J
Jan Aerts
Researcher at Katholieke Universiteit Leuven
Publications - 104
Citations - 14649
Jan Aerts is an academic researcher from Katholieke Universiteit Leuven. The author has contributed to research in topics: Genome & Visualization. The author has an hindex of 32, co-authored 100 publications receiving 11587 citations. Previous affiliations of Jan Aerts include Parco Tecnologico Padano & Wageningen University and Research Centre.
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Journal ArticleDOI
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
LaDeana W. Hillier,Webb Miller,Ewan Birney,Wesley C. Warren,Ross C. Hardison,Chris P. Ponting,Peer Bork,David W. Burt,Martien A. M. Groenen,Mary E. Delany,Jerry B. Dodgson,Asif T. Chinwalla,Paul F. Cliften,Sandra W. Clifton,Kimberly D. Delehaunty,Catrina Fronick,Robert S. Fulton,Tina Graves,Colin Kremitzki,Dan Layman,Vincent Magrini,John Douglas Mcpherson,Tracie L. Miner,Patrick Minx,William E. Nash,Michael N. Nhan,Joanne O. Nelson,Lachlan G. Oddy,Craig Pohl,Jennifer Randall-Maher,Scott M. Smith,John W. Wallis,Shiaw Pyng Yang,Michael N Romanov,Catherine M. Rondelli,Bob Paton,Jacqueline Smith,David Morrice,Laura M. Daniels,Helen G. Tempest,Lindsay Robertson,Julio S. Masabanda,Darren K. Griffin,Alain Vignal,Valerie Fillon,Lina Jacobbson,Susanne Kerje,Leif Andersson,Richard P. M. A. Crooijmans,Jan Aerts,Jan J. van der Poel,Hans Ellegren,Randolph B. Caldwell,Simon J. Hubbard,Darren Grafham,Andrzej M. Kierzek,Stuart McLaren,Ian M. Overton,Hiroshi Arakawa,Kevin J. Beattie,Yuri Bezzubov,Paul E. Boardman,James K. Bonfield,Michael D. R. Croning,Robert L. Davies,Matthew D. Francis,Sean Humphray,Carol Scott,Ruth Taylor,Cheryll Tickle,William Brown,Jane Rogers,Jean-Marie Buerstedde,Stuart A. Wilson,Lisa Stubbs,Ivan Ovcharenko,Laurie Gordon,Susan Lucas,Marcia M. Miller,Hidetoshi Inoko,Takashi Shiina,James C. Kaufman,Jan Salomonsen,Karsten Skjoedt,Gane Ka-Shu Wong,Jun Wang,Bin Liu,Jian Wang,Jun Yu,Huanming Yang,Mikhail Nefedov,Maxim Koriabine,Pieter J. deJong,Leo Goodstadt,Caleb Webber,Nicholas J. Dickens,Ivica Letunic,Mikita Suyama,David Torrents,Christian von Mering,Evgeny M. Zdobnov,Kateryna D. Makova,Anton Nekrutenko,Laura Elnitski,Pallavi Eswara,David C. King,Shan Yang,Svitlana Tyekucheva,Anusha Radakrishnan,Robert S. Harris,Francesca Chiaromonte,James Taylor,Jianbin He,Monique Rijnkels,Sam Griffiths-Jones,Abel Ureta-Vidal,Michael M. Hoffman,Jessica Severin,Stephen M. J. Searle,Andy Law,David Speed,D. Waddington,Ze Cheng,Eray Tüzün,Evan E. Eichler,Zhirong Bao,Paul Flicek,David Shteynberg,Michael R. Brent,Jacqueline M. Bye,Elizabeth J. Huckle,Sourav Chatterji,Colin N. Dewey,Lior Pachter,Andrei Kouranov,Zissimos Mourelatos,Artemis G. Hatzigeorgiou,Andrew H. Paterson,Robert Ivarie,Mikael Brandström,Erik Axelsson,Niclas Backström,Sofia Berlin,Matthew T. Webster,Olivier Pourquié,Alexandre Reymond,Catherine Ucla,Stylianos E. Antonarakis,Manyuan Long,J. J. Emerson,Esther Betrán,Isabelle Dupanloup,Henrik Kaessmann,Angie S. Hinrichs,Gill Bejerano,Terrence S. Furey,Rachel A. Harte,Brian J. Raney,Adam Siepel,W. James Kent,David Haussler,Eduardo Eyras,Robert Castelo,Josep F. Abril,Sergi Castellano,Francisco Camara,Genís Parra,Roderic Guigó,Guillaume Bourque,Glenn Tesler,Pavel A. Pevzner,Arian F.A. Smit,Lucinda Fulton,Elaine R. Mardis,Richard K. Wilson +174 more
TL;DR: A draft genome sequence of the red jungle fowl, Gallus gallus, provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes.
Journal ArticleDOI
SCENIC: single-cell regulatory network inference and clustering.
Sara Aibar,Carmen Bravo González-Blas,Thomas Moerman,Vân Anh Huynh-Thu,Hana Imrichova,Gert Hulselmans,Florian Rambow,Jean-Christophe Marine,Pierre Geurts,Jan Aerts,Joost van den Oord,Zeynep Kalender Atak,Jasper Wouters,Stein Aerts +13 more
TL;DR: On a compendium of single-cell data from tumors and brain, it is demonstrated that cis-regulatory analysis can be exploited to guide the identification of transcription factors and cell states.
Journal ArticleDOI
Origins and functional impact of copy number variation in the human genome
Donald F. Conrad,Dalila Pinto,Richard Redon,Richard Redon,Lars Feuk,Lars Feuk,Omer Gokcumen,Yujun Zhang,Jan Aerts,T. Daniel Andrews,Chris P. Barnes,Peter J. Campbell,Tomas W Fitzgerald,Min Hu,Chun Hwa Ihm,K. Kristiansson,Daniel G. MacArthur,Jeffrey R. MacDonald,Ifejinelo Onyiah,Andy Wing Chun Pang,Samuel Robson,Kathy Stirrups,Armand Valsesia,Klaudia Walter,John Wei,Chris Tyler-Smith,Nigel P. Carter,Charles Lee,Stephen W. Scherer,Stephen W. Scherer,Matthew E. Hurles +30 more
TL;DR: It is concluded that the heritability void left by genome-wide association studies will not be accounted for by common CNVs, and 30 loci with CNVs that are candidates for influencing disease susceptibility are identified.
Journal ArticleDOI
The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution
Christine G. Elsik,Christine G. Elsik,Christine G. Elsik,Ross L. Tellam,Kim C. Worley,Kim C. Worley,Richard A. Gibbs,Donna M. Muzny,George M. Weinstock,George M. Weinstock,David L. Adelson,Evan E. Eichler,Evan E. Eichler,Laura Elnitski,Roderic Guigó,Debora L. Hamernik,Steve M. Kappes,Harris A. Lewin,David J. Lynn,Frank W. Nicholas,Alexandre Reymond,Monique Rijnkels,Loren C. Skow,Evgeny M. Zdobnov,Evgeny M. Zdobnov,Evgeny M. Zdobnov,Lawrence B. Schook,James E. Womack,Tyler Alioto,Stylianos E. Antonarakis,Alex Astashyn,Charles E. Chappie,Hsiu Chuan Chen,Jacqueline Chrast,Francisco Câmara,Olga Ermolaeva,Charlotte N. Henrichsen,Wratko Hlavina,Yuri Kapustin,Boris Kiryutin,Paul Kitts,Felix Kokocinski,Melissa J. Landrum,Donna Maglott,Kim D. Pruitt,Victor Sapojnikov,Stephen M. J. Searle,Victor V. Solovyev,Alexandre Souvorov,Catherine Ucla,Carine Wyss,Juan Manuel Anzola,Daniel Gerlach,Daniel Gerlach,Eran Elhaik,Eran Elhaik,Dan Graur,Justin T. Reese,Robert C. Edgar,John C. McEwan,Gemma Marie Payne,Joy M. Raison,Thomas Junier,Thomas Junier,Evgenia V. Kriventseva,Eduardo Eyras,Mireya Plass,Ravikiran Donthu,Denis M. Larkin,James M. Reecy,Mary Qu Yang,Lin Chen,Ze Cheng,Carol G. Chitko-McKown,George E. Liu,Lakshmi K. Matukumalli,Lakshmi K. Matukumalli,Jiuzhou Song,Bin Zhu,Daniel G. Bradley,Fiona S. L. Brinkman,Lilian P.L. Lau,Matthew D. Whiteside,Angela K. Walker,Thomas T. Wheeler,Theresa Casey,J. Bruce German,J. Bruce German,Danielle G. Lemay,Nauman J. Maqbool,A.J. Molenaar,Seongwon Seo,Paul Stothard,Cynthia L. Baldwin,R. Baxter,Candice L. Brinkmeyer-Larigford,Wendy C. Brown,Christopher P. Childers,Timothy Connelley,Shirley A. Ellis,Krista L. Fritz,Elizabeth Glass,Carolyn T.A. Herzig,Antti Livanainen,Kevin K. Lahmers,Anna K. Bennett,C. Michael Dickens,James G. R. Gilbert,Darren E. Hagen,Hanni Salih,Jan Aerts,Alexandre Rodrigues Caetano,Brian P. Dalrymple,José Fernando Garcia,Clare A. Gill,Stefan Hiendleder,Erdogan Memili,D.M. Spurlock,John L. Williams,Lee Alexander,Michael J. Brownstein,Le Luo Guan,Robert A. Holt,Steven J.M. Jones,Marco A. Marra,Richard A. Moore,Stephen S. Moore,Andrew J. Roberts,Masaaki Taniguchi,Masaaki Taniguchi,Richard C. Waterman,Joseph Chacko,Mimi M. Chandrabose,Andy Cree,Marvin Diep Dao,Huyen Dinh,Ramatu Ayiesha Gabisi,Sandra Hines,Jennifer Hume,Shalini N. Jhangiani,Vandita Joshi,Christie Kovar,Lora Lewis,Yin Shin Liu,John Lopez,Margaret Morgan,Ngoc Nguyen,Geoffrey Okwuonu,San Juana Ruiz,Jireh Santibanez,Rita A. Wright,Christian J. Buhay,Yan Ding,Shannon Dugan-Rocha,Judith Herdandez,Michael Holder,Aniko Sabo,Amy Egan,Jason Goodell,Katarzyna Wilczek-Boney,Gerald R. Fowler,Matthew Hitchens,Ryan J. Lozado,Charles Moen,David Steffen,James T. Warren,Jingkun Zhang,Readman Chiu,Jacqueline E. Schein,K. James Durbin,K. James Durbin,Paul Havlak,Paul Havlak,Huaiyang Jiang,Yue Liu,Xiang Qin,Yanru Ren,Yufeng Shen,Yufeng Shen,Henry Song,Stephanie Bell,Clay Davis,Angela Jolivet Johnson,Sandra L. Lee,Lynne V. Nazareth,Bella Mayurkumar Patel,Ling Ling Pu,Selina Vattathil,Rex Lee Williams,Stacey M. Curry,Cerissa Hamilton,Erica Sodergren,Erica Sodergren,David A. Wheeler,Wes Barris,Gary L. Bennett,André Eggen,Ronnie D. Green,Gregory P. Harhay,Matthew Hobbs,Oliver C. Jann,John W. Keele,Matthew Peter Kent,Sigbjam Lien,Stephanie D. McKay,Sean McWilliam,Abhirami Ratnakumar,Robert D. Schnabel,Timothy P. L. Smith,Warren M. Snelling,Tad S. Sonstegard,Roger T. Stone,Yoshikazu Sugimoto,Akiko Takasuga,Jeremy F. Taylor,Curtis P. Van Tassell,Michael D. MacNeil,A.R.R. Abatepaulo,Colette A. Abbey,Virpi Ahola,Lassudara G. Almeida,Ariel Fernando Amadio,Elen Anatriello,Suria M. Bahadue,Fernando H. Biase,Clayton R. Boldt,Jeffery A. Carroll,W. A. Carvalho,Eliane P. Cervelatti,Elsa Chacko,Jennifer E. Chapin,Ye Cheng,Jung-Woo Choi,Adam J. Colley,Tatiana A. DeCampos,Marcos De Donato,Isabel Kinney Ferreira de Miranda Santos,Carlo José Freire de Oliveira,Heather M Deobald,Eve Devinoy,Kaitlin E. Donohue,Peter Dove,Annett Eberlein,Carolyn Fitzsimmons,Alessandra Mara Franzin,Gustavo Garcia,Sem Genini,Cody J. Gladney,Jason R. Grant,Marion L. Greaser,Jonathan A. Green,Darryl L. Hadsell,Hatam A. Hakimov,Rob Halgren,Jennifer Harrow,E. Hart,N. Hastings,Marta Hernández,Zhi-Liang Hu,Antti Iivanainen,Aaron Ingham,Terhi Iso-Touru,Catherine Jamis,Kirsty Jensen,Dimos Kapetis,Tovah Kerr,Sari S. Khalil,Hasan Khatib,D. Kolbehdari,D. Kolbehdari,Cham G. Kumar,Dinesh Kumar,Richard J. Leach,Justin C. Lee,Changxi Li,Krystin M. Logan,Roberto Malinverni,E. Marques,William F. Martin,Natália F. Martins,Sandra Regina Maruyama,Raffaele Mazza,Kim L. McLean,Juan F. Medrano,Barbara T. Moreno,Daniela D. Moré,Carl T. Muntean,Hari Prasad Nandakumar,Marcelo Fábio Gouveia Nogueira,Ingrid Olsaker,Sameer D. Pant,Francesca Panzitta,Rosemeire Conceição Parra Pastor,Mario Andres Poli,Nathan Poslusny,Satyanarayana Rachagani,Shoba Ranganathan,Shoba Ranganathan,Andrej Razpet,Penny K. Riggs,Gonzalo Rincon,Nelida Rodriguez-Osorio,Nelida Rodriguez-Osorio,Sandra L. Rodriguez-Zas,Natasha E. Romero,Anne G. Rosenwald,Lillian Sando,Sheila M. Schmutz,Libing Shen,Laura Sherman,Bruce R. Southey,Ylva Strandberg Lutzow,Jonathan V. Sweedler,Imke Tammen,Bhanu Prakash V.L. Telugu,Jennifer M. Urbanski,Yuri Tani Utsunomiya,Chris P. Verschoor,Ashley J. Waardenberg,Zhiquan Wang,Robert Ward,Rosemarie Weikard,Thomas H. Welsh,Stephen N. White,Stephen N. White,Laurens G. Wilming,Kris R. Wunderlich,Jianqi Yang,Feng-Qi Zhao +328 more
TL;DR: To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage and provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
Posted ContentDOI
SCENIC: Single-Cell Regulatory Network Inference And Clustering
Sara Aibar,Carmen Bravo González-Blas,Thomas Moerman,Jasper Wouters,Vân Anh Huynh-Thu,Hana Imrichova,Zeynep Kalender Atak,Gert Hulselmans,Michael Dewaele,Florian Rambow,Pierre Geurts,Jan Aerts,Jean-Christophe Marine,Joost van den Oord,Stein Aerts +14 more
TL;DR: SCENIC (Single Cell rEgulatory Network Inference and Clustering) is the first method to analyze scRNA-seq data using a network-centric, rather than cell-centric approach and allows for the simultaneous tracing of genomic regulatory programs and the mapping of cellular identities emerging from these programs.