J
Julien Lagarde
Researcher at Pompeu Fabra University
Publications - 39
Citations - 27845
Julien Lagarde is an academic researcher from Pompeu Fabra University. The author has contributed to research in topics: Gene & Human genome. The author has an hindex of 24, co-authored 32 publications receiving 24146 citations. Previous affiliations of Julien Lagarde include University of Geneva.
Papers
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Posted ContentDOI
Reference-free reconstruction and quantification of transcriptomes from Nanopore long-read sequencing
Ivan de la Rubia,Ivan de la Rubia,Joel A. Indi,Joel A. Indi,Silvia Carbonell-Sala,Julien Lagarde,M. Mar Albà,Eduardo Eyras +7 more
TL;DR: RATTLE is developed, the first tool to perform reference-free reconstruction and quantification of transcripts from Nanopore long reads, which accurately determines transcript sequence and abundance, is comparable to reference-based methods, and shows saturation in the number of predicted transcripts with increasing number of input reads.
Dissertation
Genomic Characterization of Human Long Noncoding RNAs
TL;DR: Using a high-throughput, targeted long-read transcriptome sequencing methodology, this study uncovers thousands of novel lncRNAs, approximately doubling the annotated transcript complexity within targeted loci.
Journal ArticleDOI
Current challenges and best practices for cell-free long RNA biomarker discovery
TL;DR: In this paper , the authors identify the main challenges and biases introduced during the different stages of biomarker discovery in liquid biopsies with cell-free RNA and propose solutions to minimize them.
Journal ArticleDOI
Current challenges and best practices for cell-free long RNA biomarker discovery
TL;DR: In this article , the authors identify the main challenges and biases introduced during the different stages of biomarker discovery in liquid biopsies with cell-free RNA and propose solutions to minimize them.
Journal ArticleDOI
Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes
Federico Abascal,Reyes Acosta,Nicholas Addleman,Jessika Adrian,Veena Afzal,Bronwen Aken,Jennifer A. Akiyama,Omar M. Al Jammal,Henry Amrhein,Stacie M. Anderson,Gregory R. Andrews,Igor Antoshechkin,Kristin G. Ardlie,Joel Armstrong,Matthew Astley,Budhaditya Banerjee,Amira A. Barkal,If H. A. Barnes,Iros Barozzi,Daniel Barrell,Gemma Barson,Daniel Bates,Ulugbek K. Baymuradov,Cassandra Bazile,Michael A. Beer,Samantha Beik,M. A. Bender,Ruth Bennett,Louis Philip Benoit Bouvrette,Bradley E. Bernstein,Andrew Berry,Anand Bhaskar,Alexandra Bignell,Steven M. Blue,David M. Bodine,Carles Boix,Nathan Boley,Tyler M. Borrman,Beatrice Borsari,Alan P. Boyle,Laurel A. Brandsmeier,Alessandra Breschi,Emery H. Bresnick,Jason A. Brooks,Michael Buckley,Christopher B. Burge,Rachel Byron,Eileen W. Cahill,Lingling Cai,Lulu Cao,Mark F. Mc Carty,Rosa Castanon,Andres Castillo,Hassan Chaib,Esther T. Chan,Daniel R. Chee,Sora Chee,Hao Chen,Huaming Chen,Jiayu Chen,Songjie Chen,Surya B. Chhetri,Jyoti S. Choudhary,Jacqueline Chrast,Dongjun Chung,Declan Clarke,Neal A.L. Cody,Candice J. Coppola,Julie Coursen,Anthony D'Ippolito,Stephen George Dalton,Cassidy Danyko,R. Davidson,Jose Davila-Velderrain,Carrie A. Davis,Alden Deran,Gilberto DeSalvo,Gloria Despacio-Reyes,Colin N. Dewey,Morgan Diegel,Mark Diekhans,Vishnu Dileep,Bo Ding,Sarah Djebali,Alexander Dobin,Daniel Dominguez,Sarah Donaldson,Jorg Drenkow,Timothy R. Dreszer,Yotam Drier,Michael O. Duff,Douglas Dunn,Catharine L. Eastman,Matthew D. Edwards,Nicole C. El-Ali,Shaimae I. Elhajjajy,Keri Elkins,Andrew Emili,Charles B. Epstein,Rachel C. Evans,Iakes Ezkurdia,Kaili Fan,Nina Farrell,Elise A. Feingold,Anne-Maud Ferreira,Katherine I. Fisher-Aylor,Stephen Fitzgerald,Paul Flicek,Chuan-Sheng Foo,Kevin Fortier,Adam Frankish,Peter Freese,Shaliu Fu,Xiang-Dong Fu,Yu Fu,Yoko Fukuda-Yuzawa,Mariateresa Fulciniti,Alister P. W. Funnell,Idan Gabdank,Timur R. Galeev,Mingshi Gao,Carlos García Girón,Tyler H. Garvin,Chelsea Gelboin-Burkhart,Grigorios Georgolopoulos,Mark Gerstein,Belinda Giardine,David K. Gifford,Daniel A. Gilchrist,Shawn M. Gillespie,Thomas R. Gingeras,Peng Gong,Alvaro J. González,José M. González,Peter Good,Alon Goren,David U. Gorkin,Brenton R. Graveley,Michael Gray,Jack Greenblatt,Edward Griffiths,Mark Groudine,Fabian Grubert,Mengting Gu,Roderic Guigó,Hongbo Guo,Yu Guo,Yuchun Guo,Gamze Gursoy,Maria Gutierrez-Arcelus,Jessica Halow,Matthew P. Hardy,Manoj Hariharan,Arif Harmanci,Anne Harrington,Jennifer Harrow,Tatsunori Hashimoto,Richard Hasz,Meital Hatan,Eric Haugen,James E Hayes,Peng He,Yupeng He,Nastaran Fadaei Heidari,David Hendrickson,Elisabeth F. Heuston,Jason A. Hilton,Benjamin C. Hitz,Abigail Hochman,Cory Holgren,Lei Hou,Shuyu Hou,Yun-Hua Esther Hsiao,Shan Chun Hsu,Hui Huang,Tim Hubbard,Jack Huey,Timothy P. Hughes,Toby Hunt,Sean Ibarrientos,Robbyn Issner,Mineo Iwata,Osagie G. Izuogu,Tommi S. Jaakkola,Nader Jameel,Camden Sinclair Jansen,Lixia Jiang,Peng Jiang,Audra K. Johnson,Rory Johnson,Irwin Jungreis,Madhura Kadaba,Maya Kasowski,M.A. Kasparian,Momoe Kato,Rajinder Kaul,Trupti Kawli,M. Kay,Judith C. Keen,Sunduz Keles,Cheryl A. Keller,David R. Kelley,Pouya Kheradpour,Daniel S Kim,Anthony Kirilusha,Birgit Knoechel,Samantha Kuan,Michael J. Kulik,Sushant Kumar,Anshul Kundaje,Tanya Kutyavin,Julien Lagarde,Bryan R. Lajoie,Nicole J. Lambert,John Lazar,Ah Young Lee,Donghoon Lee,Elizabeth Lee,Jin Wook Lee,Kristen Lee,Christina S. Leslie,Shawn Levy,Bin Li,Hairi Li,Nan Li,Xiangrui Li,Yang Li,Ying Li,Yining Li,Yue Liu,Jin Lian,Max Libbrecht,Shin Lin,Yiing Lin,Dianbo Liu,Jason Liu,Peng Li,Tingting Liu,X. Shirley Liu,Yang Liu,Yaping Liu,Maria R. Long,Shaoke Lou,Jane E. Loveland,Aiping Lu,Yun Lu,Eric Lécuyer,Lijia Ma,Brandon J. Mannion,Michael Mannstadt,Deepa Manthravadi,Georgi K. Marinov,Fergal J. Martin,Eugenio Mattei,Kenneth McCue,Megan McEown,Graham McVicker,Sarah Meadows,Alexander Meissner,Eric M. Mendenhall,C. Luke Messer,Wouter Meuleman,Clifford A. Meyer,Steve Miller,Matthew G. Milton,Tejaswini Mishra,Dianna E. Moore,Helen M. Moore,Samuel H. Moore,Jennifer L. Moran,Jonathan M. Mudge,Nikhil C. Munshi,Rabi Murad,Richard M. Myers,Vivek Nandakumar,Preetha Nandi,Anil M Narasimha,Aditi K. Narayanan,Hannah Naughton,Fabio C. P. Navarro,Patrick A. Navas,Jurijs Nazarovs,Jemma Nelson,Shane Neph,Fidencio Neri,Joseph R. Nery,Amy R. Nesmith,J. Scott Newberry,Kimberly M. Newberry,Vu Ngo,R. W. Nguyen,Thai B. Nguyen,Tung Nguyen,Andrew Nishida,William Stafford Noble,Catherine S. Novak,Eva Maria Novoa,Briana M. Nunez,Charles W. O'Donnell,Sara H. Olson,Kathrina C. Onate,Ericka Otterman,Hakan Ozadam,Michael J. Pagán,Tsultrim Palden,Xinghua Pan,Yongjin Park,E. Christopher Partridge,Benedict Paten,Florencia Pauli-Behn,Michael J. Pazin,Baikang Pei,Len A. Pennacchio,Alexander R Perez,Emily Perry,Dmitri D. Pervouchine,Nishigandha N. Phalke,Quan T. Pham,Douglas H. Phanstiel,Ingrid Plajzer-Frick,Gabriel A. Pratt,Henry Pratt,Sebastian Preissl,Jonathan K. Pritchard,Yuri Pritykin,Qian Qin,Giovanni Quinones-Valdez,Ines Rabano,Ernest Radovani,Anil Raj,Nisha Rajagopal,Oren Ram,L. Ramirez,Ricardo Ramirez,Dylan M. Rausch,Soumya Raychaudhuri,Joseph Raymond,Rozita Razavi,Timothy E. Reddy,Thomas M. Reimonn,Bing Ren,Alexandre Reymond,Alex Reynolds,Suhn K. Rhie,Miguel Rivera,Brian S. Roberts,Jose Manuel Rodriguez,Russell J. Ryan,Eric Rynes,Denis Salins,Richard Sandstrom,Takayo Sasaki,Shashank Sathe,Daniel Savic,Alexandra Scavelli,Jonathan Scheiman,Christoph N. Schlaffner,Jeffery A. Schloss,Frank W. Schmitges,Lei-Hoon See,Anurag Sethi,Manu Setty,Anthony Shafer,Shuo Shan,Eilon Sharon,Quanwen Shen,Richard I. Sherwood,Minyi Shi,Sunyoung Shin,Noam Shoresh,Kyle Siebenthall,Cristina Sisu,Teri Slifer,Cricket A. Sloan,Anna M. Smith,Valentina Snetkova,Michael Snyder,Damek V. Spacek,Sharanya Srinivasan,Rohith Srivas,George Stamatoyannopoulos,John A. Stamatoyannopoulos,Rebecca Stanton,D. Steffan,Sandra Stehling-Sun,J. Seth Strattan,Amanda Su,Balaji Sundararaman,Marie-Marthe Suner,Tahin Fahmid Syed,Matt Szynkarek,Forrest Y. Tanaka,Daniel G. Tenen,Ming Chuin Teng,Jeffrey Thomas,David Toffey,Michael L. Tress,Diane Trout,Gosia Trynka,Junko Tsuji,Sean Upchurch,Oana Ursu,Barbara Uszczynska-Ratajczak,Mia C. Uziel,Alfonso Valencia,Benjamin Van Biber,A. van der Velde,Eric L. Van Nostrand,Yekaterina Vaydylevich,Jesús Vázquez,Alec Victorsen,Jost Vielmetter,Jeff Vierstra,Anna Vlasova,Christopher M. Vockley,Simona Volpi,Shinny Vong,Hao Wang,Mengchi Wang,Qin Wang,Ruth Wang,Tao Wang,Wei Wang,Xiao-feng Wang,Yanli Wang,Nathaniel Watson,Xintao Wei,Zhijie Wei,Hendrik Weisser,Sherman M. Weissman,Rene Welch,Robert E. Welikson,Zhiping Weng,Harm-Jan Westra,John W. Whitaker,Collin White,Kevin P. White,Andre Wildberg,Brian A. Williams,D. Wine,Heather Witt,Maxim Y Wolf,James Santa Barbara Wright,Rui Xiao,Xinshu Xiao,Jie Xu,Jinrui Xu,Koon-Kiu Yan,Yongqi Yan,Hongbo Yang,Xinqiong Yang,Yi-Wen Yang,Galip Gürkan Yardımcı,Brian A. Yee,Gene W. Yeo,Taylor Young,Tianxiong Yu,Feng Yue,Chris Zaleski,C. Zang,Haoyang Zeng,Weihua Zeng,Daniel R. Zerbino,Jieru Zhai,Lijun Zhan,Ye Zhan,Bohan Zhang,Jialing Zhang,Jing Zhang,Kai Zhang,Lijun Zhang,Peng Zhang,Qi Qi Zhang,Xiao-Ou Zhang,Yanxiao Zhang,Zhizhuo Zhang,Yuan Zhao,Ye Zheng,Guoqing Zhong,Xiaoyan Zhou,Yun Zhu,Jared Zimmerman,Rizi Ai,Shantao Li,Jill Moore,Michael J. Purcaro,Yin Shen,Mark Mackiewicz,Ali Mortazavi,Diane E. Dickel,Juan Carlos Rivera-Mulia,Joel Rozowsky,Axel Visel,David Gilbert,Job Dekker,John L. Rinn,Joseph R. Ecker,Manolis Kellis,Robert J. Klein,Peggy J. Farnham,J. Michael Cherry,Barbara J. Wold,Ross C. Hardison +502 more