Publications - Jari Häkkinen

[publications] [reports] [thesis]

Colored bullets denote citation counts (May 2016) in the INSPIRE HEP information system (for high energy physics papers) and the Google Scholar (for others):
  • 1000 or more citations.
Some pdf files are links to the publisher and may have restricted access.
Compressed postscript files are preprints with unrestricted access.


    According to my page at Google Scholar there are a total of 1273 citations for 39 published papers. The mean impact is 33 citations/paper (March 2018). The h-index is 18.

    F. Salmén, S. Vickovic, L. Larsson, L. Stenbeck, J. Vallon-Christersson, A. Ehinger, J. Häkkinen, Å. Borg, J. Frisén, P. Ståhl, J. Lundeberg
    Multidimensional transcriptomics provides detailed information about immune cell distribution and identity in HER2+ breast tumors
    [preprint] (2018) at (submitted)

    P. Roswall, M. Bocci, M. Bartoschek, H. Li, G. Kristiansen, S. Jansson, S. Lehn, J. Sjölund, S. Reid, C. Larsson, P. Eriksson, C. Anderberg, E. Cortez, L.H. Saal, C. Orsmark-Pietras, E. Cordero, B.K. Haller, J. Häkkinen, I.J.G. Burvenich, E. Lim, A. Orimo, M. Höglund, L. Rydén, H. Moch, A.M. Scott, U. Eriksson, K. Pietras
    Microenvironmental control of breast cancer subtype elicited through paracrine platelet-derived growth factor-CC signaling
    Nature Medicine 24, 463-473 (2018) [journal]

    C. Brueffer, J. Vallon-Christersson, D. Grabau, A. Ehinger, J. Häkkinen, C. Hegardt, J. Malina, Y. Chen, P-O Bendahl, J. Manjer, M. Malmberg, C. Larsson, N. Loman, L. Rydén, Å. Borg, L.H. Saal
    Clinical Value of RNA Sequencing-Based Classifiers for Prediction of the Five Conventional Breast Cancer Biomarkers: A Report From the Population-Based Multicenter Sweden Cancerome Analysis Network-Breast Initiative
    JCO Precision Oncology 2, 1-18 (2018) [Open access at journal]

    H. Persson, R. Søkilde, J. Häkkinen, A.C. Pirona, J. Vallon-Christersson, A. Kvist, F. Mertens, Å. Borg, F. Mitelman, M. Höglund, C. Rovira
    Frequent miRNA-convergent fusion gene events in breast cancer
    Nature Communications 8:788 (2017)
    [journal, open access pdf]

    J. Häkkinen, N. Nordborg, O. Månsson, J. Vallon-Christersson
    Implementation of an Open Source Software solution for Laboratory Information Management and automated RNAseq data analysis in a large-scale Cancer Genomics initiative using BASE with extension package Reggie
    [preprint] (2016) at

    C. Winter, M.P. Nilsson, E. Olsson, A.M. George, Y. Chen, A. Kvist, T. Törngren, J. Vallon-Christersson, C. Hegardt, J. Häkkinen, G. Jönsson, D. Grabau, M. Malmberg, U. Kristoffersson, M. Rehn, S.K. Gruvberger-Saal, C. Larsson, Å. Borg, N. Loman, L.H. Saal
    Targeted sequencing of BRCA1 and BRCA2 across a large unselected breast cancer cohort suggests one third of mutations are somatic
    Annals of Oncology 27 (8), 1532-1538 (2016)
    [Open access at journal]

    L.H. Saal, J. Vallon-Christersson, J. Häkkinen, C. Hegardt, D. Grabau, C. Winter, C. Brueffer, M.H. Tang, C. Reuterswärd, R. Schulz, A. Karlsson, A. Ehinger, J. Malina, J. Manjer, M. Malmberg, C. Larsson, L. Rydén, N. Loman, Å Borg
    The Sweden Cancerome Analysis Network - Breast (SCAN-B) Initiative: a large-scale multicenter infrastructure towards implementation of breast cancer genomic analyses in the clinical routine
    Genome Medicine 7, (1):20 (2015)
    [Open access at journal]

    N. Loman (I contributed as ghostwriter see acknowledgment in paper)
    Svenskt samarbete för genomiska analyser av bröstcancervävnad
    Läkartidningen 2014;111:CTEY

    K. Harbst, M. Lauss, H. Cirenajwis, C. Winter, J. Howlin, T. Törngren, A. Kvist, B. Nodin, E. Olsson, J. Häkkinen, K. Jirström, J. Staaf, L. Lundgren, H. Olsson, C. Ingvar, S.K. Gruvberger-Saal, L. H Saal, G. Jönsson
    Molecular and Genetic Diversity in the Metastatic Process of Melanoma
    Journal of Pathology 233, 39-50 (2014)

    Á. Végvári, M. Rezeli, C. Sihlbom, J. Häkkinen, E. Carlsohn, J. Malm, H. Lilja, T. Laurell, G. Marko-Varga
    Molecular microheterogeneity of prostate specific antigen in seminal fluid by mass spectrometry
    Clinical Biochemistry 45, 331-8 (2012)

    Á. Végvári, M. Rezeli, J. Häkkinen, C. Sihlbom, E. Carlsohn, J. Malm, H. Lilja, T. Laurell, G. Marko-Varga
    Bioinformatic Strategies for Unambiguous Identification of Prostate Specific Antigen in Clinical Samples
    Journal of Proteomics 75, 202-10 (2011)

    M. Ringnér, E. Fredlund, J. Häkkinen, Å. Borg, J. Staaf
    GOBO: Gene expression-based outcome for breast cancer online
    PLoS One 6, e17911 (2011)

    J. Häkkinen, F. Levander
    Laboratory Data and Sample Management for Proteomics
    Methods in Molecular Biology 696, Part 2, 79-92 (2011)

    J. Vallon-Christersson, N. Nordborg, M. Svensson, J. Häkkinen
    BASE - 2nd generation software for microarray data management and analysis
    BMC Bioinformatics 10, 330 (2009)

    M. Eisenacher, L. Martens, T. Hardt, M. Kohl, H. Barsnes, K. Helsens, J. Häkkinen, F. Levander, R. Aebersold, J. Vandekerckhove, M.J. Dunn, F. Lisacek, J.A. Siepen, S.J. Hubbard, P.A. Binz, M. Blüggel, H. Thiele, J. Cottrell, H.E. Meyer, R. Apweiler, C. Stephan
    Getting a grip on proteomics data - Proteomics Data Collection (ProDaC)
    Proteomics 9, 3928-33 (2009)

    J. Häkkinen, G. Vincic, O. Månsson, K. Wårell, F. Levander
    The Proteios Software Environment - An extensible multi-user platform for management and analysis of proteomics data
    Journal of Proteome Research 8, 3037-43 (2009)

    M. Eisenacher, L. Martens, H. Barsnes, T. Hardt, M. Kohl, J. Häkkinen, R. Apweiler, H.E. Meyer, C. Stephan
    Proteomics Data Collection - 5th ProDaC Workshop: 4 March 2009, Kolympari, Crete, Greece
    Proteomics 9, 3626-9 (2009)

    M. Eisenacher, M. Kohl, L. Martens, H. Barsnes, T. Hardt, F. Levander, J. Häkkinen, R. Apweiler, H.E. Meyer, C. Stephan
    Proteomics data collection - 4th ProDaC workshop 15 August 2008, Amsterdam, The Netherlands
    Proteomics 9, 218-22 (2009)

    M. Eisenacher, T. Hardt, L. Martens, J. Häkkinen, R. Apweiler, M. Hamacher, H.E. Meyer, C. Stephan
    Proteomics Data Collection - 3(rd) ProDaC Workshop April 22(nd) 2008, Toledo, Spain
    Proteomics 8, 4163-7 (2008)

    M. Eisenacher, T. Hardt, M. Hamacher, L. Martens, J. Häkkinen, F. Levander, R. Apweiler, H.E. Meyer, C. Stephan
    Proteomics Data Collection - The 2nd ProDaC Workshop 5 october 2007, Seoul, Korea
    Proteomics 8, 1326-30 (2008)

    R. Alm, A. Ekefjärd, M. Krogh, J. Häkkinen, C. Emanuelsson
    Proteomic variation is as large within as between strawberry varieties
    Journal of Proteome Research 6, 3011-20 (2007)
    [journal abstract]

    F. Potthast, B. Gerrits, J. Häkkinen, D. Rutishauser, C.H. Ahrens, B. Roschitzki, K. Baerenfaller, R. Munton, P. Walther, S.N. Lövenich, P. Gehrig, P. Seif, P.H. Seeberger, R. Schlapbach
    The mass distance fingerprint: a statistical framework for de novo detection of predominant modifications using high-accuracy mass spectrometry
    Journal of Chromatography B854, 173-182 (2007)
    [journal local abstract]

    M. Eisenacher, T. Hardt, M. Hamacher, L. Martens, J. Häkkinen, F. Levander, R. Apweiler, H.E. Meyer, C. Stephan
    Proteomics Data Collection - The 1st ProDaC Workshop 26 April 2007 Ecole Normale Supérieur, Lyon, France
    Proteomics 7, 3034-7 (2007)

    F. Levander, M. Krogh, K. Wårell, P. Gärdén, P. James, J. Häkkinen
    Automated reporting from gel-based proteomics experiments using the open source Proteios database application
    Proteomics 7, 668-674 (2007)
    [journal local abstract]

    P. Johansson, J. Häkkinen
    Improving missing value imputation of microarray data by using spot quality weights
    BMC Bioinformatics 7, 306 (2006)
    [journal local abstract]

    R. Alm, P. Johansson, K. Hjernø, C. Emanuelsson, M. Ringnér, J. Häkkinen
    Detection and identification of protein isoforms using cluster analysis of MALDI-MS mass spectra
    Journal of Proteome Research 5, 785-792 (2006)
    [journal local abstract software]

    P. Gärdén, R. Alm, J. Häkkinen
    Proteios: an open source proteomics initiative
    Bioinformatics 21, 2085-2087 (2005)
    [journal abstract software]

    M. Ringnér, S. Veerla, S. Andersson, J. Staaf, J. Häkkinen
    ACID: a database for microarray clone information
    Bioinformatics 20, 2305-2306 (2004)
    [journal abstract software no longer maintained]

    T. Rögnvaldsson, J. Häkkinen, C. Lindberg, G. Marko-Varga, F. Potthast, J. Samuelsson
    Improving Automatic Peptide Mass Fingerprint Protein Identification by Combining Multiple Peak Sets
    Journal of Chromatography B807, 209-15 (2004)
    [journal local abstract]

    J. Häkkinen, M. Lagerholm, C. Peterson, B. Söderberg
    Local Routing Algorithms Based on Potts Neural Networks
    IEEE Transactions on Neural Networks 11, 970-977 (2000)
    [pdf ps.gz abstract]

    J. Häkkinen, M. Lagerholm, C. Peterson, B. Söderberg
    A Potts Neuron Approach to Communication Routing
    Neural Computation 10, 1587-1599 (1998)
    [pdf ps.gz abstract]

    B. Andersson, G. Gustafson, J. Häkkinen, M. Ringnér, P.J. Sutton
    Is there screwiness at the end of the QCD cascades?
    Journal of High Energy Physics 09, 014 (1998)
    [local ps.gz abstract]

    J. Häkkinen, M. Ringnér
    Bose-Einstein and colour interference in W-pair decays
    European Physical Journal C5, 275-281 (1998)
    [pdf ps.gz abstract]

    J. Häkkinen
    bb Fragmentation and Bπ Correlations
    Zeitschrift für Physik C75 35-40 (1997)
    [pdf ps.gz abstract]

    C. Friberg, G. Gustafson, J. Häkkinen
    Colour Connections in e+e- annihilation
    Nuclear Physics B490, 289-305 (1997)
    [ps.gz abstract ]

    J. Häkkinen, H. Kharraziha
    Colour: A Computer Program for QCD Colour Factor Calculations
    Computer Physics Communications 100, 311-321 (1997)
    [ps.gz abstract software v1.0.1 software v1.0 (deprecated)]

    G. Gustafson, J. Häkkinen
    Colour Interference and Confinement Effects in W pair Production
    Zeitschrift für Physik C64, 659-664 (1994)
    [ps.gz abstract]
    MC program (Link has expired, contact

    G. Gustafson, J. Häkkinen
    Deuteron production in e+e--annihilation
    Zeitschrift für Physik C61, 683-688 (1994)
    [ps.gz abstract]

    G. Gustafson, J. Häkkinen
    Lambda-polarization in e+e--annihilation at the Z0-pole
    Physics Letter B303, 350-354 (1993)
    [ps.gz abstract]


    P. Johansson, R. Alm, C. Emanuelsson, J. Häkkinen, M. Ringnér
    SPECLUST: a web tool for clustering of mass spectra
    LU TP 07-14
    [local abstract software]

    J. Häkkinen
    SWEGENE Bioinformatics Survey - Report on Current Status and Suggestions for Future Directions
    August 2002
    [ps.gz local executive summary]

    Contributions to the QCD event generators report in the
    CERN report Physics at LEP2 (CERN 96-1)
    I.G. Knowles, T. Sjöstrand, et al.
    [ps.gz abstract]


    J. Häkkinen
    Properties of Hadronization in e+e- annihilation
    Ph.D. Thesis, Lund University, 1996
    ISBN 91-628-2114-8
    [ps.gz abstract]

This page was created in April 1996.
Latest update: July 24, 2018.