Timothy R Hughes

Publication Activity (10 Years)

Years Active: 2018-2023
Publications (10 Years): 13

Top Topics

Circulating Tumor

Genome Wide Identification

Top Venues

Genome research

Scientific reports

Genes & development

Nature biotechnology

This page only lists publications with an associated author ORCID identifier.

Publications

Debashish Ray, Kaitlin U Laverty, Arttu Jolma, Kate Nie, Reuben Samson, Sara E Pour, Cyrus L Tam, Niklas von Krosigk, Syed Nabeel-Shah, Mihai Albu, Hong Zheng, Gabrielle Perron, Hyunmin Lee, Hamed Najafabadi, Benjamin J Blencowe, Jack Greenblatt, Quaid D Morris, Timothy R Hughes
RNA-binding proteins that lack canonical RNA-binding domains are rarely sequence-specific. Scientific reports 13 (1) (2023)
Sahil Sharma, Sam Kajjo, Zineb Harra, Benedeta Hasaj, Victoria Delisle, Debashish Ray, Rodrigo L Gutierrez, Isabelle Carrier, Claudia Kleinman, Quaid Morris, Timothy R Hughes, Roderick McInnes, Marc R Fabian
Uncovering a mammalian neural-specific poly(A) binding protein with unique properties. Genes & development (2023)
Debashish Ray, Kaitlin U Laverty, Arttu Jolma, Kate Nie, Reuben Samson, Sara E Pour, Cyrus L Tam, Niklas von Krosigk, Syed Nabeel-Shah, Mihai Albu, Hong Zheng, Gabrielle Perron, Hyunmin Lee, Hamed Najafabadi, Benjamin J Blencowe, Jack Greenblatt, Quaid D Morris, Timothy R Hughes
RNA-binding proteins that lack canonical RNA-binding domains are rarely sequence-specific. Scientific reports 13 (1) (2023)
Nicholas Stepankiw, Ally W H Yang, Timothy R Hughes
The human genome contains over a million autonomous exons. Genome research (2023)
David M Ichikawa, Osama Abdin, Nader Alerasool, Manjunatha Kogenaru, April L Mueller, Han Wen, David O Giganti, Gregory W Goldberg, Samantha Adams, Jeffrey M Spencer, Rozita Razavi, Satra Nim, Hong Zheng, Courtney Gionco, Finnegan T Clark, Alexey Strokach, Timothy R Hughes, Timothée Lionnet, Mikko Taipale, Philip M Kim, Marcus B Noyes
A universal deep-learning model for zinc finger design enables transcription factor reprogramming. Nature biotechnology (2023)
Kaitlin U Laverty, Arttu Jolma, Sara E Pour, Hong Zheng, Debashish Ray, Quaid Morris, Timothy R Hughes
PRIESSTESS: interpretable, high-performing models of the sequence and structure preferences of RNA-binding proteins. Nucleic acids research 50 (19) (2022)
Laura F Campitelli, Isaac Yellan, Mihai Albu, Marjan Barazandeh, Zain M Patel, Mathieu Blanchette, Timothy R Hughes
Reconstruction of full-length LINE-1 progenitors from ancestral genomes. Genetics 221 (3) (2022)
Luqian Zheng, Jingjing Liu, Lijie Niu, Mohammad Kamran, Ally W H Yang, Arttu Jolma, Qi Dai, Timothy R Hughes, Dinshaw J Patel, Long Zhang, Supriya G Prasanth, Yang Yu, Aiming Ren, Eric C Lai
Distinct structural bases for sequence-specific DNA binding by mammalian BEN domain proteins. Genes & development 36 (3-4) (2022)
Zain M Patel, Timothy R Hughes
Global properties of regulatory sequences are predicted by transcription factor recognition mechanisms. Genome biology 22 (1) (2021)
Aleksei Shkurin, Timothy R Hughes
Known sequence features can explain half of all human gene ends. NAR genomics and bioinformatics 3 (2) (2021)
Samuel A Lambert, Ally W H Yang, Alexander Sasse, Gwendolyn Cowley, Mihai Albu, Mark X Caddick, Quaid D Morris, Matthew T Weirauch, Timothy R Hughes
Similarity regression predicts evolution of transcription factor sequence specificity. Nature genetics 51 (6) (2019)
Kaitlin U Laverty, Jake M Stout, Mitchell J Sullivan, Hardik Shah, Navdeep Gill, Larry Holbrook, Gintaras Deikus, Robert Sebra, Timothy R Hughes, Jonathan E Page, Harm van Bakel
A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC/CBD acid synthase loci. Genome research 29 (1) (2018)
Marjan Barazandeh, Samuel A Lambert, Mihai Albu, Timothy R Hughes
Comparison of ChIP-Seq Data and a Reference Motif Set for Human KRAB C2H2 Zinc Finger Proteins. G3 (Bethesda, Md.) 8 (1) (2018)