9 research outputs found
Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network
- Author
- Abugessaisa Imad
- Aitken Stuart
- Aken Bronwen L.
- Alam Intikhab
- Alam Tanvir
- Alasiri Rami
- Alhendi Ahmad M. N.
- Alinejad-Rokny Hamid
- Alvarez Mariano J.
- Andersson Robin
- Arakawa Takahiro
- Araki Marito
- Arbel Taly
- Archer John
- Archibald Alan L.
- Arner Erik
- Arner Peter
- Asai Kiyoshi
- Ashoor Haitham
- Astrom Gaby
- Babina M.
- Baillie J.K.
- Bajic V.B.
- Bajpai A.
- Baker S.
- Baldarelli R.M.
- Balic A.
- Bansal M.
- Batagov A.O.
- Batzoglou S.
- Beckhouse A.G.
- Beltrami A.P.
- Beltrami C.A.
- Bertin Nicolas
- Bessière Chloé
- Bhattacharya S.
- Bickel P.J.
- Blake J.A.
- Blanchette M.
- Bodega B.
- Bonetti A.
- Bono H.
- Bornholdt J.
- Bougouffa S.
- Boyd M.
- Breda J.
- Brombacher F.
- Brown J.B.
- Bréhélin L.
- Bttcher M.
- Bult C.J.
- Burroughs A.M.
- Burt D.W.
- Busch A.
- Caglio G.
- Califano A.
- Cameron C.J.
- Cannistraci C.V.
- Carbone A.
- Carlisle A.J.
- Carninci Piero
- Carninci Piero
- Carter K.W.
- Cesselli D.
- Chang J.-C.
- Chatelain Clement
- Chen J.C.
- Chen Y.
- Chierici M.
- Christodoulou J.
- Ciani Y.
- Clark E.L.
- Coskun M.
- Dalby M.
- Dalla E.
- Daub C.O.
- Davis C.A.
- de Hoom Michiel J. L.
- de Hoom Michiel J. L.
- de Rie D.
- Denisenko E.
- Deplancke B.
- Detmar M.
- Deviatiiarov R.
- Di Bernardo D.
- Diehl A.D.
- Dieterich L.C.
- Dimont E.
- Djebali S.
- Dohi T.
- Dostie J.
- Drablos F.
- Edge A.S.B.
- Edinger M.
- Ehrlund A.
- Ekwall K.
- Elofsson A.
- Endoh M.
- Enomoto H.
- Enomoto S.
- Faghihi M.
- Fagiolini M.
- FANTOM consortium.
- Farach-Carson M.C.
- Faulkner G.J.
- Favorov A.
- Fernandes A.M.
- Ferrai C.
- Forrest A.R.R.
- Forrester L.M.
- Forsberg M.
- Fort A.
- Francescatto M.
- Freeman T.C.
- Frith Martin C.
- Frith Martin C.
- Fukuda S.
- Funayama M.
- Furlanello C.
- Furuno M.
- Furusawa C.
- Gao H.
- Gazova I.
- Gebhard C.
- Geier F.
- Geijtenbeek T.B.H.
- Ghosh S.
- Ghosheh Y.
- Gingeras T.R.
- Gojobori T.
- Goldberg T.
- Goldowitz D.
- Gough J.
- Grapotte Mathys
- Greco D.
- Gruber A.J.
- Guhl S.
- Guigo R.
- Guler R.
- Gusev O.
- Gustincich S.
- Ha T.J.
- Haberle V.
- Hale P.
- Hallstrom B.M.
- Hamada M.
- Handoko L.
- Hara M.
- Harbers M.
- Harrow J.
- Harshbarger J.
- Hase T.
- Hasegawa Akira
- Hasegawa Akira
- Hashimoto K.
- Hatano T.
- Hattori N.
- Hayashi R.
- Hayashizaki Yoshihide
- Hayashizaki Yoshihide
- Herlyn M.
- Hettne K.
- Heutink P.
- Hide W.
- Hitchens K.J.
- Hon C.C.
- Hori F.
- Horie M.
- Horimoto K.
- Horton P.
- Hou R.
- Huang E.
- Huang Y.
- Hugues R.
- Hume D.
- Ienasescu H.
- Iida K.
- Ikawa T.
- Ikemura T.
- Ikeo K.
- Inoue N.
- Ishizu Y.
- Ito Y.
- Itoh Masayoshi
- Itoh Masayoshi
- Ivshina A.V.
- Jankovic B.R.
- Jenjaroenpun P.
- Johnson R.
- Jorgensen M.
- Jorjani H.
- Joshi A.
- Jurman G.
- Kaczkowski B.
- Kai C.
- Kaida K.
- Kajiyama K.
- Kaliyaperumal R.
- Kaminuma E.
- Kanaya T.
- Kaneda H.
- Kapranov P.
- Kasianov A.S.
- Kasukawa Takeya
- Kasukawa Takeya
- Katayama T.
- Kato S.
- Kawaguchi S.
- Kawai J.
- Kawaji H.
- Kawamoto H.
- Kawamura Y.I.
- Kawasaki S.
- Kawashima T.
- Kempfle J.S.
- Kenna T.J.
- Kere J.
- Khachigian L.
- Kiryu H.
- Kishima M.
- Kitajima H.
- Kitamura T.
- Kitano H.
- Klaric E.
- Klepper K.
- Klinken S.P.
- Kloppmann E.
- Knox A.J.
- Kodama Y.
- Kogo Y.
- Kojima M.
- Kojima S.
- Kojima-Ishiyama Miki
- Komatsu N.
- Komiyama H.
- Kono T.
- Koseki H.
- Koyasu S.
- Kratz A.
- Kukalev A.
- Kulakovskiy I.
- Kundaje A.
- Kunikata H.
- Kuo R.
- Kuo T.
- Kuraku S.
- Kuznetsov V.A.
- Kwon T.J.
- Larouche M.
- Lassmann T.
- Laurent G.S.
- Law A.
- Le-Cao K.-A.
- Lecellier C.-H.
- Lecellier C.-H.
- Lee W.
- Lenhard B.
- Lennartsson A.
- Li K.
- Li R.
- Lilje B.
- Lipovich L.
- Lizio M.
- Lopez G.
- Magi S.
- Mak G.K.
- Makeev V.
- Manabe R.
- Mandai M.
- Mar J.
- Maruyama K.
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- Mason E.
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- Medvedeva Y.A.
- Meehan T.F.
- Mejhert N.
- Menichelli Christophe
- Meynert A.
- Mikami N.
- Minoda A.
- Miura H.
- Miyagi Y.
- Miyawaki A.
- Mizuno Y.
- Morikawa H.
- Morimoto M.
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- Motohashi H.
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- Murata Mitsuyoshi
- Murata Mitsuyoshi
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- Nakamura Y.
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- Nason G.P.
- Nepal C.
- Nguyen Q.H.
- Nielsen L.K.
- Nishida K.
- Nishiguchi K.M.
- Nishiyori H.
- Nishiyori-Sueki Hiromi
- Nitta K.
- Noguchi Shuhei
- Noguchi Shuhei
- Noma Shohei
- Noma Shohei
- Notredame C.
- Ogishima S.
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- Ohno H.
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- Ohtsu T.
- Okada Y.
- Okada-Hatakeyama M.
- Okazaki Y.
- Oksvold P.
- Orlando V.
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- Pachkov M.
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- Park S.-J.
- Pascarella G.
- Passier R.
- Persson H.
- Philippens I.H.
- Piazza S.
- Plessy C.
- Pombo A.
- Ponten F.
- Poulain S.
- Poulsen T.M.
- Pradhan S.
- Prezioso C.
- Pridans C.
- Qin X.-Y.
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- Ramilowski Jordan A.
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- Saito A.
- Saito M.
- Sakaguchi S.
- Sakai M.
- Sakaue S.
- Sakaue-Sawano A.
- Sandelin A.
- Sano H.
- Saraswat Manu
- Sasamoto Y.
- Sato H.
- Saxena A.
- Saya H.
- Schafferhans A.
- Schmeier S.
- Schmidl C.
- Schmocker D.
- Schneider C.
- Schueler M.
- Schultes E.A.
- Schulze-Tanzil G.
- Semple C.A.
- Seno S.
- Seo W.
- Sese J.
- Severin Jessica
- Severin Jessica
- Sheng G.
- Shi J.
- Shimoni Y.
- Shin J.W.
- SimonSanchez J.
- Sivertsson A.
- Sjostedt E.
- Soderhall C.
- Stoiber M.H.
- Sugiyama D.
- Sui S.H.
- Summers K.M.
- Suzuki A.M.
- Suzuki Harukazu
- Suzuki Harukazu
- Suzuki K.
- Suzuki M.
- Suzuki N.
- Suzuki T.
- Swanson D.J.
- Swoboda R.K.
- Tagami Michihira
- Tagami Michihira
- Taguchi A.
- Takahashi H.
- Takahashi M.
- Takamochi K.
- Takeda S.
- Takenaka Y.
- Tam K.T.
- Tanaka H.
- Tanaka R.
- Tanaka Y.
- Tang D.
- Taniuchi I.
- Tanzer A.
- Tarui H.
- Taylor M.S.
- Terada A.
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- Testa A.C.
- Thomas M.
- Thongjuea S.
- Tomii K.
- Toyoda H.
- Triglia E.T.
- Tsang H.G.
- Tsujikawa M.
- Uhlén M.
- Valen E.
- van de Wetering M.
- van Nimwegen E.
- Velmeshev D.
- Verardo R.
- Vitezic M.
- Vitting-Seerup K.
- von Feilitzen K.
- Voolstra C.R.
- Vorontsov I.E.
- Wahlestedt C.
- Wasserman Wyeth W.
- Wasserman Wyeth W.
- Watanabe K.
- Watanabe S.
- Wells C.A.
- Winteringham L.N.
- Wolvetang E.
- Yabukami H.
- Yagi K.
- Yamada T.
- Yamaguchi Y.
- Yamamoto M.
- Yamamoto Y.
- Yamamoto Y.
- Yamanaka Y.
- Yano K.
- Yasuzawa K.
- Yatsuka Y.
- Yo M.
- Yokokura S.
- Yoneda M.
- Yoshida E.
- Yoshida Y.
- Yoshihara M.
- Young R.
- Young R.S.
- Yu N.Y.
- Yumoto N.
- Zabierowski S.E.
- Zhang P.G.
- Zucchelli S.
- Zwahlen M.
- ’t Hoen P.A.C.
- Publication venue
- Nature Publishing Group
- Publication date
- 15/12/2020
- Field of study
Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism
Mortality within hospital after resuscitation from ventricular fibrillation outside hospital.
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- A A Adgey
- Adgey A.A.J.
- Aprahamian C.
- Baum R.S.
- Ch Dubois
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- Dunn H.M.
- Einarsson 0 Jakobsson F, Sigurdsson G
- Eisenberg M.S.
- Eisenberg M.S.
- Goldstein S.
- Hallstrom A.P.
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- Stults K.R.
- Tresch D.D.
- W Dickey
- Weaver W.D.
- Weaver W.D.
- Weaver W.D.
- Webb S.W.
- Publication venue
- 'BMJ'
- Publication date
- Field of study
In-Hospital Resuscitation Concept with First-Responder Defibrillation. 2-Year Experience
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- A. Mullie
- A. Zafari
- A.P. Hallstrom
- Andreas Mügge
- B. Kaernested
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- Christoph Hanefeld
- Cordula Kloppe
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- E. Katz
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- M.P. Larsen
- Nils Robert
- P. Brindley
- P. Eisenburger
- P.S. Chan
- R.J. Fairbanks
- R.O. Cummins
- R.V. Aghababian
- S. Suraseranivongse
- V.M. Nadkarni
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- Field of study
Risk Factors and Triggers of Sudden Death in the Working Generation. An Autopsy Proven Case-Control Study.
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- Burke A.P., Farb, A., Malcom, G.T., Liang, Y., Smialek, J. &
- Burke A.P., Farb, A., Malcom, G.T., Liang, Y.H., Smialek, J. &
- Cupples L.A., Gagnon, D.R. &
- El Fawal M.A., Berg, G.A., Wheatley, D.J. &
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- Folts J.D., Gering, S.A., Laibly, S.W., Bertha, B.G., Bonebrake, F.C. &
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- Jouven X., Desnos, M., Guerot, C. &
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- Reichenbach D.D., Moss, N.S. &
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- Tanabe N., Hayashi, S. &
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- Winniford M.D.
- Publication venue
- 'Tohoku University Medical Press'
- Publication date
- 01/01/1999
- Field of study
Pediatric Cardiopulmonary Arrest and Resuscitation
- Author
- A. Grenvik
- A. Langhelle
- A. Nishisaki
- A. Torres Jr
- A. Zaritsky
- A.D. Slonim
- A.G. Reis
- A.H. Idris
- A.J. Donoghue
- A.J. Donoghue
- A.P. Hallstrom
- B.S. Abella
- B.T. Smith
- C.G. Brown
- D. Yannopoulos
- D.A. Parra
- D.P. Edelson
- E.A. Hunt
- F. Schellhammer
- F.W. Tecklenburg
- G. Ceneviva
- G.O. Appleton
- H. Tunstall-Pedoe
- H.J. Dalton
- Hypothermia After Cardiac Arrest Study Group
- I. Abdallah
- I. Laurent
- J. Lopez-Herce
- J. Tibballs
- J.K. Stross
- K. Lurie
- K. Sunde
- K.D. Young
- K.G. Lurie
- K.H. Lindner
- M. Callaham
- M. Kuisma
- M. Thalmann
- M.A. DeVita
- M.B. Perondi
- M.B. Schindler
- M.C. Morris
- M.D. Berg
- N.A. Paradis
- O. Piazza
- P. Laitinen
- P. Laitinen
- P. Suominen
- P. Suominen
- P. Suominen
- P.A. Innes
- P.A. Meaney
- P.B. Berger
- P.D. Gluckman
- P.E. Sirbaugh
- P.J. Nido del
- R.A. Berg
- R.A. Dieckmann
- R.A. Samson
- R.B. Gerein
- R.J. Brilli
- R.R. Thiagarajan
- R.W. Hickey
- S. Chamnanvanakij
- S. Shankaran
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- S.B. Kinney
- S.K. Srikantan
- S.L. Caffrey
- S.R. Hintz
- T.D. Valenzuela
- T.M. Hoffman
- V.M. Nadkarni
- W. Behringer
- W.D. Graf
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- 01/01/2008
- Field of study
Update on sideline and event preparation for management of sudden cardiac arrest in athletes
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- A.P. Hallstrom
- American Academy of Family Physicians American Academy of Pediatrics, American College of Sports Medicine, American Medical Society for Sports Medicine, American Orthopedic Society for Sports Medicine, American Osteopathic Association of Sports Medicine.
- American Academy of Pediatrics
- American Heart Association
- American Heart Association
- American Heart Association
- B. Eberle
- B.J. Maron
- B.J. Maron
- B.J. Maron
- C. Basso
- D. Corrado
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- Kimberly G. Harmon
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- M. Holmberg
- M. Ruppert
- M.F. Hazinski
- M.P. Larsen
- P.D. Thompson
- R.D. White
- R.D. White
- R.D. White
- R.L. Page
- R.M. Robertson
- S.P. Camp Van
- T.D. Valenzuela
- T.J. Bunch
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- Field of study
Adaptive relationships of epoxide hydrolase in herbivorous arthropods
- Author
- A. Miyazaki
- A. Nahrstedt
- A.D. Cross
- A.D. Tomlin
- A.J. Baars
- A.M. Ajami
- A.P. Tulloch
- A.Y.H. Lu
- B. Gold
- B.A. Croft
- B.D. Hammock
- B.D. Hammock
- B.D. Hammock
- B.D. Hammock
- B.D. Hammock
- B.D. Hammock
- C.A. Mullin
- C.A. Mullin
- C.A. Mullin
- C.A. Mullin
- C.A. Mullin
- C.A. Mullin
- C.A. Mullin
- C.A. Mullin
- C.A. Mullin
- C.A. Mullin
- C.A. Mullin
- C.L. Miranda
- D. Cova
- D.H. Hutson
- D.L. Grundy
- D.M. Norris
- D.M. Soderlund
- D.V. Banthorpe
- E. Boyland
- E. Cohen
- E. Cohen
- E. Hodgson
- E. McCord Jr.
- E.S. Oonnithan
- F. Oesch
- F.M. Dean
- G.D. Prestwich
- G.E. Pratt
- G.J.P. Singh
- G.R. Hartmann
- G.T. Brooks
- G.T. Brooks
- G.T. Brooks
- G.T. Brooks
- G.T. Brooks
- G.T. Brooks
- H. Breuer
- H.H. Rees
- I. Hallstrom
- I. Kubo
- J. Seidegard
- J.-I. Fukami
- J.-L. Fukami
- J.A. Ottea
- J.A. Ottea
- J.A. Ottea
- J.E. Casida
- J.E. Casida
- J.F. Fitzloff
- J.O. Nelson
- J.R. Wisniewski
- K.D. Wing
- L.B. Brattsten
- L.B. Brattsten
- L.O. Ruzo
- M. Gadot
- M. Jansen
- M. Rothschild
- M. Slade
- M. Slade
- M. Slade
- M. Slade
- M. Slade
- M.E. Schroeder
- M.T.S. Hsia
- P.E. Kolattukudy
- P.F. Dowd
- P.J. Holloway
- P.J. Holloway
- P.M. Fox
- R. Croteau
- R. Feyereisen
- R. Feyereisen
- R.A. White
- R.B. Yamasaki
- R.J. Kuhr
- R.N. Wixtrom
- R.R. Scheune
- S. Ahmad
- S. Ahmad
- S.J. Kramer
- S.J. Yu
- S.J. Yu
- S.J. Yu
- S.J. Yu
- S.J. Yu
- S.J. Yu
- S.S. Gill
- T.A. Beek Van
- T.A. Miller
- T.C. Sparks
- T.W. Bell
- W.C. Burnett Jr.
- W.E. Scott
- W.R. Martin
- W.S. Bowers
- Y. Fujimoto
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- Field of study
Conserved RB functions in development and tumor suppression
- Author
- A. Bergmann
- A. Chicas
- A. Hirschi
- A. Ianari
- A. Sharma
- A.C. Bester
- A.G. Knudson Jr.
- A.J. Ruthenburg
- A.L. Manning
- A.P. Feinberg
- A.P. Young
- B. Li
- B. Ren
- B.D. Dynlacht
- B.N. Nicolay
- B.N. Nicolay
- B.O. Williams
- B.S. Taylor
- C. Attwooll
- C. Milet
- C. Stirzaker
- C. Treins
- C.E. Isaac
- C.H. Coschi
- C.J. Sherr
- C.W. Miller
- D. Chen
- D. Ferres-Marco
- D. Ginsberg
- D. Kanber
- D. Pan
- D.D. Sarbassov
- D.K. Dimova
- D.L. Burkhart
- D.M. Thomas
- D.W. Goodrich
- E. Bier
- E. Calo
- E. Hernando
- E.E. Bosco
- E.S. Knudsen
- E.V. Benevolenskaya
- F. Bunz
- F. Foijer
- F.A. Dick
- F.J. Kaye
- F.J. Stott
- G. Ferbeyre
- G. Mulligan
- G.M. Gordon
- H. Müller
- H. Tanaka
- H. Toyoshima
- H. Wang
- H.A. Rogoff
- H.S. Zhang
- H.Z. Chen
- J. Bartkova
- J. Christensen
- J. Kato
- J. Li
- J. Lukas
- J. Sage
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- J.L. Chong
- J.M. Schvartzman
- J.R. Burke
- J.S. Searle
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- K. Polyak
- K. Tschöp
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- R.J. Bourgo
- R.J. Klose
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- S. Gonzalo
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- S.E. Wirt
- S.H. Friend
- S.M. Rubin
- S.W. Hiebert
- T. Harn van
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- Y. Takahashi
- Y. Zhang
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- Field of study
Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network
- Author
- Abugessaisa Imad
- Aitken Stuart
- Aken Bronwen L.
- Alam Intikhab
- Alam Tanvir
- Alasiri Rami
- Alhendi Ahmad M. N.
- Alinejad-Rokny Hamid
- Alvarez Mariano J.
- Andersson Robin
- Arakawa Takahiro
- Araki Marito
- Arbel Taly
- Archer John
- Archibald Alan L.
- Arner Erik
- Arner Peter
- Asai Kiyoshi
- Ashoor Haitham
- Astrom Gaby
- Babina M.
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- Bertin Nicolas
- Bessière Chloé
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- Blake J.A.
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- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- 02/06/2021
- Field of study
10.1038/s41467-021-23143-7Nature Communications121329