Jan Bert van Klinken

researcher

Vakgebied(en)

  • systems biology (mathematical modelling, simulation, stoichiometric analysis)
  • pathway analysis
  • data integration
  • multivariate statistics
  • indirect calorimetry

Publications

van Klinken JB, Willems van Dijk, K (2015) FluxModeCalculator: an efficient tool for large-scale flux mode computation. Bioinformatics [in press]

Draisma HH, Pool R, Kobl M, Jansen R, Petersen AK, Vaarhorst AA, Yet I, Haller T, Demirkan A, Esko T, Zhu G, Böhringer S, Beekman M, van Klinken JB, Römisch-Margl W, Prehn C, Adamski J, . . . , Boomsma DI. (2015) Genome-wide association study identifies novel genetic variants contributing to variation in blood metabolite levels. Nat Commun. 6:7208

Heemskerk MM, van Harmelen VJ, van Dijk KW, van Klinken JB (2015) Reanalysis of mGWAS results and in vitro validation show that lactate dehydrogenase interacts with branched-chain amino acid metabolism. Eur J Hum Genet [in press]

van Beek L, van Klinken JB, Pronk AC, van Dam AD, Dirven E, Rensen PC, Koning F, Willems van Dijk K, van Harmelen V. (2015) The limited storage capacity of gonadal adipose tissue directs the development of metabolic disorders in male C57Bl/6J mice. Diabetologia 58(7):1601-9

Demirkan A, Henneman P, Verhoeven A, Dharuri H, Amin N, van Klinken JB, Karssen LC, de Vries B, Meissner A, Göraler S, van den Maagdenberg AM, Deelder AM, C 't Hoen PA, van Duijn CM, van Dijk KW. (2015) Insight in genome-wide association of metabolite quantitative traits by exome sequence analyses. PLoS Genet. 11(1):e1004835

Bakker LE, Guigas B, van Schinkel LD, van der Zon GC, Streefland TC, van Klinken JB, Jonker JT, Lamb HJ, Smit JW, Pijl H, Meinders AE, Jazet IM. (2014) Middle-aged overweight South Asian men exhibit a different metabolic adaptation to short-term energy restriction compared with Europeans. Diabetologia 58(1):165-77

Lips MA, Van Klinken JB, van Harmelen V, Dharuri HK, 't Hoen PA, Laros JF, van Ommen GJ, Janssen IM, Van Ramshorst B, Van Wagensveld BA, Swank DJ, Van Dielen F, Dane A, Harms A, Vreeken R, Hankemeier T, Smit JW, Pijl H, Willems van Dijk K. (2014) Roux-en-Y Gastric Bypass Surgery, but Not Calorie Restriction, Reduces Plasma Branched-Chain Amino Acids in Obese Women Independent of Weight Loss or the Presence of Type 2 Diabetes Mellitus. Diabetes Care 37(12):3150-6

Wit JM, van Duyvenvoorde HA, van Klinken JB, Caliebe J, Bosch CA, Lui JC, Gijsbers AC, Bakker E, Breuning MH, Oostdijk W, Losekoot M, Baron J, Binder G, Ranke MB, Ruivenkamp CA. (2014) Copy Number Variants in Short Children Born Small for Gestational Age. Horm Res Paediatr. 82(5):310-8

Kühnast S, van der Tuin SJ, van der Hoorn JW, van Klinken JB, Simic B, Pieterman E, Havekes LM, Landmesser U, Lüscher TF, Willems van Dijk K, Rensen PC, Jukema JW, Princen HM. (2014) Anacetrapib reduces progression of atherosclerosis, mainly by reducing non-HDL-cholesterol, improves lesion stability and adds to the beneficial effects of atorvastatin. Eur Heart J 36(1):39-48

Dharuri H, 't Hoen PA, van Klinken JB, Henneman P, Laros JF, Lips MA, El Bouazzaoui F, van Ommen GJ, Janssen I, van Ramshorst B, van Wagensveld BA, Pijl H, Willems van Dijk K, van Harmelen V. (2014) Downregulation of the acetyl-CoA metabolic network in adipose tissue of obese diabetic individuals and recovery after weight loss. Diabetologia 57(11):2384-92

Dharuri H, Demirkan A, van Klinken JB, Mook-Kanamori DO, van Duijn CM, 't Hoen PA, Willems van Dijk K. (2014) Genetics of the human metabolome, what is next? Biochim Biophys Acta S0925-4439(14)00158-6

Bakker LE, Boon MR, van der Linden RA, Arias-Bouda LP, van Klinken JB, Smit F, Verberne HJ, Jukema JW, Tamsma JT, Havekes LM, van Marken Lichtenbelt WD, Jazet IM, Rensen PC. (2014) Brown adipose tissue volume in healthy lean south Asian adults compared with white Caucasians: a prospective, case-controlled observational study. Lancet Diabetes Endocrinol 2(3):210-7

Heemskerk MM, van den Berg SA, Pronk AC, van Klinken JB, Boon MR, Havekes LM, Rensen PC, van Dijk KW, van Harmelen V. (2014) Long-term niacin treatment induces insulin resistance and adrenergic responsiveness in adipocytes by adaptive downregulation of phosphodiesterase 3B. Am J Physiol Endocrinol Metab 306(7):E808-13

Bakker LE, van Schinkel LD, Guigas B, Streefland TC, Jonker JT, van Klinken JB, van der Zon GC, Lamb HJ, Smit JW, Pijl H, Meinders AE, Jazet IM. (2014) A 5-day high-fat, high-calorie diet impairs insulin sensitivity in healthy, young South Asian men but not in Caucasian men. Diabetes 63(1):248-58

Dharuri H, Henneman P, Demirkan A, van Klinken JB, Mook-Kanamori DO, Wang-Sattler R, Gieger C, Adamski J, Hettne K, Roos M, Suhre K, Van Duijn CM; EUROSPAN Consortia, van Dijk KW, 't Hoen PA. (2013) Automated workflow-based exploitation of pathway databases provides new insights into genetic associations of metabolite profiles. BMC Genomics 14:865

Kühnast S, Louwe MC, Heemskerk MM, Pieterman EJ, van Klinken JB, van den Berg SA, Smit JW, Havekes LM, Rensen PC, van der Hoorn JW, Princen HM, Jukema JW. (2013) Niacin Reduces Atherosclerosis Development in APOE*3Leiden.CETP Mice Mainly by Reducing NonHDL-Cholesterol. PLoS One 8(6):e66467

Lips MA, Pijl H, van Klinken JB, de Groot GH, Janssen IM, Van Ramshorst B, Van Wagensveld BA, Swank DJ, Van Dielen F, Smit JW. (2013) Roux-en-Y gastric bypass and calorie restriction induce comparable time-dependent effects on thyroid hormone function tests in obese female subjects. Eur J Endocrinol 169(3):339-47

Lips MA, de Groot GH, van Klinken JB, Aarts E, Berends FJ, Janssen IM, Van Ramshorst B, Van Wagensveld BA, Swank DJ, Van Dielen F, Willems van Dijk K, Pijl H. (2014) Calorie Restriction is a Major Determinant of the Short-Term Metabolic Effects of Gastric Bypass Surgery in Obese Type 2 Diabetic Patients. Clin Endocrinol (Oxf) 80(6):834-42

van den Berg SA, Heemskerk MM, Geerling JJ, van Klinken JB, Schaap FG, Bijland S, Berbée JF, van Harmelen VJ, Pronk AC, Schreurs M, Havekes LM, Rensen PC, van Dijk KW. (2013) Apolipoprotein A5 deficiency aggravates high-fat diet-induced obesity due to impaired central regulation of food intake. FASEB J 27(8):3354-62.

van Klinken JB, van den Berg SA, van Dijk KW. (2013) Practical aspects of estimating energy components in rodents. Front Physiol 4:94:10.3389/fphys.2013.00094.

Vroegrijk IO, van Klinken JB, van Diepen JA, van den Berg SA, Febbraio M, Steinbusch LK, Glatz JF, Havekes LM, Voshol PJ, Rensen PC, van Dijk KW, van Harmelen V. (2013) CD36 is important for adipocyte recruitment and affects lipolysis. Obesity (Silver Spring) 21(10):2037-45

Berbée JF, Wong MC, Wang Y, van der Hoorn JW, Khedoe PP, van Klinken JB, Mol IM, Hiemstra PS, Tsikas D, Romijn JA, Havekes LM, Princen HM, Rensen PC (2013) Resveratrol protects against atherosclerosis, but does not add to the antiatherogenic effect of atorvastatin, in APOE*3-Leiden.CETP mice. J Nutr Biochem 24(8):1423-30

Coomans CP, van den Berg SA, Houben T, van Klinken JB, van den Berg R, Pronk AC, Havekes LM, Romijn JA, Willems van Dijk K, Biermasz NR, Meijer JH (2013) Detrimental effects of constant light exposure and high-fat diet on circadian energy metabolism and insulin sensitivity. FASEB J 27(4):1721-32

Van Klinken JB, van den Berg SA, Havekes LM, Willems Van Dijk K (2012) Estimation of activity related energy expenditure and resting metabolic rate in freely moving mice from indirect calorimetry data. PLoS One 7(5):e36162

Bijland S, Pieterman EJ, Maas AC, van der Hoorn JW, van Erk MJ, van Klinken JB, Havekes LM, van Dijk KW, Princen HM, Rensen PC (2010) Fenofibrate increases very low density lipoprotein triglyceride production despite reducing plasma triglyceride levels in APOE*3-Leiden.CETP mice. J Biol Chem 285(33):25168-75

van den Berg SA, Nabben M, Bijland S, Voshol PJ, van Klinken JB, Havekes LM, Romijn JA, Hoeks J, Hesselink MK, Schrauwen P, van Dijk KW (2010) High levels of whole-body energy expenditure are associated with a lower coupling of skeletal muscle mitochondria in C57Bl/6 mice. Metabolism 59(11):1612-8

Chiarugi D, Degano P, van Klinken JB, Marangoni R (2008) Cells in Silico: A Holistic Approach. In: Formal methods for computational systems biology, LNCS 5016, Springer, Berlin, pp 366-386

 


Software

Component analysis of energy expenditure

The MATLAB toolbox for estimating activity related and resting energy expenditure from metabolic chamber / indirect calorimetry data can be downloaded here

 

FluxModeCalculator

The MATLAB toolbox for computing the elementary flux modes, extreme pathways or minimal generating sets in stoichiometric models can be downloaded here


Contactgegevens

Leids Universitair Medisch Centrum
Gebouw 2
Kamer T-03-054

Einthovenweg 20
2333 ZC Leiden
Tel: (0)715269472

Postzone S4-P
Postbus 9600
2300 RC Leiden

E-mail: j.b.van_klinken@lumc.nl