[publications] [reports] [thesis]
| Colored bullets denote citation counts (April 2021) in the INSPIRE HEP information system (for high energy physics papers) and the Google Scholar (for others): | |
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Some pdf files are links to the publisher and may have restricted access. Compressed postscript files are preprints with unrestricted access. |
V. Hafstað, J. Häkkinen, H. Persson
Fast and sensitive validation of fusion transcripts in
whole-genome sequencing data
BMC Bioinformatics
24, 359 (2023) [journal]
S. Stordal Bjørklund, M. Ragle Aure,
J. Häkkinen, J. Vallon-Christersson, S. Kumar,
K. Bull Evensen, T. Fleischer, J. Tost,
K. K. Sahlberg, A. Mathelier, G. Bhanot,
S. Ganesan, X. Tekpli, V. N. Kristensen
Subtype and cell type specific expression of lncRNAs provide
insight into breast cancer
Communications
Biology 5 834 (2022) [journal]
J. Staaf, J. Häkkinen, C. Hegardt,
L.H. Saal, S. Kimbung, I. Hedenfalk, T. Lien,
T. Sørlie, B. Naume, H. Russnes,
R. Marcone, A. Ayyanan, C. Brisken,
R.R. Malterling, B. Asking, H. Olofsson,
H. Lindman, P.O. Bendahl, A. Ehinger,
C. Larsson, N. Loman, L. Rydén,
M. Malmberg, Å. Borg, J. Vallon-Christersson
RNA sequencing-based single sample predictors of
molecular subtype and risk of recurrence for clinical assessment of
early-stage breast cancer
npj Breast Cancer
8, 94 (2022) [Open access at journal, early
version at medRxiv]
V. Hafstað, R. Søkilde, J. Häkkinen,
M. Larsson J. Vallon-Christersson, C. Rovira,
H. Persson
Regulatory networks and 5' partner
usage of miRNA host gene fusions in breast cancer
International Journal of Cancer 151 1 (2022)
[journal]
M. Dahlgren, A.M. George, C. Brueffer,
S. Gladchuk, Y. Chen, J. Vallon-Christersson,
C. Hegardt, J. Häkkinen, L. Rydén,
M. Malmberg, C. Larsson, S.K. Gruvberger-Saal,
A. Ehinger, N. Loman, Å. Borg, L.H. Saal
Preexisting Somatic Mutations of Estrogen Receptor
Alpha (ESR1) in Early-Stage Primary Breast Cancer
JNCI Cancer Spectrum 5, 2 (2021) [journal]
M. Aine, C. Boyaci, J. Hartman,
J. Häkkinen, S. Mitra, A. Bosch Campos,
E. Nimeus, A. Ehinger, J. Vallon-Christersson,
Å. Borg, J. Staaf
Molecular analyses of
triple-negative breast cancer in the young and elderly
Breast Cancer Research 23, 20 (2021) [Open
access at journal]
C. Brueffer, S. Gladchuk, C. Winter,
J. Vallon-Christersson, C. Hegardt, J. Häkkinen,
A.M. George, Y. Chen, A. Ehinger, C. Larsson,
N. Loman, M. Malmberg, L. Rydén,
Å. Borg, L.H. Saal
The Mutational
Landscape of the SCAN-B Real-World Primary Breast Cancer
Transcriptome
EMBO Molecular Medicine
12, e12118 (2020) [Open access at journal, early
version at bioRxiv]
D. Glodzik, A. Bosch, J. Hartman, M. Aine,
J. Vallon-Christersson, C. Reuterswärd,
A. Karlsson, S. Mitra, E.. Niméus,
K. Holm, J. Häkkinen, C. Hegardt,
L.H. Saal, C. Larsson, M. Malmberg,
L. Rydén, A. Ehinger, N. Loman, A. Kvist,
H. Ehrencrona, S. Nik-Zainal, Å. Borg,
J. Staaf
Comprehensive molecular comparison of
BRCA1 hypermethylated and BRCA1 mutated triple negative breast
cancers
Nature Communications
11, 3747 (2020) [journal]
C. Larsson, A. Ehinger, S. Winslow,
K. Leandersson, M. Klintman, L. Dahl,
J. Vallon-Christersson, J. Häkkinen, C. Hegardt,
J. Manjer, L.H. Saal, L. Rydén,
M. Malmberg, Å. Borg, N. Loman
Prognostic implications of the expression levels of
different immunoglobulin heavy chain-encoding RNAs in early breast
cancer
npj Breast Cancer 6, 28
(2020) [journal]
A. Sanna, K. Harbst, I. Johansson,
G. Christensen, M. Lauss, S. Mitra,
F. Rosengren, J. Häkkinen,
J. Vallon-Christersson, H. Olsson, Å. Ingvar,
K. Isaksson, C. Ingvar, K. Nielson,
G. Jönsson
Tumor genetic heterogeneity
analysis of chronic sun-damaged melanoma
Pigment
Cell & Melanoma Research 33, 480-489 (2020) [journal]
H. Persson, R. Søkilde, J. Häkkinen,
J. Vallon-Christersson, F. Mitelman, Å. Borg,
M. Höglund, C. Rovira
Analysis of fusion
transcripts indicates widespread deregulation of snoRNAs and their
host genes in breast cancer
International Journal
of Cancer 146, 3343-3353 (2020) [journal]
J. Staaf, D. Glodzik, A. Bosch,
J. Vallon-Christersson, C. Reuterswärd,
J. Häkkinen, A. Degasperi, T.D. Amarante,
L.H. Saal, C. Hegardt, H. Stobart, A. Ehinger,
C. Larsson, L. Rydén, N. Loman,
M. Malmberg, A. Kvist, H. Ehrencrona,
H.R. Davies, Å. Borg, S. Nik-Zainal
Whole-genome sequencing of triple-negative breast cancers in
a population-based clinical study
Nature Medicine 25, 1526-1533 (2019) [journal]
J. Vallon-Christersson, J. Häkkinen, C. Hegardt,
L.H. Saal, C. Larsson, A. Ehinger, H. Lindman,
H. Olofsson, T. Sjöblom, F. Wärnberg,
L. Rydén, N. Loman, M. Malmberg,
Å. Borg, J. Staaf
Cross comparison and
prognostic assessment of breast cancer multigene signatures in a
large population-based contemporary clinical series
Scientific Reports 9, Article number: 12184
(2019) [journal]
C. Lundgren, P.O. Bendahl, Å. Borg,
A. Ehinger, C. Hegardt, C. Larsson, N. Loman,
M. Malmberg, H. Olofsson, L.H. Saal, T. Sjöblom,
H. Lindman, M. Klintman, J. Häkkinen,
J. Vallon-Christersson, M. Fernö,
L. Rydén, M. Ekholm
Agreement between
molecular subtyping and surrogate subtype classification: a
contemporary population-based study of ER-positive/HER2-negative
primary breast cancer
Breast Cancer Research and
Treatment 178, 459-467 (2019) [journal]
L. Dihge, J. Vallon-Christersson, C. Hegardt,
L.H. Saal, J. Häkkinen, C. Larsson,
A. Ehinger, N. Loman, M. Malmberg, P.O. Bendahl,
A. Borg, J. Staaf, L. Rydén
Prediction of lymph node metastasis in breast cancer by gene
expression and clinicopathological models: Development and
validation within a population based cohort
Clinical Cancer Research 25, 6338-81 (2019) [journal]
B. Phung, M. Cieśla, A. Sanna, N. Guzzi,
G. Beneventi, P.C.T. Ngoc, M. Lauss, R. Cabrita,
E. Cordero, A. Bosch, F. Rosengren,
J. Häkkinen, K. Griewank, A. Paschen,
K. Harbst, H. Olsson, C. Ingvar, A. Carneiro,
H. Tsao, D. Schadendorf, K. Pietras, C. Bellodi,
G. Jönsson
The X-Linked DDX3X RNA Helicase
Dictates Translation Reprogramming and Metastasis in
Melanoma
Cell Reports 27,
P3573-3586.E7 (2019) [Open access at
journal]
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 https://bioRxiv.org
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 https://bioRxiv.org
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
[journal]
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)
[journal]
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)
[journal]
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)
[journal]
M. Ringnér, E. Fredlund, J. Häkkinen,
Å. Borg, J. Staaf
GOBO: Gene
expression-based outcome for breast cancer online
PLoS One 6, e17911 (2011)
[journal]
J. Häkkinen, F. Levander
Laboratory Data
and Sample Management for Proteomics
Methods in
Molecular Biology 696, Part 2, 79-92 (2011)
[journal]
J. Vallon-Christersson, N. Nordborg, M. Svensson,
J. Häkkinen
BASE - 2nd generation software
for microarray data management and analysis
BMC
Bioinformatics 10, 330 (2009)
[journal]
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)
[journal]
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)
[journal]
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)
[journal]
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)
[journal]
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)
[journal]
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)
[journal]
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)
[journal]
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 pdf abstract]
P. Johansson, J. Häkkinen
Improving
missing value imputation of microarray data by using spot quality
weights
BMC Bioinformatics 7,
306 (2006)
[journal 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
abstract
software]
P. Gärdén, R. Alm, J. Häkkinen
Proteios: an open source proteomics initiative
Bioinformatics 21, 2085-2087 (2005)
[journal
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
pdf 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)
[journal]
J. Häkkinen, M. Lagerholm, C. Peterson,
B. Söderberg
A Potts Neuron Approach to
Communication Routing
Neural Computation
10, 1587-1599 (1998)
[journal]
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)
[pdf journal]
J. Häkkinen, M. Ringnér
Bose-Einstein and colour interference in W-pair
decays
European Physical Journal
C5, 275-281 (1998)
[pdf
journal]
J. Häkkinen
bb Fragmentation and Bπ
Correlations
Zeitschrift für Physik
C75 35-40 (1997)
[pdf
journal]
C. Friberg, G. Gustafson, J. Häkkinen
Colour Connections in e+e-
annihilation
Nuclear Physics B490,
289-305 (1997)
[journal]
J. Häkkinen, H. Kharraziha
Colour: A
Computer Program for QCD Colour Factor Calculations
Computer Physics Communications 100, 311-321 (1997)
[journal
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)
[journal]
MC program (Link has expired, contact
jari.hakkinen@med.lu.se).
G. Gustafson, J. Häkkinen
Deuteron
production in e+e--annihilation
Zeitschrift für Physik C61, 683-688 (1994)
[journal]
G. Gustafson, J. Häkkinen
Lambda-polarization in e+e--annihilation at
the Z0-pole
Physics Letter
B303, 350-354 (1993)
[jounal]
P. Johansson, R. Alm, C. Emanuelsson,
J. Häkkinen, M. Ringnér
SPECLUST: a web tool for clustering of mass spectra
LU TP 07-14
[pdf abstract software]
J. Häkkinen
SWEGENE Bioinformatics Survey -
Report on Current Status and Suggestions for Future
Directions
August 2002
[pdf 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.
[Report at CERN
Dcoument Server]