Publications

Spheromics Publications and Contributions since September 2007

* Co-authorship was offered by the authors

 

Peer-reviewed journals

 

 

2016

 

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"
submitted

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 confriamtion of potential gene classifiers of human clear cell renal carcinoma using next-generation sequencing (RNAseq)"
submitted

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

2015

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

2014


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."
Journal of Hypertension, in press, 2014.

 

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.



2013 


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


2012

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

 

2011    
  

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


2010


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.


2009      



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


2007    


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


2013      


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)


 

2010    
  


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

 

 

2009      


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

John Wiley & Sons, Inc. 2009, ISBN 978-0-470-74138-2

www.the-batch-effect-book.org
To purchase a copy, follow this link:
Batch Effect Book-Scherer


Therein:

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


2013

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)

2012

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


2010

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
.

 

2008      

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

 

2007   
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

 

 

2007      

Founding of Spheromics in September 2007