Page tree
Skip to end of metadata
Go to start of metadata

Contents



Official publication list in the SciLifeLab database

https://publications.scilifelab.se/label/Bioinformatics%20Long-term%20Support%20WABI
All service, collaborative and development projects.



Publications related to supported projects

2017

Genome-Based Sexing Provides Clues about Behavior and Social Structure in the Woolly Mammoth. Pečnerová P, Díez-del-Molino D, Dussex N, Feuerborn T, von Seth J, van der Plicht J, Nikolskiy P, Tikhonov A, Vartanyan S, Dalén L, Current Biology - (-) - [2017-11-00; online 2017-11-00] [Advisory program]

The Evolution of Dark Matter in the Mitogenome of Seed Beetles. Sayadi A,Immonen E, Tellgren-Roth C,Arnqvist G, (2017) Genome Biology and Evolution 9:2697–2706 https://doi.org/10.1093/gbe/evx205

TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data. Eisfeldt J, Vezzi F, Olason P, Nilsson D, Lindstrand A (2017) . F1000Research 2017, 6:664 (doi: 10.12688/f1000research.11168.2)

SweGen: A whole-genome data resource of genetic variability in a cross-section of the Swedish population. Ameur A, Dahlberg J, Olason P, Vezzi F, Karlsson R, Martin M, Viklund J, Kähäri A, Lundin P, Che H, Thutkawkorapin J, Eisfeldt J, Lampa S, Dahlberg M, Hagberg J, Jareborg N, Liljedahl U, Jonasson I, Johansson Å, Feuk L, Lundeberg J, Syvänen AC, Lundin S, Nilsson D, Nystedt B, Magnusson P, Gyllensten U (2017)  European Journal of Human Genetics, accepted

Spatially resolved transcriptome profiling in model plant species. Giacomello S, Salmén F, Terebieniec BK, Vickovic S, Navarro JF, Alexeyenko A, Reimegård J, McKee LS, Mannapperuma C, Bulone V, Ståhl PL, Sundström JF, Street NR, Lundeberg J. (2017) Nature Plants 3:17061. (Also featured in Nature Reviews Genetics.)

Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana, Reimegård J, Kundu S, Pendle A, Irish VF, Shaw P, Nakayama N, Sundström JF, Emanuelsson O. (2017) Nucleic Acids Res. 45:3253-3265.

Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandifloraSteige KA, Laenen B, Reimegård J, Scofield DG, Slotte T. (2017) Proceedings of the National Academy of Sciences USA 114:1087-1092.

Identification of endoribonuclease specific cleavage positions reveals novel targets of RNase III in Streptococcus pyogenesLe Rhun A, Lécrivain AL, Reimegård J, Proux-Wéra E, Broglia L, Della Beffa C, Charpentier E. (2017) Nucleic Acids Research 45:2329-2340.

Massive parallel sequencing questions the pathogenic role of missense variants in dilated cardiomyopathy. Dalin M, Engström PG, Ivarsson EG, Unneberg P, Light S, Schaufelberger M, Giljam T, Andersson B, Bergö MO (2017) International Journal of Cardiology 228:742-748. 

Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialisZhu Y*, Engström PG*, Tellgren-Roth C, Baudo CD, Kennell JC, Sun S, Billmyre RB, Schröder MS, Andersson A, Holm T, Sigurgeirsson B, Wu G, Sankaranarayanan SR, Siddharthan R, Sanyal K, Lundeberg J, Nystedt B, Boekhout T, Dawson TL Jr, Heitman J, Scheynius A§, Lehtiö J§ (2017) Nucleic Acids Research 45:2629-2643.

Single-Cell Analysis Reveals a Close Relationship between Differentiating Dopamine and Subthalamic Nucleus Neuronal Lineages.  Kee N, Volakaki N, Kirkeby A, Dahl L, Storvall H, Nolbrant S, Lahti L, Björklund ÅK, Gillberg L, Joodmardi E, Sandberg R, Parmar M, Perlmann T. (2017) Cell Stem Cell 20:29-40.

2016

A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them. Humble E, Martinez-Barrio A, Forcada J, Trathan PN, Thorne MA, Hoffmann M, Wolf JB, Hoffman JI. (2016) Molecular Ecology Resources. 16:909-921.

Cloche is a bHLH-PAS transcription factor that drives haemato-vascular specification. Reischauer S, Stone OA, Villasenor A, Chi N, Jin SW, Martin M, Lee MT, Fukuda N, Marass M, Witty A, Fiddes I, Kuo T, Chung WS, Salek S, Lerrigo R, Alsiö J, Luo S, Tworus D, Augustine SM, Mucenieks S, Nystedt B, Giraldez AJ, Schroth GP, Andersson O, Stainier DY. (2016) Nature 535:294-298.

Deep targeted sequencing in pediatric acute lymphoblastic leukemia unveils distinct mutational patterns between genetic subtypes and novel relapse-associated genes. Lindqvist CM, Lundmark A, Nordlund J, Freyhult E, Ekman D, Almlöf JC, Raine A, Övernäs E, Abrahamsson J, Frost BM, Grandér D, Heyman M, Palle J, Forestier E, Lönnerholm G, Berglund EC, Syvänen AC. (2016) Oncotarget 7:64071-64088.

Distinct transcription factor complexes act on a permissive chromatin landscape to establish regionalized gene expression in CNS stem cells. Hagey D, Zaouter C, Combeau G, Andersson Lendahl M, Andersson O, Huss M, Muhr J. (2016) Genome Research 26:908-917

Evolutionary history of host use, rather than plant phylogeny, determines gene expression in a generalist butterfly. Celorio-Mancera de la Paz M, Wheat CW, Huss M, Vezzi F, Neethiraj R, Reimegård J, Nylin S, Janz N. (2016) BMC Evolutionary Biology 16:59.

Identification of Shared and Unique Serum Lipid Profiles in Diabetes Mellitus and Myocardial Infarction. Kjellqvist S, Klose C, Surma MA, Hindy G, Mollet IG, Johansson A, Chavaux P, Gottfries J, Simons K, Melander O, Fernandez C. (2016) Journal of the American Heart Assocication 5:e004503.

Massive and parallel expression profiling using microarrayed single-cell sequencing. Vickovic S, Ståhl PL, Salmén F, Giatrellis S, Westholm JO, Mollbrink A, Navarro JF, Custodio J, Bienko M, Sutton LA, Rosenquist R, Frisén J, Lundeberg J. (2016) Nature Communications 7:13182.

Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity. Corcoran MM, Phad GE, Bernat NV, Stahl-Hennig C, Sumida N, Persson MA, Martin M, Karlsson Hedestam GB. (2016) Nature Communications 7:13642.

RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes. Le Rhun A, Beer YY, Reimegård J, Chylinski K, Charpentier E. (2016) RNA Biology 13:177-95.

SweGen: A whole-genome map of genetic variability in a cross-section of the Swedish population. Ameur A, Dahlberg J, Olason P, Vezzi F, Karlsson R, Lundin P, Che H, Thutkawkorapin J, Kahari A, Dahlberg M, Viklund J, Hagberg J, Jareborg N, Jonasson I, Johansson Å, Lundin S, Nilsson D, Nystedt B, Magnusson P, Gyllensten U (2016) bioRxiv 081505.

The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing. Martinez Barrio A, Lamichhaney S, Fan G, Rafati N, Pettersson M, Zhang H, Dainat J, Ekman D, Höppner M, Jern P, Martin MNystedt B, Liu X, Chen W, Liang X, Shi C, Fu Y, Ma K, Zhan X, Feng C, Gustafson U, Rubin CJ, Sällman Almén M, Blass M, Casini M, Folkvord A, Laikre L, Ryman N, Ming-Yuen Lee S, Xu X, Andersson L. (2016) eLife 5:e12081.

The Impact of Endurance Training on Human Skeletal Muscle Memory, Global Isoform Expression and Novel Transcripts. Lindholm ME*, Giacomello S*, Werne Solnestam B, Fischer H, Huss M, Kjellqvist S§, Sundberg CJ§. (2016) PLoS Genetics 12:e1006294.

The role of germline alterations in the DNA damage response genes BRIP1 and BRCA2 in melanoma susceptibility. Tuominen R, Engström PG, Helgadottir H, Eriksson H, Unneberg PKjellqvist S, Yang M, Lindén D, Edsgärd D, Hansson J, Höiom V. (2016) Genes, Chromosomes and Cancer 55:601-611.

The role of transposable elements for gene expression in Capsella hybrids and allopolyploids. Reimegård J

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Ståhl P, Salmén F, Vickovic S, Lundmark A, Fernández Navarro J, Magnusson J, Giacomello S, Asp M, Westholm J, Huss M, Mollbrink A, Linnarsson S, Codeluppi S, Borg Å, Pontén F, Costea P, Sahlén P, Mulder J, Bargmann O, Lundeberg J, Frisén J. (2016) Science 353:78-82.

2015

Cis-regulatory changes associated with a recent mating system shift and floral adaptation in Capsella. Steige KA, Reimegård J, Koenig D, Scofield DG, Slotte T. (2015)  Molecular Biology and Evolution 32:2501-2514.

Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers. Burri R, Nater A, Kawakami T, Mugal CF, Olason PI, Smeds L, Suh A, Dutoit L, Bureš S, Garamszegi LZ, Hogner S, Moreno J, Qvarnström A, Ružić M, Sæther SA, Sætre GP, Török J, Ellegren H. (2015) Genome Research 25:1656-1665.

The human cardiac and skeletal muscle proteomes defined by transcriptomics and antibody-based profiling. Lindskog C, Linné J, Fagerberg L, Hallström BM, Sundberg CJ, Lindholm M, Huss M, Kampf C, Choi H, Liem DA, Ping P, Väremo L, Mardinoglu A, Nielsen J, Larsson E, Pontén F, Uhlén M. (2015) BMC Genomics 16:475.

The human gut microbiome as a transporter of antibiotic resistance genes between continents. Bengtsson-Palme J, Angelin M, Huss MKjellqvist S, Kristiansson E, Palmgren H, Larsson DG, Johansson A. (2015) Antimicrob Agents and Chemotherapy 59:6551-6560.

The Mutational Landscape in Pediatric Acute Lymphoblastic Leukemia Deciphered by Whole Genome Sequencing. Lindqvist CM, Nordlund J, Ekman D, Johansson A, Moghadam BT, Raine A, Overnäs E, Dahlberg J, Wahlberg P, Henriksson N, Abrahamsson J, Frost BM, Grandér D, Heyman M, Larsson R, Palle J, Söderhäll S, Forestier E, Lönnerholm G, Syvänen AC, Berglund EC. (2015) Human Mutation 36:118-28.

2014

The genomic landscape underlying phenotypic integrity in the face of gene flow in crows. Poelstra JW, Vijay N, Bossu CM, Lantz H, Ryll B, Müller I, Baglione V, Unneberg P, Wikelski M, Grabherr MG, Wolf JB. (2014) Science 344:1410-4.

The human skeletal muscle transcriptome: sex differences, alternative splicing, and tissue homogeneity assessed with RNA sequencing. Lindholm ME, Huss M, Solnestam BW, Kjellqvist S, Lundeberg J, Sundberg CJ. (2014) The FASEB Journal 28:4571-4581.



Publications related to method development and knowledge building outside of supported projects

2016

WhatsHap: fast and accurate read-based phasing. Martin M, Patterson M, Garg S, Fischer SO, Pisanti N, Klau GW, Schoenhuth A, Marschall T. (2016) bioRxiv 085050.

Read-Based Phasing of Related Individuals. Garg S, Martin M, Marschall T. (2016) Bioinformatics 32: i234-i242.

Computational Pan-Genomics: Status, Promises and Challenges. The Computational Pan-Genomics Consortium. (2016) Briefings in Bioinformatics, advance online publication.

2015

Assessing the consistency of public human tissue RNA-seq data sets. Danielsson F, James T, Gomez-Cabrero D, Huss M. (2015) Briefings in Bioinformatics 16:941-949.

 

Publications related to old projects, but with SciLifeLab affiliation

2017

Neuropilin-1 Is Expressed on Lymphoid Tissue Residing LTi-like Group 3 Innate Lymphoid Cells and Associated with Ectopic Lymphoid AggregatesMedya Mara Shikhagaie, Åsa K Björklund, Jenny Mjösberg, Jonas S Erjefält, Anne S Cornelissen, Xavier Romero Ros, Suzanne M Bal, Jasper J Koning, Reina E Mebius, Michiko Mori, Melanie Bruchard, Bianca Blom, Hergen Spits. Cell Reports 18 (7), 1761-1773

Genome-wide identification of Grainy head targets in Drosophila reveals regulatory interactions with the POU-domain transcription factor, Vvl
Yao L, Wang S, Westholm JO, Dai Q, Matsuda R, Hosono C, Bray S, Lai EC, Samakovlis C. Development 144(17):3145-3155, 2017.

Fast and general tests of genetic interaction for genome-wide association studies. Mattias Frånberg, Rona J Strawbridge, Anders Hamsten, PROCARDIS Consortium, Ulf De Faire, Jens Lagergren, and Bengt Sennblad. PLoS Comp Biol, 2017 vol. 13 (6) p. e1005556.

Genome-wide association study with additional genetic and post-transcriptional analyses reveals novel regulators of plasma factor XI levels. Bengt Sennblad, Saonli Basu, Johanna Mazur, Pierre Suchon, Angel Martinez-Perez, Astrid van Hylckama Vlieg, Vinh Truong, Yuhuang Li, Jesper R Gådin, Weihong Tang, Vera Grossman, Hugoline G de Haan, Niklas Handin, Angela Silveira, Juan Carlos Souto, Anders Franco-Cereceda, Pierre-Emmanuel Morange, France Gagnon, José Manuel Soria, Per Eriksson, Anders Hamsten, Lars Maegdefessel, Frits R Rosendaal, Philipp Wild, Aaron R Folsom, David-Alexandre Trégouët, and Maria Sabater-Lleal. Human Molecular Genetics, 2017.

Impact of common genetic determinants of Hemoglobin A1c on type 2 diabetes risk and diagnosis in ancestrally diverse populations: A transethnic genome-wide meta-analysis. Eleanor Wheeler, Aaron Leong, Ching-Ti Liu, Marie-France Hivert, Rona J Strawbridge, Clara Podmore, Man Li, Jie Yao, Xueling Sim, Jaeyoung Hong, Audrey Y Chu, Weihua Zhang, Xu wang, Peng Chen, Nisa M Maruthur, Bianca C Porneala, Stephen J Sharp, Yucheng Jia, Edmond K Kabagambe, li-Ching Chang, Wei-Min Chen, Cathy E Elks, Daniel S Evans, Qiao Fan, Franco Giulianini, Min Jin Go, Jouke-Jan Hottenga, Yao Hu, Anne U Jackson, Stavroula Kanoni, Young Jin kim, Marcus E Kleber, Claes Ladenvall, Cecile Lecoeur, Sing-Hui Lim, Yingchang Lu, Anubha Mahajan, Carola Marzi, Mike A Nalls, Pau Navarro, Ilja M Nolte, Lynda M Rose, Denis V Rybin, Serena Sanna, Yuan Shi, Daniel O Stram, Fumihiko Takeuchi, Shu Pei Tan, Peter J van der Most, Jana V Van Vliet-Ostaptchouk, Andrew Wong, Loic Yengo, Wanting Zhao, Anuj Goel, María Teresa Martínez-Larrad, Dörte Radke, Perttu Salo, Toshiko Tanaka, Erik P A van Iperen, Goncalo Abecasis, Saima Afaq, Behrooz Z Alizadeh, Alain G Bertoni, Amelie Bonnefond, Yvonne Böttcher, Erwin P Bottinger, Harry Campbell, Olga D Carlson, Chien-Hsiun Chen, Yoon Shin Cho, W Timothy Garvey, Christian Gieger, Mark O Goodarzi, Harald Grallert, Anders Hamsten, Catharina A Hartman, Christian Herder, Chao Agnes Hsiung, Jie Huang, Michiya Igase, Masato Isono, Tomohiro Katsuya, Chiea-Chuen Khor, Wieland Kiess, Katsuhiko Kohara, Peter Kovacs, Juyoung Lee, Wen-Jane Lee, Benjamin Lehne, Huaixing Li, Jianjun Liu, Stéphane Lobbens, Jian'an Luan, Valeriya Lyssenko, Thomas Meitinger, Tetsuro Miki, Iva Miljkovic, Sanghoon Moon, Antonella Mulas, Gabriele Müller, Martina Müller-Nurasyid, Ramaiah Nagaraja, Matthias Nauck, James S Pankow, Ozren Polasek, Inga Prokopenko, Paula S Ramos, Laura Rasmussen-Torvik, Wolfgang Rathmann, Stephen S Rich, Neil R Robertson, Michael Roden, Ronan Roussel, Igor Rudan, Robert A Scott, William R Scott, Bengt Sennblad, David S Siscovick, Konstantin Strauch, Liang Sun, Morris Swertz, Salman M Tajuddin, Kent D Taylor, Yik Ying Teo, Yih Chung Tham, Anke Tönjes, Nicholas J Wareham, Gonneke Willemsen, Tom Wilsgaard, Aroon D Hingorani, EPIC-CVD Consortium, EPIC-InterAct Consortium, LifeLines Cohort Study, Josephine Egan, Luigi Ferrucci, G Kees Hovingh, Antti Jula, Mika Kivimaki, Meena Kumari, Inger Njølstad, Colin N A Palmer, Manuel Serrano-Ríos, Michael Stumvoll, Hugh Watkins, Tin Aung, Matthias Blüher, Michael Boehnke, Dorret I Boomsma, Stefan R Bornstein, John C Chambers, Daniel I Chasman, Yii-Der Ida Chen, Yduan-Tsong Chen, Ching-Yu Cheng, Francesco Cucca, Eco J C de Geus, Panos Deloukas, Michele K Evans, Myriam Fornage, Yechiel Friedlander, Philippe Froguel, Leif Groop, Myron D Gross, Tamara B Harris, Caroline Hayward, Chew-Kiat Heng, Erik Ingelsson, Norihiro kato, Bong-Jo Kim, Woon-Puay Koh, Jaspal S Kooner, Antje Körner, Diana Kuh, Johanna Kuusisto, Markku Laakso, Xu Lin, Yongmei Liu, Ruth J F Loos, Patrik K E Magnusson, Winfried März, Mark I McCarthy, Albertine J Oldehinkel, Ken K Ong, Nancy L Pedersen, Mark A Pereira, Annette Peters, Paul M Ridker, Charumathi Sabanayagam, Michele Sale, Danish Saleheen, Juha Saltevo, Peter EH Schwarz, Wayne H-H Sheu, Harold Snieder, Timothy D Spector, Yasuharu Tabara, Jaakko Tuomilehto, Rob M van Dam, James G Wilson, James F Wilson, Bruce H R Wolffenbuttel, Tien Yin Wong, Jer-Yuarn Wu, Jian-Min Yuan, Alan B Zonderman, Nicole Soranzo, Xiuqing Guo, David J Roberts, Jose C Florez, Robert Sladek, Josée Dupuis, Andrew P Morris, E Shyong Tai, Elizabeth Selvin, Jerome I Rotter, Claudia Langenberg, Inês Barroso, and James B Meigs. PLoS Med, 2017 vol. 14 (9) p. e1002383.

Integrative Studies Implicate Matrix Metalloproteinase 12 as a Culprit Gene for Large-Artery Atherosclerotic Stroke. Hovsep Mahdessian, Ljubica Perisic Matic, Mariette Lengquist, Karl Gertow, Bengt Sennblad, Damiano Baldassarre, Fabrizio Veglia, Steve E Humphries, Rainer Rauramaa, Ulf De Faire, Andries J Smit, Philippe Giral, Sudhir Kurl, Elmo Mannarino, Elena Tremoli, Anders Hamsten, Per Eriksson, Ulf Hedin, Anders Malarstig, and IMPROVE study group. J Intern Med, 2017.


An Expanded Genome-Wide Association Study of Type 2 Diabetes in Europeans. Robert A Scott, Laura J Scott, Reedik Mägi, Letizia Marullo, Kyle J Gaulton, Marika Kaakinen, Natalia Pervjakova, Tune H Pers, Andrew D. Johnson, John D Eicher, Anne U Jackson, Teresa Ferreira, Yeji Lee, Clement Ma, Valgerdur Steinthorsdottir, Gudmar Thorleifsson, Lu Qi, Natalie R van Zuydam, Anubha Mahajan, Han Chen, Peter Almgren, Ben F Voight, Harald Grallert, Martina Müller-Nurasyid, Janina S Ried, William N Rayner, Neil Robertson, Lennart C Karssen, Elisabeth M van Leeuwen, Sara M Willems, Christian Fuchsberger, Phoenix Kwan, Tanya M Teslovich, Pritam Chanda, Man Li, Yingchang Lu, Christian Dina, Dorothee Thuillier, Loic Yengo, Longda Jiang, Thomas Sparso, Hans A Kestler, Himanshu Chheda, Lewin Eisele, Stefan Gustafsson, Mattias Frånberg, Rona J Strawbridge, Rafn Benediktsson, Astradur B Hreidarsson, Augustine Kong, Gunnar Sigurðsson, Nicola D Kerrison, Jian'an Luan, Liming Liang, Thomas Meitinger, Michael Roden, Barbara Thorand, Tõnu Esko, Evelin Mihailov, Caroline Fox, Ching-Ti Liu, Denis Rybin, Bo Isomaa, Valeriya Lyssenko, Tiinamaija Tuomi, David J Couper, James S Pankow, Niels Grarup, Christian T Have, Marit E Jorgensen, Torben Jørgensen, Allan Linneberg, Marilyn C. Cornelis, Rob M van Dam, David J. Hunter, Peter Kraft, Qi Sun, Sarah Edkins, Katharine R Owen, John RB Perry, Andrew R Wood, Eleftheria Zeggini, Juan Tajes-Fernandes, Gonçalo R Abecasis, Lori L Bonnycastle, Peter S Chines, Heather M Stringham, Heikki A Koistinen, Leena Kinnunen, Bengt Sennblad, Thomas W Mühleisen, Markus M Nöthen, Sonali Pechlivanis, Damiano Baldassarre, Karl Gertow, Steve E Humphries, Elena Tremoli, Norman Klopp, Julia Meyer, Gerald Steinbach, Roman Wennauer, Johan G Eriksson, Satu Mаnnisto, Leena Peltonen, Emmi Tikkanen, Guillaume Charpentier, Elodie Eury, Stéphane Lobbens, Bruna Gigante, Karin Leander, Olga McLeod, Erwin P Bottinger, Omri Gottesman, Douglas Ruderfer, Matthias Blüher, Peter Kovacs, Anke Tönjes, Nisa M Maruthur, Chiara Scapoli, Raimund Erbel, Karl-Heinz Jöckel, Susanne Moebus, Ulf De Faire, Anders Hamsten, Michael Stumvoll, Panagiotis Deloukas, Peter J Donnelly, Timothy M Frayling, Andrew T Hattersley, Samuli Ripatti, Veikko Salomaa, Nancy L Pedersen, Bernhard O Boehm, Richard N Bergman, Francis S Collins, Karen L Mohlke, Jaakko Tuomilehto, Torben Hansen, Oluf Pedersen, Inês Barroso, Lars Lannfelt, Erik Ingelsson, Lars Lind, Cecilia M Lindgren, Stephane Cauchi, Philippe Froguel, Ruth Jf Loos, Beverley Balkau, Heiner Boeing, Paul W Franks, Aurelio Barricarte Gurrea, Domenico Palli, Yvonne T van der Schouw, David Altshuler, Leif C Groop, Claudia Langenberg, Nicholas J Wareham, Eric Sijbrands, Cornelia M Van Duijn, Jose C Florez, James B Meigs, Eric Boerwinkle, Christian Gieger, Konstantin Strauch, Andres Metspalu, Andrew D Morris, Colin NA Palmer, Frank B. Hu, Unnur Thorsteinsdottir, Kari Stefansson, Josée Dupuis, Andrew P Morris, Michael Boehnke, Mark I McCarthy, Inga Prokopenko, and DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium. Diabetes, 2017 10.2337/db16-1253.

Genome-wide meta-analysis of 241,258 adults accounting for smoking behaviour identifies novel loci for obesity traits. Anne E Justice, Thomas W Winkler, Mary F Feitosa, Misa Graff, Virginia A Fisher, Kristin Young, Llilda Barata, Xuan Deng, Jacek Czajkowski, David Hadley, Julius S Ngwa, Tarunveer S Ahluwalia, Audrey Y Chu, Nancy L Heard-Costa, Elise Lim, Jeremiah Perez, John D Eicher, Zoltán Kutalik, Luting Xue, Anubha Mahajan, Frida Renstrom, Joseph Wu, Qibin Qi, Shafqat Ahmad, Tamuno Alfred, Najaf Amin, Lawrence F Bielak, Amelie Bonnefond, Jennifer Bragg, Gemma Cadby, Martina Chittani, Scott Coggeshall, Tanguy Corre, Nese Direk, Joel Eriksson, Krista Fischer, Mathias Gorski, Marie Neergaard Harder, Momoko Horikoshi, Tao Huang, Jennifer E Huffman, Anne U Jackson, Johanne Marie Justesen, Stavroula Kanoni, Leena Kinnunen, Marcus E Kleber, Pirjo Komulainen, Meena Kumari, Unhee Lim, Jian'an Luan, Leo-Pekka Lyytikäinen, Massimo Mangino, Ani Manichaikul, Jonathan Marten, Rita P S Middelberg, Martina Müller-Nurasyid, Pau Navarro, Louis Perusse, Natalia Pervjakova, Cinzia Sarti, Albert Vernon Smith, Jennifer A Smith, Alena Stancakova, Rona J Strawbridge, Heather M Stringham, Yun Ju Sung, Toshiko Tanaka, Alexander Teumer, Stella Trompet, Sander W van der Laan, Peter J van der Most, Jana V Van Vliet-Ostaptchouk, Sailaja L Vedantam, Niek Verweij, Jacqueline M Vink, Veronique Vitart, Ying Wu, Loic Yengo, Weihua Zhang, Jing Hua Zhao, Martina E Zimmermann, Niha Zubair, Gonçalo R Abecasis, Linda S Adair, Saima Afaq, Uzma Afzal, Stephan J L Bakker, Traci M Bartz, John Beilby, Richard N Bergman, Sven Bergmann, Reiner Biffar, John Blangero, Eric Boerwinkle, Lori L Bonnycastle, Erwin Bottinger, Daniele Braga, Brendan M Buckley, Steve Buyske, Harry Campbell, John C Chambers, Francis S Collins, Joanne E Curran, Gert J de Borst, Anton J M de Craen, Eco J C de Geus, George Dedoussis, Graciela E Delgado, Hester M den Ruijter, Gudny Eiriksdottir, Anna L Eriksson, Tõnu Esko, Jessica D Faul, Ian Ford, Terrence Forrester, Karl Gertow, Bruna Gigante, Nicola Glorioso, Jian Gong, Harald Grallert, Tanja B Grammer, Niels Grarup, Saskia Haitjema, Göran Hallmans, Anders Hamsten, Torben Hansen, Tamara B Harris, Catharina A Hartman, Maija Hassinen, Nicholas D Hastie, Andrew C Heath, Dena Hernandez, Lucia Hindorff, Lynne J Hocking, Mette Hollensted, Oddgeir L Holmen, Georg Homuth, Jouke Jan Hottenga, Jie Huang, Joseph Hung, Nina Hutri-Kähönen, Erik Ingelsson, Alan L James, John-Olov Jansson, Marjo-Riitta Järvelin, Min A Jhun, Marit E Jorgensen, Markus Juonala, Mika Kähönen, Magnus Karlsson, Heikki A Koistinen, Ivana Kolcic, Genovefa Kolovou, Charles Kooperberg, Bernhard K Krämer, Johanna Kuusisto, Kirsti Kvaløy, Timo A Lakka, Claudia Langenberg, Lenore J Launer, Karin Leander, Nanette R Lee, Lars Lind, Cecilia M Lindgren, Allan Linneberg, Stéphane Lobbens, Marie Loh, Mattias Lorentzon, Robert Luben, Gitta Lubke, Anja Ludolph-Donislawski, Sara Lupoli, Pamela A F Madden, Reija Männikkö, Pedro Marques-Vidal, Nicholas G Martin, Colin A McKenzie, Barbara McKnight, Dan Mellström, Cristina Menni, Grant W Montgomery, Aw Bill Musk, Narisu Narisu, Matthias Nauck, Ilja M Nolte, Albertine J Oldehinkel, Matthias Olden, Ken K Ong, Sandosh Padmanabhan, Patricia A Peyser, Charlotta Pisinger, David J Porteous, Olli T Raitakari, Tuomo Rankinen, D C Rao, Laura J Rasmussen-Torvik, Rajesh Rawal, Treva Rice, Paul M Ridker, Lynda M Rose, Stephanie A Bien, Igor Rudan, Serena Sanna, Mark A Sarzynski, Naveed Sattar, Kai Savonen, David Schlessinger, Salome Scholtens, Claudia Schurmann, Robert A Scott, Bengt Sennblad, Marten A Siemelink, Günther Silbernagel, P Eline Slagboom, Harold Snieder, Jan A Staessen, David J Stott, Morris A Swertz, Amy J Swift, Kent D Taylor, Bamidele O Tayo, Barbara Thorand, Dorothee Thuillier, Jaakko Tuomilehto, Andre G Uitterlinden, Liesbeth Vandenput, Marie-Claude Vohl, Henry Völzke, Judith M Vonk, Gerard Waeber, Melanie Waldenberger, R G J Westendorp, Sarah Wild, Gonneke Willemsen, Bruce H R Wolffenbuttel, Andrew Wong, Alan F Wright, Wei Zhao, M Carola Zillikens, Damiano Baldassarre, Beverley Balkau, Stefania Bandinelli, Carsten A Boger, Dorret I Boomsma, Claude Bouchard, Marcel Bruinenberg, Daniel I Chasman, Yii-DerIda Chen, Peter S Chines, Richard S Cooper, Francesco Cucca, Daniele Cusi, Ulf de Faire, Luigi Ferrucci, Paul W Franks, Philippe Froguel, Penny Gordon-Larsen, Hans-Jörgen Grabe, Vilmundur Gudnason, Christopher A Haiman, Caroline Hayward, Kristian Hveem, Andrew D. Johnson, J Wouter Jukema, Sharon L R Kardia, Mika Kivimaki, Jaspal S Kooner, Diana Kuh, Markku Laakso, Terho Lehtimäki, Loic Le Marchand, Winfried März, Mark I McCarthy, Andres Metspalu, Andrew P Morris, Claes Ohlsson, Lyle J Palmer, Gerard Pasterkamp, Oluf Pedersen, Annette Peters, Ulrike Peters, Ozren Polasek, Bruce M Psaty, Lu Qi, Rainer Rauramaa, Blair H Smith, Thorkild I A Sørensen, Konstantin Strauch, Henning Tiemeier, Elena Tremoli, Pim van der Harst, Henrik Vestergaard, Peter Vollenweider, Nicholas J Wareham, David R Weir, John B Whitfield, James F Wilson, Jessica Tyrrell, Timothy M Frayling, Inês Barroso, Michael Boehnke, Panagiotis Deloukas, Caroline S Fox, Joel N Hirschhorn, David J. Hunter, Tim D Spector, David P Strachan, Cornelia M Van Duijn, Iris M Heid, Karen L Mohlke, Jonathan Marchini, Ruth J F Loos, Tuomas O Kilpeläinen, Ching-Ti Liu, Ingrid B Borecki, Kari E North, and L Adrienne Cupples. Nat Commun, 2017 vol. 8 p. 14977.

Mapping of 79 loci for 83 plasma protein biomarkers in cardiovascular disease. Lasse Folkersen, Eric Fauman, Maria Sabater-Lleal, Rona J Strawbridge, Mattias Frånberg, Bengt Sennblad, Damiano Baldassarre, Fabrizio Veglia, Steve E Humphries, Rainer Rauramaa, Ulf De Faire, Andries J Smit, Philippe Giral, Sudhir Kurl, Elmo Mannarino, Stefan Enroth, Åsa Johansson, Sofia Bosdotter Enroth, Stefan Gustafsson, Lars Lind, Cecilia Lindgren, Andrew P Morris, Vilmantas Giedraitis, Angela Silveira, Anders Franco-Cereceda, Elena Tremoli, IMPROVE study group, Ulf Gyllensten, Erik Ingelsson, Søren Brunak, Per Eriksson, Daniel Ziemek, Anders Hamsten, and Anders Malarstig. PLoS Genetics, 2017 vol. 13 (4) p. e1006706.


2016

Genetic Variants in CHIA and CHI3L1 Are Associated with the IgE Response to the Ascaris Resistance Marker ABA-1 and the Birch Pollen Allergen Bet v 1. Acevedo N, Bornacelly A, Mercado D, Unneberg P, Mittermann I, Valenta R, Kennedy M, Scheynius A, Caraballo L. (2016) PLoS One 11:e0167453.

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. (2016) Nature immunology 17:451-460

Genome-wide association study with additional genetic and post-transcriptional analyses reveals novel regulators of plasma factor XI levels. Bengt Sennblad, Saonli Basu, Johanna Mazur, Pierre Suchon, Angel Martinez-Perez, and (26 further authors).  Human Molecular Genetics, (accepted), 2016.

Soluble CD93 is involved in metabolic dysregulation but does not influence carotid intima-media thickness. Rona J Strawbridge, Agneta Hilding, Angela Silveira, Cecilia Österholm, Bengt Sennblad, and (20 further authors).  Diabetes, 65(10):2888–2899, 2016.

Discovery and refinement of genetic loci associated with cardiometabolic risk using dense imputation maps. Valentina Iotchkova, Jie Huang, John A Morris, (...31 authors ...), Bengt Sennblad, and (36 further authors).  Nat. Genet., 2016.

Analysis with the exome array identifies multiple new independent variants in lipid loci. Stavroula Kanoni, Nicholas G D Masca, Kathleen E Stirrups, (. . . 33 authors . . . ), Bengt Sennblad, and (28 further authors).  Human Molecular Genetics, 2016.

Correction: The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study. Thomas W Winkler, Anne E Justice, Mariaelisa Graff, (...244 authors ...), Bengt Sennblad, and (200 further authors).  PLoS Genetics, 12(6):e1006166, 2016.

Genetic loci on chromosome 5 are associated with circulating levels of interleukin-5 and eosinophil count in a European population with high risk for cardiovascular disease. Olga McLeod, Angela Silveira, Elsa Valdes-Marquez, (. . . 8 authors . . . ), Bengt Sennblad, and (14 further authors). Cytokine, 81:1–9, 2016.

A meta-analysis of 120 246 individuals identifies 18 new loci for fibrinogen concentration. Paul S de Vries, Daniel I Chasman, Maria Sabater-Lleal, (...62 authors ...), Bengt Sennblad, and (68 further authors). Human Molecular Genetics, 25(2):358–370, 2016. 

2015

Aberrant splicing of genes involved in haemoglobin synthesis and impaired terminal erythroid maturation in SF3B1 mutated refractory anaemia with ring sideroblasts. Conte S, Katayama S, Vesterlund L, Karimi M, Dimitriou M, Jansson M, Mortera-Blanco T, Unneberg P, Papaemmanuil E, Sander B, Skoog T, Campbell P, Walfridsson J, Kere J, Hellström-Lindberg E. Br J Haematol. 2015 Nov;171(4):478-90

High-throughput mutational screening adds clinically important information in myelodysplastic syndromes and secondary or therapy-related acute myeloid leukemia. Karimi M, Nilsson C, Dimitriou M, Jansson M, Matsson H, Unneberg P, Lehmann S, Kere J, Hellström-Lindberg E. Haematologica. 2015 Jun;100(6):e223-5

Genome-wide identification of Wig-1 mRNA targets by RIP-Seq analysisBersani C, Huss M, Giacomello S, Xu L-D,  Bianchi J, Eriksson S, Jerhammar F, Alexeyenko A, Vilborg A, Lundeberg J, Lui W-O, Wiman KG. Oncotarget, 10.18632/oncotarget.6557 (2015).

Polymorphisms in DCDC2 and S100B associate with developmental dyslexia. Matsson H, Huss M, Persson H, Einarsdottir E, Tiraboschi E, Nopola-Hemmi J, Schumacher J, Neuhoff N, Warnke A, Lyytinen H, Schulte-Körne G, Nöthen MM, Leppänen PH, Peyrard-Janvid M, Kere J. J Hum Genet. 2015 Jul;60(7):399-401.

Common and distinct DNA-binding and regulatory activities of the BEN-solo transcription factor family. Dai Q, Ren A, Westholm JO, Duan H, Patel DJ, Lai EC. Genes Dev. 2015 Jan 1;29(1):48-62.

Reprogramming of Yersinia from Virulent to Persistent Mode Revealed by Complex In Vivo RNA-seq Analysis. Avican K, Fahlgren A, Huss M, Heroven AK, Beckstette M, Dersch P, Fällman M. PLoS Pathog. 2015 Jan 15;11(1)

Targeted gene mutation in tetraploid potato through transient TALEN expression in protoplasts. Nicolia A, Proux-Wéra E, Åhman I, Onkokesung N, Andersson M, Andreasson E, Zhu LH. J Biotechnol. 2015 (204) 17-24.

Clade- and species-specific features of genome evolution in the SaccharomycetaceaeWolfe KH, Armisén D, Proux-Wera E, ÓhÉigeartaigh SS, Azam H, Gordon JL, Byrne KP. FEMS Yeast Res. 2015 Aug;15(5).

A novel workflow correlating RNA-seq data to Phythophthora infestans resistance levels in wild Solanum species and potato clones. Frades I, Abreha KB, Proux-Wéra E, Lankinen Å, Andreasson E, Alexandersson E. Front. Plant Sci. 6. 2015 Sept.

Mitochondrial DNA variation in the Viking age population of Norway. Maja Krzewińska, Gro Bjørnstad, Pontus Skoglund, Pall Isolfur Olason, Jan Bill, Anders Götherström, Erika Hagelberg. Philos Trans R Soc Lond B Biol Sci. 2015 Jan 19;370(1660):20130384. doi: 10.1098/rstb.2013.0384.

Amelanism in the corn snake is associated with the insertion of an LTR-retrotransposon in the OCA2 gene. Suzanne V. Saenko, Sangeet Lamichhaney, Alvaro Martinez Barrio, Nima Rafati, Leif Andersson & Michel C. Milinkovitch.  Sci. Rep. 5, 17118  (2015) doi: 10.1038/srep17118

Evolution of Darwin/'s finches and their beaks revealed by genome sequencing. Sangeet Lamichhaney, Jonas Berglund, Markus Sällman Almén, Khurram Maqbool, Manfred Grabherr, Alvaro Martinez Barrio, Marta Promerová, Carl-Johan Rubin, Chao Wang, Neda Zamani, B Rosemary Grant, Peter R Grant, Matthew T Webster, Leif Andersson  Nature 518, 371–375 (2015) doi:10.1038/nature14181

2014

Differences in gene expression between mouse and human for dynamically regulated genes in early embryo. Madissoon E, Töhönen V, Vesterlund L, Katayama S, Unneberg P, Inzunza J, Hovatta O, Kere J. (2014) PLoS One 9:e102949.

Association and Mutation Analyses of the IRF6 Gene in Families With Nonsyndromic and Syndromic Cleft Lip and/or Cleft Palate. Pegelow M, Koillinen H, Magnusson M, Fransson I, Unneberg P, Kere J, Karsten A, Peyrard-Janvid M. (2014) The Cleft Palate-Craniofacial Journal 51:49-55

A method to map changes in bacterial surface composition induced by regulatory RNAs in Escherichia coli and Staphylococcus aureus.Hammann P, Parmentier D, Cerciat M, Reimegård J, Helfer AC, Boisset S, Guillier M, Vandenesch F, Wagner EG, Romby P, Fechter P. Biochimie. 2014 Nov;106:175-9. 

The Dictyostelium discoideum RNA-dependent RNA polymerase RrpC silences the centromeric retrotransposon DIRS-1 post-transcriptionally and is required for the spreading of RNA silencing signals. Wiegand S, Meier D, Seehafer C, Malicki M, Hofmann P, Schmith A, Winckler T, Földesi B, Boesler B, Nellen W, Reimegård J, Käller M, Hällman J, Emanuelsson O, Avesson L, Söderbom F, Hammann C. (2014) Nucleic Acids Research 42:3330-3345.

Dominant mutations in GRHL3 cause Van der Woude Syndrome and disrupt oral periderm development. Peyrard-Janvid M, Leslie EJ, Kousa YA, Smith TL, Dunnwald M, Magnusson M, Lentz BA, Unneberg P, Fransson I, Koillinen HK, Rautio J, Pegelow M, Karsten A, Basel-Vanagaite L, Gordon W, Andersen B, Svensson T, Murray JC, Cornell RA, Kere J, Schutte BC. (2014) Am Journal of Human Genetics 94:23-32.

The Chironomus tentans genome sequence and the organization of the Balbiani ring genes. Kutsenko A, Svensson T, Nystedt B, Lundeberg J, Björk P, Sonnhammer E, Giacomello S, Visa N, Wieslander L. (2014) BMC Genomics 15:819.

Genome-wide Analysis of Drosophila Circular RNAs Reveals Their Structural and Sequence Properties and Age-Dependent Neural Accumulation. Westholm JO, Miura P, Olson S, Shenker S, Joseph B, Sanfilippo P, Celniker SE, Graveley BR, Lai EC. (2014) Cell Reports 9:1966-80.

Evaluation and integration of functional annotation pipelines for newly sequenced organisms: the potato genome as a test case. David Amar, Itziar Frades, Agnieszka Danek, Tatyana Goldberg, Sanjeev K Sharma, Pete E Hedley, Estelle Proux-Wera, Erik Andreasson, Ron Shamir, Oren Tzfadia and Erik Alexandersson. (2014) BMC Plant Biology 14:329.

Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication. M Carneiro, CJ Rubin, F Di Palma, FW Albert, J Alföldi, AM Barrio, et al. (2014) Science 345:1074-1079.

BESST - Efficient scaffolding of large fragmented assemblies. Sahlin K, Vezzi F, Nystedt B, Lundeberg J, Arvestad L (2014) BMC Bioinformatics 15:281.

Efficient de novo assembly of large and complex genomes by massively parallel sequencing of Fosmid pools. Alexeyenko A, Nystedt B, Vezzi F, Sherwood E, Ye R, Knudsen B, Simonsen M, Turner B, de Jong P, Wu CC, Lundeberg J. (2014) BMC Genomics 15:439.

Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche. Perry et al (Kjellqvist S) (2014) Nature 514:92-97.

A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution. Kawakami T, Smeds L, Backström N, Husby A, Qvarnström A, Mugal CF, Olason P, Ellegren H. (2014) Molecular Ecology 23:4035-4058.

Estimation of linkage disequilibrium and interspecific gene flow in Ficedula flycatchers by a newly developed 50k single-nucleotide polymorphism array. Kawakami T, Backström N, Burri R, Husby A, Olason P, Rice AM, Ålund M, Qvarnström A, Ellegren H. (2014) Molecular Ecology Resources 14:1248-1260.

Abolished InsP3R2 function inhibits sweat secretion in both humans and mice. Klar J, Hisatsune C, Baig SM, Tariq M, Johansson AC, Rasool M, Malik NA, Ameur A, Sugiura K,Feuk L, Mikoshiba K, Dahl N. (2014) J Clin Invest. 124:4773-80.

Assessment of whole genome amplification for sequence capture and massively parallel sequencing. Hasmats J, Gréen H, Orear C, Validire P, Huss M, Käller M, Lundeberg J. (2014) PLoS One 9:e84785.

Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. Fagerberg L, Hallström BM, Oksvold P, Kampf C, Djureinovic D, Odeberg J, Habuka M, Tahmasebpoor S, Danielsson A, Edlund K, Asplund A, Sjöstedt E, Lundberg E, Szigyarto CA, Skogs M, Takanen JO, Berling H, Tegel H, Mulder J, Nilsson P, Schwenk JM, Lindskog C, Danielsson F, Mardinoglu A, Sivertsson A, von Feilitzen K, Forsberg M, Zwahlen M, Olsson I, Navani S, Huss M, Nielsen J, Ponten F, Uhlén M. (2014) Mol Cell Proteomics. 13:397-406.

HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics. Branca RM, Orre LM, Johansson HJ, Granholm V, Huss M, Pérez-Bercoff Å, Forshed J, Käll L, Lehtiö J. (2014) Nat Methods 11(1):59-62.

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Brownstein CA, [...], Huss M, [...] Margulies DM. (2014) Genome Biology 15:R53.

Differences in gene expression between mouse and human for dynamically regulated genes in early embryo. Madissoon E, Töhönen V, Vesterlund L, Katayama S, Unneberg P, Inzunza J, Hovatta O, Kere J. (2014) PLoS One. 9:e102949.

 

  • No labels