| |
|
|
| Bibliography
for Joakim Lundeberg 2000-2007 |
| Peer Reviewed Articles |
| 1 - 65 publications from
1990 -1999 |
| 66. |
Odeberg J., Wood T.,
Blücher Å., Raphter J., Norstedt G., and Lundeberg
J. A modified cDNA RDA protocol on solid-phase technology
suited for analysis of gene expression in small tissue samples.
2000, Biomol Engineering, 17(1), 1-9 |
| 67. |
Blomstergren A.,
O’ Meara D., Lukacs M., Uhlén M., and Lundeberg
J., Cooperative oligonucleotides in enrichment
of cycle sequencing products. 2000, BioTechniques,
29(2), 352-358 |
68. |
Ahmadian A., Lundeberg
J., Nyrén P, Uhlén M., and Ronaghi M.
Analysis of the p53 tumor suppressor gene by pyrosequencing,
2000, BioTechniques 28, 140-147 |
69. |
Savolainen P., Arvestad
L., and Lundeberg J. mtDNA tandem repeats in domestic
dog and wolves; mutation mechanism revealed by analysis
of the sequence of imperfect repeats, 2000, Mol Biol
Evol, 17(4), 474-488 |
70. |
Tollet-Egnell P., Flores-Morales
A., Odeberg J., Lundeberg J., and Norstedt G. Differential
cloning of growth hormone regulated hepatic transcripts
in the aged rat. 2000, Endocrinology 141, 910-921 |
71. |
Savolainen P., Arvestad
L., and Lundeberg J. A novel method for forensic
DNA investigation based on repeat type sequence analysis
of domestic dog and wolf mtDNA. 2000, J. Foren Sci,
45(5), 990-999 |
72. |
Ahmadian A., Gharizadeh
B., Gustafsson A., Sterky F., Uhlén M., and Lundeberg
J. Single nucleotide polymorphism analysis by pyrosequencing.
2000, Anal Biochem 280, 103-110 |
73. |
Røsok Ø.,
Pedeutour F., Odeberg J., Lundeberg J., and Aasheim H-C.
2000. The C1orf9 gene encodes a putative transmembrane member
of a novel protein family, Biochem. Biophys Res Commun
267(3), 855-62 |
74. |
Nygren M., Reizenstein
E., Ronaghi M., and Lundeberg J. Polymorphisms
in the pertussis toxin promotor region affecting the DNA-based
diagnosis of Bordetella infection. 2000, J Clin Microbiol
38, 55-60 |
75. |
Garcia C.A., Ahmadian
A., Lundeberg J., Garizadeh B., J. Lundeberg, M. Ronaghi
M., Nyrén P. Mutation detection by pyrosequencing:
sequencing of exons 5 to 8 of the p53 tumor suppressor gene
2000, Gene 253(2), 249-257 |
76. |
Girnita L., Girnita
A., Brodin B., Zie Y., Nilsson G., Dricu A., Lundeberg J.,
Wejde J., Bartolazzi A., Wiman KG, Larsson O. Increased
expression of insulin-like growth factor I receptor in malignant
cells expressing aberrant p53: functional impact. 2000,
Cancer Res 60(18), 5278-5283 |
77. |
Persson Å.E.,
Ling G., Williams C., Bäckvall H., Pontén
J., Pontén F. and Lundeberg J. Analysis
of p53 mutations in single cells obtained from histological
tissue sections. 2000, Anal Biochem, 287, 25-31 |
78. |
Nygren M., Ronaghi
M., Nyrén P., Albert J., Uhlén M. and Lundeberg
J. Quantification of HIV-1 using multiple quantitative
PCR standards and bioluminometric detection, 2001, Anal
Biochem, 288, 28-38 |
79. |
O’Meara D., Wilbe
K., Albert J., and Lundeberg J. Monitoring resistance
to HIV-1 protease inhibitors by pyrosequencing. 2001, J
Clin Micro, 39, 464-473 |
80. |
Hertzberg M.,
Sivertzon M., Aspeborg H., Nilsson P., Sandberg G., and
Lundeberg J. cDNA microarray analysis of small
plant tissue samples using a cDNA tag target amplification
protocol. 2001, Plant J, 25(5), 585-591 |
81. |
Boräng S., Andersson
T., Larsson M., Thelin A., Odeberg J. and Lundeberg J.
Characterization of a candidate drug by solid-phase representation
difference analysis. 2001, Gene 271, 183-192 |
82. |
Sterky F., Sundberg
B., Bhalerao R., Gustafsson P., Jansson S., Jones A., Moritz
T., Nilsson O., Teeri T., Uhlén M., Lundeberg J.,
and Sandberg G. Tree genomics in Sweden: a national
network of biological and technological expertise, 2001,
AgBiotechNet, 3, 1-5 |
83. |
Gustafsson A., Guo
Z., Huo X. Ahmadian A., Brodin B., Pontén J., Pontén
F. and Lundeberg J. Determination of the codon 72
polymorphism in the p53 tumor suppressor gene in cervical
squamous cell cancer and adenomacarcinoma. 2001, Acta
Dermatology, 125-129 |
84. |
Brodin B., Haslam K.,
Yang K, Bartolazzi A., Xie Y., Starborg M., Lundeberg J.
and Larsson O. Cloning and characterisation of spliced
fusion transcripts of synovila sarcoma: SYT/SSX4 , SYT/SSX4v
and SYT/SSX2v. Possible regulatory role of the fusion gene
product in wild type SYT expression. 2001. Gene
268, 173-82 |
85. |
Ling Gao, Persson Åsa,
Berne Berit, Lundeberg Joakim, Ponten Fredrik: Persistent
p53 mutations in single cells from normal human skin. American
Journal of Pathology 159: 1247-1253, 2001 |
86. |
Ahmadian A., Gharizade
B., O’Meara D. and Lundeberg J. Genotyping
by apyrase mediated allele specific extension. 2001, Nucleic
Acids Res, 29 (24), e121, 1-5 |
87. |
Hertzberg M., Aspeborg
H., Schrader J., Anderson A., Blomqvist K., Bhalereo R.,
Rahman D., Marchant A., Melerowicz E.J., Bennett M., Uhlén
M., Teeri T., Lundeberg J., Sundberg B., Nilsson P., Sandberg
G. A transcriptional roadmap to wood formation, 2001,
Proc Natl Acad Sci USA, 98, 14732-14737 |
88. |
Ling Gao, Ahmadian
Afshin, Persson Åsa, Unden Anne Birgitte, Afink Gjis,
Williams Cecilia, Uhlen Mathias, Toftgård Rune, Lundeberg
Joakim, Ponten Fredrik: PATCHED and p53 gene alterations
in sporadic and hereditary basal cell cancer. Oncogene
20: 7770-7778, 2001 |
89. |
Flores-Morales A.,
Stahlberg N., Tollet-Egnell P, Lundeberg J, Malek RL, Quackenbush
J., Lee N., Malek R. and Norstedt G. Microarray analysis
of the in vivo effects of hypophysectomy and growth hormone
treatment on gene expression in rat. 2001 Endocrinology
142(7): 3163-76 |
90. |
Gustafsson A.,
Kiljas J., Alderborn A., Uhlén M., Andersson L.,
and Lundeberg J. Screening of single nucleotide
polymorphisms in the pig melanocortin receptor 1 using
pyrosequencing technology. 2002, Animal Biotech,
145-154 |
91. |
Kaessmann H., Zöllner
S., Gustafsson A., Wiebe V., Laan M., Lundeberg J., Uhlen
M., and Pääbo S. Extensive linkage disequilibrium
in small human populations in Eurasia. 2002 Am J of
Hum Genet, 70, 673-685 |
92. |
Agaton C., Sievertzon
M., Holmberg A., Larsson M., Unneberg P., Odeberg J., Uhlén
M., and Lundeberg J. Gene expression analysis by
signature pyrosequencing. 2002, Gene, 289, 31-39 |
93. |
Andersson T., Boräng
S., Larsson M., Thelin A., Ekstrand-Hammarström B.,
Lundeberg J., and Odeberg J. Novel candidate genes
for atherosclerosis are identified by representational difference
analysis-based transcript profiling of cholesterol-loaded
macrophages.. 2002, Pathobiology, 69(6):303-14
|
94. |
Andersson T., Unneberg
P, Nilsson P, Odeberg J, Quackenbush J and Lundeberg J.,
Monitoring of representational difference analysis subtraction
procedures by global microarrays, 2002, Biotechniques,
32:1348-1358 |
95. |
O' Meara D., Ahmadian
A., Odeberg J. and Lundeberg J. SNP typing by apyrase-mediated
allele-specific primer extension on DNA microarrays. 2002,
Nucleic Acids Res 30 (15) e75 |
96. |
Johansson H., Sterky
F., Amini B., Lundeberg J., and Kleczkowski L.A.
Molecular cloning of UDP-Glucose Dehydrogenase from cambium
of Poplar (Populus tremula x tremuloides), 2002, Biochim
Biophys Acta. 2002 Jun 7;1576(1-2):53-8 |
97. |
Ehn M, Ahmadian A.,
Nilsson P., Lundeberg J. and Hober S. Esherichia
coli Single-stranded DNA-binding protein (SSB), a molecular
tool for improved sequence quality in pyrosequencing. 2002
Electrophoresis, 23:3289-3299 |
98. |
Sivertsson A, Platz
A, Hansson J, Lundeberg J Pyrosequencing as an alternative
to single-strand conformation polymorphism analysis for
detection of N-ras mutations in human melanoma metastases.
Clin Chem. 2002 Dec;48(12):2164-70 |
99. |
Persson AE, Edstrom
DW, Backvall H, Lundeberg J, Ponten F, Ros AM, Williams
C. The Mutagenic Effect of UVA1 in Human Skin: An
analysis of the p53 gene in single keratinocytes. 2002,
Photoderm, Photoimm and Photomed, 2002 Dec;18(6):287-93 |
100. |
Savolainen P.,.Zhang
Y., Luo J, Lundeberg J, and Leitner T.Genetic evidence
of an East Asian origin of domestic dogs, Science,
2002, Nov 22;298(5598):1610-3 |
101. |
Bhalerao R, Keskitalo
J, Sterky F, Erlandsson R, Bjorkbacka H, Birve SJ, Karlsson
J, Gardestrom P, Gustafsson P, Lundeberg J, Jansson S.
Gene expression in autumn leaves. Plant Physiol.
2003 Feb;131(2):430-42 |
102. |
Andersson T., Boräng
S., Wirta V., Thelin A., Lundeberg J., and Odeberg J
Shotgun sequencing and microarray analysis of RDA transcripts,
2003, Gene, 310, 39-47 |
103. |
Ericsson, O., Sivertsson,
Å., Lundeberg, J. and Ahmadian, A.: Microarray
based re-sequencing by apyrase-mediated allele-specific
extension. Electrophoresis, 2003, 24:3330-8 |
104. |
Agaton C., Galli J.,
Ingmarie Höidén Guthenberg, Lars Janzon, Marianne
Hansson, Anna Asplund, Eva Brundell, Susanne Lindberg, Irene
Ruthberg, Kenneth Wester, Dorothee Wurtz, Christer Höög,
Joakim Lundeberg, Stefan Ståhl, Fredrik Pontén
and Mathias Uhlén.: Analysis of human chromosome
21 using reporter ligand proteomics. Mol Cell Proteomics,
2003, 2(6), 405-414 |
105. |
Gharizadeh B, Kaller
M, Nyren P, Andersson A, Uhlen M, Lundeberg J, Ahmadian
A.Viral and microbial genotyping by a combination
of multiplex competitive hybridization and specific extension
followed by hybridization to generic tag arrays. Nucleic
Acids Res. 2003 Nov 15;31(22):e146. |
106. |
Boräng S., Anderssson
T., Thelin A., Odeberg J., and Lundeberg J..Vascular
gene expression in atherosclerotic plaque prone regions
analysed by representational difference analysis. Pathobiology
2004, 71, 107-14 |
107. |
Johansson T, Le Quere
A, Ahren D, Soderstrom B, Erlandsson R, Lundeberg J, Uhlen
M, and Tunlid A. Transcriptional responses of Paxillus
involutus and Betula pendula during formation of ectomycorrhizal
root tissue. Mol Plant Microbe Interact. 2004 Feb;17(2):202-15 |
108. |
Westberg J., Persson
A., Holmberg A., Goesmann A., Lundeberg J., Johansson K-E.,
Pettersson B., and Uhlen M. The genome sequence of
Mycoplasma mycoides subsp mycoides SC, the causative agent
of contagious bovine pleuropneumonia (CBPP). Genome
Research, 2004, 14, 221-7 |
109. |
Andersson A., Keskitalo
J., Bhalerao R., Sjödin A., Sterky F., Wissel K., Bhalerao
R., Gustafsson P., Karlsson J., Lundeberg J., Moyle R.,
Nilsson O., Sandberg G., Sundberg B., Tandre K., Uhlen M,
Jansson S., Nilsson P.. A transcriptional timetable
of autumn senescence. Genome Biol. 2004;5(4) |
110. |
Blomstergren A., Lundin
A., Nilsson, C., Engstrand, L. and Lundeberg J. Comparative
analysis of the complete cag pathogenicity island sequence
in four Helicobacter pylori isolates. Gene. 2004
17;328:85-93 |
111. |
Sterky F., Bhalerao
R., Unneberg P., Segerman B., Nilsson P., Brunner A., Charbnonel-Campaa
L., Jonsson Lindvall J., Tandre K., Strauss S., Sundberg
B., Gustafsson P., Uhlen M., Bhalerao R., Nilsson O., Sandberg
G., Karlsson J., Lundeberg J., and Jansson S. A Populus
EST resource for plant functional genomics. Proc Natl
Acad Sci 2004, USA, 101, 13951-6 |
112. |
Bäckvall H., Strömberg
S., Gustafsson, A.C., Asplund A., Sivertsson Å., Lundeberg
J., Pontén F. Mutation Spectra of Epidermal
p53 Clones adjacent to Basal Cell Carcinoma and Squamous
Cell Carcinoma. (2004). Exp. Dermatology. 13, 643-50 |
113. |
Hilson P, Allemeersch
J., Altmann T., Aubourg S., Lundeberg J.,...Zabeau M.,
Small I.Versatile Gene-Specific Sequence Tags for Arabidopsis
Functional Genomics: Transcript Profiling and Reverse Genetics
Applications. 2004 Genome Research, 14, 2176-89 |
114. |
Ehn M., Nourizad N.,
Bergström K., Ahmadian A., Nyren P., Lundeberg J. and
Hober S. Toward pyrosequencing on surface-attached
genetic material by use of DNA-binding luciferase fusions
protein. Anal Biochem, 2004, 329, 11-20 |
115. |
Sivertzon M., Agaton
C., Nilsson P. and Lundeberg J. Transcriptome amplification
from small tissue samples Biotechniques. 2004;36(2):253-9 |
116. |
Savolainen P, Leitner
T, Wilton A, Matisoo-Smith E, Lundeberg J. A detailed
picture of the origin of the Australian dingo, obtained
from the study of mitochondrial DNA. 2004, Proc Natl
Acad Sci USA, 101(33), 12387-12390 |
117. |
Fitzsimmons CJ, Savolainen
P, Amini B, Hjälm G, Lundeberg J, Andersson L.
Detection of sequence polymorphisms in red junglefowl and
White Leghorn ESTs. 2004, Animal Genetics, 35,
391-6 |
118. |
Schrader J., Moyle
R., Bhalerao R., Hertzberg M., Lundeberg J., Nilsson P.
and Bhalerao R.P. Cambial meristem dormancy in trees
involves extensive remodelling of the transcriptome. 2004.
Plant J., 40, 173-87 |
119. |
Kaller M, Ahmadian
A, Lundeberg Microarray-based AMASE as a novel approach
for mutation detection. J. Mutat Res 2004, 554,
77-88 |
120. |
Holmberg, A., Lukacs,
M., Holmberg, K., Lundeberg, J. and Uhlen, M. The
biotin-streptavidin interaction can be reversibly broken
with non-ionic solutions at elevated temperatures, 2005.
Electrophoresis, 26, 501-10 |
121. |
Gustafsson A.C., Ren
Z., Asplund A., Pontén F. and Lundeberg J.
The Role of p53 Codon 72 and HPV Status of Cutaneous Squamous
Cell Carcinoma in the Swedish Population. 2005 Acta
Dermatology, 84, 439-44 |
122. |
Wirta V., Lukacs M.,
Holmberg A., Bhalearo R., Nilsson P., Uhlen,M., and Lundeberg
J.. A whole genome Arabidopsis thaliana microarray
prepared using a novel probe purification technology. 2005,
BMC Biotechnology 5, 5 |
123. |
Savolainen P., Fitzsimmons
C., Arvestad L., Andersson L, and Lundeberg J.. EST
analysis of brain and testis cDNA libraries from White leghorn
and Red Jungle Fowl, Cytogenet Genome Res. 2005;111(1):79-87 |
124. |
Asplund A., Gustafsson
A.C., Wikonkal N.M., Lundeberg J., Brash D.E. and Pontén
F. PTCH Codon 1315 Polymorphism and Risk for Non
Melanoma Skin Cancer. Br J Dermatol. 2005 May;152(5):868-73 |
125. |
Gustafsson A.C., Kupershmidt
I., Edlundh-Rose E., Parasassi T., Grecco G., Bracci-Laudiero
L., Lundeberg J. Global Gene Expression Analysis
in Time Series Following N-Acetyl L-Cysteine Induced Epithelial
Differentiation of Human Normal and Cancer cells in vitro.
BMC Cancer. 2005 Jul 7;5:75 |
126. |
Käller M, Hultin
E., Zheng B., Gharizadeh B., Wallin K-L, Lundeber J and
Ahmadian A. HPV Genotyping by Competitive Hybridization
and Extension Detected on Signature-Tagged Microarrays.
J Virol Methods. 2005 129(2):102-12 |
127. |
Sievertzon M, Wirta
V, Mercer A., Meletis K, Erlandsson R., Wikström L,
Frisén J, Lundeberg J. Transcriptome analysi
in primary neural stem cells using a tag cDNA amplification
method. BMC Neuroscience, 2005 Apr 15;6(1):28 |
128. |
Backvall H, Asplund
A, Gustafsson A, Sivertsson A, Lundeberg J, Ponten F.
Genetic tumor archeology: microdissection and genetic heterogeneity
in squamous and basal cell carcinoma. Mutat Res.
2005, 571(1-2):65-79. |
129. |
Hultin E, Kaller M,
Ahmadian A, Lundeberg J.Competitive enzymatic reaction
to control allele-specific extensions. Nucleic Acids
Res. 2005 Mar 14;33(5):e48. |
130. |
Parasassi T.,Brunelli
R. , Bracci-Laudiero L, Greco G., Gustafsson A., Krasnowska
E., Lundeberg J., Lundeberg T., Pittaluga E., Romano MC,
and Serafino A. Differentiation of normal and cancer
cells induced by sulfhydryl-reduction. Biochemical and molecular
mechanisms, Cell Death Differ. 2005 Oct;12(10):1285-96 |
131. |
Edlundh-Rose E,., Kupershmidt
I, Gustafsson A.C., Parasassi T., Grecco G., Bracci-Laudiero
L., Lundeberg J. Gene expression analysis of human
epidermal keratinocytes over time following the addition
of the antioxidant N-Acetyl L-Cysteine using spotted cDNA
microarrays. 2005, Pathobiology, 72(4): 203-12 |
132. |
Sievertzon M, Wirta
V, Mercer A, Frisén J, Lundeberg J. Epidermal
growth factor (EGF) withdrawal masks gene expression differences
in the study of pituitary adenylate cyclase-activating polypeptide
(PACAP) activation of primary neural stem cell proliferation
BMC Neurosci. 2005 Aug 28;6:55 |
133. |
Arvestad L, Visa N,
Lundeberg J, Wieslander L, and Savolainen P. ESTs
from midgut and an epithelial cell line of Chironomus tentans:
annotation, bioinformatic classification of unknown transcripts
and analysis of expression levels. Insect Mol. Biol.
2005: 14(6):689-95 |
134. |
Velazquez-Fernandez,
D, Laurell, C, Geli, J, Höög, A, Odeberg, J, Kjellman,
M, Lundeberg, J, Hamberger, B, Nilsson, P and Bäckdahl,
M: Expression profiling of adrenocortical tumors suggests
a molecular signature of malignancy. Surgery 2005,
138(6):1087-94 |
135. |
Käller M., Tuominen
R., Ahmadian A., Magnusson V., Egyhazi S., Hansson J. and
Lundeberg J. Detection of mutations in MC1R with
PrASE as an alternative to direct sequencing. 2005, Clin
Chem 51(12):2388-91. |
136. |
Janzi M, Odling J,
Pan-Hammarstrom Q, Sundberg M, Lundeberg J, Uhlen M, Hammarstrom
L, Nilsson P. Serum microarrays for large scale screening
of protein levels. Mol Cell Proteomics. 4(12):1942-1947.] |
137. |
Asplund A, Sivertsson
A, Backvall H, Ahmadian A, Lundeberg J, Ponten F
Genetic mosaicism in basal cell carcinoma. Exp Dermatol.
2005 Aug;14(8):593-600 |
138. |
Ka S, Fitzsimmons C,
Jacobsson L, Savolainen P, Lundeberg J, Siegel PB, Andersson
L, Hallbook F. Expression analysis of growth and
energy regulation-associated genes in two divergent chicken
strains. Ann N Y Acad Sci. 2005 Apr;1040:357-9 |
139. |
Uhlén, M, Björling,
E., Agaton, C., Al-Khalili Szigyarto, C., Amini, B., Andersen,
E., Andersson, A.-C., Angelidou, P., Asplund, A., Asplund,
C., Berglund, L., Bergström, K., Brumer, H., Cerjan,
D., Ekström, M., Elobeid, A., Eriksson, C., Fagerberg,
L., Falk, R., Fall, J., Forsberg, M., Björklund, M.G.,
Gumbel, K., Halimi, A., Hallin, I., Hamsten, C., Hansson,
M., Hedhammar, M., Hercules. G., Kampf, C., Larsson, K.,
Lindskog, M., Lodewyckx, W., Lund, J., Lundeberg, J., Magnusson,
K., Malm, E., Nilsson, P., Ödling, J., Oksvold, P.,
Olsson, I., Öster, E., Ottosson, J., Paavilainen, L.,
Persson, A., Rimini, R., Rockberg, J., Runeson, M., Sivertsson,
Å., SköllermoA., Steen, J., Stenvall, M., Sterky,
F., Strömberg, S., Sundberg, M., Tegel, H., Tourle,
S., Wahlund, E., WaldénA., Wan, J., Wernérus,
H., Westberg, J., Wester, K., Wrethagen, U., Xu, L.-L.,
Hober, S. & Pontén, F., A human protein
atlas for normal and cancer tissues based on antibody proteomics,
2005 Mol Cell Proteomics. 4(12):1920-1932. |
140. |
Meletis K, Wirta V.,
Hede SM., Nistér M., Lundeberg J. and Frisén
J. p53 suppresses the self-renewal of adult neural
stem cells. Development. 2006 Jan;133(2):363-9 |
141. |
Unneberg P., Strömberg
M., Lundeberg J., Jansson S. and Sterky F. Analysis
of 70,000 EST sequences to study divergence between two
closely related Populus species. 2006 Tree Genetics
and Genomes, 1:109-115 |
142. |
Lindberg J., af Klint
E., Ulfgren AK., Stark A., Andersson T., Nilsson P., Klareskog
L, Lundeberg J., Investigation of tissue heterogeniety
between multiple biopsies retreived from the same synovial
joint, Arthritis Res Ther. 2006 Feb 16;8(2):R47 |
143, |
Richter, K., Wirta,
V., Dahl, L., Bruce, SK., Lundeberg, J., Carlsson, L. and
Williams C. (2006). Global gene expression analyses
of hematopoietic stem cell-like cell lines with inducible
Lhx2 expression. BMC Genomics 7, 75 |
144. |
Käller M., Hultin
E., Holmberg K., Persson M-L, Odeberg J., Lundeberg J. and
Ahmadian A. Comparison of PrASE and Pyrosequencing
for SNP GenotypinG, BMC Genomics. 2006 Nov 16;7:291. |
145. |
Williams, C., Wirta,
V., Meletis, K., Wikstrom, L., Carlsson, L., Frisen, J.,
and Lundeberg, J. (2006). Catalog of gene expression
in adult neural stem cells and their in vivo microenvironment.
Exp Cell Res., 2006 Jun 10;312(10):1798-812 |
146. |
Liu T., Laurell C.,
Selivanova G., Lundeberg J, Nilsson P. and Wiman K.G.
Hypoxia induces p53-dependent transactivation and Fas-dependent
apoptosis, Cell Death Differ. 2007 Mar;14(3):411-21.
Epub 2006 Aug 18. |
147. |
Petterson E., Lindskog
M., Lundeberg J and Ahmadian A. Tri-nucleotide threading
for parallel amplification of minute amounts of genomic
DNA. Nucleic Acids Res. 2006 Mar 31;34(6):e49 |
148. |
Laurell C, Nilsson
P., and Lundeberg J. Comparative analysis of an exponential
DNA versus a linear RNA amplification approach for microarray
analysis. J Biotechnol. 2007 Jan 20;127(4):638-46.
Epub 2006 Sep 25 |
149. |
Edlundh-Rose E, Egyházi
S, Omholt K, Månsson-Brahme E, Hansson J, and Lundeberg
J. Lower age at diagnosis in melanomas with BRAF
as compared to NRAS mutations., Melanoma Res. 2006
Dec;16(6):471-8. |
150. |
Lindberg J., af Klint
E., Catrina A., Nilsson P., Klareskog L, Ulfgren AK and
Lundeberg J. Effect of infliximab on mRNA expression
profiles in synovial tissue of RA patients, Arthritis
Res Ther. 2006;8(6):R179. |
151. |
Natanaelsson C, Oskarsson
M, Angleby H, Lundeberg J, Kirkness E and Savolainen P.
Dog Y chromosomal DNA sequence: identification, sequencing
and SNP discovery. BMC Genet. 2006 Oct 6;7:45. |
152. |
Lindqvist C, Janczak
AM, Nätt D, Baranowska I, Lindqvist N, Wichman A, Lundeberg
J, Lindberg J Torjesen PA & Jensen P. Transmission
of Stress-induced Learning Impairment and Associated Brain
Gene Expression from Parents to Offspring in Chickens. PLoS
ONE. 2007 Apr 11;2:e364 |
153. |
Svensson P., Williams
C, Lundeberg J, Ryden P, I Bergqvist I. and Edlund H.
Gene array identification of Ipf1/Pdx1 -/- regulated genes
in pancreatic progenitor cells. BMC Dev Biol. 2007
Nov 23;7:129. |
154. |
Rubin. C-J, Lindberg.
J, Fitzsimmons. C, Savolainen. P , Jensen. P, Lundeberg.
J, Andersson. L, Kindmark. A Differential gene expression
in femoral bone from Red junglefowl and domestic chicken,
differering for bone phenotypic traits.BMC Genomics.
2007 Jul 2;8:208 |
155. |
Ståhl PL, Gantelius
J, Natanaelsson C, Ahmadian A, Andersson-Svahn H and Lundeberg
J. Visual DNA - identification of DNA sequence variations
by bead trapping. Genomics. 2007 Dec;90(6):741-5.
Epub 2007 Oct 24. |
156. |
Gry Björklund
M, Natanaelsson C, Hao Y, and Lundeberg J. Array
analysis using disiloxyl 70mer oligonucleotides. Nucleic
Acids Res. 2008 Mar;36(4):1334-42. Epub 2008 Jan 10 |
157. |
Ribacke U, Mok BW,
Wirta V, Normark J, Lundeberg J, Kironde F, Egwang TG, Nilsson
P, Wahlgren M. Genome wide gene amplifications and
deletions in Plasmodium falciparum. Mol Biochem Parasitol.
2007 Sep;155(1):33-44. Epub 2007 May 18 |
158. |
Apostolova G, Dorn
R, Ka S, Hallbook F, Lundeberg J, Liser K, Hakim V, Brodski
C, Michaelidis TM, Dechant G. Neurotransmitter phenotype-specific
expression changes in developing sympathetic neurons.Mol
Cell Neurosci. 2007 Jul;35(3):397-408. Epub 2007 Apr
|
| Review articles, Book chapters
etc |
| 1 – 15 reviews from 1990 -1999 |
16. |
Sterky F., and Lundeberg
J. Sequencing genes and genomes, J Bacteriology,
76 (2000), 1-31 |
17. |
Sivertzon M and Lundeberg
J. Kapplöpningen om kartläggningen av den
mänskliga arvsmassan Hugo projeketet, slutet på
början. 2000 Tidskriften Medikament, 5, 77-80 |
18. |
Savolainen P. and Lundeberg
J. Dog genetic data and forensic evidence. In The
genetics of the dog. Eds Ruvanski and Sampson, 2001,
521-536 |
19. |
Persson Å., Bäckvall
H., Ponten F., Uhlen M. and Lundeberg J. Single cell
gene mutation analysis using laser-assisted microdissection
of tissue sections. 2002 Meth Enzym, 356, 334-343 |
20. |
Ahmadian A. and Lundeberg
J., Brief history of genetic variation analysis,
2002, Biotechniques, 2002 May;32(5):1122-1128 |
21. |
O'Meara D and Lundeberg
J, DNA methods in viral epidemiology In The Molecular
Epidemiology of human viruses. (Ed Leitner T), 2002,
11-25 |
22. |
Ponten F. and Lundeberg
J. Principles of tumor biology and pathogenesis of
BCCs and SCCs. Dermatology, Harcourt Health Sciences
Publishers Ltd, 2003. |
23. |
Micke P., Östman
A., Lundeberg J and Ponten F. Laser-assisted cell
microdissection using the PALM system. Methods Mol Biol.
2005;293:151-66 |
24. |
Sivertzon M, Nilsson
P. and Lundeberg J. Improving reliability and performance
of DNA microarrays, Expert Review of Molecular Diagnostics,
Expert Rev Mol Diagn. 2006 May;6(3):481-92. Review. |
25. |
Ponten F. Asplund
A. and Lundeberg J. Neoplasma of skin. Principles
of tumor biology and pathogenesis of BCCs and SCCs. Dermatology
(2nd edition), Harcourt Health Sciences Publishers Ltd,
2008. in press |
26. |
Käller M., Lundeberg
J and Ahmadian A. Arrayed identification of DNA signatures,
Expert Rev Mol Diagn. 2007 Jan;7(1):65-76. Review |
Patents |
1. |
Allele-specific primer
extension assay
Inventor: AHMADIAN AFSHIN; NYREN PAL; LUNDEBERG JOAKIM
Applicant : PYROSEQUENCING AB
EC: C12Q1/68B10A; C12Q1/68D2G IPC: C12Q1/68; C12Q1/68
Publiceringsinformation: AU2002233540 - 2008-02-14 |
2. |
METHOD FOR AMPLIFICATION
Inventor: AHMADIAN AFSHIN (SE); PETTERSSON ERIK (SE); LUNDEBERG
JOAKIM Sökande: SEDNA BIOTECHNOLOGIES AB (SE)
EC: C12Q1/68D4 IPC: C12Q1/68; C12Q1/68
Publiceringsinformation: EP1874957 - 2008-01-09 |
3. |
Allele-specific mutation
detection assay
Inventor: AHMADIAN AFSHIN (SE); LUNDEBERG JOAKIM (SE)
EC: C12Q1/68B6 IPC: C12Q1/68; C12P19/34; C12P19/00 (+1)
Publiceringsinformation: US2006088872 - 2006-04-27 |
4. |
The use of modular
oligonucleotides as probes or primers in nucleic acid based
assay
Inventor: LUNDEBERG JOAKIM (SE); UHLEN MATHIAS (SE)
Applicant: DYNAL BIOTECH ASA OSLO OSLO (NO)
EC: C12Q1/68B8; C12Q1/68D2; (+1) IPC: C12Q1/68; G01N33/543;
C12N15/09 (+4)
Publiceringsinformation: DE69732419T - 2006-04-06 |
5. |
Method of assessing
the amount of nucleic acid in a sample
Inventor: LUNDEBERG JOAKIM (SE); RONAGHI MOSTAFA (US)
EC: C12Q1/68D2C IPC: C12Q1/68; C12Q1/68; (IPC1-7): C12Q1/68
(+1)
Publiceringsinformation: US2003157499 - 2003-08-21 |
6. |
Allele-specific primer
extension assay
Inventor: LUNDEBERG JOAKIM (SE); AHMADIAN AFSHIN (SE); (+1)
Applicant: PYROSEQUENCING AB (SE); DZIEGLEWSKA HANNA (GB);
(+3)
EC: C12Q1/68B10A; C12Q1/68D2G IPC: C12Q1/68; C12Q1/68; (IPC1-7):
C12Q1/68
Publiceringsinformation: WO02068684 - 2002-09-06 |
7. |
Allele specific primer
extension
Inventor: AHMADIAN AFSHIN (SE); LUNDEBERG JOAKIM (SE); (+1)
Applicant: PYROSEQUENCING AB (US)
EC: C12Q1/68D2G; C12Q1/68E IPC: C12Q1/68; C12Q1/68; (IPC1-7):
C12Q1/68 (+1)
Publiceringsinformation: US2003104372 - 2003-06-05 |
8. |
Method of isolation
primer extension products with modular oligonucleotides
Inventor: LUNDEBERG JOAKIM (SE); UHLEN MATHIAS (SE)
Applicant: DYNAL AS (NO); JONES ELIZABETH LOUISE (GB); (+2)
EC: C12Q1/68B8; C12Q1/68B10; (+1) IPC: C12N15/09; C12Q1/68;
C12N15/09 (+2)
Publiceringsinformation: WO0015842 - 2000-03-23 |
9. |
Method of isolation
primer extension products with modular
oligonucleotides
Inventor: LUNDEBERG JOAKIM; UHLEN MATHIAS Sökande:
DYNAL ASA
EC: IPC: C12Q1/68; C12Q1/68; (IPC1-7): C12Q1/68
Publiceringsinformation: AU773108B - 2004-05-13 |
10. |
Activating a reversibly
inactivated immobilized enzyme by
release from an immobilizing moiety
Inventor: LUNDEBERG JOAKIM (SE); UHLEN MATHIAS (SE)
Applicant: DYNAL AS (NO)
EC: C07K14/315; C07K14/705B26; (+3) IPC: G01N33/58; C07K14/315;
C07K14/735 (+13)
Publiceringsinformation: US6610479 - 2003-08-26 |
11. |
Method for quantifying
nucleic acid using multiple competitor nucleic acids
Inventor: LUNDEBERG JOAKIM (SE); UHLEN MATHIAS (SE)
Applicant :DYNAL AS (NO); DZIEGLEWSKA HANNA EVA (GB); (+2)
EC: C12Q1/68D2C; C12Q1/70B2B IPC: C12Q1/68; C12Q1/70; C12Q1/68
Publiceringsinformation: WO9712058 - 1997-04-03 |
12. |
Chemical method for
the analysis of DNA sequences
Inventor: UHLEN MATHIAS (SE); LUNDEBERG JOAKIM (SE)
Applicant: CEMU BIOTEKNIK AB (SE)
EC: C12Q1/68B10; C12Q1/68D2G; (+1) IPC: C12N15/09; C12Q1/68;
C12N15/09 (+5)
Publiceringsinformation: US5534424 - 1996-07-09 |
| Bibliography
for Afshin Ahmadian 2000-2007 |
| Peer Reviewed Articles |
| 1. |
A. Ahmadian, B. Gharizadeh, A.C.
Gustafsson, F. Sterky, P. Nyren, M. Uhlen, and J. Lundeberg,
Single-nucleotide polymorphism analysis by pyrosequencing.
Anal Biochem 280 (2000) 103-10. |
2. |
A. Ahmadian, J. Lundeberg, P. Nyren,
M. Uhlen, and M. Ronaghi, Analysis of the p53 tumor
suppressor gene by pyrosequencing. Biotechniques
28 (2000) 140-4, 146-7. |
3. |
C.A. Garcia, A. Ahmadian, B. Gharizadeh,
J. Lundeberg, M. Ronaghi, and P. Nyren, Mutation
detection by pyrosequencing: sequencing of exons 5-8 of
the p53 tumor suppressor gene. Gene 253 (2000)
249-57 |
4. |
A. Ahmadian, B. Gharizadeh, D. O'Meara,
J. Odeberg, and J. Lundeberg, Genotyping by apyrase-mediated
allele-specific extension. Nucleic Acids Res 29
(2001) E121. |
5. |
A.C. Gustafsson, Z. Guo, X. Hu,
A. Ahmadian, B. Brodin, A. Nilsson, J. Ponten, F. Ponten,
and J. Lundeberg, HPV-related cancer susceptibility
and p53 codon 72 polymorphism. Acta Derm Venereol
81 (2001) 125-9. |
6. |
G. Ling, A. Ahmadian, A. Persson,
A.B. Unden, G. Afink, C. Williams, M. Uhlen, R. Toftgard,
J. Lundeberg, and F. Ponten, PATCHED and p53 gene
alterations in sporadic and hereditary basal cell cancer.
Oncogene 20 (2001) 7770-8. |
7. |
A. Ahmadian, and J. Lundeberg,
A brief history of genetic variation analysis. Biotechniques
32 (2002) 1122-4, 1126, 1128 passim |
8. |
A. Ahmadian, A. Russom, H. Andersson,
M. Uhlen, G. Stemme, and P. Nilsson, SNP analysis
by allele-specific extension in a micromachined filter chamber.
Biotechniques 32 (2002) 748, 750, 752, 754. |
9. |
M. Ehn, A. Ahmadian, P. Nilsson,
J. Lundeberg, and S. Hober, Escherichia coli single-stranded
DNA-binding protein, a molecular tool for improved sequence
quality in pyrosequencing. Electrophoresis 23 (2002)
3289-99. |
10. |
B. Gharizadeh, T. Nordstrom, A.
Ahmadian, M. Ronaghi, and P. Nyren, Long-read pyrosequencing
using pure 2'-deoxyadenosine-5'-O'-(1-thiotriphosphate)
Sp-isomer. Anal Biochem 301 (2002) 82-90 |
11. |
D. O'Meara, A. Ahmadian, J. Odeberg,
and J. Lundeberg, SNP typing by apyrase-mediated
allele-specific primer extension on DNA microarrays.
Nucleic Acids Res 30 (2002) e75. |
12. |
O. Ericsson, A. Sivertsson, J. Lundeberg,
and A. Ahmadian, Microarray-based resequencing by
apyrase-mediated allele-specific extension. Electrophoresis
24 (2003) 3330-8. |
13. |
B. Gharizadeh, M. Kaller, P. Nyren,
A. Andersson, M. Uhlen, J. Lundeberg, and A. Ahmadian,
Viral and microbial genotyping by a combination of multiplex
competitive hybridization and specific extension followed
by hybridization to generic tag arrays. Nucleic Acids
Res 31 (2003) e146. |
14. |
A. Russom, A. Ahmadian, H. Andersson,
P. Nilsson, and G. Stemme, Single-nucleotide polymorphism
analysis by allele-specific extension of fluorescently labeled
nucleotides in a microfluidic flow-through device. Electrophoresis
24 (2003) 158-61 |
15. |
M. Ehn, N. Nourizad, K. Bergstrom,
A. Ahmadian, P. Nyren, J. Lundeberg, and S. Hober,
Toward pyrosequencing on surface-attached genetic material
by use of DNA-binding luciferase fusion proteins. Anal
Biochem 329 (2004) 11-20. |
16. |
M. Kaller, A. Ahmadian, and J. Lundeberg,
Microarray-based AMASE as a novel approach for mutation
detection. Mutat Res 554 (2004) 77-88. |
17. |
A. Asplund, A. Sivertsson, H. Backvall,
A. Ahmadian, J. Lundeberg, and F. Ponten, Genetic
mosaicism in basal cell carcinoma. Exp Dermatol
14 (2005) 593-600. |
18. |
B. Gharizadeh, M. Oggionni, B. Zheng,
E. Akom, N. Pourmand, A. Ahmadian, K.L. Wallin, and P. Nyren,
Type-specific multiple sequencing primers: a novel strategy
for reliable and rapid genotyping of human papillomaviruses
by pyrosequencing technology. J Mol Diagn 7 (2005)
198-205 |
19. |
E. Hultin, M. Kaller, A. Ahmadian,
and J. Lundeberg, Competitive enzymatic reaction
to control allele-specific extensions. Nucleic Acids
Res 33 (2005) e48. |
20. |
M. Kaller, E. Hultin, B. Zheng,
B. Gharizadeh, K.L. Wallin, J. Lundeberg, and A. Ahmadian,
Tag-array based HPV genotyping by competitive hybridization
and extension. J Virol Methods 129 (2005) 102-12. |
21. |
M. Kaller, R. Tuominen, A. Ahmadian,
V. Magnusson, S. Egyhazi, J. Hansson, and J. Lundeberg,
Detection of MC1R polymorphisms with protease-mediated allele-specific
extension as an alternative to direct sequencing. Clin
Chem 51 (2005) 2388-91. |
22. |
A. Ahmadian, M. Ehn, and S. Hober,
Pyrosequencing: history, biochemistry and future. Clin
Chim Acta 363 (2006) 83-94. |
23. |
M. Kaller, E. Hultin, K. Holmberg,
M.L. Persson, J. Odeberg, J. Lundeberg, and A. Ahmadian,
Comparison of PrASE and Pyrosequencing for SNP Genotyping.
BMC Genomics 7 (2006) 291. |
24. |
E. Pettersson, M. Lindskog, J. Lundeberg,
and A. Ahmadian, Tri-nucleotide threading for parallel
amplification of minute amounts of genomic DNA. Nucleic
Acids Res 34 (2006) e49. |
25. |
M. Kaller, J. Lundeberg, and A.
Ahmadian, Arrayed identification of DNA signatures.
Expert Rev Mol Diagn 7 (2007) 65-76. |
26. |
P.L. Stahl, J. Gantelius, C. Natanaelsson,
A. Ahmadian, H. Andersson-Svahn, and J. Lundeberg,
Visual DNA -- identification of DNA sequence variations
by bead trapping. Genomics 90 (2007) 741-5. |
27. |
E. Pettersson, P. Zajac, P.L. Stahl,
J.A. Jacobsson, R. Fredriksson, C. Marcus, H.B. Schioth,
J. Lundeberg, and A. Ahmadian, Allelotyping by massively
parallel pyrosequencing of SNP-carrying trinucleotide threads.
Hum Mutat 29 (2008) 323-9. |
28. |
P. Zajac, E. Pettersson, M. Gry,
J. Lundeberg, and A. Ahmadian, Expression profiling
of signature gene sets with trinucleotide threading. Genomics
91 (2008) 209-17. |
| List of Patent |
| 1. |
Allele-specific primer extension
assay
Inventor: AHMADIAN AFSHIN; NYREN PAL; LUNDEBERG JOAKIM
Applicant : PYROSEQUENCING AB
EC: C12Q1/68B10A; C12Q1/68D2G IPC: C12Q1/68; C12Q1/68
Publiceringsinformation: AU2002233540 - 2008-02-14 |
| 2. |
Method for amplification
Inventor: AHMADIAN AFSHIN (SE); PETTERSSON ERIK (SE); LUNDEBERG
JOAKIM
Sökande: SEDNA BIOTECHNOLOGIES AB (SE)
EC: C12Q1/68D4 IPC: C12Q1/68; C12Q1/68
Publiceringsinformation: EP1874957 - 2008-01-09 |
| 3. |
Allele-specific mutation detection
assay
Inventor: AHMADIAN AFSHIN (SE); LUNDEBERG JOAKIM (SE)
EC: C12Q1/68B6 IPC: C12Q1/68; C12P19/34; C12P19/00 (+1)
Publiceringsinformation: US2006088872 - 2006-04-27 |
| 4. |
Allele-specific primer extension
assay
Inventor: LUNDEBERG JOAKIM (SE); AHMADIAN AFSHIN (SE)
Applicant: PYROSEQUENCING AB (SE); DZIEGLEWSKA HANNA (GB);
EC: C12Q1/68B10A; C12Q1/68D2G IPC: C12Q1/68; C12Q1/68; (IPC1-7):
C12Q1/68
Publiceringsinformation: WO02068684 - 2002-09-06 |
| 5. |
Allele specific primer extension
Inventor: AHMADIAN AFSHIN (SE); LUNDEBERG JOAKIM (SE);
Applicant: PYROSEQUENCING AB (US)
EC: C12Q1/68D2G; C12Q1/68E IPC: C12Q1/68; C12Q1/68; (IPC1-7):
C12Q1/68
Publiceringsinformation: US2003104372 - 2003-06-05 |
Bibliography Peter
Nilsson 2000-2007 |
| H. Gräns, B. Evengård
and P. Nilsson (2007), Transcriptome analysis of
peripheral blood mononuclear cells from patients with Chronic
Fatigue Syndrome J Chronic Fatigue Syndrome 14
(3): 7-25 |
| L. Henríquez-Hernández,
A. Flores-Morales, R. Santana-Farré, M. Axelson,
P. Nilsson, G. Norstedt and L. Fernández-Pérez
(2007), Role of pituitary hormones on 17a-ethinylestradiol-induced
cholestasis in rat J Pharmacol Exp Ther 320 (2):
695-705 |
| C. Laurell, V. Wirta,
P. Nilsson and J. Lundeberg (2007), Comparative analysis
of a 3' end tag PCR and a linear RNA amplification approach
for microarray analysis Journal of Biotechnology
127 (4): 638-646 |
| T. Liu, C. Laurell,
G. Selivanova, J. Lundeberg, P. Nilsson and K. G. Wiman
(2007), Hypoxia induces p53-dependent transactivation and
Fas-dependent apoptosis Cell Death & Differentiation
14 (3): 411-421 |
| B. W. Mok, U. Ribacke,
G. Winter, B. H. Yip, C.-S. Tan, V. Fernandez, Q. Chen,
P. Nilsson and M. Wahlgren (2007), Comparative Transcriptomal
Analysis of Isogenic Plasmodium falciparum Clones of Distinct
Antigenic and Adhesive Phenotypes Molecular and Biochemical
Parasitology 151 (2): 184-192 |
| Z. Pei, H. Yu, M. Theurer,
A. Waldén, P. Nilsson, M. Yan and O. Ramström
(2007), Photogenerated Carbohydrate Microarrays ChemBioChem
8 (2): 166-168 |
| U. Ribacke, B. W. Mok,
V. Wirta, J. Normark, J. Lundeberg, F. Kironde, T. G. Egwang,
P. Nilsson and M. Wahlgren (2007), Genome Wide Gene
Amplifications and Deletions in Plasmodium falciparum
Molecular and Biochemical Parasitology 155 33-44 |
| J. Schwenk, J. Lindberg,
M. Sundberg, M. Uhlén and P. Nilsson (2007),
Determination of binding specificities in highly multiplexed
bead based assays for antibody proteomics Molecular
and Cellular Proteomics 6 (1): 125-132 |
| S. Strömberg, M.
G. Björklund, C. Asplund, A. Sköllermo, A. Persson,
K. Wester, C. Kampf, P. Nilsson, A.-C. Andersson, M. Uhlen,
J. Kononen, F. Ponten and A. Asplund (2007), A high-throughput
strategy for protein profiling in cell microarrays using
automated image analysis Proteomics 7 (13): 2142-2150 |
| S. Andersson-Gunnerås,
E. Mellerowicz, J. Love, B. Segerman, Y. Ohmiya, P. Coutinho,
P. Nilsson, B. Henrissat, T. Moritz and B. Sundberg
(2006), Biosynthesis of cellulose-enriched tension wood
in Populus: global analysis of transcripts and metabolites
identifies biochemical and developmental regulators in secondary
wall biosynthesis Plant J 45 (2): 144-16 |
| A. Andersson, M. Lundgren,
S. Eriksson, M. Rosenlund, R. Bernander and P. Nilsson
(2006), Global analysis of RNA stability in the archaeon
Sulfolobus Genome Biology 7 (10): R99 |
| S. J. J. Brouns, J.
Walther, A. P. L. Snijders, H. J. G. v. d. Werken, H. L.
D. M. Willemen, P. Worm, M. G. J. d. Vos, A. Andersson,
M. Lundgren, H. F. M. Mazon, R. H. H. v. d. Heuvel, P. Nilsson,
L. Salmon, W. M. d. Vos, P. C. Wright, R. Bernander and
J. v. d. Oost (2006), Identification of the missing
links in the prokaryotic pentose oxidation pathway: evidence
for enzyme recruitment J Biol Chem 281 27378-27388 |
| C. Eriksson, C. Agaton,
R. Kånge, M. Sundberg, P. Nilsson, B. Ek, M. Uhlén,
M. Gustafsson and S. Hober (2006), Microfluidic analysis
of antibody specificity in a compact disc format J Proteome
Research 5 (7): 1568-1574 |
| K. Larsson, K. Wester,
P. Nilsson, M. Uhlen, S. Hober and H. Wernérus
(2006), Multiplexed PrEST-immunization for high-throughput
affinity proteomics J Immunol Methods 315 (1-2):
110-120 |
| J. Lindberg, E. a. Klint,
A.-K. Ulfgren, A. Stark, T. Andersson, P. Nilsson, L. Klareskog
and J. Lundeberg (2006), Variability in synovial
inflammation in rheumatoid arthritis investigated by microarray
technology Arthritis Research & Therapy 8 (2):
R47 |
| J. Lindberg, E. a. Klint,
A. I. Catrina, P. Nilsson, L. Klareskog, A.-K. Ulfgren and
J. Lundeberg (2006), Effect of infliximab on mRNA
expression profiles in synovial tissue of RA patients Arthritis
Research & Therapy 8 (6): R179 |
| S.-T. Pang, W.-H. Weng,
A. Flores-Morales, B. Johansson, M. R. Pourian, P. Nilsson,
B. Byström, Å. Pousette, C. Larsson and G. Norstedt
(2006), Cytogenetic and expression profiles associated with
transformation to androgen-resistant prostate cancer The
Prostate 66 (2): 157-172 |
| M. Sievertzon, P. Nilsson
and J. Lundeberg (2006), Improving reliability and
performance of DNA microarrays Expert Review of Molecular
Diagnostics 6 (3): 481-492 |
| A. Sjödin, M. Bylesjö,
O. Skogström, D. Eriksson, P. Nilsson, P. Rydén,
S. Jansson and J. Karlsson (2006), UPSC-BASE –Populus
transcriptomics online Plant J 48 (5): 806-817 |
| N. R. Street, O. Skogström,
A. Sjödin, J. Tucker, M. Rodríguez-Acosta, P.
Nilsson, S. Jansson and G. Taylor (2006), The Genetics
and Genomics of drought response in Populus Plant J
48 (3): 321-341 |
| A. Andersson, R. Bernander
and P. Nilsson (2005), Dual-genome primer design
for construction of DNA microarrays Bioinformatics
21 (3): 325-332 |
| H. Aspeborg, J. Schrader,
P. M. Coutinho, M. Stam, Å. Kallas, S. Djerbi, P.
Nilsson, S. Denman, B. Amini, F. Sterky, E. Master, G. Sandberg,
E. Mellerowicz, B. Sundberg, B. Henrissat and T. T. Teeri
(2005), Carbohydrate-active enzymes involved in the secondary
cell wall biogenesis in hybrid aspen Plant Physiol
137 (3): 983-997 |
| E. Edlundh-Rose, I.
Kupershmidt, A. Gustafsson, T. Parasassi, L. Bracci-Laudiero,
G. Greco, E. Krasnowska, M. Romano, T. Lundeberg, P. Nilsson
and J. Lundeberg (2005), Gene expression analysis
of human epidermal keratinocytes after N-acetyl L-cysteine
treatment demonstrates cell cycle arrest and increased differentiation.
Pathobiology 72 (4): 203-212 |
| H. Gräns, P. Nilsson
and B. Evengård (2005), Gene expression profiling
of Swedish patients with Chronic Fatigue Syndrome J
Internal Medicin 258 388-390 |
| M. Janzi, J. Ödling,
Q. Pan-Hammarström, M. Sundberg, J. Lundeberg, M. Uhlen,
L. Hammarström and P. Nilsson (2005), Serum
microarrays for large scale screening of protein levels
Molecular and Cellular Proteomics 4 1942-1947 |
| A. Lundin, B. Björkholm,
I. Kupershmidt, M. Unemo, P. Nilsson, D. I. Andersson and
L. Engstrand (2005), Slow Genetic Divergence of Helicobacter
pylori During Long-term Colonization Infection and Immunity
73 4818-4822 |
| I. M. Lönnstedt,
R. Rimini and P. Nilsson (2005), Bayesian microarray one-way
anova and grouping cell lines by equal expression levels
Statistical Applications in Genetics and Molecular Biology
4 (1): Article 7C. Moreau, N. Aksenov, M. Garcia, B. Segerman,
C. Funk, P. Nilsson, S. Jansson and H. Tuominen (2005),
In silico analysis of an EST database to investigate developmental
cell death in wood tissues of Populus trees Genome Biology
6 R34 |
| P. Nilsson, L. Paavilainen,
K. Larsson, J. Ödling, M. Sundberg, A.-C. Andersson,
C. Kampf, A. Persson, C. A.-K. Szigyarto, J. Ottosson, E.
Björling, S. Hober, H. Wernérus, K. Wester,
F. Pontén and M. Uhlen (2005), Towards a human
proteome atlas: high-throughput generation of mono-specific
antibodies for tissue profiling Proteomics 5 4327-4337 |
| H. Nordström, K.
Falk, G. Lindegren, M. Mouzavi-Jazi, A. Johansson, F. Elgh,
P. Nilsson and Å. Lundkvist (2005), Microarray
based detection and identification of seven pathogenic flaviviruses
J Med Virol 77 (4): 528-540 |
| M. Uhlén, E.
Björling, C. Agaton, C. A.-K. Szigyarto, B. Amini,
E. Andersen, A.-C. Andersson, P. Angelidou, A. Asplund,
C. Asplund, L. Berglund, K. Bergström, D. Cerjan, M.
Ekström, A. Elobeid, C. Eriksson, L. Fagerberg, R.
Falk, J. Fall, M. Forsberg, K. Gumbel, A. Halimi, I. Hallin,
C. Hamsten, M. Hansson, M. Hedhammar, G. Hercules, C. Kampf,
K. Larsson, M. Lindskog, J. Lund, J. Lundeberg, K. Magnusson,
E. Malm, P. Nilsson, P. Oksvold, I. Olsson, J. Ottosson,
J. Ödling, E. Öster, L. Paavilainen, A. Persson,
R. Rimini, J. Rockberg, M. Runeson, Å. Sivertsson,
A. Sköllermo, J. Steen, M. Stenvall, F. Sterky, S.
Strömberg, M. Sundberg, H. Tegel, S. Tourle, E. Wahlund,
J. Wan, H. Wernérus, J. Westberg, K. Wester, U. Wrethagen,
L. L. Xu, S. Hober and F. Pontén (2005), A
human protein atlas for normal and cancer tissues based
on antibody proteomics Molecular and Cellular Proteomics
4 1920-1932 |
| D. Velazquez-Fernandez,
C. Laurell, J. Geli, A. Höög, J. Odeberg, M. Kjellman,
J. Lundeberg, B. Hamberger, P. Nilsson and M. Bäckdahl
(2005), Expression profiling of adrenocortical tumors suggests
a molecular signature of malignancy Surgery 138
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| V. Wirta, M. Lukasc,
A. Holmberg, P. Nilsson, M. Uhlén, R. P. Bhalerao
and J. Lundeberg (2005), Assembly of a gene sequence
tag microarray for transcript analysis of Arabidopsis thaliana
BMC Biotechnology 5 5 |
| A. Andersson, J. Keskitalo,
A. Sjodin, R. Bhalerao, F. Sterky, K. Wissel, K. Tandre,
H. Aspeborg, R. Moyle, Y. Ohmiya, A. Brunner, P. Gustafsson,
J. Karlsson, J. Lundeberg, O. Nilsson, G. Sandberg, S. Strauss,
B. Sundberg, M. Uhlen, S. Jansson and P. Nilsson
(2004), A transcriptional timetable of autumn senescence
Genome Biol 5 (4): R24 |
| S. Djerbi, H. Aspeborg,
P. Nilsson, B. Sundberg, E. Mellerowicz, K. Blomqvist and
T. T. Teeri (2004), Identification and expression
analysis of genes encoding putative cellulose synthases
(CesA) in the hybrid aspen, Populus tremula (L.) x P. tremuloides
(Michx.) Cellulose 11 (3-4): 301-312 |
| D. Kemmer, M. Faxen,
E. Hodges, J. Lim, E. Herzog, E. Ljungström, A. Lundmark,
R. Podowski, E. L. L. Sonnhammer, P. Nilsson, M. Reimers,
M. K. Olsen, S. L. Roberds, C. Wahlestedt, C. Höög,
P. Agarwal and W. W. Wasserman (2004), Exploring
the Foundation of Genomics: A Northern Blot Reference Set
for the Comparative Analysis of Transcript Profiling Technologies
Comparative and Functional Genomics 5 (8): 584-595 |
| M. Lundgren, A. Andersson,
L. Chen, P. Nilsson and R. Bernander (2004), Three
replication origins in Sulfolobus species: synchronous initiation
of chromosome replication and asynchronous termination Proc
Natl Acad Sci U S A 101 (18): 7046-51 |
| K. K. Mantripragada,
I. Tapia-Paez, E. Blennow, P. Nilsson, A. Wedell and J.
P. Dumanski (2004), DNA copy-number analysis of the
22q11 deletion-syndrome region using array-CGH with genomic
and PCR-based targets Int J Mol Med 13 (2): 273-9 |
| H. Nordström, P.
Johansson, Q. G. Li, A. Lundkvist, P. Nilsson and F. Elgh
(2004), Microarray technology for identification
and distinction of hantaviruses J Med Virol 72
(4): 646-55 |
| J. Schrader, J. Nilsson,
E. Mellerowicz, A. Berglund, P. Nilsson, M. Hertzberg and
G. Sandberg (2004), A high-resolution transcript
profile across the wood-forming meristem of poplar identifies
potential regulators of cambial stem cell identity Plant
Cell 16 (9): 2278-92 |
| J. Schrader, R. Moyle,
R. Bhalerao, M. Hertzberg, J. Lundeberg, P. Nilsson and
R. P. Bhalerao (2004), Cambial meristem dormancy
in trees involves extensive remodelling of the transcriptome
Plant J 40 (2): 173-87 |
| M. Sievertzon, C. Agaton,
P. Nilsson and J. Lundeberg (2004), Amplification
of mRNA populations by a cDNA tag strategy Biotechniques
36 (2): 253-9 |
| F. Sterky, R. R. Bhalerao,
P. Unneberg, B. Segerman, P. Nilsson, A. M. Brunner, L.
Charbonnel-Campaa, J. J. Lindvall, K. Tandre, S. H. Strauss,
B. Sundberg, P. Gustafsson, M. Uhlen, R. P. Bhalerao, O.
Nilsson, G. Sandberg, J. Karlsson, J. Lundeberg and S. Jansson
(2004), A Populus EST resource for plant functional
genomics Proc Natl Acad Sci U S A 101 (38): 13951-6 |
| M. Israelsson, M. E.
Eriksson, M. Hertzberg, H. Aspeborg, P. Nilsson and T. Moritz
(2003), Changes in gene expression in the wood-forming tissue
of transgenic hybrid aspen with increased secondary growth
Plant Mol Biol 52 (4): 893-903 |
| A. Russom, A. Ahmadian,
H. Andersson, P. Nilsson and G. Stemme (2003), Single-nucleotide
polymorphism analysis by allele-specific extension of fluorescently
labeled nucleotides in a microfluidic flow-through device
Electrophoresis 24 (1-2): 158-61 |
| A. Ahmadian, A. Russom,
H. Andersson, M. Uhlen, G. Stemme and P. Nilsson
(2002), SNP analysis by allele-specific extension in a micromachined
filter chamber Biotechniques 32 (4): 748, 750,
752, 754 |
| T. Andersson, P. Unneberg,
P. Nilsson, J. Odeberg, J. Quackenbush and J. Lundeberg
(2002), Monitoring of representational difference
analysis subtraction procedures by global microarrays Biotechniques
32 (6): 1348-50, 1352, 1354-6, 1358. |
| M. Ehn, A. Ahmadian,
P. Nilsson, J. Lundeberg and S. Hober (2002), Escherichia
coli single-stranded DNA-binding protein, a molecular tool
for improved sequence quality in pyrosequencing Electrophoresis
23 (19): 3289-99. |
| H. Andersson, W. van
der Wijngaart, P. Nilsson, P. Enoksson and G. Stemme
(2001), Valve-Less Diffuser Micropump for Microfluidic Analytical
Systems Sensors Actuat B 72 259-265 |
| M. Ehn, P. Nilsson,
M. Uhlen and S. Hober (2001), Overexpression, rapid
isolation, and biochemical characterization of Escherichia
coli single-stranded DNA-binding protein Protein Expr
Purif 22 (1): 120-7. |
| M. Hertzberg, M. Sievertzon,
H. Aspeborg, P. Nilsson, G. Sandberg and J. Lundeberg
(2001), cDNA microarray analysis of small plant tissue samples
using a cDNA tag target amplification protocol Plant
J 25 (5): 585-91 |
| M. Hertzberg, H. Aspeborg,
J. Schrader, A. Andersson, R. Erlandsson, K. Blomqvist,
R. Bhalerao, M. Uhlen, T. T. Teeri, J. Lundeberg, B. Sundberg,
P. Nilsson and G. Sandberg (2001), A transcriptional
roadmap to wood formation Proc Natl Acad Sci U S A
98 (25): 14732-7 |
Bibliography Peter
Savolainen 2000-2007 |
| Peer Reviewed Articles |
1. |
Savolainen P, Arvestad
L, Lundeberg J. mtDNA tandem repeats in domestic
dogs and wolves: mutation mechanism studied by analysis
of the sequence of imperfect repeats. Mol. Biol. Evol. 2000:17,474-488. |
2. |
Savolainen P, Arvestad
L, Lundeberg J. A novel method for forensic DNA investigations,
based on repeat type sequence analysis of domestic dog mtDNA.
J. Forensic Sci. 2000:45,990-999. |
3. |
Savolainen P, Zhang
Y-P, Luo J, Lundeberg J, Leitner T. Genetic evidence
for an East Asian origin of domestic dogs. Science 2002:298,1610-1613. |
4. |
Savolainen P, Leitner
T, Wilton A, Matisoo-Smith E, Lundeberg J. A detailed
picture of the origin of the Australian dingo, obtained
from the study of mitochondrial DNA. Proc. Natl. Acad. Sci.
USA 2004:101,12387-12390. |
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Tellgren Å, Berglund
AC, Savolainen P, Janis CM, Liberles DA. Myostatin
rapid sequence evolution in ruminants predates domestication.
Mol. Phylogenet. Evol. 2004:33,782-790. |
6. |
Fitzsimmons CJ, Savolainen
P, Amini B, Hjälm G, Lundeberg J, Andersson L.
Detection of sequence polymorphisms in red junglefowl and
White Leghorn ESTs. Anim. Genet. 2004:35,391-396. |
7. |
Angleby H, Savolainen
P. A study of the forensic usefulness of the mitochondrial
DNA variation among and within populations, breeds and types
of domestic dogs. Forensic Sci Int. 2005:154,99-110. |
8. |
Savolainen P, Fitzsimmons
C, Arvestad L, Andersson L, Lundeberg J. ESTs from
brain and testis of White Leghorn and red junglefowl: annotation,
bioinformatic classification of unknown transcripts and
analysis of expression levels. Cytogenet. Genome Res. 2005:111,79-87. |
9. |
Coward K, Ponting CP,
Chang H-Y, Hibbitt O, Savolainen P, Jones KT, Parrington
J. Phospholipase C{zeta}, the trigger of egg activation
in mammals, is present in a non-mammalian species. Reproduction.
2005:130,157-63. |
10. |
Ka S, Fitzsimmons C,
Jacobsson L, Savolainen P, Lundeberg J, Siegel PB, Andersson
L, Hallbook F. Expression analysis of growth and
energy regulation-associated genes in two divergent chicken
strains. Ann. N. Y. Acad. Sci. 2005:1040,357-9. |
11. |
Arvestad L, Visa N,
Lundeberg J, Wieslander L, Savolainen P. Expressed
sequence tags from the midgut and an epithelial cell line
of Chironomus tentans: annotation, bioinformatic classification
of unknown transcripts and analysis of expression levels.
Insect Mol Biol. 2005:14,689-95. |
12. |
Guo S, Savolainen P,
Su J, Zhang Q, Qi D, Zhao X, Liu J. Origin of mitochondrial
DNA diversity of domestic yaks. BMC Evol Biol. 2006:6,73. |
13. |
Natanaelsson C, Oskarsson
MC, Angleby H, Lundeberg J, Kirkness EF, Savolainen P.
Dog Y chromosomal DNA sequence: identification, sequencing
and SNP discovery. BMC Genet. 2006:7,45. |
14. |
Rubin C-J, Lindberg
J, Fitzsimmons C, Savolainen P, Jensen P, Lundeberg J, Andersson
L, Kindmark A.. Differential gene expression in femoral
bone from red junglefowl and domestic chicken, differing
for bone phenotypic traits. BMC Genomics. 2007:8,208. |
15. |
Hillbertz NH, Isaksson
M, Karlsson EK, Hellmén E, Pielberg G, Savolainen
P, Wade CM, von Euler H, Gustafson U, Hedhammar A, Nilsson
M, Lindblad-Toh K, Andersson L, Andersson G.. A duplication
of FGF3, FGF4, FGF9 and ORAOV1 causes the hair ridge and
predisposes to dermoid sinus in Ridgeback dogs. Nat Genet.
2007:39,1318-20. |
Book
chapters |
1. |
Savolainen P and Lundeberg
J. Dog genetic data and forensic evidence. In: Eds.
Ruvinsky A, Sampson J. The Genetics of the dog.
2001. CABI Publishing, New York. |
2. |
Savolainen P.
mtDNA studies of the origin of dogs. In: Eds. Ostrander
EA, Giger U, Lindbladh-Toh K. The dog and its genome.
2006. Cold Spring Harbor Laboratory Press, New York. |
3. |
Savolainen P.
Domestication of dogs. In: Ed. Jensen P. The behavioural
biology of dogs. 2007. CAB International, Wallingford. |
Popular
science |
1. |
Cederlund B and Savolainen
P. Från Asiatisk varg till både pekingeser
och schäfer. Hundsport 2003:9,18-22. |
2. |
Savolainen P.
Asien – die Wiege aller Hunde? Studie über den
Ursprung der Hunde. Teil 1/2. Hundemagazin WUFF
2004:3,38-41 |
3. |
Savolainen P.
Asien – die Wiege aller Hunde? Studie über den
Ursprung der Hunde. Teil 2/2. Hundemagazin WUFF
2004:4,42-45 |
Bibliography Fredrik
Sterky 2000-2007 |
| Peer Reviewed Journal Articles |
1. |
Tuskan, G.A. –
(…, Sterky, F., …) – Rokhsar, D.
The genome of black cottonwood, Populus trichocarpa (Torr.
& Gray). Science. 2006 Sep 15;313(5793):1596-604. |
2. |
Uhlen, M. – (…,
Sterky, F., …) – Ponten, F. A human protein
atlas for normal and cancer tissues based on antibody proteomics
Mol Cell Proteomics. 2005 Dec;4(12):1920-1932 |
3. |
Unneberg, P, Strömberg,
M, Lundeberg, J, Jansson, S & Sterky, F. Analysis
of 70,000 EST sequences to study divergence between two
closely related Populus species Tree Genetics and Genomes
(2005) 1:109-115 |
4. |
Djerbi, S., Lindskog,
M., Arvestad, L., Sterky, F., Teeri, T.T. The genome
sequence of black cottonwood (Populus trichocarpa) reveals
18 conserved cellulose synthase (CesA) genes. Planta.(2005)
221(5):739-46 |
5. |
Lindskog, M., Rockberg,
J., Uhlen, M., Sterky, F. Selection of protein epitopes
for antibody production. Biotechniques 38:723-727
(2005) |
6. |
Sterck, L., Rombauts,
S., Jansson S., Sterky, F., Rouze, P., Van de Peer, Y.
EST data suggest that poplar is an ancient polyploid. New
Phytol 167:165-170 (2005) |
7. |
Unneberg, P., M. Stromberg,
M., Sterky, F. SNP discovery using advanced algorithms
and neural networks. Bioinformatics 21:2528-2530
(2005) |
8. |
Aspeborg, H., Schrader,
J., Coutinho, P. M., Stam, M., Kallas, A., Djerbi, S., Nilsson,
P., Denman, S., Amini, B., Sterky, F., Master, E., Sandberg,
G., Mellerowicz, E., Sundberg, B., Henrissat, B. & Teeri,
T. T. Carbohydrate-active enzymes involved in the
secondary cell wall biogenesis in hybrid aspen. Plant
Physiol 137, 983-97 (2005). |
9. |
Sterky, F., Bhalerao,
R. R., Unneberg, P., Segerman, B., Nilsson, P., Brunner,
A. M., Charbonnel-Campaa, L., Lindvall, J. J., Tandre, K.,
Strauss, S. H., Sundberg, B., Gustafsson, P., Uhlen, M.,
Bhalerao, R. P., Nilsson, O., Sandberg, G., Karlsson, J.,
Lundeberg, J. & Jansson, S. A Populus EST resource
for plant functional genomics. Proc Natl Acad Sci U
S A 101, 13951-6 (2004). |
10. |
Karpinska, B., Karlsson,
M., Srivastava, M., Stenberg, A., Schrader, J., Sterky,
F., Bhalerao, R. & Wingsle, G. MYB transcription
factors are differentially expressed and regulated during
secondary vascular tissue development in hybrid aspen.
Plant Mol Biol 56, 255-70 (2004). |
11. |
Gray-Mitsumune, M.,
Mellerowicz, E. J., Abe, H., Schrader, J., Winzell, A.,
Sterky, F., Blomqvist, K., McQueen-Mason, S., Teeri, T.
T. & Sundberg, B. Expansins abundant in secondary
xylem belong to subgroup A of the alpha-expansin gene family.
Plant Physiol 135, 1552-64 (2004). |
12. |
Andersson, A., Keskitalo,
J., Sjodin, A., Bhalerao, R., Sterky, F., Wissel, K., Tandre,
K., Aspeborg, H., Moyle, R., Ohmiya, Y., Brunner, A., Gustafsson,
P., Karlsson, J., Lundeberg, J., Nilsson, O., Sandberg,
G., Strauss, S., Sundberg, B., Uhlen, M., Jansson, S. &
Nilsson, P. A transcriptional timetable of autumn
senescence. Genome Biol 5, R24 (2004). |
13. |
Bhalerao, R., Keskitalo,
J., Sterky, F., Erlandsson, R., Bjorkbacka, H., Birve, S.
J., Karlsson, J., Gardestrom, P., Gustafsson, P., Lundeberg,
J. & Jansson, S. Gene expression in autumn leaves.
Plant Physiol 131, 430-42 (2003). |
14. |
Johansson, H., Sterky,
F., Amini, B., Lundeberg, J. & Kleczkowski, L.
A. Molecular cloning and characterization of a cDNA encoding
poplar UDP-glucose dehydrogenase, a key gene of hemicellulose/pectin
formation. Biochim Biophys Acta 1576, 53-8 (2002). |
15. |
Ahmadian, A., Gharizadeh,
B., Gustafsson, A. C., Sterky, F., Nyrén, P., Uhlén,
M. & Lundeberg, J. Single-nucleotide polymorphism
analysis by pyrosequencing. Analytical Biochemistry
280, 103-10 (2000). |
| Reviews, book chapters,
books |
1. |
Finkelstein, D., Ewing,
R., Gollub, J., Sterky, F., Cherry, J. M. & Somerville,
S. Microarray data quality analysis: lessons from
the AFGC project. Arabidopsis Functional Genomics Consortium.
Plant Mol Biol 48, 119-31 (2002).(R) |
2. |
Sterky, F., Sundberg,
B., Bhalerao, R., Gustafsson, P., Jansson, S., Jones, A.,
Moritz, T., Nilsson, O., Teeri, T. T., Uhlen, M., Lundeberg,
J. & Sandberg, G. Tree genomics in Sweden: a
national network of biological and technological expertise.
AgBiotechNet 3, 1-5 (2001).(R) |
3. |
Finkelstein, D., Gollub,
J., Ewing, R., Sterky, F., Somerville, S. & Cherry,
J. M. in Methods of Microarray Data Analysis: Papers
from CAMDA 2000 (eds. Lin, S. M. & Johnson, K. F.) (Kluwer
Academic Publishers, Boston, 2001).(B) |
4. |
Sterky, F. & Lundeberg,
J. Sequence analysis of genes and genomes. Journal
of Biotechnology 76, 1-31 (2000). (R) |
| Publicly available softwares |
1. |
Forage: Software for SNP discovery (Unneberg
et al, 2005)
http://biobase.biotech.kth.se/forage/ |
2. |
Bishop: Software for selection of optimal
epitopes in (human) genes (Lindskog et al, 2005) http://biobase.biotech.kth.se/bishop/ |
|
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