Franke, Prof. Lude
Lude Franke is Associate Professor at the Genetics Department of the University of Groningen/University Medical Centre Groningen and Head of Research and Education in the Dept. of Genetics, UMCG. He is a statistical geneticist, working on analyzing data on the genetics of complex and autoimmune diseases (e.g. celiac disease). He has been awarded an ERC Starting grant (2014), NWO VIDI grant (2014), NWO VENI grant (2009) and a Horizon Grant (2009) to work on identifying molecular effects due to disease-causing mutations.
Jonge Akademie, Lude Franke
In his spare time he is also a graphic designer. This chance combination of skills can sometimes make life as a genetics researcher a bit easier: if you can explain your research visually, more people can understand what you are doing. Lude Franke is one of the founding members of the Young Academy Groningen and has also been appointed member of De Jonge Akademie (National Young Academy).
In 2021 Franke was awarded a Vici grant. Many diseases have a genetic basis, but cancer is often caused by mutations that arise during life, whereas other diseases are caused by genetic differences that are inherited from parents. Frankes project uses gene networks to test whether a unifying principle exists that links these different types of mutations.
Previously in the news
- Lude Franke awarded Vici grant
- Mental health at lowest ebb since the start of the coronavirus pandemic
- UMCG investigating resistance to Covid-19 among group of Lifelines participants
- Why does corona affect people differently?
- Biobanks collaborate on big data to unravel disease processes
- New method opens opportunities for large-scale studies of cancer development
- ERC Starting Grant for Lude Franke
- VIDI for Lude Franke
2024
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R., Mooiweer, J.,
Ramírez-Sánchez, A. D., Oelen,
R., Franke, L., Wijmenga, C.,
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Bourgonje, A. R., Netea, M. G., Lansdorp, P.,
Aubert, G., Bonder, M. J., Franke, L. H.,
Vogl, T., van der Wijst, M. G. P., Melé,
M., van Baarle, D., Fu, J., &
Zhernakova, A. (2024). Antibody signatures against
viruses and microbiome reflect past and chronic exposures and
associate with aging and inflammation.
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Neavin,
D., Senabouth, A., Arora, H., Lee, J. T. H., Ripoll-Cladellas,
A., Franke, L., Prabhakar, S., Ye, C. J., McCarthy, D.
J., Melé, M., Hemberg, M., & Powell, J. E. (2024).
Demuxafy: improvement in droplet assignment by integrating
multiple single-cell demultiplexing and doublet detection
methods. Genome Biology,
25(1), Article 94. https://doi.org/10.1186/s13059-024-03224-8
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S., Bonder, M. J., Westra, H.-J.,
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Zhernakova, A., Fu, J., Hoogerland, J.
A., & Zhernakova, D. V. (2024).
Epigenome-wide association study on the plasma metabolome
suggests self-regulation of the glycine and serine pathway through
DNA methylation. Clinical Epigenetics,
16, Article 104. https://doi.org/10.1186/s13148-024-01718-7
Akeju,
O., Mens, M. M. J., Warmerdam, R., Dijkema, M., van
den Biggelaar, A. H. J., Franke, L., Goudsmit, J.,
& Wu, J. W. (2024). Genetic Correlates of Biological
Aging and the Influence on Prediction of Mortality.
Journals of Gerontology - Series A Biological Sciences
and Medical Sciences, 79(4), Article glae024.
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Karthikeyan, S., Oliver-Williams, C., Sliz, E., Allara, E., Fung,
W. T., Surendran, P., Zhang, W., Jousilahti, P., Kristiansson, K.,
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(2024). Genome-wide characterization of circulating metabolic
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V., Oelen, R., Groot, H. E.,
Benjamins, J. W., Brambs, S., Kaiser, R., Gottschlich, A.,
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(2024). Multiomic analyses uncover immunological signatures
in acute and chronic coronary syndromes. Nature
Medicine, 30, 1696–1710. https://doi.org/10.1038/s41591-024-02953-4
Vochteloo,
M., Deelen, P., Vink, B., Bios Consortium ,
Tsai, E. A., Runz, H., Andreu-Sánchez, S.,
Fu, J., Zhernakova, A., Westra,
H.-J., & Franke, L. (2024). Picalo:
principal interaction component analysis for the identification of
discrete technical, cell-type, and environmental factors that
mediate eQTLs. Genome Biology,
25(1), Article 29. https://doi.org/10.1186/s13059-023-03151-0
ABCTB
Investigators, Kentistou, K. A., Kaisinger, L. R., Stankovic, S.,
Vaudel, M., Mendes de Oliveira, E., Messina, A., Walters, R. G.,
Liu, X., Busch, A. S., Helgason, H., Thompson, D. J., Santoni, F.,
Petricek, K. M., Zouaghi, Y., Huang-Doran, I., Gudbjartsson, D. F.,
Bratland, E., Lin, K., ... Ong, K. K. (2024). Publisher
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across the allele frequency spectrum. Nature
genetics. Advance online publication. https://doi.org/10.1038/s41588-024-01857-w
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Blokland, I. V., Oelen, R., Groot, H.
E., Benjamins, J. W., Pekayvaz, K., Losert, C.,
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Harst, P., Franke, L., & van der
Wijst, M. G. P. (2024). Single-Cell Dissection of the
Immune Response After Acute Myocardial Infarction.
Circulation. Genomic and precision medicine,
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ABCTB
Investigators, Perry, J. R. B., & Ong, K. K. (2024).
Understanding the genetic complexity of puberty timing across
the allele frequency spectrum. Nature
genetics, 56(7), 1397-1411. https://doi.org/10.1038/s41588-024-01798-4
2023
COVID-19
Host Genetics Initiative (2023). A second update on mapping
the human genetic architecture of COVID-19.
Nature, 621(7977), E7-E26. https://doi.org/10.1038/s41586-023-06355-3
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Klein, N., Tsai, E. A., Vochteloo, M., Baird,
D., Huang, Y., Chen, C. Y., van Dam, S., Oelen,
R., Deelen, P., Bakker, O. B., El
Garwany, O., Ouyang, Z., Marshall, E. E., Zavodszky, M. I., van
Rheenen, W., Bakker, M. K., Veldink, J., Gaunt, T. R., Runz,
H., ... Westra, H. J. (2023). Brain expression
quantitative trait locus and network analyses reveal downstream
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COVID-19
Host Genetics Initiative (2023). Erratum to: Mapping the
human genetic architecture of COVID-19 (Nature, (2021), 600, 7889,
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Nature, 621(7977), E7-E26. https://doi.org/10.1093/1476-4687
HUNT
All-In Stroke, CADISP group, International Consortium for Blood
Pressure (ICBP), The International Headache Genetics Consortium
(IHGC), International Stroke Genetics Consortium, ISGC Intracranial
Aneurysm Working Group, Bakker, M. K., Kanning, J. P., Abraham, G.,
Martinsen, A. E., Winsvold, B. S., Zwart, J. A., Bourcier, R.,
Sawada, T., Koido, M., Kamatani, Y., Morel, S., Amouyel, P.,
Debette, S., ... Ruigrok, Y. M. (2023). Genetic Risk Score
for Intracranial Aneurysms: Prediction of Subarachnoid Hemorrhage
and Role in Clinical Heterogeneity.
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BBJ,
BioMe, BioVU, Canadian Partnership for Tomorrow's Health/OHS, China
Kadoorie Biobank Collaborative Group, Colorado Center for
Personalized Medicine, deCODE Genetics, ESTBB, FinnGen, Generation
Scotland, Genes & Health, LifeLines, Mass General Brigham
Biobank, Michigan Genomics Initiative, QIMR Berghofer Biobank,
Taiwan Biobank, The HUNT Study, UCLA ATLAS Community Health
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analyses provide lessons for developing polygenic risk scores
across diverse cohorts. Cell Genomics,
3(1), Article 100241. https://doi.org/10.1016/j.xgen.2022.100241
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T., de Vries, D. H., Korshevniuk, M., Losert,
C., Oelen, R., van Blokland, I. V.,
Groot, H. E., Swertz, M. A., van der
Harst, P., Westra, H. J., van der Wijst,
M. G. P., Heinig, M., & Franke, L. (2023).
Identification of genetic variants that impact gene
co-expression relationships using large-scale single-cell
data. Genome Biology, 24,
Article 80. https://doi.org/10.1186/s13059-023-02897-x
Boahen,
C. K., Oelen, R., Le, K., Netea,
M. G., Franke, L., Wijst, M. G. P. V.
D., & Kumar, V. (2023). Integration
of Candida albicans-induced single-cell gene expression data and
secretory protein concentrations reveal genetic regulators of
inflammation. Frontiers in Immunology,
14, Article 1069379. https://doi.org/10.3389/fimmu.2023.1069379
Genomics
England Research Consortium, Boulogne, F., Claus, L.
R., Wiersma, H., Oelen, R., Schukking,
F., de Klein, N., Li, S., Westra,
H. J., van der Zwaag, B., van Reekum, F., Sierks, D.,
Schönauer, R., Li, Z., Bijlsma, E. K., Bos, W. J. W.,
Halbritter, J., Knoers, N. V. A. M., Besse, W., ...
van Eerde, A. M. (2023). KidneyNetwork: Using kidney-derived
gene expression data to predict and prioritize novel genes involved
in kidney disease. European Journal of Human
Genetics, 31, 1300–1308. https://doi.org/10.1038/s41431-023-01296-x
BIOS
Consortium, Dekkers, K. F., Slieker, R. C., Ioan-Facsinay, A., van
Iterson, M., Ikram, M. A., van Greevenbroek, M. M. J., Veldink, J.
H., Franke, L., Boomsma, D. I., Slagboom, P. E.,
Jukema, J. W., & Heijmans, B. T. (2023). Lipid-induced
transcriptomic changes in blood link to lipid metabolism and
allergic response. Nature
Communications, 14, Article 544. https://doi.org/10.1038/s41467-022-35663-x
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K., Losert, C., Knottenberg, V., van Blokland, I.
V., Oelen, R., Groot, H. E.,
Benjamins, J. W., Brambs, S., Kaiser, R., Eivers, L.,
Polewka, V., Escaig, R., Joppich, M., Janjic, A., Popp, O.,
Petzold, T., Zimmer, R., Enard, W., Saar, K., ... Stark, K. (2023).
Multi-Omic Factor Analysis uncovers immunological
signatures with pathophysiologic and clinical implications in
coronary syndromes. MedRxiv. https://doi.org/10.1101/2023.05.02.23289392
eQTLgen
Consortium, Dai, Q., Zhou, G., Zhao, H., Võsa,
U., Franke, L., Battle, A., Teumer, A.,
Lehtimäki, T., Raitakari, O. T., Esko, T., Epstein, M. P.,
& Yang, J. (2023). OTTERS: a powerful TWAS framework
leveraging summary-level reference data. Nature
Communications, 14, Article 1271. https://doi.org/10.1038/s41467-023-36862-w
The
Netherlands A. C. M./P. L. N. Registry, Lifelines Cohort
Study, Lopera-Maya, E. A., Li, S.,
de Brouwer, R., Nolte, I. M., van Breen,
J., Jongbloed, J. D. H., Swertz, M.
A., Snieder, H., Franke, L.,
Wijmenga, C., de Boer, R. A., Deelen,
P., van der Zwaag, P. A., & Sanna,
S. (2023). Phenotypic and Genetic Factors Associated
with Absence of Cardiomyopathy Symptoms in PLN:c.40_42delAGA
Carriers. Journal of cardiovascular translational
research, 16, 1251–1266. https://doi.org/10.1007/s12265-022-10347-5
Kellmann,
A., Lanting, P., Franke, L.
H., van Enckevort, E., & Swertz, M.
A. (2023). Semiautomatic translation of medicine usage
data (in Dutch, free-text) from Lifelines COVID-19 questionnaires
to ATC codes. Database-The journal of biological
databases and curation, 2023. https://doi.org/10.1093/database/baad019
ABCTB
Investigators, Kentistou, K. A., Kaisinger, L. R., Stankovic, S.,
Vaudel, M., de Oliveira, E. M., Messina, A., Walters, R. G., Liu,
X., Busch, A. S., Helgason, H., Thompson, D. J., Santon, F.,
Petricek, K. M., Zouaghi, Y., Huang-Doran, I., Gudbjartsson, D. F.,
Bratland, E., Lin, K., ... Ong, K. K. (2023).
Understanding the genetic complexity of puberty timing
across the allele frequency spectrum. MedRxiv. https://doi.org/10.1101/2023.06.14.23291322
Lifelines
Corona Research initiative, Mobach, M. P., Boezen, H.
M., Mierau, J. O., Franke, H.
L., Dekens, J., Deelen, P.,
Lanting, P., Vonk, J. M., Nolte,
I., Ori, A. P. S., Claringbould,
A., Boulogne, F., Dijkema, M. X. L.,
Wiersma, H. H., Warmerdam, R.,
Jankipersadsing, S. A., van Blokland, I.,
de Bock, G. T. H., ... Wijmenga, C. (2023).
Workplace impact on employees: A Lifelines Corona Research
Initiative on the return to work. PLoS
ONE, 18(1), Article e0279902. https://doi.org/10.1371/journal.pone.0279902
2022
COVID-19
Host Genetics Initiative (2022). A first update on mapping
the human genetic architecture of COVID-19.
Nature, 608, E1–E10. https://doi.org/10.1038/s41586-022-04826-7
Lifelines
Cohort Study, Zhernakova, D. V., Sinha,
T., Andreu Sánchez, S., Prins,
J., Kurilshikov, A., Balder, J.-W.,
Sanna, S., Franke, L. H., Kuivenhoven, J.
A., Zhernakova, A., & Fu, J.
(2022). Age-dependent sex differences in cardiometabolic risk
factors. Nature Cardiovascular
Research, 1, 844–854. https://doi.org/10.1038/s44161-022-00131-8
Lifelines
Cohort Study, Lopera-Maya, E. A., Kurilshikov,
A., van der Graaf, A., Hu,
S., Andreu-Sánchez, S., Chen,
L., Vila, A. V., Gacesa, R.,
Sinha, T., Collij, V., Klaassen, M. A.
Y., Bolte, L. A., Gois, M. F. B.,
Neerincx, P. B. T., Swertz, M. A.,
Harmsen, H. J. M., Wijmenga, C., Fu,
J., ... Sanna, S. (2022). Author
Correction: Effect of host genetics on the gut microbiome in 7,738
participants of the Dutch Microbiome Project (Nature Genetics,
(2022), 54, 2, (143-151), 10.1038/s41588-021-00992-y).
Nature genetics, 54(9), 1448. https://doi.org/10.1038/s41588-022-01164-2
SLALOM
Consortium, PARALS Consortium, SLAGEN Consortium, SLAP Consortium,
van Rheenen, W., van der Spek, R. A. A., Bakker, M. K., van Vugt,
J. J. F. A., Hop, P. J., Zwamborn, R. A. J., de Klein,
N., Westra, H.-J., Bakker, O.
B., Deelen, P., Shireby, G., Hannon, E.,
Moisse, M., Baird, D., Restuadi, R., ... Veldink, J. H. (2022).
Author Correction: Common and rare variant association
analyses in amyotrophic lateral sclerosis identify 15 risk loci
with distinct genetic architectures and neuron-specific biology
(vol 53, pg 1636, 2021). Nature
genetics, 54(3), 361-361. https://doi.org/10.1038/s41588-022-01020-3
Lopera-Maya,
E. A., Kurilshikov, A., van der Graaf,
A., Hu, S., Lifelines Cohort Study,
Andreu-Sánchez, S., Chen, L., Vila,
A. V., Gacesa, R., Sinha,
T., Collij, V., Klaassen, M. A. Y.,
Bolte, L. A., Brandao Gois, M. F.,
Neerincx, P. B. T., Swertz, M. A.,
Harmsen, H. J. M., Wijmenga, C., Fu,
J., ... Sanna, S. (2022). Effect of host
genetics on the gut microbiome in 7,738 participants of the Dutch
Microbiome Project. Nature genetics,
54, 143-151. https://doi.org/10.1038/s41588-021-00992-y
BIOS
Consortium (2022). Functional genomics analysis identifies T
and NK cell activation as a driver of epigenetic clock
progression. Genome Biology,
23(1), 24. https://doi.org/10.1186/s13059-021-02585-8
Andreu-Sánchez,
S., Aubert, G., Ripoll-Cladellas, A., Henkelman, S.,
Zhernakova, D. V., Sinha, T.,
Kurilshikov, A., Cenit, M. C., Jan Bonder,
M., Franke, L., Wijmenga,
C., Fu, J., van der Wijst, M. G.
P., Melé, M., Lansdorp, P., &
Zhernakova, A. (2022). Genetic, parental and lifestyle
factors influence telomere length. Communications
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BIOS
Consortium, Brain MEND Consortium, Hop, P. J., Zwamborn, R. A. J.,
Hannon, E., Shireby, G. L., Nabais, M. F., Walker, E. M., van
Rheenen, W., van Vugt, J. J. F. A., Dekker, A. M., Westeneng, H.
J., Tazelaar, G. H. P., van Eijk, K. R., Moisse, M., Baird, D., Al
Khleifat, A., Iacoangeli, A., Ticozzi, N., ... Veldink, J. H.
(2022). Genome-wide study of DNA methylation shows
alterations in metabolic, inflammatory, and cholesterol pathways in
ALS. Science Translational Medicine,
14(633), Article eabj0264. https://doi.org/10.1126/scitranslmed.abj0264
deCODE
Genetics, Estonian Biobank, FinnGen, Generation Scotland, Genes
& Health Research Team, LifeLines, Mass General Brigham
Biobank, Michigan Genomics Initiative, National Biobank of Korea,
Penn Medicine BioBank, Qatar Biobank, The QSkin Sun and Health
Study, Taiwan Biobank, The HUNT Study, UCLA ATLAS Community Health
Initiative, Uganda Genome Resource, UK Biobank, Biobank of the
Americas, BioBank Japan Project, ... Sanna, S. (2022).
Global Biobank Meta-analysis Initiative: Powering genetic
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Genomics, 2(10), Article 100192. https://doi.org/10.1016/j.xgen.2022.100192
Uniken
Venema, W. T. C., Ramírez-Sánchez, A.
D., Bigaeva, E., Withoff,
S., Jonkers, I., McIntyre, R. E., Ghouraba, M.,
Raine, T., Weersma, R. K., Franke,
L., Festen, E. A. M., & van der
Wijst, M. G. P. (2022). Gut mucosa dissociation
protocols influence cell type proportions and single-cell gene
expression levels. Scientific Reports,
12, Article 9897. https://doi.org/10.1038/s41598-022-13812-y
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A., Dijkema, M. X. L., Snieder, H., Vonk,
J. M., Boezen, H. M., Deelen,
P., & Franke, L. H. (2022). Increased
genetic contribution to wellbeing during the COVID-19
pandemic. PLoS genetics,
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Corona Research initiative, Qi, Y., Lepe,
A., Almansa, J., Ots, P., de
Kroon, M. L. A., Boezen, H. M., Mierau,
J. O., Franke, H. L., Dekens,
J., Deelen, P., Lanting, P.,
Vonk, J. M., Nolte, I., Ori, A. P.
S., Claringbould, A., Boulogne,
F., Dijkema, M. X. L., Wiersma, H. H.,
... Brouwer, S. (2022). Increases in symptoms of
depression and anxiety in adults during the initial phases of the
COVID-19 pandemic are limited to those with less resources: Results
from the Lifelines Cohort Study. Journal of
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Bios
Consortium , Porcu, E., Claringbould, A., Weihs, A.,
Lepik, K., Richardson, T. G., Voelker, U., Santoni, F. A., Teumer,
A., Franke, L., Reymond, A., & Kutalik, Z. (2022).
Limited evidence for blood eQTLs in human sexual
dimorphism. Genome medicine,
14(1), Article 89. https://doi.org/10.1186/s13073-022-01088-w
Global
Biobank Meta-analysis Initiative, Kanai, M., Elzur, R., Zhou, W.,
Daly, M. J., & Finucane, H. K. (2022). Meta-analysis
fine-mapping is often miscalibrated at single-variant
resolution. Cell Genomics,
2(12), Article 100210. https://doi.org/10.1016/j.xgen.2022.100210
Estonian
Biobank Research Team, Lepamets, M., Auwerx, C., Nõukas,
M., Claringbould, A., Porcu, E., Kals, M.,
Jürgenson, T., Morris, A. P., Võsa, U.,
Bochud, M., Stringhini, S., Wijmenga, C.,
Franke, L., Peterson, H., Vilo, J., Lepik, K., Mägi,
R., & Kutalik, Z. (2022). Omics-informed CNV calls reduce
false-positive rates and improve power for CNV-trait
associations. Human Genetics and Genomics
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23andMe
Research Team, Social Science Genetic Association Consortium,
Okbay, A., Wu, Y., Wang, N., Jayashankar, H., Bennett, M., Nehzati,
S. M., Sidorenko, J., Kweon, H., Goldman, G., Gjorgjieva, T.,
Jiang, Y., Hicks, B., Tian, C., Hinds, D. A., Ahlskog, R.,
Magnusson, P. K. E., Oskarsson, S., ... Young, A. I. (2022).
Polygenic prediction of educational attainment within and
between families from genome-wide association analyses in 3 million
individuals. Nature genetics,
54(4), 437-449. https://doi.org/10.1038/s41588-022-01016-z
Lifelines
Cohort Study, Zhernakova, D. V., Sinha,
T., Andreu-Sánchez, S., Prins, J.
R., Kurilshikov, A., Balder, J. W.,
Sanna, S., Franke, L., Kuivenhoven, J.
A., Zhernakova, A., & Fu, J.
(2022). Publisher Correction: Age-dependent sex differences
in cardiometabolic risk factors . Nature
Cardiovascular Research, 1(10), 961. https://doi.org/10.1038/s44161-022-00146-1
Single-Cell
EQTLGen Consortium, Bios Consortium , Oelen, R.,
de Vries, D. H., Brugge, H., Gordon, M.
G., Vochteloo, M., Ye, C. J., Westra,
H.-J., Franke, L., & van der Wijst,
M. G. P. (2022). Single-cell RNA-sequencing of
peripheral blood mononuclear cells reveals widespread,
context-specific gene expression regulation upon pathogenic
exposure. Nature Communications,
13(1), Article 3267. https://doi.org/10.1038/s41467-022-30893-5
BIOS
Consortium, Vochteloo, M., Deelen, P.,
Vink, B., Tsai, E. A., Runz, H., Andreu-Sánchez,
S., Fu, J., Zhernakova, A.,
Westra, H.-J., & Franke, L. (2022).
Unbiased identification of unknown cellular and
environmental factors that mediate eQTLs using principal
interaction component analysis. BioRxiv. https://doi.org/10.1101/2022.07.28.501849
Lifelines
Corona Research initiative, Dite, G. S., Murphy, N. M., Spaeth, E.,
& Allman, R. (2022). Validation of a clinical and genetic
model for predicting severe COVID-19. Epidemiology
And Infection, 150, Article e91. https://doi.org/10.1017/S0950268822000541
GenOMICC
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