Publications by authors named "Peter J van der Spek"

100Publications

A Novel Text-Mining Approach for Retrieving Pharmacogenomics Associations From the Literature.

Front Pharmacol 2020 10;11:602030. Epub 2020 Nov 10.

Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece.

View Article and Find Full Text PDF
November 2020

Cas9 Modulates the Transcriptome in Caco-2 Intestinal Epithelial Cells.

Genes (Basel) 2020 Oct 14;11(10). Epub 2020 Oct 14.

Host-Microbe Interactomics, Wageningen University and Research, 6708 WD Wageningen, The Netherlands.

View Article and Find Full Text PDF
October 2020

Molecular Binding Mechanism and Pharmacology Comparative Analysis of Noscapine for Repurposing against SARS-CoV-2 Protease.

J Proteome Res 2020 11 4;19(11):4678-4689. Epub 2020 Sep 4.

Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi 110007, India.

View Article and Find Full Text PDF
November 2020

Molecular data show conserved DNA locations distinguishing lung cancer subtypes and regulation of immune genes.

Lung Cancer 2020 08 20;146:341-349. Epub 2020 Jun 20.

University of Groningen and University Medical Center Groningen, Departments of Pulmonary Diseases and Pathology and Medical Biology, Hanzeplein 1, 9713 GZ, Groningen, the Netherlands. Electronic address:

View Article and Find Full Text PDF
August 2020

The tissue-specific aspect of genome-wide DNA methylation in newborn and placental tissues: implications for epigenetic epidemiologic studies.

J Dev Orig Health Dis 2021 Feb 24;12(1):113-123. Epub 2020 Apr 24.

Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Centre Rotterdam, Postbus 2040, 3000 CARotterdam, The Netherlands.

View Article and Find Full Text PDF
February 2021

Precursor lesions of vulvar squamous cell carcinoma - histology and biomarkers: A systematic review.

Crit Rev Oncol Hematol 2020 Mar 15;147:102866. Epub 2020 Jan 15.

Department of Pathology, Erasmus MC, University Medical Centre Rotterdam, the Netherlands. Electronic address:

View Article and Find Full Text PDF
March 2020

Molecular clustering of genes related to the atopic syndrome: Towards a more tailored approach and personalized medicine?

Clin Transl Allergy 2019 10;9:34. Epub 2019 Jul 10.

4Department of Pathology, Division of Bioinformatics, Erasmus MC University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands.

View Article and Find Full Text PDF
July 2019

Increased serum levels of leptin and insulin in both schizophrenia and major depressive disorder: A cross-disorder proteomics analysis.

Eur Neuropsychopharmacol 2019 07 21;29(7):835-846. Epub 2019 Jun 21.

Antes Center for Mental Health Care, Poortugaal, the Netherlands; Department of Psychiatry, Erasmus Medical Center, Rotterdam, the Netherlands; Department of Neuroscience, Erasmus Medical Center, Rotterdam, the Netherlands. Electronic address:

View Article and Find Full Text PDF
July 2019

Towards a rational design of faecal transplant analogues.

Sci Rep 2019 04 3;9(1):5558. Epub 2019 Apr 3.

Vrije Universiteit Amsterdam, Athena Institute, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.

View Article and Find Full Text PDF
April 2019

Galaxy mothur Toolset (GmT): a user-friendly application for 16S rRNA gene sequencing analysis using mothur.

Gigascience 2019 02;8(2)

Erasmus University Medical Center Rotterdam, Department of Pathology, Bioinformatics group, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.

View Article and Find Full Text PDF
February 2019

On the origin of proteins in human drusen: The meet, greet and stick hypothesis.

Prog Retin Eye Res 2019 05 17;70:55-84. Epub 2018 Dec 17.

UCL Institute of Ophthalmology, University College London, London, UK; Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University, Belfast, Northern Ireland, UK.

View Article and Find Full Text PDF
May 2019

First trimester physiological development of the fetal foot position using three-dimensional ultrasound in virtual reality.

J Obstet Gynaecol Res 2019 Feb 18;45(2):280-288. Epub 2018 Nov 18.

Department of Obstetrics and Gynecology, Division of Obstetrics and Prenatal Medicine, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, the Netherlands.

View Article and Find Full Text PDF
February 2019

A multidisciplinary review of triphalangeal thumb.

J Hand Surg Eur Vol 2019 Jan 14;44(1):59-68. Epub 2018 Oct 14.

1 Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.

View Article and Find Full Text PDF
January 2019

Evaluation of First-Trimester Physiological Midgut Herniation Using Three-Dimensional Ultrasound.

Fetal Diagn Ther 2019 15;45(5):332-338. Epub 2018 Aug 15.

Division of Obstetrics and Prenatal Medicine, Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Centre, Rotterdam, The Netherlands.

View Article and Find Full Text PDF
December 2019

De Novo and Inherited Loss-of-Function Variants in TLK2: Clinical and Genotype-Phenotype Evaluation of a Distinct Neurodevelopmental Disorder.

Am J Hum Genet 2018 06 31;102(6):1195-1203. Epub 2018 May 31.

Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Craniofacial Unit, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK. Electronic address:

View Article and Find Full Text PDF
June 2018

Genome-wide association meta-analysis highlights light-induced signaling as a driver for refractive error.

Authors:
Milly S Tedja Robert Wojciechowski Pirro G Hysi Nicholas Eriksson Nicholas A Furlotte Virginie J M Verhoeven Adriana I Iglesias Magda A Meester-Smoor Stuart W Tompson Qiao Fan Anthony P Khawaja Ching-Yu Cheng René Höhn Kenji Yamashiro Adam Wenocur Clare Grazal Toomas Haller Andres Metspalu Juho Wedenoja Jost B Jonas Ya Xing Wang Jing Xie Paul Mitchell Paul J Foster Barbara E K Klein Ronald Klein Andrew D Paterson S Mohsen Hosseini Rupal L Shah Cathy Williams Yik Ying Teo Yih Chung Tham Preeti Gupta Wanting Zhao Yuan Shi Woei-Yuh Saw E-Shyong Tai Xue Ling Sim Jennifer E Huffman Ozren Polašek Caroline Hayward Goran Bencic Igor Rudan James F Wilson Peter K Joshi Akitaka Tsujikawa Fumihiko Matsuda Kristina N Whisenhunt Tanja Zeller Peter J van der Spek Roxanna Haak Hanne Meijers-Heijboer Elisabeth M van Leeuwen Sudha K Iyengar Jonathan H Lass Albert Hofman Fernando Rivadeneira André G Uitterlinden Johannes R Vingerling Terho Lehtimäki Olli T Raitakari Ginevra Biino Maria Pina Concas Tae-Hwi Schwantes-An Robert P Igo Gabriel Cuellar-Partida Nicholas G Martin Jamie E Craig Puya Gharahkhani Katie M Williams Abhishek Nag Jugnoo S Rahi Phillippa M Cumberland Cécile Delcourt Céline Bellenguez Janina S Ried Arthur A Bergen Thomas Meitinger Christian Gieger Tien Yin Wong Alex W Hewitt David A Mackey Claire L Simpson Norbert Pfeiffer Olavi Pärssinen Paul N Baird Veronique Vitart Najaf Amin Cornelia M van Duijn Joan E Bailey-Wilson Terri L Young Seang-Mei Saw Dwight Stambolian Stuart MacGregor Jeremy A Guggenheim Joyce Y Tung Christopher J Hammond Caroline C W Klaver

Nat Genet 2018 06 28;50(6):834-848. Epub 2018 May 28.

Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands.

View Article and Find Full Text PDF
June 2018

Accuracy of fetal sex determination in the first trimester of pregnancy using 3D virtual reality ultrasound.

J Clin Ultrasound 2018 May 19;46(4):241-246. Epub 2017 Oct 19.

Department of Obstetrics and Gynecology, Division of Obstetrics and Prenatal Medicine, Erasmus MC, University Medical Centre, Rotterdam, the Netherlands.

View Article and Find Full Text PDF
May 2018

Early- and late-onset preeclampsia and the tissue-specific epigenome of the placenta and newborn.

Placenta 2017 Oct 30;58:122-132. Epub 2017 Aug 30.

Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Centre Rotterdam, Postbus 2040, 3000 CA Rotterdam, The Netherlands. Electronic address:

View Article and Find Full Text PDF
October 2017

Identification of Associated Genes and Diseases in Patients With Congenital Upper-Limb Anomalies: A Novel Application of the OMT Classification.

J Hand Surg Am 2017 Jul;42(7):533-545.e4

Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands. Electronic address:

View Article and Find Full Text PDF
July 2017

A Novel Heterozygous Mutation in the SH2 Domain Causes Chronic Mucocutaneous Candidiasis, Atypically Diverse Infections, Autoimmunity, and Impaired Cytokine Regulation.

Front Immunol 2017 13;8:274. Epub 2017 Mar 13.

Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands; Department of Internal Medicine, Division of Clinical Immunology, Erasmus University Medical Center, Rotterdam, Netherlands.

View Article and Find Full Text PDF
March 2017

An International Ki67 Reproducibility Study in Adrenal Cortical Carcinoma.

Am J Surg Pathol 2016 Apr;40(4):569-76

Departments of *Pathology ∥Bioinformatics ¶¶¶Medical Oncology ∥∥∥Internal Medicine, Division of Endocrinology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam ††Laboratory for Pathology, PAL Dordrecht, Dordrecht ###Department of Pathology, Reinier de Graaf Hospital, Delft ****Department of Pathology, University Medical Center Utrecht, Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands †Department of Histopathology, King's College Hospital, London ***Department of Pathology, University Hospitals Birmingham, Birmingham †††Department of Histopathology, Royal Hallamshire Hospital, Sheffield, UK ‡Department of Clinical and Molecular Medicine, Pathology Unit, Sant' Andrea Hospital, Sapienza University, Rome ¶Department of Oncology, University of Turin at San Luigi Hospital, Orbassano, Italy §Department of Pathology, Department of Internal Medicine, University of Michigan Comprehensive Cancer Center, University of Michigan Health System, Ann Arbor, MI #Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI **Department of Pathology and Laboratory Medicine, Tufts Medical Center, Tufts University School of Medicine ‡‡Department of Pathology, Massachusetts General Hospital, Boston, MA §§Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN ∥∥Department of Pathology, University Health Network, University of Toronto, Toronto, ON, Canada ¶¶Department of Anatomical Pathology, Royal North Shore Hospital and University of Sydney, Sydney, NSW, Australia ##Department of Pathology and Molecular Genetics and Research Laboratory, Hospital Universitari Arnau de Vilanova, IRBLLEIDA, University of Lleida, Lleida, Spain ‡‡‡INSERM U1016 CNRS UMR8104, Institut Cochin, Paris Descartes University, Sorbonne Paris Cité §§§Department of Pathology, Pitié-Salpetrière Hospital, APHP, Pierre and Marie Curie Univers

View Article and Find Full Text PDF
April 2016

FuMa: reporting overlap in RNA-seq detected fusion genes.

Bioinformatics 2016 04 10;32(8):1226-8. Epub 2015 Dec 10.

Department of Bioinformatics, Erasmus University Medical Center, Rotterdam, 3000 CA, The Netherlands.

View Article and Find Full Text PDF
April 2016

Comparison of Mouse and Human Retinal Pigment Epithelium Gene Expression Profiles: Potential Implications for Age-Related Macular Degeneration.

PLoS One 2015 30;10(10):e0141597. Epub 2015 Oct 30.

Department of Clinical Genetics, Academic Medical Centre, Amsterdam, The Netherlands; The Netherlands Institute for Neuroscience (NIN-KNAW), Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands; Department of Ophthalmology, Academic Medical Centre, Amsterdam, The Netherlands.

View Article and Find Full Text PDF
June 2016

Gain-of-Function Mutations in ZIC1 Are Associated with Coronal Craniosynostosis and Learning Disability.

Am J Hum Genet 2015 Sep;97(3):378-88

Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK; Craniofacial Unit, Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK. Electronic address:

View Article and Find Full Text PDF
September 2015

Tumor-specific mutations in low-frequency genes affect their functional properties.

J Neurooncol 2015 May 19;122(3):461-70. Epub 2015 Feb 19.

Department of Neurology, Be 430A, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.

View Article and Find Full Text PDF
May 2015

Retinal pigment epithelial cells display specific transcriptional responses upon TNF-α stimulation.

Br J Ophthalmol 2015 May 13;99(5):700-4. Epub 2015 Feb 13.

Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center Rotterdam, The Netherlands.

View Article and Find Full Text PDF
May 2015

Pollitt syndrome patients carry mutation in TTDN1.

Meta Gene 2014 Dec 30;2:616-8. Epub 2014 Aug 30.

Department of Bioinformatics, Erasmus University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands.

View Article and Find Full Text PDF
December 2014

A novel mutation in FGFR2.

Am J Med Genet A 2015 Jan 25;167A(1):123-7. Epub 2014 Nov 25.

Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center, Rotterdam, the Netherlands; Department of Bioinformatics, Erasmus MC, University Medical Center, Rotterdam, the Netherlands.

View Article and Find Full Text PDF
January 2015

Design and validation of a 3D virtual reality desktop system for sonographic length and volume measurements in early pregnancy evaluation.

J Clin Ultrasound 2015 Mar 9;43(3):164-70. Epub 2014 Jul 9.

Department of Obstetrics and Gynaecology, Division of Obstetrics and Prenatal Medicine, Erasmus MC, University Medical Center Rotterdam, Room Na15.23, PO Box 2040, 3000, CA Rotterdam, The Netherlands.

View Article and Find Full Text PDF
March 2015

First-trimester hand measurements in euploid and aneuploid human fetuses using virtual reality.

Prenat Diagn 2014 Oct 29;34(10):961-9. Epub 2014 May 29.

Department of Obstetrics and Gynaecology, Division of Obstetrics and Prenatal Medicine, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands.

View Article and Find Full Text PDF
October 2014

Early pregnancy placental bed and fetal vascular volume measurements using 3-D virtual reality.

Ultrasound Med Biol 2014 Aug 3;40(8):1796-803. Epub 2014 May 3.

Division of Obstetrics and Prenatal Medicine, Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.

View Article and Find Full Text PDF
August 2014

Differential gene expression of the intermediate and outer interzone layers of developing articular cartilage in murine embryos.

Stem Cells Dev 2014 Aug 16;23(16):1883-98. Epub 2014 Jun 16.

1 Equine University Hospital, Department of Companion Animals and Horses, University of Veterinary Medicine Vienna , Vienna, Austria .

View Article and Find Full Text PDF
August 2014

First-Trimester Detection of Surface Abnormalities: A Comparison of 2- and 3-Dimensional Ultrasound and 3-Dimensional Virtual Reality Ultrasound.

Reprod Sci 2014 Aug 18;21(8):993-999. Epub 2014 Jan 18.

Department of Obstetrics and Gynaecology, Division of Obstetrics and Prenatal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.

View Article and Find Full Text PDF
August 2014

Metabolic alterations due to IDH1 mutation in glioma: opening for therapeutic opportunities?

Acta Neuropathol Commun 2014 Jan 9;2. Epub 2014 Jan 9.

Department of Pathology, Erasmus Medical Center, Dr, Molewaterplein 50, 3000 CA, Rotterdam, The Netherlands.

View Article and Find Full Text PDF
January 2014

Gene expression and functional annotation of the human and mouse choroid plexus epithelium.

PLoS One 2013 31;8(12):e83345. Epub 2013 Dec 31.

Department of Clinical and Molecular Ophthalmogenetics, the Netherlands Institute for Neuroscience (NIN), Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam, The Netherlands ; Department of Ophthalmology, Academic Medical Centre (AMC), Amsterdam, The Netherlands ; Department of Clinical Genetics, Academic Medical Centre (AMC), Amsterdam, The Netherlands.

View Article and Find Full Text PDF
August 2014

Microarray and morphological analysis of early postnatal CRB2 mutant retinas on a pure C57BL/6J genetic background.

PLoS One 2013 6;8(12):e82532. Epub 2013 Dec 6.

Department of Neuromedical Genetics, The Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands.

View Article and Find Full Text PDF
July 2014

Gene expression analysis of peripheral cells for subclassification of pediatric inflammatory bowel disease in remission.

PLoS One 2013 18;8(11):e79549. Epub 2013 Nov 18.

Department of Paediatrics, Erasmus MC - Sophia Children's Hospital, Rotterdam, The Netherlands ; Department of Paediatric Gastroenterology, Wilhelmina Children's Hospital, UMC Utrecht, Utrecht, The Netherlands.

View Article and Find Full Text PDF
July 2014

Is there an effect of obstructive sleep apnea syndrome on oxidative stress and inflammatory parameters in patients with craniofacial anomalies?

J Craniofac Surg 2013 Nov;24(6):1908-13

From the Departments of *Plastic, Reconstructive and Hand Surgery, †Bioinformatics, ‡Intensive Care Medicine, and §Department of Biochemistry, Academic Medical Center, Amsterdam, and ∥Pediatrics, Dutch Craniofacial Centre, Erasmuc Medical Center, Sophia Children's Hospital, Rotterdam, The Netherlands.

View Article and Find Full Text PDF
November 2013

In silico analysis of the molecular machinery underlying aqueous humor production: potential implications for glaucoma.

J Clin Bioinforma 2013 Oct 28;3(1):21. Epub 2013 Oct 28.

Department of Clinical and Molecular Ophthalmogenetics the Netherlands Institute for Neuroscience (NIN), Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam, the Netherlands.

View Article and Find Full Text PDF
October 2013

NetWeAvers: an R package for integrative biological network analysis with mass spectrometry data.

Bioinformatics 2013 Nov 4;29(22):2946-7. Epub 2013 Sep 4.

Department of Bioinformatics, Erasmus University Medical Center, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands, Department of Mathematics and Computer Science, Metropolitan State University of Denver, Colorado, USA, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, Meibergdreef 9, Amsterdam, 1105AZ, The Netherlands, Netherlands Proteomics Centre, H.R. Kruytgebouw, Padualaan 8, 3584CH Utrecht, The Netherlands and Netherlands Bioinformatics Centre, Geert Grooteplein 28, 6525GA Nijmegen, The Netherlands.

View Article and Find Full Text PDF
November 2013

Boston type craniosynostosis: report of a second mutation in MSX2.

Am J Med Genet A 2013 Oct 15;161A(10):2626-33. Epub 2013 Aug 15.

Department of Plastic, Reconstructive and Hand Surgery, Dutch Craniofacial Centre, Erasmus Medical Centre Sophia Children's Hospital, Rotterdam, The Netherlands.

View Article and Find Full Text PDF
October 2013

Loss of E-cadherin is not a necessity for epithelial to mesenchymal transition in human breast cancer.

Breast Cancer Res Treat 2013 Feb 22;138(1):47-57. Epub 2013 Jan 22.

Department of Medical Oncology, Josephine Nefkens Institute, Erasmus University Medical Center-Daniel den Hoed Cancer Center, Rotterdam, The Netherlands.

View Article and Find Full Text PDF
February 2013

Gene expression and functional annotation of the human ciliary body epithelia.

PLoS One 2012 18;7(9):e44973. Epub 2012 Sep 18.

Department of Clinical and Molecular Ophthalmogenetics, the Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands.

View Article and Find Full Text PDF
March 2013

Collagenase matrix metalloproteinase-8 expressed in atherosclerotic carotid plaques is associated with systemic cardiovascular outcome.

Eur Heart J 2011 Sep 2;32(18):2314-25. Epub 2011 Feb 2.

Experimental Cardiology Laboratory, Division heart and Lungs, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, The Netherlands.

View Article and Find Full Text PDF
September 2011

Virtual reality for embryonic measurements requiring depth perception.

Fertil Steril 2011 Feb;95(2):773-4

Division of Obstetrics and Prenatal Medicine, Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Center Rotterdam, the Netherlands.

View Article and Find Full Text PDF
February 2011