Spheromics Publications and Contributions since September 2007

* Co-authorship was offered by the authors


Peer-reviewed journals


Landolt L, Furriol J, Babickova J, Ahmed L, Eikrem Ø, Skogstrand T, Scherer A, Suliman S, Leh S, Lorens JB, Gausdal G, Marti HP, Osman T.

AXL targeting reduces fibrosis development in experimental unilateral ureteral obstruction.
Physiol Rep. 2019 May;7(10):e14091. doi: 10.14814/phy2.14091.

Koch E, Finne K, Eikrem Ø, Landolt L, Beisland C, Leh S, Delaleu N, Granly M, Vikse BE, Osman T, Scherer A, Marti HP.

Transcriptome-proteome integration of archival human renal cell carcinoma biopsies enables identification of molecular mechanisms.

Am Am J Physiol Renal Physiol. 2019 May 1;316(5):F1053-F1067. doi: 10.1152/ajprenal.00424.201




Strauss P, Marti HP, Beisland C, Scherer A, Lysne V, Leh S, Flatberg A, Koch E, Beisvag V, Landolt L, Skogstrand T, Eikrem Ø.

Expanding the Utilization of Formalin-Fixed, Paraffin-Embedded Archives: Feasibility of miR-Seq for Disease Exploration and Biomarker Development from Biopsies with Clear Cell Renal Cell Carcinoma.

Int J Mol Sci. 2018 Mar 10;19(3). pii: E803. doi: 10.3390/ijms19030803.


Landolt L, Eikrem Ø, Strauss P, Scherer A, Lovett DH, Beisland C, Finne K, Osman T, Ibrahim MM, Gausdal G, Ahmed L, Lorens JB, Thiery JP, Tan TZ, Sekulic M, Marti HP. Clear Cell Renal Cell Carcinoma is linked to Epithelial-to-Mesenchymal Transition and to Fibrosis.

Physiol Rep. 2017 Jun;5(11). pii: e13305. doi: 10.14814/phy2.13305





Marti H.-P., Jeffs A., Scherer A.*, Leader J., Leader C., Bedford J., Walker R. "Renal fibrosis mRNA classifier: Validation in experimental lithium-induced interstitial fibrosis in the rat kidney"
PLoS One. 2016 Dec 21;11(12):e0168240. doi: 10.1371/journal.pone.0168240. eCollection 2016

Eikrem O., Strauss P., Beisland C., Scherer A.*, Landolt L., Flatberg A., Leh S., Beisvag V., Hjelle K., Shresta A., Marti H.P. "Development and confiemation of potential gene classifiers of human clear cell renal carcinoma using next-generation sequencing (RNAseq)"
Scand J Urol, 2016; DOI 10.1080/21681805.2016.1238007

Eikrem O, Beisland C., Hjelle K., Flatberg A., Scherer A.*, Landolt L., Skogstrand T., Leh., Besivag V., Marti H.-P. "Transcriptome sequencing (RNAseq) enables utilization of formalin-fixed, paraffin-embedded biopsies with clear cell renal carcinoma for exploration of disease biology and biomarker development"
PLoS One 2016 11(2):e0149743. doi: 10.1371; PMID: 26901863

Finne K., Marti H.-P., Leh S., Skogstrand T., Vethe H., Tenstad O., Berven F.S., Scherer A.*, Vikse B.E. "Proteomic analysis of normal or minimally damaged renal tubular tissue demonstrates extensive changes in two-kidney-one-clip hypertensive rats"
Nephron 2016; 132(1):70-80. doi: 10.1159/000442825; PMID: 26745798


Vethe H., Finne K., Skogstrand T., Vaudel M., Vikse B.E., Hultström M., Placier S., Scherer A.*, Tenstad O., Hans-Peter Marti H.-P. “Distinct protein signature of hypertension-induced damage in the renal proteome of the two-kidney, one-clip (2K1C) rat model.”
J Hypertension, 2015 Jan;33(1):126-135. doi: 10.1097/HJH.0000
000000000370. PMID:25304470


Su Z.Q., Labaj P., Li S.,…Scherer, A.,…,Shi L. “Power and Limitations of RNA-Seq”, The SEQC Consortium,
Nature Biotechnology, 2014;32(9):903-914.

Wang C., Gong B.,…,Scherer A.,…,Tong W. “A comprehensive study design reveals treatment- and abundance-dependent concordance between RNA-Seq and microarrays”, The SEQC consortium,
Nature Biotechnology, 2014; 32(9):926-932

Nicole Hartmann, Evert Luesink, Edward Khokhlovich, Joseph D. Szustakowski, Lukas Baeriswyl, Joshua Peterson, Andreas Scherer*, Nirmala R. Nanguneri, Frank Staedtler. “The use of haplotype-specific transcripts improves sample annotation consistency.”
Biomarker Research 2014; 2:17. PMID: 25285214.

Martin Letzkus, Evert Luesink, Sandrine Starck-Schwertz, Marc Bigaud, Fareed Mirza, Nicole Hartmann, Bernhard Gerstmayer, Uwe Janssen, Andreas Scherer*, Martin Schumacher, Aurelie Verles, Alessandra Vitaliti, Nanguneri Nirmala, Keith J Johnson, Frank Staedtler. “Gene expression profiling of immunomagnetically separated cells directly from stabilized whole blood for multicenter clinical trials.”
Clinical and Translational Medicine 201
4; 3:36. DOI: 10.1186/s40169-014-0036z.

Heidrun Vethe, Kenneth Finne, Trude Skogstrand, Marc Vaudel, Bjørn E. Vikse, Michael Hultström, Sandrine Placier, Andreas Scherer*, Olav Tenstad, Hans-Peter Marti. “Distinct protein signature of hypertension-induced damage in the renal proteome of the two-kidney, one-clip (2K1C) rat model."
J Hypertens. 2015 Jan;33(1):126-35. doi: 10.1097/HJH.0000000000000370.


Marti H-P, Fuscoe JC, Kwekel JC, Anagnostopoulou A, Scherer A. "Metzincins and Related Genes (MARGS) in Experimental Renal Aging: Towards a Unifying Fibrosis Classifier across Species."
Nephrology Dialysis Transplantation 2014, gfu027.

Borchers C, Kast J, Foster L, Siu M, Overall CM, Binkowski A, Hildebrand W, Scherer A*, Mansoor M, Keown P; for the Human Proteome Organization Chromosome 6 Consortium. The Human Proteome Organization Chromosome 6 Consortium: integrating chromosome-centric and biology/disease-driven strategies.

Journal of Proteomics. 2014; 100: 60-67.


Andreas Scherer (editorial). Clinical and Ethical Considerations of Massively Parallel Sequencing in Transplantation Science.
World J Transpl. 2013, Dec;3(4):62-67.

Staedtler F, Hartmann N, Letzkus M, Bongiovanni S, Scherer A*, Marc P, Johnson KJ, and Schumacher MM. Robust and tissue independent gender-specific transcript biomarkers.
Biomarkers 2013, Aug;18(5):436-45.

Andreas Scherer, Oliver Gunther, Robert Balshaw, Zsuzsanna Hollander, Janet McManus, Raymond Ng, W Robert McMaster, Bruce McManus, and Paul Keown. Alteration of the human gene expressioon profile in uremia.
BMC Medical Genomics 2013, Jun 28;6(1):23


Jensen JM, Scherer A*, Wanke C, Brautigam M, Bongiovanni S, Letzkus M, Staedtler F, Kehren J, Zuehlsdorf M, Schwarz T, Weichenthal M, Folster-Holst R, Proksch E. Gene expression is differently affected by pimecrolimus and betamethasone in lesional skin of atopic dermatitis.
Allergy 2012, 67: 413-423



Jens-Michael Jensen, Kerstin Ahrens, Josef Meingassner, Andreas Scherer*, Matthias Bräutigam, Anton Stütz, Thomas Schwarz, Regina Fölster-Holst, Jürgen Harder, Regine Gläser, Ehrhardt Proksch. Differential suppression of epidermal antimicrobial protein expression in atopic dermatitis and EFAD mice by pimecrolimus compared to corticosteroids.
Experimental Dermatology 2011, 20: 783-788

Roedder S, Scherer A*, Koerner M, Marti HP. A subset of metzincins and related genes constitutes a marker of human solid organ fibrosis.
European Journal of Pathology 2011, 458: 487-496


Shi L, Campbell G, Jones WD,..., Scherer A,...,Wolfinger R. The MAQC-II Project: A comprehensive study of common practices for the development and validation of microarray-based predictive models.
Nature Biotechnology 2010;28:827-838.

J. Luo, M. Schumacher, A. Scherer, D. Sanoudou, D. Megherbi, T. Davison, T. Shi, W. Tong, L. Shi, H. Hong, C. Zhao, F. Elloumi, W. Shi, R. Thomas, S. Lin, G. Tillinghast, G. Liu, Y. Zhou, D. herman, Y. Li, Y. deng, H. Fang, M. Woods, P. Bushel, M. Woods, J. Zhang. A Comparison of Batch Effect Removal Methods for Enhancement of Cross-Batch Prediction Performance Using MAQC-II Microarray Gene Expression Data. The Pharmacogenomics Journal, 2010;10:247-257.


S. Roedder, A. Scherer*, M. Koerner, U. Eisenberger, A. Hertig, F. Raulf, E. Rondeau, H-P. Marti . Meta-Analyses Qualify Metzincins and Related Genes as Acute Rejection Markers in Renal Transplant Patients.
American Journal of Transplantation 2009;10:296-297.

Oliver P. Günther, Robert F. Balshaw, Andreas Scherer*, Zsuzsanna Hollander, Alice Mui, Tim Triche, Gabriela Cohen Freue, Guiyun Li, Raymond Ng, Janet Wilson-McManus, W. Robert McMaster, Bruce M. McManus, Paul A. Keown. Functional Genomic Analysis of Peripheral Blood During Early Acute Renal Allograft Rejection.
Transplantation 2009;88:942-951.


A. Scherer, W. Gwinner, M. Mengel, T. Kirsch, F. Raulf, N. Hartmann, F. Staedtler, G. Engel, J. Klupp, A. Korn, J. Kehren, H. Haller. Transcriptome Changes in Renal Allograft Protocol Biopsies at Three Months Precede the Onset of Interstitial Fibrosis/Tubular Atrophy (IF/TA) at Six Months. Nephrology Dialysis Transplantation (NDT) 2009:24:2567-2575.


S. Rödder, A. Scherer*, F. Raulf, C.C. Berthier, A. Hertig, E. Rondeau, H.-P. Marti. Renal Allografts with IF/TA Display Distinct Expression Profiles of Metzincins and Related Genes.
American Journal of Transplantation (AJT), 2009, Vol.9 (3): 517-526


Cohen Freue GV, Hollander Z, Shen E, Zamar RH, Balshaw R, Scherer A*, McManus B, Keown P, McMaster WR, Ng RT. MDQC: a new quality assessment method for microarrays based on quality control reports.
Bioinformatics. 2007 Dec 1;23(23):3162-9


Book chapters/Books


Andreas Scherer
, Manhong Dai, Fan Meng. Impact of Experimental Noise and Annotation Imprecision in Data Quality in Microarray Experiments. In:  "Statistical Methods for Microarray Data Analysis", pages 155 – 176. Editors: Andrei Y. Yakovlev, Lev Klebanov, Daniel Gaile.

Springer Methods in Molecular Biology 972. ISBN: 978-1-60327-336-7 (Print) 978-1-60327-337-4 (Online)



David Lin, Andreas Scherer*, Raymond Ng, Robert Balshaw, Shawna Flynn, Paul Keown, Rob McMaster, Bruce McManus. Clinical Validation and Biomarkers Translation. In ”Biomarkers in Drug Development: A Handbook of Practice, Application, and Strategy”, Editors: MR Bleavins, C Carini, M Jurima-Romet, and R Rahbari.

John Wiley & Sons, Inc. 2010, ISBN 978-0-470-16927-8




Batch Effects and Noise in Microarray Experiments: Sources and Solutions . Andreas Scherer, editor

John Wiley & Sons, Inc. 2009, ISBN 978-0-470-74138-2
To purchase a copy, follow this link:
Batch Effect Book-Scherer


Andreas Scherer. Variation, Variability, Batches and Bias in Microarray Experiments: An Introduction.
In: "Batch Effects and Noise in Microarray Experiments: Sources and Solutions", editor: Andreas Scherer                                                              John Wiley & Sons, Inc. 2009, ISBN 978-0-470-74138-2

Martin Schumacher, Frank Staedtler, Wendell Jones, and Andreas Scherer. Aspects of Technical Bias.
In: "Batch Effects and Noise in Microarray Experiments: Sources and Solutions", editor: Andreas Scherer                                                              John Wiley & Sons, Inc. 2009, ISBN 978-0-470-74138-2

Lev Klebanov and Andreas Scherer.  Toward Integration of Biological Noise: Aggregation Effect in Microarray Data Analysis.
In: "Batch Effects and Noise in Microarray Experiments: Sources and Solutions", editor: Andreas Scherer                                                         John Wiley & Sons, Inc. 2009, ISBN 978-0-470-74138-2

Gabriella Rustici, Andreas Scherer, and John Quackenbush. Data, Analysis, and Standardization.
In: "Batch Effects and Noise in Microarray Experiments: Sources and Solutions", editor: Andreas Scherer                                                            John Wiley & Sons, Inc. 2009, ISBN 978-0-470-74138-2


Oral Presentations, Posters and Abstracts


Hans-Peter Marti, James C. Fucsoe, Joshua C. Kwekel, Aikaterini Anagnostopoulou, and Andreas Scherer. Fibrosis of Kidneys and other solid organs: towards a unifying classsifier across species. American Society of Nephrology, Kidney Week 2013, Annual Meeting, Nov 7-10, Atlanta, GA, USA (Poster)


Andreas Scherer. Introduction to Gene Expression Profiling For Biomarker Discovery in Renal Disease. University of Otago Research Theme: The Kidney in Health and Disease2012, University of Otago, Dunedin, NZ


A. Scherer*, J.-M. Jensen, M. Braeutigam,..., and E. Proksch. Gene expression profiles are differently affected by pimecrolimus and beta-methasone in leasional skin in atopic dermatitis . Poster                                                      
40th Annual Meeting of the European Society for Dermatological Research (ESRD); 8.-11. Sept. 2010, Helsinki, Finland

S. Roedder, A. Scherer*, M. Koerner, and H.-P. Marti. Successful cross-organ classification of fibrosis based on microarray meta-analysis applying a classifier model of renal transplant IF/TA.                                                                        
Oral presentation; XXIII International Congress of The Transplantation Society, 2010, Vancouver, CA

O.P. Guenther, A. Scherer*, D. Lin,..., and P.A. Keown. Classification of acute renal rejecion with proteogenomic ensemble classifiers.         
Oral presentation;   XXIII International Congress of The Transplantation Society, 2010, Vancouver, CA

S. Roedder, A. Scherer*, and H.-P. Marti. Expression Signatures of Extracellular Matrix Related Transcript Sets Linked Renal Allograft Interstitial Fibrosis/Tubular Atrophy with Acute T-cell mediated Rejection.
Oral presentation; 1st International Conference on Transplantomics and Biomarkers in Organ Transplantation; San Francisco, Feb 24-26, 2010



Paul Keown, Andreas Scherer*, Oliver Gùˆnther, Zsuzsanna Hollander, Gabriela Cohen-Freue, David Lin, Janet Wilson-McManus, Robert Balshaw, Raymond Ng, Robert McMaster and Bruce McManus. Longitudinal Pattern of Differential Gene Expression Within the First 3 Months Following Renal Transplantation. Poster                                                            
XXII International Congress of The Transplantation Society in Sydney, August 2008


Silke Roedder, Andreas Scherer*, Friedrich Raulf, Celine Berthier, Alexandre Hertig, Eric Rondeau,and Hans Peter Marti. Differential Expression of Metzincins and Related Genes, including MMP7, -9 and THBS2, discriminates Acute Rejection from Chronic Dysfunction in Renal Allografts. Poster.   American Society of Nephrology (ASN) Renal Week 2008, November 4 - November 9, 2008


S Roedder, A Scherer*, F Raulf, C Berthier, A Hertig, E Rondeau, HP Marti. Renal Allografts with Non- Specified Chronic Dysfunction are Characterized by Distinct Expression Profiles of Metzincins and Related Genes International Society of Nephrology (ISN). Poster.
Nexus Symposium on Transplantation and the Kidney; Rome, Italy, Sept 25-28, 2008


Biomarkers in Renal Transplantation: The Vancouver Biomarkers Program                                                          
Canadian Society of Transplantation Annual Scientific Meeting (CST), March 2008, Quebec, CA


Translational Program for Applied Health- Biomarkers in Transplantation-A Canada-Wide Trial and Biomarker Assay Development    Genome British Columbia Biomarker in Transplantation; Grant proposal (accepted)


Silke Roedder, Hans-Peter Marti. Gene Expression Profiling Reveals Dysregulation of Matrix Metalloproteinases and Extracellular Matrix-Related Genes in Chronic Allograft Nephropathy American Society of Nephrology (ASN), Nov 2007, San Francisco, USA




Founding of Spheromics in September 2007