Bioinformatics, 1367-4803

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  1. 2021
  2. BigDataProcessor2: A free and open-source Fiji plugin for inspection and processing of TB sized image data

    Christian Tischer, Ashis Ravindran, Sabine Reither, Nicolas Chiaruttini, Rainer Pepperkok & Nils Norlin, 2021 Feb 17, In: Bioinformatics (Oxford, England).

    Research output: Contribution to journalArticle

  3. multiclassPairs: An R package to train multiclass pair-based classifier

    Nour-Al-Dain Marzouka & Pontus Eriksson, 2021 Feb 5, (Accepted/In press) In: Bioinformatics (Oxford, England). 2 p., btab088.

    Research output: Contribution to journalDebate/Note/Editorial

  4. 2020
  5. Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences

    Erand Smakaj, Lmar Babrak, Mats Ohlin, Mikhail Shugay, Bryan Briney, Deniz Tosoni, Christopher Galli, Vendi Grobelsek, Igor D'Angelo, Branden Olson, Sai Reddy, Victor Greiff, Johannes Trück, Susanna Marquez, William Lees & Enkelejda Miho, 2020, In: Bioinformatics (Oxford, England). 36, 6, p. 1731-1739 9 p.

    Research output: Contribution to journalArticle

  6. 2019
  7. RTNduals an R/Bioconductor package for analysis of co-regulation and inference of dual regulons

    Vinicius S. Chagas, Clarice S. Groeneveld, Kelin G. Oliveira, Sheyla Trefflich, Rodrigo C. de Almeida, Bruce A.J. Ponder, Kerstin B. Meyer, Steven J.M. Jones, A. Gordon Robertson & Mauro A.A. Castro, 2019 Dec 15, In: Bioinformatics (Oxford, England). 35, 24, p. 5357-5358 2 p.

    Research output: Contribution to journalLetter

  8. Pair Matcher (PaM): fast model-based optimization of treatment/case-control matches

    Eran Elhaik & Desmond M Ryan, 2019 Jul 1, In: Bioinformatics (Oxford, England). 35, 13, p. 2243-2250

    Research output: Contribution to journalArticle

  9. SMSSVD: SubMatrix Selection Singular Value Decomposition

    Rasmus Henningsson & Magnus Fontes, 2019, In: Bioinformatics (Oxford, England). 35, 3, p. 478-486 9 p.

    Research output: Contribution to journalArticle

  10. Uncertainty quantification, propagation and characterization by Bayesian analysis combined with global sensitivity analysis applied to dynamical intracellular pathway models

    Olivia Eriksson, Alexandra Jauhiainen, Sara Maad Sasane, Andrei Kramer, Anu G. Nair, Carolina Sartorius & Jeanette Hellgren Kotaleski, 2019, In: Bioinformatics (Oxford, England). 35, 2, p. 284-292 9 p.

    Research output: Contribution to journalArticle

  11. 2018
  12. Using standard microbiome reference groups to simplify beta-diversity analyses and facilitate independent validation

    Marlena Maziarz, Ruth M. Pfeiffer, Yunhu Wan & Mitchell H. Gail, 2018 Oct 1, In: Bioinformatics. 34, 19, p. 3249-3257 9 p.

    Research output: Contribution to journalArticle

  13. 2017
  14. LoFtool: a gene intolerance score based on loss-of-function variants in 60 706 individuals

    João Fadista, Nikolay Oskolkov, Ola Hansson & Leif Groop, 2017, In: Bioinformatics. 33, 4, p. 471-474

    Research output: Contribution to journalArticle

  15. 2016
  16. PON-Sol: Prediction of effects of amino acid substitutions on protein solubility

    Yang Yang, Abhishek Niroula, Bairong Shen & Mauno Vihinen, 2016 Jul 1, In: Bioinformatics. 32, 13, p. 2032-2034

    Research output: Contribution to journalArticle

  17. 2015
  18. Automatic determination of NET (neutrophil extracellular traps) coverage in fluorescent microscopy images

    Luis Pedro Coelho, Catarina Pato, Ana Friães, Ariane Neumann, Maren von Köckritz-Blickwede, Mário Ramirez & João André Carriço, 2015 Jul 15, In: Bioinformatics. 31, 14, p. 2364-70 7 p.

    Research output: Contribution to journalArticle

  19. DIANA - algorithmic improvements for analysis of data-independent acquisition MS data.

    Johan Teleman, Hannes Röst, George Rosenberger, Uwe Schmitt, Lars Malmström, Johan Malmström & Fredrik Levander, 2015, In: Bioinformatics. 31, 4, p. 555-562

    Research output: Contribution to journalArticle

  20. EVpedia: A Community Web Portal for Extracellular Vesicles Research.

    Dae-Kyum Kim, Jaewook Lee, Sae Rom Kim, Dong-Sic Choi, Yae Jin Yoon, Ji Hyun Kim, Gyeongyun Go, Dinh Nhung, Kahye Hong, Su Chul Jang, Si-Hyun Kim, Kyong-Su Park, Oh Youn Kim, Hyun Taek Park, Ji Hye Seo, Elena Aikawa, Monika Baj-Krzyworzeka, Bas W M van Balkom, Mattias Belting, Lionel Blanc & 75 others, Vincent Bond, Antonella Bongiovanni, Francesc E Borràs, Luc Buée, Edit I Buzás, Lesley Cheng, Aled Clayton, Emanuele Cocucci, Charles S Dela Cruz, Dominic M Desiderio, Dolores Di Vizio, Karin Ekström, Juan M Falcon-Perez, Chris Gardiner, Bernd Giebel, David W Greening, Julia Christina Gross, Dwijendra Gupta, An Hendrix, Andrew F Hill, Michelle M Hill, Esther Nolte-'t Hoen, Do Won Hwang, Jameel Inal, Medicharla V Jagannadham, Muthuvel Jayachandran, Young-Koo Jee, Malene Jørgensen, Kwang Pyo Kim, Yoon-Keun Kim, Thomas Kislinger, Cecilia Lässer, Dong Soo Lee, Hakmo Lee, Johannes van Leeuwen, Thomas Lener, Ming-Lin Liu, Jan Lötvall, Antonio Marcilla, Suresh Mathivanan, Andreas Möller, Jess Morhayim, François Mullier, Irina Nazarenko, Rienk Nieuwland, Diana N Nunes, Ken Pang, Jaesung Park, Tushar Patel, Gabriella Pocsfalvi, Hernando Del Portillo, Ulrich Putz, Marcel I Ramirez, Marcio L Rodrigues, Tae-Young Roh, Felix Royo, Susmita Sahoo, Raymond Schiffelers, Shivani Sharma, Pia Siljander, Richard J Simpson, Carolina Soekmadji, Philip Stahl, Allan Stensballe, Ewa Stępień, Hidetoshi Tahara, Arne Trummer, Hadi Valadi, Laura J Vella, Sun Nyunt Wai, Kenneth Witwer, María Yáñez-Mó, Hyewon Youn, Reinhard Zeidler & Yong Song Gho, 2015, In: Bioinformatics. 31, 6, p. 933-939

    Research output: Contribution to journalArticle

  21. 2013
  22. SBSI: an extensible distributed software infrastructure for parameter estimation in systems biology

    Richard Adams, Allan Clark, Azusa Yamaguchi, Neil Hanlon, Nikos Tsorman, Shakir Ali, Galina Lebedeva, Alexey Goltsov, Anatoly Sorokin, Ozgur E. Akman, Carl Troein, Andrew J. Millar, Igor Goryanin & Stephen Gilmore, 2013, In: Bioinformatics. 29, 5, p. 664-665

    Research output: Contribution to journalArticle

  23. Ultranet: efficient solver for the sparse inverse covariance selection problem in gene network modeling.

    Linnea Järvstråt, M Johansson, Urban Gullberg & B. Nilsson, 2013, In: Bioinformatics. 29, 4, p. 511-512

    Research output: Contribution to journalArticle

  24. 2012
  25. Analysis of case-control association studies with known risk variants

    Noah Zaitlen, Bogdan Pasaniuc, Nick Patterson, Samuela Pollack, Benjamin Voight, Leif Groop, David Altshuler, Brian E. Henderson, Laurence N. Kolonel, Loic Le Marchand, Kevin Waters, Christopher A. Haiman, Barbara E. Stranger, Emmanouil T. Dermitzakis, Peter Kraft & Alkes L. Price, 2012, In: Bioinformatics. 28, 13, p. 1729-1737

    Research output: Contribution to journalArticle

  26. 2009
  27. Modified variational bayes EM estimation of hidden markov tree model of cell lineages

    Victor Olariu, Daniel Coca, Stephen A. Billings, Peter Tonge, Paul Gokhale, Peter W. Andrews & Visakan Kadirkamanathan, 2009 Nov 1, In: Bioinformatics. 25, 21, p. 2824-2830 7 p.

    Research output: Contribution to journalArticle

  28. RAMI: a tool for identification and characterization of phylogenetic clusters in microbial communities

    Thomas Pommier, Bjorn Canback, Per Lundberg, Ake Hagstrom & Anders Tunlid, 2009, In: Bioinformatics. 25, 6, p. 736-742

    Research output: Contribution to journalArticle

  29. Ultrasome: efficient aberration caller for copy number studies of ultra-high resolution

    Björn Nilsson, Mikael Johansson, Fatima Al-Shahrour, Anne E. Carpenter & Benjamin L. Ebert, 2009, In: Bioinformatics. 25, 8, p. 1078-1079

    Research output: Contribution to journalArticle

  30. 2008
  31. Model-based prediction of sequence alignment quality.

    Virpi Ahola, Tero Aittokallio, Mauno Vihinen & Esa Uusipaikka, 2008, In: Bioinformatics. 24, 19, p. 2165-2171

    Research output: Contribution to journalArticle

  32. 2007
  33. Continuous-index hidden Markov modelling of array CGH copy number data.

    Susann Stjernqvist, Tobias Rydén, Martin Sköld & Johan Staaf, 2007, In: Bioinformatics. 23, p. 1006-1014

    Research output: Contribution to journalArticle

  34. Multiple spaced seeds for homology search

    Lucian Ilie & Silvana Ilie, 2007, In: Bioinformatics. 23, 22, p. 2969-2977

    Research output: Contribution to journalArticle

  35. Regression analysis and modelling of data acquisition for SELDI-TOF mass spectrometry.

    Martin Sköld, Tobias Rydén, Viktoria Samuelsson, Charlotte Welinder, Lars Ekblad, Håkan Olsson & Bo Baldetorp, 2007, In: Bioinformatics. 23, 11, p. 1401-1409

    Research output: Contribution to journalArticle

  36. Robust smooth segmentation approach for array CGH data analysis

    J Huang, Arief Gusnanto, Kathleen O'Sullivan, Johan Staaf, Åke Borg & Yudi Pawitan, 2007, In: Bioinformatics. 23, 18, p. 2463-2469

    Research output: Contribution to journalArticle

  37. 2005
  38. CoGenT++: an extensive and extensible data environment for computational genomics

    Leon Goldovsky, Paul Janssen, Dag Ahrén, Benjamin Audit, Ildefonso Cases, Nikos Darzentas, Anton Enright, Núria López-Bigas, José Peregrin-Alvarez, Mike Smith, Sophia Tsoka, Victor Kunin & Christos Ouzounis, 2005, In: Bioinformatics. 21, 19, p. 3806-3810

    Research output: Contribution to journalArticle

  39. Modeling the organization of the WUSCHEL expression domain in the shoot apical meristem

    Henrik Jönsson, M Heisler, GV Reddy, V Agrawal, V Gor, BE Shapiro, E Mjolsness & EM Meyerowitz, 2005, In: Bioinformatics. 21, Suppl 1, p. I232-I240

    Research output: Contribution to journalArticle

  40. PROTEIOS: an open source proteomics initiative

    Per Gärdén, Rikard Alm & Jari Häkkinen, 2005, In: Bioinformatics. 21, 9, p. 2085-2087

    Research output: Contribution to journalArticle

  41. 2004
  42. ACID: a database for microarray clone information

    Markus Ringnér, Srinivas Veerla, S Andersson, Johan Staaf & Jari Häkkinen, 2004, In: Bioinformatics. 20, 14, p. 2305-2306

    Research output: Contribution to journalArticle

  43. Approximate geodesic distances reveal biologically relevant structures in microarray data

    Jens Nilsson, Thoas Fioretos, Mattias Höglund & Magnus Fontes, 2004, In: Bioinformatics. 20, 6, p. 874-880

    Research output: Contribution to journalArticle

  44. Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprinting

    J Samuelsson, D Dalevi, Fredrik Levander & T Rognvaldsson, 2004, In: Bioinformatics. 20, 18, p. 3628-3635

    Research output: Contribution to journalArticle

  45. 2003
  46. Efficient estimation of emission probabilities in profile hidden Markov models.

    Virpi Ahola, Tero Aittokallio, Esa Uusipaikka & Mauno Vihinen, 2003, In: Bioinformatics. 19, 18, p. 2359-2368

    Research output: Contribution to journalArticle

  47. RankViaContact: ranking and visualization of amino acid contacts.

    Bairong Shen & Mauno Vihinen, 2003, In: Bioinformatics. 19, 16, p. 2161-2162

    Research output: Contribution to journalArticle

  48. 2002
  49. Binary tree-structured vector quantization approach to clustering and visualizing microarray data

    M. Sultan, D. A. Wigle, C. A. Cumbaa, M. Maziarz, J. Glasgow, M. S. Tsao & I. Jurisica, 2002 Jan 1, In: Bioinformatics. 18, SUPPL. 1

    Research output: Contribution to journalArticle

  50. A novel approach to local reliability of sequence alignments.

    Maximilian Schlosshauer & Mattias Ohlsson, 2002, In: Bioinformatics. 18, 6, p. 847-854

    Research output: Contribution to journalArticle

  51. 2001
  52. BioWAP, mobile Internet service for bioinformatics

    P Riikonen, J Boberg, T Salakoski & Mauno Vihinen, 2001, In: Bioinformatics. 17, 9, p. 855-856

    Research output: Contribution to journalArticle

  53. 1999
  54. MUTbase: maintenance and analysis of distributed mutation databases

    P Riikonen & Mauno Vihinen, 1999, In: Bioinformatics. 15, 10, p. 852-859

    Research output: Contribution to journalArticle

  55. 1995
  56. MIST - A user-friendly metabolic simulator

    M Ehlde & Guido Zacchi, 1995, In: Computer Applications in the Biosciences. 11, 2, p. 201-207

    Research output: Contribution to journalArticle

  57. 1992
  58. MULTICOMP - A PROGRAM PACKAGE FOR MULTIPLE SEQUENCE COMPARISON

    Mauno Vihinen, A EURANTO, P LUOSTARINEN & O NEVALAINEN, 1992, In: Computer Applications in the Biosciences. 8, 1, p. 35-38

    Research output: Contribution to journalArticle

  59. 1988
  60. AN ALGORITHM FOR SIMULTANEOUS COMPARISON OF SEVERAL SEQUENCES

    Mauno Vihinen, 1988, In: Computer Applications in the Biosciences. 4, 1, p. 89-92

    Research output: Contribution to journalArticle