Publications

 

» Citations of Mikael Kubista

 

BBMRI (Biobanks Europe) Newsletter 6, 2017 
Trust Quality Experience Knowledge
CEN/ISO Specifications

 

Irma Virant-Klun, Anders Ståhlberg, Mikael Kubista, and Thomas Skutella
MicroRNAs: From Female Fertility, Germ Cells, and Stem Cells to Cancer in Humans
Stem Cells International, Volume 2016, Article ID 3984937,

 

Tobias M. Gorges, Andra Kuske, Katharina Röck,  Oliver Mauermann,  Volkmar Muller, Sven Peine, Karl Verpoort, Vendula Novosadova, Mikael Kubista, Sabine Riethdorf, and Klaus Pantel Accession of Tumor Heterogeneity by Multiplex Transcriptome Profiling of Single Circulating Tumor Cells

Clinical Chemistry 62:11, 1504–1515 (2016)


 

Oskar Karlsson, Lova Segerström, Robert Sjöback, Ingrid Nylander, Mats Borén          qPCR based mRNA quality score show intact mRNA after heat stabilization
Biomolecular Detection and Quantification, Volume 7, March 2016, Pages 21–26

 

J. Björkman, D. Švec, E. Lott, M. Kubista, R. Sjöback
Differential amplicons (ΔAmp)—a new molecular method to assess RNA integrity
Biomolecular Detection and Quantification, Volume 6, January 2016, Pages 4–12

 

Sabine Conrad, Hossein Azizi, Maryam Hatami, Mikael Kubista, Michael Bonin, Jörg Hennenlotter, Karl-Dietrich Sievert, Thomas Skutella
Expression of Genes Related to Germ Cell Lineage and Pluripotency in Single Cells and Colonies of Human Adult Germ Stem Cells
Stem Cells International, Vol 2016 (2016), Article ID 8582526, 17 pages, http://dx.doi.org/10.1155/2016/8582526

 

 Kap M, Sieuwerts AM, Kubista M, Oomen M, Arshad S, Riegman P.
The influence of tissue procurement procedures on RNA integrity, gene expression, and morphology in porcine and human liver tissue.
Biopreserv Biobank. 2015 Jun;13(3):200-6

 

Mikael Kubista
Addressing biological heterogeneity with single cell profiling
European Pharmaceutical Reviews (2015)

 

Daniel Andersson, Nina Akrap, David Svec, Tony E Godfrey, Mikael Kubista, Göran Landberg, Anders Ståhlberg
Properties of targeted preamplification in DNA and cDNA quantification 2015
Expert Rev. Mol. Diagn. Early online, 1–16 (2015)

 

Monika Sidova, Radek Sindelka, Mirco Castoldi, Vladimir Benes, Mikael Kubista
Intracellular microRNA profiles form in the Xenopus laevis oocyte that may contribute to asymmetric cell division
Nature Scientific Reports 5, Article number: 11157, doi:10.1038/srep11157

 

David Svec , Ales Tichopad, Vendula Novosadova, Michael W. Pfaffl, Mikael Kubista
How good is a PCR efficiency estimate: Recommendations for precise and robust qPCR efficiency assessments
Biomolecular Detection and Quantification (2015) doi:10.1016/j.bdq.2015.01.005

 

Monika Sidova, Silvie Tomankova, Pavel Abaffy, Mikael Kubista, Radek Sindelka
Effects of post-mortem and physical degradation on RNA integrity and quality
Biomolecular Detection and Quantification 2015

 

Elena Kallea, Mikael Kubistab, Christopher Rensingd
Multi-template polymerase chain reaction
Biomolecular Detection and Quantification 2 (2014) 11–29

 

Francesca Malentacchi, Mario Pazzagli, Lisa Simi, Claudio Orlando, Ralf Wyrich, Kalle Günther, Paolo Verderio, Sara Pizzamiglio, Chiara Maura Ciniselli, Hui Zhang, Vlasta Korenkova, Lynne Rainen, Tzachi Bar, Mikael Kubista, Stefania Gelmini
Second External Quality Assessment for the Pre-Analytical Phase of Blood Samples Used for RNA Based Analyses
PlosOne, 9(11), e112293 (November 2014)

 

Hui Zhang1, Vlasta Korenkova, Robert Sjöback3, David Svec, Jens Björkman, Mogens Kruhøffer, Paolo Verderio, Sara Pizzamiglio, Chiara Maura Ciniselli, Ralf Wyrich, Uwe Oelmueller, Mikael Kubista, Torbjørn Lindahl, Anders Lönneborg, Edith Rian
Biomarkers for Monitoring Pre-Analytical Quality Variation of mRNA in Blood Samples
PlosOne, 9(11), e111644 (November 2014)

 

Mikael Kubista
Prime time for qPCR – raising the quality bar
European Pharmaceutical Review 19(3), (2014)

 

Jana Slyskova, Francesca Cordero, Barbara Pardini, Vlasta Korenkova, Veronika Vymetalkova, Ludovit Bielik, Ludmila Vodickova, Pavel Pitule, Vaclav Liska, Vit Martin Matejka, Miroslav Levy, Tomas Buchler, Mikael Kubista, Alessio Naccarati, and Pavel Vodicka
Post-Treatment Recovery of Suboptimal DNA Repair Capacity and Gene Expression Levels in Colorectal Cancer Patients
Mol Carcinog. (2014) DOI 10.1002

 

Hamdi Joda, Valerio Beni, Noora Alakulppi, Jukka Partanen, Kristina Lind, Linda Strömbom, Daniel Latta, Julian Höth, Ioanis Katakis, Ciara K. O’Sullivan
Medium-high resolution electrochemical genotyping of HLA-DQ2 DQ8 for detection of predisposition to coeliac disease
Anal Bioanal Chem (15 March 2014) DOI 10.1007/s00216-014-7650-x

 

Anders Ståhlberg, Mikael Kubista
The workflow of single cell profiling using qPCR
Expert Rev. Mol. Diagn. 14(3), (2014)

 

Sabine Conrad, Hossein Azizi, Maryam Hatami, Mikael Kubista, Michael Bonin, Jörg Hennenlotter, Markus Renninger, Thomas Skutella
Differential Gene Expression Profiling of Enriched Human Spermatogonia after Short- and Long-Term Culture
BioMed Research International Volume 2014, Article ID 138350, http://dx.doi.org/10.1155/2014/138350


Anders Ståhlberg, Pierre Åman,Linda Strömbom, Neven Zoric, Alfredo Diez, Olle Nilsson, Mikael Kubista, Börje Ridell
Comparison of Reverse Transcription Quantitative Real-Time PCR Flow Cytometry and Immunohistochemistry for Detection of Monoclonality in Lymphomas
ISRN Oncology Volume 2014, Article ID 796210 (2014) http://dx.doi.org/10.1155/2014/796210


Novel approach to single cell analysis: multiple analyte measurements from a single cell
www.lifetechnologies.com (2013)

 

David Svec, Daniel Andersson, Milos Pekny, Robert Sjöback, Mikael Kubista, Anders Ståhlberg
Direct cell lysis for single-cell gene expression profiling
Frontiers in Oncology Volume 3 Article 274 (November 2013)


Stephen A Bustin et al.
The need for transparency and good practices in the qPCR literature
Nature Methods 11:1063-1067 (November 2013)


Sarah Webb
Getting over qPCR’s technical hurdles
BioTechniques 55:165-168 (October 2013) doi: 10.2144/000114085

 

Monika Flachsova, Radek Sindelka, Mikael Kubista
Single blastomere expression profiling of Xenopus laevis embryos of 8 to 32-cells reveals developmental asymmetry
Scientific Reports 3, 2278 (2013) doi: 10.1038/srep02278


F. Malentacchi, M. Pazzagli, L. Simi, C. Orlando, R. Wyrich, C.C. Hartmann, P. Verderio, S. Pizzamiglio, C.M. Ciniselli, A. Tichopad, M. Kubista, S. Gelmini
SPIDIA-DNA: An External Quality Assessment for the pre-analytical phase of blood samples used for DNA-based analyses
Clinica Chimica Acta 424, 274–286 (2013)


Vendula Rusnakova, Pavel Honsa, David Dzamba, Anders Ståhlberg, Mikael Kubista, Miroslava Anderova
Heterogeneity of Astrocytes: From Development to Injury-Single Cell Gene Expression
PloS One 8(8), e69734 (2013)

 

Mikael Kubista, Anders Ståhlberg
Unrevealing biological secrets by single cell expression profiling
Drug Discovery World, 59-65 (Summer 2013)

 

Vivien Marx
PCR: living life amplified and standardized
Nature Methods 10, 391–395 (2013) doi:10.1038/nmeth.2443

 

Jim F. Huggett, Carole A. Foy, Vladimir Benes, Kerry Emslie, Jeremy A. Garson, Ross Haynes, Jan Hellemans, Mikael Kubista, Reinhold D. Mueller, Tania Nolan, Michael W. Pfaffl, Gregory L. Shipley, Jo Vandesompele, Carl T. Wittwer,and Stephen A. Bustin
Guidelines for Minimum Information for Publication of Quantitative Digital PCR Experiments
Clin Chem 59:6 (2013)

 

M. Pazzagli, F. Malentacchi, L. Simi, C. Orlando, R. Wyrich, K. Günther, C.C. Hartmann,P. Verderio, S. Pizzamiglio, C.M. Ciniselli, A. Tichopad, M. Kubista, S. Gelmini
SPIDIA-RNA: First external quality assessment for the pre-analytical phase of blood samples used for RNA based analyses
Methods 59, 20-31 (2013)

 

Irma Virant-Klun, Thomas Skutella, Mikael Kubista, Andrej Vogler, Jasna Sinkovec, and Helena Meden-Vrtovec
Expression of Pluripotency and Oocyte-Related Genes in Single Putative Stem Cells from Human Adult Ovarian Surface Epithelium Cultured In Vitro in the Presence of Follicular Fluid
BioMed Research International, vol. 2013, ArticleID 861460, 18 pages, 2013. doi:10.1155/2013/861460

 

Anders Ståhlberg, Vendula Rusnakova and Mikael Kubista
The added value of single-cell gene expression profiling
Briefings in Functional Genomics (2013) doi: 10.1093/bfgp/elt001 First published online: Feb 7, 2013

David Svec, Vendula Rusnakova, Vlasta Korenkova and Mikael Kubista
Dye-Based High-Throughput qPCR in Microfluidic Platform BioMark
PCR Technology: Current Innovations, Third Edition. Ch 23 (2013)


Christer Slotte, Maria Lennerås, Catharina Göthberg, Felicia Suska, Neven Zoric, Peter Thomsen, Ulf Nannmark
Gene Expression of Inflammation and Bone Healing in Peri-Implant Crevicular Fluid after Placement and Loading of Dental Implants. A Kinetic Clinical Pilot Study Using Quantitative Real-Time PCR
Clinical Implant Dentistry and Related Research, Volume 14, Number 5, 2012

Mikael Kubista, Jens Björkman, David Svec, and Robert Sjöback
RNA quality matters
European_Pharmaceutical_Reviews Vol 17, Issue 6, 2012


Anders Ståhlberg, Vendula Rusnakova, Amin Forootan, Miroslava Anderova, Mikael Kubista
RT-qPCR work-flow for single-cell data analysis
Methods 59, 80-88 (2013)



Q&A
European Pharmaceutical Review Vol 17, Issue 5, 2012


Mikael Kubista, Ales Tichopad
Setting the bar
European Pharmaceutical Review Vol 17, Issue 5, 2012


Monya Baker
Digital PCR hits its stride
Nature methods, vol.9 no.6, June 2012, p.541-544



Hamdi Joda, Valerio Beni, Deirdre Curnane, Ioanis Katakis, Noora Alakulppi, Jukka Partanen, Kristina Lind, Linda Strömbom, Ciara K. O’Sullivan
Low–medium resolution HLA-DQ2/DQ8 typing for coeliac disease predisposition analysis by colorimetric assay
Anal Bioanal Chem (2012) 403:807–819. DOI 10.1007/s00216-012-5898-6


 

Anders Ståhlberg, Christer Thomsen, David Ruff, and Pierre Åman.
Quantitative PCR Analysis of DNA, RNAs, and Proteins in the Same Single Cell
Clinical Chemistry 58:12 (2012)



Joakim Håkansson, Anders Ståhlberg, Fredrik Wolfhagen Sand, Holger Gerhardt, Henrik Semb
N-CAM Exhibits a Regulatory Function in Pathological Angiogenesis in Oxygen Induced Retinopathy
PloS_One, 2011, 6 (1)


Karin Norrman, Anna Strömbeck, Henrik Semb, Anders Ståhlberg
Distinct gene expression signatures in human embryonic stem cells differentiated towards definitive endoderm at single-cell level

Methods 59, 59 (2013)


Mikael Kubista.
I See the Light! And I See It Again and Again!
Clinical Chemistry 58:11 (2012)


Mikael Kubista, Vendula Rusnakova, David Svec, Björn Sjögreen and Ales Tichopad.
Chapter 4 “Genex: Data Analysis Software” in Quantitative Real-time PCR in Applied Microbiology. Editor: Martin Filion, ISBN: 978-1-908230-01-0. Publisher: Caister Academic Press (2012)


Mikael Kubista.
Drivers and Hurdles for qPCR 
Genetic Engineering & Biotechnology News, May 1, 2012 (Vol.32, No.9)


Kalle Günther, Francesca Malentacchi, Paolo Verderio, Sara Pizzamiglio, Chiara Maura Ciniselli, Ales Tichopad, Mikael Kubista, Ralf Wyrich, Mario Pazzagli, Stefania Gelmini.
Implementation of a proficiency testing for the assessment of the preanalytical phase of blood samples used for RNA based analysis.
Clinica Chimica Acta 413 (2012) 779–786


Martin Stimpfe, Thomas Skutella, Mikael Kubista, ElviraMalicev, Sabine Conrad, and Irma Virant-Klun. 
Potential Stemness of Frozen-Thawed Testicular Biopsies without Spermin Infertile Men Included into the In Vitro Fertilization Programme
Journal of Biomedicine and Biotechnology Volume 2012, Article ID 291038, 15 pages


Jana Benesova, Vendula Rusnakova, Pavel Honsa, Helena Pivonkova, David Dzamba, Mikael Kubista, Miroslava Anderova.
Distinct Expression/Function of Potassium and Chloride Channels Contributes to the Diverse Volume Regulation in Cortical Astrocytes of GFAP/EGFP Mice.
PLoS ONE, 2012, 7(1), 1-13



Henrik Laurell, Jason S. Iacovoni, Anne Abot, David Svec, Jean-Jose Maoret, Jean-Francois Arnal and Mikael Kubista.
Correction of RT–qPCR data for genomic DNA-derived signals with ValidPrime.
Nucleic Acids Research, 2012, 1–10



Chris Tachibana
qPCR Innovations and Blueprints
Science DOI: 10.1126/science.opms.p1100058 (2011)


Bibova I, Linhartova I, Stanek O, Rusnakova V, Kubista M, Suchanek M, Vasakova M, Sebo P.
Detection of immune cell response to M. tuberculosis–specific antigens by quantitative polymerase chain reaction.
Diagn Microbiol Infect Dis. 2011 Nov 14.



Joakim Håkansson, Anders Ståhlberg, Fredrik Wolfhagen Sand, Holger Gerhardt, Henrik Semb.
N-CAM Exhibits Regulatory Function in Pathological Angiogenesis in Oxygen Induced Retinopathy.
PLoS ONE, 2011, 6(10), 1-11


Brevik A, Rusnakova V, Duale N, Slagsvold HH, Olsen AK, Storeng R, Kubista M, Brunborg G, Lindeman. B.
Preconceptional paternal glycidamide exposure affects embryonic gene expression: Single embryo gene expression study following in vitro fertilization.
Reprod Toxicol. 2011 Sep 29. [Epub ahead of print].



Tzachi Bar, Mikael Kubista and Ales Tichopad.
SURVEY AND SUMMARY. Validation of kinetics similarity in qPCR.
Nucleic Acids Research, 1–12 (2011).


Mikael Kubista and Anders Stahlberg.
DNA diagnostics get digitised.
Drug Discovery World (2011).


Anders Stahlberg, Mikael Kubista and Pierre Aman.
Single-cell gene-expression profiling and its potential diagnostic applications.
Expert Rev. Mol. Diagn. 11(7), 735–740 (2011).


Mikael Kubista and Ales Tichopad.
qPCR Round Table.
International Drug Discovery Aug/Sept (2011).


Mikael Kubista, Linda Strombom, David Svec, Vendula Rusnakova, Anders Stahlberg.
High throughput single cell expression profiling: Taking a closer look on biological response.
European Pharmaceutical Review. 2011 16(2):20-24.


Stephen A. Bustin, Vladimir Benes, Jeremy A. Garson, Jan Hellemans, Jim Huggett, Mikael Kubista, Reinhold Mueller, Tania Nolan, Michael W. Pfaffl, Gregory L. Shipley, Jo Vandesompele, and Carl T. Wittwer.
Primer Sequence Disclosure: A Clarification of the MIQE Guidelines.
Clin. Chem., 201116295 March 18, 2011.


Anders Stahlberg, Daniel Andersson, Johan Aurelius, Maryam Faiz, Marcela Pekna, Mikael Kubista, Milos Pekny.
Defining cell populations with single-cell gene expression profiling: correlations and identification of astrocyte subpopulations.
Nucleic Acids Research, 2010, 1–12.


Kolostova K, Pinterova D, Tesarova P, Bobek V, Mikulova V, Kubecova M, Brychta M, Rusnakova V, Kasimir-Bauer S, Kubista M.
Gene expression profiling in circulation cells(CTCS)of breast carcinoma patients.
Annals of Oncology 21:49-50 Suppl. 4,99P MAY(2010).


Kozubenko N, Turnovcova K, Kapcalova M, Butenko O, Anderova M, Rusnakova V, Kubista M, Hampl A, Jendelova P, Sykova E.
Analysis of in vitro and in vivo characteristics of human embryonic stem cell-derived neural precursors.
Cell Transplant 19(4):471-86 (2010).


Anna Coll, Anna Nadal, Rosa Collado, Gemma Capellades, Mikael Kubista, Joaquima Messeguer, Maria Pla.
Natural variation explains most transcriptomic changes among maize plants of MON810 and comparable non-GM varieties subjected to two N-fertilization farming practices.
Plant Mol Biol 73:349–362 (2010).


Mikael Kubista.
REAL-TIME PCR: where we are and where are we heading.
Drug Discovery World Spring (2010).


Radek Sindelka, Monika Sidova, David Svec, Mikael Kubista.
Spatial expression profiles in the Xenopus laevis oocytes measured with qPCR tomography.
Methods 51:87-91(2010).


Ales Tichopad, Tzachi Bar, Ladislav Pecen, Robert R Kitchen, Mikael Kubista, Michael W. Pfaffl.
Quality control for quantitative PCR based on amplification compatibility test.
Methods 50:308–312(2010).


Robert R. Kitchen, Mikael Kubista, Ales Tichopad.
Statistical aspects of quantitative real-time PCR experiment design.
Methods 50:231–236 (2010).


Anders Bergkvist, Vendula Rusnakova, Radek Sindelka, Jose Manuel Andrade Garda, Björn Sjögreen, Daniel Lindh, Amin Forootan, Mikael Kubista.
Gene expression profiling – Clusters of possibilities.
Methods 50:323–335(2010).


Tichopad A, Kitchen R, Riedmaier I, Becker C, Stahlberg A, Kubista M.
Design and Optimization of Reverse-Transcription Quantitative PCR Experiments.
Clinical Chemistry 55:101816–1823 (2009).


Mášová A, Šindelka R, Kubista M, Kindl J, Jiráček J.
Gene expression responses in larvae of the fleshfly Sarcophaga bullata after immune stimulation.
Folia Biol (Praha). 2009;55(3):98-106.


Mikael Kubista.
Intracellular Gene Expression Profiles Revealed with Real-time PCR Tomography.
Research Spotlight: Gene Expression (2009).


Stephen A. Bustin, Vladimir Benes, Jeremy A. Garson, Jan Hellemans, Jim Huggett, Mikael Kubista, Reinhold Mueller, Tania Nolan, Michael W. Pfaffl, Gregory L. Shipley, Jo Vandesompele,5 and Carl T. Wittwer.
The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments.
Clinical Chemistry 55,4 (2009).


Kubista M.
What future holds for real-time PCR.
European Pharmaceutical Reviews Industry Focus (2009).


Kristina Lind, Joakim Norbeck
A QPCR-based reporter system to study post-transcriptional regulation via the 3′ untranslated region of mRNA in S cerevisiae
yeast (2009) (www.interscience.wiley.com) DOI: 10.1002/yea.1675

 

Niazi A,Yazdanipour A, Ghasemi J, Amini A, Bozorgzad S, Kubista M.
Spectrophotometric Investigation of the Acidity Constants of Fluorescein in Various Water-Organic Solvent Media.
Chemical Engineering Communications. 2008; 195:1257–1268.


M. W. Pfaffl, J. Vandesompele and M. Kubista.
Data Analysis Software: Chapter 5 in Real-Time PCR: Current Technology and Applications.
Publisher: Caister Academic Press. Editor: Julie Logan, Kirstin Edwards and Nick Saunders ISBN: 978-1-904455-39-4, 2009.


Kubista M, Eliasson J, Lennerĺs M, Andersson S and Sjöback R.
What is needed to measure a difference with real-time PCR?
Eppendorf BioNews Application Notes 2008.


Kubista M.
Emerging real-time PCR applications.
Drug Discovery World Summer 2008.


Bergkvist A, Forootan A, Zoric N, Strombom L, Sjoback R, Kubista M.
Choosing a normalization strategy for RT-PCR.
Genetic Engineering & Biotechnology News. 2008 Jul; 28 (13):26


Li LZ, Lundkvist A, Andersson D, Wilhelmsson U, Nagai N, Pardo AC, Nodin C, Stahlberg A, Aprico K, Larsson K, Yabe T, Moons L, Fotheringham A, Davies I, Carmeliet P, Schwartz JP, Pekna M, Kubista M, Blomstrand, Maragakis N, Nilsson M, Pekny M.
Protective role of reactive astrocytes in brain ischemia.
Journal of Cerebral Blood Flow and Metabolism. 2008 Mar; 28(3):468-481.


Stahlberg A, Elbing K, Andrade-Garda JM, Sjögreen B, Forootan A, Kubista M.
Multiway real-time PCR gene expression profiling in yeast Saccharomyces cerevisiae reveals altered transcriptional response of ADH-genes to glucose stimuli.
BMC Genomics. 2008 Apr 16;9:17


Sindelka R, Jonák J, Hands R, Bustin SA, Kubista M.
Intracellular expression profiles measured by real-time PCR tomography in the Xenopus laevis oocyte.
Nucleic Acids Res. 2008 Feb;36(2):387-92


Pamela Pinzani, Kristina Lind, Francesca Malentacchi, Gabriella Nesi, Francesca Salvianti, Donata Villari, Mikael Kubista, Mario Pazzagli, Claudio Orlando
Prostate-specific antigen mRNA and protein levels in laser microdissected cells of human prostate measured by real-time reverse transcriptase–quantitative polymerase chain reaction and immuno–quantitative polymerase chain reaction
Human Pathology (2008) 39, 1474–1482


Kristina Lind, Joakim Norbeck
Immuno-qPCR detection of the tandem affinity purification (TAP)-tag as a sensitive and accurate tool suitable for large-scale protein quantification
Proteomics 2007, 7, 4414–4423. DOI 10.1002/pmic.200700577

 

I. M. Mackay, S. A. Bustin, J. M. Andrade, M. Kubista and T. P Sloots.
Quantification of Micro-Organisms: Not Human, Not Simple, Not Quick. Chapter 5 in Real-Time PCR in Microbiology: From Diagnosis to Characterization.
Publisher: Caister Academic Press. Editor: Ian M. Mackay Sir Albert Sakzewski Virus Research Centre, Queensland, Australia. ISBN: 978-1-904455-18-9 (2007).


M.G.H.M. Beld, C. Birch, P.A. Cane, W. Carman, E.C.J. Claas, J.P. Clewley, E. Domingo, J. Druce, C. Escarmis, R.A.M. Fouchier, V. Foulongne, M.G. Ison, L.C. Jennings, B. Kaltenboeck, I.D. Kay, M. Kubista, O. Landt, I.M. Mackay, J. Mackay, H.G.M. Niesters, M.D. Nissen, S. Palladino, N.G. Papadopoulos, A. Petrich, M,W. Pfaffl, W. Rawlinson, U. Reischl, N.A. Saunders, C. Savolainen-Kopra, O. Schildgen, G.M. Scott, M. Segondy, R. Seibl, T.P. Sloots, Y-W. Tang, R. Tellier and P.C.Y. Woo.
Experts Roundtable: Real-Time PCR and Microbiology.Chapter 10 in Real-Time PCR in Microbiology: From Diagnosis to Characterization.
Publisher: Caister Academic Press. Editor: Ian M. Mackay Sir Albert Sakzewski Virus Research Centre, Queensland, Australia.ISBN: 978-1-904455-18-9 (2007).


Andrade JM, Kubista M, Carlosena A, Prada D.
3-Way characterization of soils by Procrustes rotation, matrix-augmented principal components analysis and parallel factor analysis.
Anal Chim Acta. (2007), 603(1): 20-9.


M. Kubista, R. Sindelka, A. Tichopad, A. Bergkvist, D. Lindh, A. Forootan.
The Prime Technique. Real-time PCR data analysis.
G.I.T. Laboratory Journal (2007), 9-10, 33-35.


L. Li, A. Lundkvist, D. Andersson, U. Wilhelmsson, N. Nagai, A. C. Pardo, C. Nodin, A. Sta°hlberg, K. Aprico, K. Larsson, T. Yabe, L. Moons, A. Fotheringham, I. Davies, P. Carmeliet, J. P. Schwartz, M. Pekna, M. Kubista, F. Blomstrand, N. Maragakis, M. Nilsson and M.Pekny.
Protective role of reactive astrocytes in brain ischemia.
Journal of Cerebral Blood Flow & Metabolism (2007), 1–14


M.G.H.M. Beld, C. Birch, P.A. Cane, W. Carman, E.C.J. Claas, J.P. Clewley, E. Domingo, J. Druce, C. Escarmis, R.A.M. Fouchier, V. Foulongne, M.G. Ison, L.C. Jennings, B. Kaltenboeck, I.D. Kay, M. Kubista, O. Landt, I.M. Mackay, J. Mackay, H.G.M. Niesters, M.D. Nissen, S. Palladino, N.G. Papadopoulos, A. Petrich, M,W. Pfaffl, W. Rawlinson, U. Reischl, N.A. Saunders, C. Savolainen-Kopra, O. Schildgen, G.M. Scott, M. Segondy, R. Seibl, T.P. Sloots, Y-W. Tang, R. Tellier and P.C.Y. Woo
Real-Time PCR in Microbiology: From Diagnosis to Characterization, Experts Roundtable: Real-Time PCR and Microbiology
Publisher: Caister Academic Press, Editor: Ian M. Mackay Sir Albert Sakzewski Virus Research Centre, Queensland, Australia, Publication date: September 2007, ISBN: 978-1-904455-18-9


AAA Real-Time PCR Tech Guide – Volume 3


AAA Real-Time PCR Tech Guide – Volume 2


AAA Real-Time PCR Tech Guide – Volume 1


M. Kubista, B. Sjogreen, A. Forootan, R. Sindelka, J. Jonak, JM. Andrade.
Real-time PCR gene expression profiling.
European Pharmaceutical Reviews (2007), Vol. 1.

K. Lind, A.Ståhlberg, N. Zoric, and M. Kubista.
Combining sequence-specific probes and DNA binding dyes in real-time PCR for specific nucleic acid quantification and melting curve analysis.
Biotechniques 40, 315-18 (2006).See also: Thinking outside the BOXTO, BioSpotlight, Biotechniques (2006), Vol. 3, 40, 251.


M. Kubista, J. M. Andrade, M. Bengtsson, A. Forootan, J. Jonák, K. Lind, R. Sindelka, R. Sjöback, B. Sjögreen, L. Strömbom, A.Ståhlberg & N. Zoric.
The Real-time Polymerase Chain Reaction.
Molecular Aspects of Medicine 27, 95-125 (2006).


M. Leijon, M. Mousavi-Jasi, & M. Kubista.
LightUp Probes in Clinical Diagnostics.
Molecular Aspects of Medicine (2006).


A. Niazi,, A. Yazdanipour, J. Ghasemi and M. Kubista.
Spectrophotometric and thermodynamic study on the dimerization equilibrium of ionic dyes in water by chemometrics method.
Spectrochimica Acta Part A 65: 73–78 (2006).


K. Noaksson, N. Zoric, X. Zeng, M. S. Rao, J. Hyllner, H. Semb, M. Kubista, P. Sartipy.
Monitoring Differentiation of Human Embryonic Stem Cells Using Real-Time PCR.
Stem Cells 23, 1460-1467 (2005).


M. Bengtsson, A. Ståhlberg, P. Rorsman, and M. Kubista
Gene expression profiling in single cells from the pancreatic islets of Langerhans reveals lognormal distribution of mRNA levels.
Genome Research 15, 1388-1392 (2005).

See also: Research Highlights in Nature Review Genetics 6, 1758 (2005).



K. Lind and M. Kubista
Development and evaluation of three real-time immuno-PCR assemblages for quantification of PS.
J.Immunological Methods 304, 107-116 (2005).



M. Kubista, J. Ghasemi, B. Sjögreen & A. Forootan
Trilinear Fluorescence Spectroscopy.
Spectroscopy Asia 1, 22-27 (2005)


J. Håkansson, X. Xian, L. He, A. Ståhlberg, S. Nelander, T. Samuelsson, M. Kubista, H. Semb.
Neural Cell Adhesion Molecule-Deficient ß-Cell Tumorigenesis Results in Diminished Extracellular Matrix Molecule Expression and Tumour Cell-Matrix Adhesion.
Tumor Biology 26, 103-112 (2005).



A. Ståhlberg, N. Zoric, P. Åman & M. Kubista.
Quantitative real-time PCR for cancer detection: the lymphoma case.
Expert Reviews in Molecular Diagnostics 5, 221-230 (2005)



M. Kubista, J. Karlsson, M. Bengtsson, N. Zoric & G. Westman.
DNA-binding fluorophores.
Encyclopedia of Medical Genomics and Proteomics (2004)



M. Kubista & N. Zoric.
PCR platforms.
Encyclopedia of Medical Genomics and Proteomics (2004)


M. Kubista, J. Ghasemi, B. Sjögreen & A. Forootan
Trilinear Fluorescence Spectroscopy.
Spectroscopy Europe 16, 8 (2004)


M. Kubista.
Nucleic acid-based technologies: application amplified.
Pharmacogenomics 5(7), 767-773 (2004)


Anders Ståhlberg, Mikael Kubista, and Michael Pfaffl
Comparison of Reverse Transcriptases in Gene Expression Analysis
Clinical Chemistry 50, No. 9, 2004



J. M. Andrade, M, P. Gómez-Carracedo, W. Krzanowski & M. Kubista.
Procrustes rotation in analytical chemistry, a tutorial.
Chemometrics and Intelligent Laboratory Systems 72 123 (2004).



M. Kubista, I. H. Ismail, A. Forootan, & B., Sjögreen.
Determination of Protolytic Constants by Trilinear Fluorescence Spectroscopy.
J. Fluorescence 14, 139 (2004).



Anders Ståhlberg, Joakim Håkansson, Xiaojie Xian, Henrik Semb, and Mikael Kubista
Properties of the Reverse Transcription Reaction in mRNA Quantification
Clinical Chemistry 50:3, 509-515, 2004



J. Ghasemi, A. Niazi, G. Westman, &, M. Kubista
Thermodynamic characterization of the dimerization equilibrium of an asymmetric dye by spectral titration and chemometric analysis.
Talanta 62, 835 (2004).



J. Ghasemi, S. Ahmadi, M. Kubista, and A. Forootan.
Determination of Acidity.



J. M. Andrade, M. P. Gómez-Carracedo, E. Fernández, A. Elbergali, M. Kubista and D. Prada.
Classification of commercial apple beverages using a minimum set of mid-IR wavenumbers selected by Procrustes rotation.
Analyst, 128, 1193-1199 (2003).



T. Bar, A. Ståhlberg, A. Muszta and M. Kubista.
Kinetic Outlier Detection (KOD) in real-time PCR
Acids Res. 31, e105 (2003).


M. Bengtsson, J. Karlsson, G. Westman and M. Kubista.
A new minor groove binding asymmetric cyanine reporter dye for real-time PCR.
Nucl. Acids Res. 31, e45 (2003).


T. Bar, M. Bengtsson, J. Karlsson, K. Lind, A. Stålberg, G. Westman, N. Zoric & M. Kubista.
The TATAA Biocenter, Sweden.
InFocus 4, 6-7.



A. Ståhlberg, P. Åman, B. Ridell, P. Mostad & M. Kubista.
Quantitative Real-Time PCR Method for Detection of B-Lymphocyte Monoclonality by Comparison of k and l Immunoglobulin Light Chain Expression.
Clin. Chem. 49, 51-59 (2003).



K. Lind & M. Kubista.
Real-Time Immuno-PCR on the iCycler iQ System.
Bioradiations 109, 32-33 (2002).


J. Ghasemi, A. Niazi, M. Kubista & A. Elbergali.
Spectrophotometric determination of acidity constants of 4-(2-pyridylazo)resorcinol in binary methanol-water mixtures.
Anal. Chimica Acta, 455, 335-342 (2002).



M. Kubista, A. Ståhlberg & T. Bar.
Light-up probe based real-time Q-PCR. In Genomics and Proteomics Technologies (Eds. R. Raghavachari & W. Tan).
Proceedings of SPIE, 4264, 53-58 (2001).


N. Svanvik, J. Nygren, G. Westman & M. Kubista.
Free-probe Fluorescence of Light-up probes.
J. Amer. Chem. Soc., 123, 803-809 (2001).


N.Svanvik, A. Ståhlberg, U. Sehlstedt, R. Sjöback & M. Kubista.
Detection of PCR Products in Real-time Using Light-up Probes.
Anal. Biochem. 287, 179-182 (2000).

 

Isacsson, H. Cao, L. Ohlsson, S. Nordgren, N. Svanvik, G. Westman, M. Kubista, R. Sjöback, & U. Sehlstedt.
Rapid and specific detection of PCR products using light-up probes.
Molecular and Cellular Probes, 14, 321-328 (2000).



N. Svanvik, G. Westman, W. Dongyuan & M. Kubista.
Light-up Probes Thiazole Orange Conjugated PNA for Detection of Nucleic Acid in Homogeneous Solution.
Anal. Biochem. 281, 26-35 (2000).



C. M. Gustafsson, H. Spåhr, J. Beve & M. Kubista.
Temporal Regulation of RNA Polymerase II by Srb10 and Kin28 Cyclindependent Kinases.
ChemTracts, 12, 933-937 (1999).



H. R. Widlund, P. N. Kuduvalli, M. Bengtsson, H. Cao, T. D. Tullius & M. Kubista.
Nucleosome structural features and intrinsic properties of the (TATAAACGCC)-repeat sequence.
J. Biol. Chem. 274, 31847-31852 (1999).



A.-C. Thåström, P. Lowary, H. Widlund, M. Kubista & J. Widom.
Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences.
J. Mol. Biol. 288, 213-229 (1999).



L. Antonov, G. Gergov, V. Petrov & M. Kubista.
UV-Vis spectroscopic and chemometric study on the aggregation of ionic dyes in water.
Talanta 49, 99-106 (1999).



M. Kubista, J. Nygren, A. Elbergali & R. Sjöback.
Eliminating the need for reference samples.
Critical Reviews in Analytical Chemistry 29, 1-28 (1999).



T. Simonsson, H. Widlund & M. Kubista.
Structure-Function Correlations of the Insulin-linked Polymorphic Region.
Chemtract 12, 210-217 (1999).



A. Elbergali, J. Nygren & M. Kubista.
An automated procedure to predict the number of components in spectroscopic data.
Anal. Chim. Acta 379, 143-158 (1999).



R. Sjöback, J. Nygren & M. Kubista.
Characterization of fluorescein-oligonucleotide conjugates and measurement of local electrostatic potential.
Biopolymers 46, 445-453 (1998).



H. Cao, H. Widlund, T. Simonson & M. Kubista.
TGGA-repeats impair nucleosome formation.
J. Mol. Biol. 281, 253-260 (1998).


J. Nygren, A. Elbergali & M. Kubista.
Unambiguous Characterization of a Single Test Sample by Fluorescence Spectroscopy and Solvent Extraction without Use of Standards.
Analytical Chemistry 70, 4841-4846 (1998).



J. Nygren, N. Svanvik & M. Kubista.
The interaction between the fluorescent dye thiazole orange and DNA.
Biopolymers 46, 39-51 (1998).


T. Simonson, P. Pecinka & M. Kubista.
DNA tetraplex formation in the control region of c-myc
Nucl. Acids Res., 26, 1167-1172 (1998).


R. Sjöback, C. M. Gustafsson & M. Kubista.
Determination of DNA protein affinity constants using chemometric analysis of tryptophan fluorescence quenching data.
J. Luminescence, 72-74, 610-611 (1997).



H. Widlund, H. Cao, S. Simonson, E. Magnusson, T. Simonson, J. D. Kahn, D. M. Crothers, P. E. Nielsen, M. Kubista.
Identification and Characterization of genomic nucleosome positioning sequences.
J. Mol. Biol., 267, 807-817 (1997).



J. Nygren, J. M. Andrade, & M. Kubista.
Characterization of a single sample by Combining thermodynamic and Spectroscopic Information in Spectral Analysis.
Anal. Chem. 68, 1706-1710 (1996).



M. Kubista, T. Simonson, R. Sjöback, H. Widlund, & A. Johansson.
Towards an Understanding of the Mechanism of DNA Strand Exchange Promoted by RecA Protein. in ‘Biological Structure and Dynamics’
Eds. Ramaswamy H. Sarma and Mukti H. Sarma, pp. 49-60, Adenine press (1996).



A. Carlosena, J. M. Andrade, M. Kubista, D. Prada.
Procrustes Rotation as a way to Compare Different Sampling Seasons in Soils.
Anal. Chem. 67, 2373-2378 (1995).



R. Sjöback, J. Nygren & M. Kubista.
Absorption and Fluorescence properties of Fluorescein.
Spetrochimica Acta Part A 51, L7-L21 (1995).



M. Kubista, R. Sjöback & J. Nygren.
Quantitative Spectral Analysis of Multicomponent Equilibria.
Analytica Chimica Acta 302, 121-125 (1995).



P. Wittung, J. Kajanus, M. Kubista, & B. Malmström.
Absorption flattening in the optical spectra of liposome-entrapped substances.
Febs Lett. , 352, 37-40 (1994).



P. Samuelsson, K. Jansen & M. Kubista.
Long-range Interactions between DNA-bound Ligands.
J. Mol. Recogn. 7, 233-241 (1994).



T. Simonson, M. Kubista, R. Sjöback, H. Ryberg & M. Takahashi.
Properties of RecA-oligonucleotide Complexes.
J. Mol. Recogn. 7, 199-206 (1994).



M. Kubista, B. Nordén & M. Takahashi.
Properties of RecA Complexes with Homopolymeric DNA strands depend on Sequence Complementarity. Implications for the Mechanism of Strand Exchange.
Nucleosides & Nucleotides 13(1-3), 753-772 (1994).



M. Kubista, R: Sjöback, S. Eriksson & B. Albinsson.
Experimental Correction for the Inner-filter Effect in Fluorescence Spectra.
Analyst 119, 417-419 (1994).



K. Jansen, B. Nordén& M. Kubista.
Sequence Dependence of 4’,6-Diamidino-2-phenylindole (DAPI)-DNA Interactions.
J. Amer. Chem.Soc. 115, 10527-10530 (1993).



M. Kubista, R. Sjöback & B. Albinsson.
Determination of Equilibrium Constants by Chemometric Analysis of Spectroscopic Data.
Anal. Chem. 65, 994-998 (1993).



T. Simonson & M. Kubista.
DNA Orientation in Shear Flow.
Biopol. 33, 1225-1235 (1993).


I. Scarminio & M. Kubista.
Analysis of Correlated Spectral Data.
Anal. Chem. 65, 409-418 (1993).


S. Kim, S. Eriksson, M. Kubista, & B. Nordén.
Interaction of 4’,6-Diamidino-2-phenylindole (DAPI) with Poly[d(G-C)2] and Poly[d(G-m5C)2]: Evidence for Major Groove Binding of a DNA Probe.
J. Amer. Chem. Soc. 115, 3441-3447 (1993).



S. Eriksson, S. Kim, M. Kubista, & B. Nordén.
Binding of 4’,6-Diamidino-2-phenylindole (DAPI) to AT Regions of DNA: Evidence for an Allosteric Conformational Change.
Biochem. 32, 2987-2998 (1993).



 M. Kubista, S. Eriksson & B. Albinsson.
Quantitative Spectral Analysis Without Reference Samples.
Spectrosc.Europe 4, 28-29 (1992).


B. Nordén, C. Elvingson, M. Kubista, B. Sjöberg, H. Ryberg, M. Ryberg, K. Mortensen, & M. Takahashi.
Structure of a RecA-DNA Complexes Studied by Combination of Linear Dichroism and Small-angle Neutron-scattering Measurements on Flow-oriented Samples.
J. Mol. Biol. 226, 1175-1191 (1992).



B. Nordén, M. Kubista, & T. Kurucsev.
Linear Dichroism of Nucleic Acids.
Quart. Rev. Biophys. 25, 51-170 (1992).


B. Nordén, C. Elvingson, P. Hagmar, M. Kubista, D. Baty, K. Mortensen, & M. Takahashi.
RecA-protein-DNA Complexes Studied by Flow Linear Dichroism, Fluorescence and Small Angle Neutron Scattering. Structure & Function. Vol. 2: Proteins.
Eds. R. H. Sarma & M. H. Sarma. 61-68 (1992).



P. Hagmar, S. Pierrou, P. Nielsen, B. Nordén, & M. Kubista.
Ionic Strength Dependence of the Binding of Methylene Blue to Chromatin and Calf Thymus DNA.
J. Biomol. Struct. Dyn. 9, 667-679 (1992).



B. Albinsson, S. Eriksson, R. Lyng, & M. Kubista.
The Electronically Excited States of 2-phenylindole.
Chem. Phys. 151, 149-157(1991).



M. Takahashi, M. Kubista, & B. Nordén.
Co-ordination of Multiple DNA molecules in RecA fiber Evidenced by Linear Dichroism Spectroscopy.
Biochemie, 73, 219-226 (1991).



B. Persson, J. Rydström, & M. Kubista.
A Circular Dichroism Study of Mitochondrial Transhydrogenase from Beef Heart.
Biophys. Chem. 39, 267-272(1991).


B. Nordén, S. Eriksson, S. Kim, M. Kubista, R. Lyng, & B. Åkerman.
DNA Drug Interactions Studied with Polarized Light Spectroscopy: The DAPI case. The 23rd Jerusalem Symposium on Quantum Chemistry and Biochemistry.
Eds B. Pullman & J. Jortner. Vol. 23. Kluwer Acad. Publ. Dordrecht. 23-41 (1990).



B. Nordén, C. Elvingson, T. Eriksson, M. Kubista, B. Sjöberg, M. Takahashi, & K. Mortensen.
Structure of a RecA-DNA Complex from Linear Dichroism and Small-angle Neutron-scattering in Flow-oriented Solution.
J. Mol. Biol. 216, 223-228 (1990).



S. Boström, J. Deinum, J.-E. Löfroth, M. Wirth, & M. Kubista.
Conformational Differences between Latent and Active Plasminogen ActivatorInhibitor, PAI-1: A Spectroscopic Study.
Thromb. Res. 59, 851-858 (1990).



B. Albinsson, M. Kubista, K. Sandros, & B. Nordén. Electronic
Linear Dichroism Spectrum and Transition Moment Directions of the Hypermodified Nucleic Acid Base Wye.
J. Phys. Chem. 94, 4006-4011 (1990).



M. Chiesa, I. Domini, B. Samori, S. Eriksson, M. Kubista & B. Nordén.
Multisite Distribution of Solute Molecules in Micelles. Benzene in a Nematic Phase of Potassium Laurate/Decanol/Water.
Gaz. Chim. Ital. 120, 667-670 (1990).



M. Kubista, P. Hagmar, P. Nielsen & B. Nordén.
Reinterpretation of Linear Dichroism of Chromatin Supports a Perpendicular Linker Orientation in the Folded State.
J. Biomol. Struct. Dyn. 1, 37-54 (1990).



M. Kubista, M. Takahashi & B. Nordén.
Stoichiometry, Base Orientation, and Nuclease Accessibility of RecA-DNA Complexes Seen by Polarized Light in Flow-oriented Solution. Implications for the mechanism of genetic recombination.
J. Biol. Chem. 265, 18891-18897 (1990).



M. Kubista.
A New Method for the Analysis of Correlated Data Using Procrustes Rotation which is Suitable for Spectral Analysis.
Chemomet. and Intell. Lab. Syst. 7, 273-279 (1990).



B. Albinsson, M. Kubista, B. Nordén & E. Thulstrup.
Near-Ultraviolet Electronic Transitions of the Tryptophan Chromophore: Linear Dichroism, Fluorescence anisotropy, and Magnetic Circular Dichroism Spectra of Some Indole Derivatives.
J. Phys. Chem. 93, 6646-6654 (1989).



P. Hagmar, R. Marquet, P. Colson, M. Kubista, P. Nielsen, B. Nordén, & C. Houssier.
Electric and Flow Linear Dichroism of Unfolded and Condensed Chromatin: A Comparative Study at Low and Intermediate Ionic Strength.
J. Biomol. Struct. Dyn. 7, 19-33 (1989).



M. Kubista, B. Åkerman & B. Albinsson.
Characterization of the Electronic Structure of 4’,6-Diamidino-2-phenylindole. J. Amer. Chem. Soc. 111, 7031-7035 (1989).
J. Amer. Chem. Soc. 111, 7031-7035 (1989).



M. Takahashi, M. Kubista, & B. Nordén.
Binding of RecA Protein to Z-form DNA Studied with Circular and Linear Dichroism Spectroscopy.
J. Biol. Chem. 264, 8568-8574 (1989).



M. Takahashi, M. Kubista, & B. Nordén.
Binding Stoichiometry and Structureof RecA-DNA Complexes Studied by Flow Linear Dichroism and Fluorescence Spectroscopy. Evidence for multiple heterogeneous DNA co-ordination.
J. Mol. Biol. 205, 137-147 (1989).



M. Kubista, B. Albinsson, B.?kerman, R. Lyng & B. Nordén.
Characterization of Spectroscopic Properties of Aromatic Molecules by Polarized Spectroscopy.
Finn. Chem. Lett. 38-39 (1988).



M. Kubista.
Protein-DNA Complexes Studied with Polarized Light Spectroscopy. Doctoral thesis.
Chalmers University of Technology.


M. Kubista, M. Takahashi & B. Nordén.
Competitive Binding between Unmodified and Etheno DNA provides information about Structure and Stoichiometries of RecA-DNA Complexes.
Nucleosides & Nucleotides 7(5&6), 783-786 (1988).



B. Nordén & M. Kubista.
Linear Dichroism and Induced Circular Dichroism for Studying Structure and Interactions of DNA. In ‘Polarized Spectroscopy of Ordered Systems’.
Eds. B. Samori & E. Thulstrup. NATO ASI Series C, 242. 133-165 (1988).



M. Kubista, P. Nielsen & B. Nordén.
Flow Linear Dichroism supports an Accordion Model for the Salt-induced Condensation of Chromatin.
Biochem. Pharm. 17, 1813-1814 (1988).



M. Kubista, B. Åkerman & B. Nordén.
Induced Circular Dichroism in Nonintercalative DNA-Drug Complexes. Sector Rules for Structural Applications.
J. Phys. Chem. 92, 2352-2356 (1988).



M. Kubista.
A Study of Non-Intercalator DNA Interactions with Polarised Light Spectroscopy. Licentiate thesis.
Chalmers University of Technology.



M. Kubista, B. Åkerman & B. Nordén.
Characterization of Interaction between DNA and 4’,6-Diamidino-2-phenylindole by Optical Spectroscopy.
Biochem. 26, 4545-4553 (1987).



M. Takahashi, M. Kubista, & B. Nordén.
Linear Dichroism Study of RecA-DNA Complexes. Structural evidence and binding stoichiometries.
J. Biol. Chem. 292, 8109-8111 (1987).



M. Kubista, M. Takahashi & B. Nordén.
Linear Dichroism – A potential method for studying DNA-protein interactions.
Springer Ser. Biophys. I. 145-147 (1987).



M. Kubista, T. Härd, P. Nielsen & B. Nordén.
Structural Transition of Chromatin at Low Salt Concentrations: A Flow Linear Dichroism Study.
Biochem. 24, 6336-6342 (1985).