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Marc Jan Bonder

European Molecular Biology Laboratory

68H-index
238Paper Count
3.1WCitation Count
Published Papers 68
Publication Date
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Molecular co-accessibility identifies coordinated regulation between distant cis-regulatory elements
errMolecular Cell
IF16.6
err2026-08-12
err0
errOAAI
errMathias Boulanger; Kasit Chatsirisupachai; Yuliya Badayeva; Rene Snajder; Marc Jan Bonder; Karine Lapouge; Kim Remans; Arnaud R. Krebs
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Cell-to-cell variability and gain of methylation at polycomb CpG islands as a hallmark of aging
errNature Communications
IF15.7
err2026-06-09
err0
errOAAI
errHagit Masika; Shmuel Ruppo; Stephen J. Clark; Marc Jan Bonder; Ferdinand von Meyenn; Merav Hecht; Shari Orlanski; Efrat Katsman; Oriya Vardi-Yaakov; Abraham Zlotogorski; Tahel Fachler-Sharp; Sharona Elgavish; Yuval Dor; Wolf Reik; Tommy Kaplan; Howard Cedar
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Genetic architecture and mechanisms of host-microbiome interactions from a multi-cohort analysis of outbred laboratory rats
errNature Communications
IF15.7
err2025-12-18
err0
errOAAI
errHélène Tonnelé; Denghui Chen; Felipe Morillo; Jorge Garcia-Calleja; Apurva S. Chitre; Benjamin B. Johnson; Thiago Missfeldt Sanches; Riyan Cheng; Marc Jan Bonder; Antonio Gonzalez; Tomasz Kosciolek; Anthony M. George; Wenyan Han; Katie Holl; Aidan Horvath; Keita Ishiwari; Christopher P. King; Alexander C. Lamparelli; Connor D. Martin; Angel Garcia Martinez; Alesa H. Netzley; Jordan A. Tripi; Tengfei Wang; Elena Bosch; Peter A. Doris; Oliver Stegle; Hao Chen; Shelly B. Flagel; Paul J. Meyer; Jerry B. Richards; Terry E. Robinson; Leah C. Solberg Woods; Oksana Polesskaya; Rob Knight; Abraham A. Palmer; Amelie Baud
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A genome-scale single-cell CRISPRi map of trans gene regulation across human pluripotent stem cell lines
errCell Genomics
IF9
err2025-12-01
err0
errOAAI
errClaudia Feng; Elin Madli Peets; Yan Zhou; Luca Crepaldi; Sunay Usluer; Alistair Dunham; Jana M. Braunger; Jing Su; Magdalena E. Strauss; Daniele Muraro; Kimberly Ai Xian Cheam; Marc Jan Bonder; Edgar Garriga Nogales; Sarah Cooper; Andrew Bassett; Steven Leonard; Yong Gu; Bo Fussing; David Burke; Leopold Parts
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Author Correction: Complex genetic variation in nearly complete human genomes
errNature
IF48.5
err2025-08-26
err0
errOAAI
errGlennis A. Logsdon; Peter Ebert; Peter A. Audano; Mark Loftus; David Porubsky; Jana Ebler; Feyza Yilmaz; Pille Hallast; Timofey Prodanov; DongAhn Yoo; Carolyn A. Paisie; William T. Harvey; Xuefang Zhao; Gianni V. Martino; Mir Henglin; Katherine M. Munson; Keon Rabbani; Chen-Shan Chin; Bida Gu; Hufsah Ashraf; Stephan Scholz; Olanrewaju Austine-Orimoloye; Parithi Balachandran; Marc Jan Bonder; Haoyu Cheng; Zechen Chong; Jonathan Crabtree; Mark Gerstein; Lisbeth A. Guethlein; Patrick Hasenfeld; Glenn Hickey; Kendra Hoekzema; Sarah E. Hunt; Matthew Jensen; Yunzhe Jiang; Sergey Koren; Youngjun Kwon; Chong Li; Heng Li; Jiaqi Li; Paul J. Norman; Keisuke K. Oshima; Benedict Paten; Adam M. Phillippy; Nicholas R. Pollock; Tobias Rausch; Mikko Rautiainen; Yuwei Song; Arda Söylev; Arvis Sulovari; Likhitha Surapaneni; Vasiliki Tsapalou; Weichen Zhou; Ying Zhou; Qihui Zhu; Michael C. Zody; Ryan E. Mills; Scott E. Devine; Xinghua Shi; Michael E. Talkowski; Mark J. P. Chaisson; Alexander T. Dilthey; Miriam K. Konkel; Jan O. Korbel; Charles Lee; Christine R. Beck; Evan E. Eichler; Tobias Marschall
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Unveiling genetic signatures of immune response in immune-related diseases through single-cell eQTL analysis across diverse conditions
errNature Communications
IF15.7
err2025-08-04
err0
errOAAI
errZhenhua Zhang; Wenchao Li; Qiuyao Zhan; Michelle Aillaud; Javier Botey-Bataller; Martijn Zoodsma; Rob ter Horst; Leo A. B. Joosten; Christoph Bock; Leon N. Schulte; Cheng-Jian Xu; Mihai G. Netea; Marc Jan Bonder; Yang Li
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Complex genetic variation in nearly complete human genomes
errNature
IF48.5
err2025-07-23
err0
errOAAI
errGlennis A. Logsdon; Peter Ebert; Peter A. Audano; Mark Loftus; David Porubsky; Jana Ebler; Feyza Yilmaz; Pille Hallast; Timofey Prodanov; DongAhn Yoo; Carolyn A. Paisie; William T. Harvey; Xuefang Zhao; Gianni V. Martino; Mir Henglin; Katherine M. Munson; Keon Rabbani; Chen-Shan Chin; Bida Gu; Hufsah Ashraf; Stephan Scholz; Olanrewaju Austine-Orimoloye; Parithi Balachandran; Marc Jan Bonder; Haoyu Cheng; Zechen Chong; Jonathan Crabtree; Mark Gerstein; Lisbeth A. Guethlein; Patrick Hasenfeld; Glenn Hickey; Kendra Hoekzema; Sarah E. Hunt; Matthew Jensen; Yunzhe Jiang; Sergey Koren; Youngjun Kwon; Chong Li; Heng Li; Jiaqi Li; Paul J. Norman; Keisuke K. Oshima; Benedict Paten; Adam M. Phillippy; Nicholas R. Pollock; Tobias Rausch; Mikko Rautiainen; Yuwei Song; Arda Söylev; Arvis Sulovari; Likhitha Surapaneni; Vasiliki Tsapalou; Weichen Zhou; Ying Zhou; Qihui Zhu; Michael C. Zody; Ryan E. Mills; Scott E. Devine; Xinghua Shi; Michael E. Talkowski; Mark J. P. Chaisson; Alexander T. Dilthey; Miriam K. Konkel; Jan O. Korbel; Charles Lee; Christine R. Beck; Evan E. Eichler; Tobias Marschall
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Linking the gut microbiome to host DNA methylation by a discovery and replication epigenome-wide association study
errBMC GENOMICS
IF3.7
err2024-12-19
err0
errOAAI
errDemirkan, Ayse; van Dongen, Jenny; Finnicum, Casey T.; Westra, Harm-Jan; Jankipersadsing, Soesma; Willemsen, Gonneke; Ijzerman, Richard G.; Boomsma, Dorret I.; Ehli, Erik A.; Bonder, Marc Jan; Fu, Jingyuan; Franke, Lude; Wijmenga, Cisca; de Geus, Eco J. C.; Kurilshikov, Alexander; Zhernakova, Alexandra
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An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes
errGENOME RESEARCH
IF5.5
err2024-12-05
err0
PREAI
errLi, Chong; Bonder, Marc Jan; Syed, Sabriya; Jensen, Matthew; Human Genome Structural Variation Consortium HGSVC, Mark B.; HGSVC Functional Analysis Working Group, Michael C.; Gerstein, Mark B.; Zody, Michael C.; Chaisson, Mark J. P.; Talkowski, Michael E.; Marschall, Tobias; Korbel, Jan O.; Eichler, Evan E.; Lee, Charles; Shi, Xinghua
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scEpiAge: an age predictor highlighting single-cell ageing heterogeneity in mouse blood
errNATURE COMMUNICATIONS
IF15.7
err2024-08-31
err0
errOAAI
errBonder, Marc Jan; Clark, Stephen J.; Krueger, Felix; Luo, Siyuan; de Sousa, Joao Agostinho; Hashtroud, Aida M.; Stubbs, Thomas M.; Stark, Anne-Katrien; Rulands, Steffen; Stegle, Oliver; Reik, Wolf; von Meyenn, Ferdinand
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Epigenome-wide association study on the plasma metabolome suggests self-regulation of the glycine and serine pathway through DNA methylation
errCLINICAL EPIGENETICS
IF4.4
err2024-08-13
err0
errOAAI
errWu, Jiafei; Palasantzas, Victoria; Andreu-Sanchez, Sergio; Ploesch, Torsten; Leonard, Sam; Li, Shuang; Bonder, Marc Jan; Westra, Harm-Jan; van Meurs, Joyce; Ghanbari, Mohsen; Franke, Lude; Zhernakova, Alexandra; Fu, Jingyuan; Hoogerland, Joanne A.; Zhernakova, Daria V.
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Expression profiling of cerebrospinal fluid identifies dysregulated antiviral mechanisms in multiple sclerosis
errBRAIN
IF11.7
err2023-12-01
err3
errOAAI
errBan, Maria; Bredikhin, Danila; Huang, Yuanhua; Bonder, Marc Jan; Katarzyna, Kania; Oliver, Amanda J.; Wilson, Nicola K.; Coupland, Paul; Hadfield, James; Goettgens, Berthold; Madissoon, Elo; Stegle, Oliver; Sawcer, Stephen
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pycoMeth: a toolbox for differential methylation testing from Nanopore methylation calls
errGENOME BIOLOGY
IF9.4
err2023-04-20
err4
errOAAI
errSnajder, Rene; Leger, Adrien; Stegle, Oliver; Bonder, Marc Jan
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Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures
errCELL GENOMICS
IF9
err2023-04-01
err11
errOAAI
errRausch, Tobias; Snajder, Rene; Leger, Adrien; Simovic, Milena; Giurgiu, Madalina; Villacorta, Laura; Henssen, Anton G.; Froehling, Stefan; Stegle, Oliver; Birney, Ewan; Bonder, Marc Jan; Ernst, Aurelie; Korbel, Jan O.
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Genetic, parental and lifestyle factors influence telomere length
errCOMMUNICATIONS BIOLOGY
IF5.1
err2022-06-09
err34
errOAAI
errAndreu-Sanchez, Sergio; Aubert, Geraldine; Ripoll-Cladellas, Aida; Henkelman, Sandra; Zhernakova, Daria, V; Sinha, Trishla; Kurilshikov, Alexander; Cenit, Maria Carmen; Bonder, Marc Jan; Franke, Lude; Wijmenga, Cisca; Fu, Jingyuan; van der Wijst, Monique G. P.; Mele, Marta; Lansdorp, Peter; Zhernakova, Alexandra
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Single-cell Atlas of common variable immunodeficiency shows germinal center-associated epigenetic dysregulation in B-cell responses
errNATURE COMMUNICATIONS
IF15.7
err2022-04-01
err33
errOAAI
errRodriguez-Ubreva, Javier; Arutyunyan, Anna; Bonder, Marc Jan; Del Pino-Molina, Lucia; Clark, Stephen J.; de la Calle-Fabregat, Carlos; Garcia-Alonso, Luz; Handfield, Louis-Francois; Ciudad, Laura; Andres-Leon, Eduardo; Krueger, Felix; Catala-Moll, Francesc; Rodriguez-Cortez, Virginia C.; Polanski, Krzysztof; Mamanova, Lira; van Dongen, Stijn; Kiselev, Vladimir Yu; Martinez-Saavedra, Maria T.; Heyn, Holger; Martin, Javier; Warnatz, Klaus; Lopez-Granados, Eduardo; Rodriguez-Gallego, Carlos; Stegle, Oliver; Kelsey, Gavin; Vento-Tormo, Roser; Ballestar, Esteban
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Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression
errNATURE GENETICS
IF31.8
err2021-09-02
err736
errOAAI
errVosa, Urmo; Claringbould, Annique; Westra, Harm-Jan; Bonder, Marc Jan; Deelen, Patrick; Zeng, Biao; Kirsten, Holger; Saha, Ashis; Kreuzhuber, Roman; Yazar, Seyhan; Brugge, Harm; Oelen, Roy; de Vries, Dylan H.; van der Wijst, Monique G. P.; Kasela, Silva; Pervjakova, Natalia; Alves, Isabel; Fave, Marie-Julie; Agbessi, Mawusse; Christiansen, Mark W.; Jansen, Rick; Seppala, Ilkka; Tong, Lin; Teumer, Alexander; Schramm, Katharina; Hemani, Gibran; Verlouw, Joost; Yaghootkar, Hanieh; Flitman, Reyhan Sonmez; Brown, Andrew; Kukushkina, Viktorija; Kalnapenkis, Anette; Rueger, Sina; Porcu, Eleonora; Kronberg, Jaanika; Kettunen, Johannes; Lee, Bernett; Zhang, Futao; Qi, Ting; Hernandez, Jose Alquicira; Arindrarto, Wibowo; Beutner, Frank; Dmitrieva, Julia; Elansary, Mahmoud; Fairfax, Benjamin P.; Georges, Michel; Heijmans, Bastiaan T.; Hewitt, Alex W.; Kahonen, Mika; Kim, Yungil; Knight, Julian C.; Kovacs, Peter; Krohn, Knut; Li, Shuang; Loeffler, Markus; Marigorta, Urko M.; Mei, Hailang; Momozawa, Yukihide; Mueller-Nurasyid, Martina; Nauck, Matthias; Nivard, Michel G.; Penninx, Brenda W. J. H.; Pritchard, Jonathan K.; Raitakari, Olli T.; Rotzschke, Olaf; Slagboom, Eline P.; Stehouwer, Coen D. A.; Stumvoll, Michael; Sullivan, Patrick; 't Hoen, Peter A. C.; Thiery, Joachim; Tonjes, Anke; van Dongen, Jenny; van Iterson, Maarten; Veldink, Jan H.; Voelker, Uwe; Warmerdam, Robert; Wijmenga, Cisca; Swertz, Morris; Andiappan, Anand; Montgomery, Grant W.; Ripatti, Samuli; Perola, Markus; Kutalik, Zoltan; Dermitzakis, Emmanouil; Bergmann, Sven; Frayling, Timothy; van Meurs, Joyce; Prokisch, Holger; Ahsan, Habibul; Pierce, Brandon L.; Lehtimaki, Terho; Boomsma, Dorret, I; Psaty, Bruce M.; Gharib, Sina A.; Awadalla, Philip; Milani, Lili; Ouwehand, Willem H.; Downes, Kate; Stegle, Oliver; Battle, Alexis; Visscher, Peter M.; Yang, Jian; Scholz, Markus; Powell, Joseph; Gibson, Greg; Esko, Tonu; Franke, Lude
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Mitochondrial DNA variants modulate N-formylmethionine, proteostasis and risk of late-onset human diseases
errNATURE MEDICINE
IF50
err2021-08-23
err35
errOAAI
errCai, Na; Gomez-Duran, Aurora; Yonova-Doing, Ekaterina; Kundu, Kousik; Burgess, Annette, I; Golder, Zoe J.; Calabrese, Claudia; Bonder, Marc J.; Camacho, Marta; Lawson, Rachael A.; Li, Lixin; Williams-Gray, Caroline H.; Di Angelantonio, Emanuele; Roberts, David J.; Watkins, Nick A.; Ouwehand, Willem H.; Butterworth, Adam S.; Stewart, Isobel D.; Pietzner, Maik; Wareham, Nick J.; Langenberg, Claudia; Danesh, John; Walter, Klaudia; Rothwell, Peter M.; Howson, Joanna M. M.; Stegle, Oliver; Chinnery, Patrick F.; Soranzo, Nicole
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Optimizing expression quantitative trait locus mapping workflows for single-cell studies
errGENOME BIOLOGY
IF9.4
err2021-06-24
err36
errOAAI
errCuomo, Anna S. E.; Alvari, Giordano; Azodi, Christina B.; McCarthy, Davis J.; Bonder, Marc Jan
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Large-scale association analyses identify host factors influencing human gut microbiome composition
errNATURE GENETICS
IF31.8
err2021-01-18
err954
errOAAI
errKurilshikov, Alexander; Medina-Gomez, Carolina; Bacigalupe, Rodrigo; Radjabzadeh, Djawad; Wang, Jun; Demirkan, Ayse; Le Roy, Caroline, I; Garay, Juan Antonio Raygoza; Finnicum, Casey T.; Liu, Xingrong; Zhernakova, Daria, V; Bonder, Marc Jan; Hansen, Tue H.; Frost, Fabian; Ruhlemann, Malte C.; Turpin, Williams; Moon, Jee-Young; Kim, Han-Na; Lull, Kreete; Barkan, Elad; Shah, Shiraz A.; Fornage, Myriam; Szopinska-Tokov, Joanna; Wallen, Zachary D.; Borisevich, Dmitrii; Agreus, Lars; Andreasson, Anna; Bang, Corinna; Bedrani, Larbi; Bell, Jordana T.; Bisgaard, Hans; Boehnke, Michael; Boomsma, Dorret, I; Burk, Robert D.; Claringbould, Annique; Croitoru, Kenneth; Davies, Gareth E.; van Duijn, Cornelia M.; Duijts, Liesbeth; Falony, Gwen; Fu, Jingyuan; van der Graaf, Adriaan; Hansen, Torben; Homuth, Georg; Hughes, David A.; Ijzerman, Richard G.; Jackson, Matthew A.; Jaddoe, Vincent W. V.; Joossens, Marie; Jorgensen, Torben; Keszthelyi, Daniel; Knight, Rob; Laakso, Markku; Laudes, Matthias; Launer, Lenore J.; Lieb, Wolfgang; Lusis, Aldons J.; Masclee, Ad A. M.; Moll, Henriette A.; Mujagic, Zlatan; Qibin, Qi; Rothschild, Daphna; Shin, Hocheol; Sorensen, Soren J.; Steves, Claire J.; Thorsen, Jonathan; Timpson, Nicholas J.; Tito, Raul Y.; Vieira-Silva, Sara; Volker, Uwe; Volzke, Henry; Vosa, Urmo; Wade, Kaitlin H.; Walter, Susanna; Watanabe, Kyoko; Weiss, Stefan; Weiss, Frank U.; Weissbrod, Omer; Westra, Harm-Jan; Willemsen, Gonneke; Payami, Haydeh; Jonkers, Daisy M. A. E.; Vasquez, Alejandro Arias; de Geus, Eco J. C.; Meyer, Katie A.; Stokholm, Jakob; Segal, Eran; Org, Elin; Wijmenga, Cisca; Kim, Hyung-Lae; Kaplan, Robert C.; Spector, Tim D.; Uitterlinden, Andre G.; Rivadeneira, Fernando; Franke, Andre; Lerch, Markus M.; Franke, Lude; Sanna, Serena; D'Amato, Mauro; Pedersen, Oluf; Paterson, Andrew D.; Kraaij, Robert; Raes, Jeroen; Zhernakova, Alexandra
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Research Directions

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Co-authors
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