometry analysis and antibody-based confocal microscopy. The study was perform...

Emma Lundberg, Linn Fagerberg, Daniel Klevebring, Ivan Matic, Tamar Geiger, Juergen Cox, Cajsa Algenäs, Joakim Lundeberg, Matthias Mann, Mathias Uhlen (2010) Mol Syst Biol 6:

Classification of DNA sequences using Bloom filters.

2011-05-09T20:48:50Z

New generation sequencing technologies producing increasingly complex datasets demand new efficient and specialized sequence analysis algorithms. Often, it is only the 'novel' sequences in a complex dataset that are of interest and the superfluous sequences need to be removed.

Henrik Stranneheim, Max Käller, Tobias Allander, Björn Andersson, Lars Arvestad, Joakim Lundeberg (2010) Bioinformatics 26: 13 1595-1600

Analysis of transcript and protein overlap in a human osteosarcoma cell line.

2011-05-09T20:58:58Z

An interesting field of research in genomics and proteomics is to compare the overlap between the transcriptome and the proteome. Recently, the tools to analyse gene and protein expression on a whole-genome scale have been improved, including the availability of the new generation sequencing instruments and high-throughput antibody-based methods to analyze the presence and localization of proteins...

Daniel Klevebring, Linn Fagerberg, Emma Lundberg, Olof Emanuelsson, Mathias Uhlén, Joakim Lundeberg (2010) BMC Genomics 11:

Chk1 promotes replication fork progression by controlling replication initiation.

2011-05-09T20:45:37Z

DNA replication starts at initiation sites termed replication origins. Metazoan cells contain many more potential origins than are activated (fired) during each S phase. Origin activation is controlled by the ATR checkpoint kinase and its downstream effector kinase Chk1, which suppresses origin firing in response to replication blocks and during normal S phase by inhibiting the cyclin-dependent ki...

Eva Petermann, Mick Woodcock, Thomas Helleday (2010) Proc Natl Acad Sci U S A 107: 37 16090-16095

6-thioguanine selectively kills BRCA2-defective tumors and overcomes PARP inhibitor resistance.

2011-05-09T20:44:07Z

Familial breast and ovarian cancers are often defective in homologous recombination (HR) due to mutations in the BRCA1 or BRCA2 genes. Cisplatin chemotherapy or poly(ADP-ribose) polymerase (PARP) inhibitors were tested for these tumors in clinical trials. In a screen for novel drugs that selectively kill BRCA2-defective cells, we identified 6-thioguanine (6TG), which induces DNA double-strand brea...

Natalia Issaeva, Huw D Thomas, Tatjana Djureinovic, Tatjana Djurenovic, Janneke E Jaspers, Ivaylo Stoimenov, Suzanne Kyle, Nicholas Pedley, Ponnari Gottipati, Rafal Zur, Kate Sleeth, Vicky Chatzakos, Evan A Mulligan, Cecilia Lundin, Evgenia Gubanova, Ariena Kersbergen, Adrian L Harris, Ricky A Sharma, Sven Rottenberg, Nicola J Curtin, Thomas Helleday (2010) Cancer Res 70: 15 6268-6276