A
Aki Minoda
Researcher at Epigenomics AG
Publications - 40
Citations - 5377
Aki Minoda is an academic researcher from Epigenomics AG. The author has contributed to research in topics: Chromatin & Gene. The author has an hindex of 21, co-authored 34 publications receiving 4759 citations. Previous affiliations of Aki Minoda include London Research Institute & University of California, Berkeley.
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Journal ArticleDOI
Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE
Sushmita Roy,Jason Ernst,Peter V. Kharchenko,Pouya Kheradpour,Nicolas Nègre,Matthew L. Eaton,Jane M. Landolin,Christopher A. Bristow,Lijia Ma,Michael F. Lin,Stefan Washietl,Bradley I. Arshinoff,Ferhat Ay,Patrick E. Meyer,Nicolas Robine,Nicole L. Washington,Luisa Di Stefano,Eugene Berezikov,Christopher D. Brown,Rogerio Candeias,Joseph W. Carlson,Adrian Carr,Irwin Jungreis,Daniel Marbach,Rachel Sealfon,Michael Y. Tolstorukov,Sebastian Will,Artyom A. Alekseyenko,Carlo G. Artieri,Benjamin W. Booth,Angela N. Brooks,Qi Dai,Carrie A. Davis,Michael O. Duff,X. Feng,Andrey A. Gorchakov,Tingting Gu,Jorja G. Henikoff,Philipp Kapranov,Renhua Li,Heather K. MacAlpine,John H. Malone,Aki Minoda,Jared T. Nordman,Katsutomo Okamura,Marc D. Perry,Sara K. Powell,Nicole C. Riddle,Akiko Sakai,Anastasia Samsonova,Jeremy E. Sandler,Yuri B. Schwartz,Noa Sher,Rebecca Spokony,David Sturgill,Marijke J. van Baren,Kenneth H. Wan,Li Yang,Charles Yu,Elise A. Feingold,Peter J. Good,Mark S. Guyer,Rebecca F. Lowdon,Kami Ahmad,Justen Andrews,Bonnie Berger,Steven E. Brenner,Michael R. Brent,Lucy Cherbas,Sarah C. R. Elgin,Thomas R. Gingeras,Robert L. Grossman,Roger A. Hoskins,Thomas C. Kaufman,W. J. Kent,Mitzi I. Kuroda,Terry L. Orr-Weaver,Norbert Perrimon,Vincenzo Pirrotta,James W. Posakony,Bing Ren,Steven Russell,Peter Cherbas,Brenton R. Graveley,Suzanna E. Lewis,Gos Micklem,Brian Oliver,Peter J. Park,Susan E. Celniker,Steven Henikoff,Gary H. Karpen,Eric C. Lai,David M. MacAlpine,Lincoln Stein,Kevin P. White,Manolis Kellis +95 more
TL;DR: The Drosophila Encyclopedia of DNA Elements (modENCODE) project as mentioned in this paper has been used to map transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines.
Journal ArticleDOI
Comprehensive analysis of the chromatin landscape in Drosophila melanogaster
Peter V. Kharchenko,Artyom A. Alekseyenko,Artyom A. Alekseyenko,Yuri B. Schwartz,Aki Minoda,Nicole C. Riddle,Jason Ernst,Jason Ernst,Peter J. Sabo,Erica Larschan,Erica Larschan,Erica Larschan,Andrey A. Gorchakov,Andrey A. Gorchakov,Tingting Gu,Daniela Linder-Basso,Annette Plachetka,Annette Plachetka,Gregory A. Shanower,Michael Y. Tolstorukov,Michael Y. Tolstorukov,Lovelace J. Luquette,Ruibin Xi,Youngsook L. Jung,Youngsook L. Jung,Richard W. Park,Richard W. Park,Eric P. Bishop,Eric P. Bishop,Theresa K. Canfield,Richard Sandstrom,Robert E. Thurman,David M. MacAlpine,John A. Stamatoyannopoulos,Manolis Kellis,Manolis Kellis,Sarah C. R. Elgin,Mitzi I. Kuroda,Mitzi I. Kuroda,Vincenzo Pirrotta,Gary H. Karpen,Peter J. Park,Peter J. Park,Peter J. Park +43 more
TL;DR: In this article, the authors present a genome-wide chromatin landscape for Drosophila melanogaster based on eighteen histone modifications, summarized by nine prevalent combinatorial patterns.
Journal Article
Comprehensive analysis of the chromatin landscape in Drosophila melanogaster
Peter V. Kharchenko,Artyom A. Alekseyenko,Artyom A. Alekseyenko,Yuri B. Schwartz,Aki Minoda,Nicole C. Riddle,Jason Ernst,Jason Ernst,Peter J. Sabo,Erica Larschan,Erica Larschan,Erica Larschan,Andrey A. Gorchakov,Andrey A. Gorchakov,Tingting Gu,Daniela Linder-Basso,Annette Plachetka,Annette Plachetka,Gregory A. Shanower,Michael Y. Tolstorukov,Michael Y. Tolstorukov,Lovelace J. Luquette,Ruibin Xi,Youngsook L. Jung,Youngsook L. Jung,Richard W. Park,Richard W. Park,Eric P. Bishop,Eric P. Bishop,Theresa K. Canfield,Richard Sandstrom,Robert E. Thurman,David M. MacAlpine,John A. Stamatoyannopoulos,Manolis Kellis,Manolis Kellis,Sarah C. R. Elgin,Mitzi I. Kuroda,Mitzi I. Kuroda,Vincenzo Pirrotta,Gary H. Karpen,Peter J. Park,Peter J. Park,Peter J. Park +43 more
TL;DR: It is found that active genes display distinct chromatin signatures that are correlated with disparate gene lengths, exon patterns, regulatory functions and genomic contexts, and a diversity of signatures among Polycomb targets that include a subset with paused polymerase.
Journal ArticleDOI
Double-Strand Breaks in Heterochromatin Move Outside of a Dynamic HP1a Domain to Complete Recombinational Repair
Irene Chiolo,Aki Minoda,Serafin U Colmenares,Aris Polyzos,Sylvain V. Costes,Gary H. Karpen,Gary H. Karpen +6 more
TL;DR: It is proposed that the spatial and temporal control of DSB repair in heterochromatin safeguards genome stability by preventing aberrant exchanges between repeats.
Journal ArticleDOI
An assessment of histone-modification antibody quality
Thea A. Egelhofer,Aki Minoda,Aki Minoda,Sarit Klugman,Sarit Klugman,Kyungjoon Lee,P. Kolasinska-Zwierz,Artyom A. Alekseyenko,Ming Sin Cheung,Daniel S. Day,Sarah Gadel,Andrey A. Gorchakov,Tingting Gu,Peter V. Kharchenko,Samantha Kuan,Samantha Kuan,Isabel J. Latorre,Daniela Linder-Basso,Ying Luu,Ying Luu,Que-Minh Ngo,Que-Minh Ngo,Marc D. Perry,Andreas Rechtsteiner,Nicole C. Riddle,Yuri B. Schwartz,Gregory A. Shanower,A. Vielle,Julie Ahringer,Sarah C. R. Elgin,Mitzi I. Kuroda,Vincenzo Pirrotta,Bing Ren,Bing Ren,Susan Strome,Peter J. Park,Gary H. Karpen,Gary H. Karpen,R. David Hawkins,R. David Hawkins,Jason D. Lieb +40 more
TL;DR: The specificity and utility of histone-modification antibodies raised against 57 different histone modifications in Drosophila melanogaster, Caenorhabditis elegans and human cells are tested.