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1 - 24 of 24 items

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Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome

Cai Li , Boris Lenhard , Nicholas M. Luscombe
Genome Research,28(5),676-688 (2018-04-04) , Cold Spring Harbor Laboratory Press , info:doi/10.1101/gr.231449.117 , © 2018 Li et al. , publisher

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Intron retention and nuclear loss of SFPQ are molecular hallmarks of ALS

Raphaelle Luisier , Giulia E. Tyzack , Claire E. Hall , Jamie S. Mitchell , Helen Devine , Doaa M. Taha , Bilal Malik , Ione Meyer , Linda Greensmith , Jia Newcombe , Jernej Ule , Nicholas M. Luscombe , Rickie Patani
Nature Communications,9(1), (2018-05-22) , Nature Research , info:doi/10.1038/s41467-018-04373-8 , © 2018 The Author(s). , publisher

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Heteromeric RNP Assembly at LINEs Controls Lineage-Specific RNA Processing

Jan Attig , Federico Agostini , Clare Gooding , Anob M. Chakrabarti , Aarti Singh , Nejc Haberman , Julian A. Zagalak , Warren Emmett , Christopher W.J. Smith , Nicholas M. Luscombe , Jernej Ule
Cell,174(5),1067-1081.e17 (2018-08-02) , Elsevier Inc. , info:doi/10.1016/j.cell.2018.07.001 , © 2018 The Authors. , publisher

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Machine learning models in electronic health records can outperform conventional survival models for predicting patient mortality in coronary artery disease

Andrew J. Steele , Spiros C. Denaxas , Anoop D. Shah , Harry Hemingway , Nicholas M. Luscombe
PLOS ONE,13(8),e0202344 (2018-08-31) , Public Library of Science , info:doi/10.1371/journal.pone.0202344 , © 2018 Steele et al. , publisher

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Nervous System Regionalization Entails Axial Allocation before Neural Differentiation

Vicki Metzis , Sebastian Steinhauser , Edvinas Pakanavicius , Mina Gouti , Despina Stamataki , Kenzo Ivanovitch , Thomas Watson , Teresa Rayon , S. Neda Mousavy Gharavy , Robin Lovell-Badge , Nicholas M. Luscombe , James Briscoe
Cell,175(4),1105-1118.e17 (2018-10-18) , Elsevier Inc , info:doi/10.1016/j.cell.2018.09.040 , © 2018 The Author(s). , publisher

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Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis

Anna R. Poetsch , Simon J. Boulton , Nicholas M. Luscombe
Genome Biology,19(1),215 (2018-12-07) , BMC , info:doi/10.1186/s13059-018-1582-2 , © 2018 The Author(s). , publisher

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Target-Specific Precision of CRISPR-Mediated Genome Editing

Anob M. Chakrabarti , Tristan Henser-Brownhill , Josep Monserrat , Anna R. Poetsch , Nicholas M. Luscombe , Paola Scaffidi
Molecular Cell,73(4),699-713.e6 (2018-12-13) , Elsevier Inc. , info:doi/10.1016/j.molcel.2018.11.031 , © 2018 The Author(s). , publisher

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A systems view of spliceosomal assembly and branchpoints with iCLIP

Michael Briese , Nejc Haberman , Christopher R. Sibley , Rupert Faraway , Andrea S. Elser , Anob M. Chakrabarti , Zhen Wang , Julian König , David Perera , Vihandha O. Wickramasinghe , Ashok R. Venkitaraman , Nicholas M. Luscombe , Luciano Saieva , Livio Pellizzoni , Christopher W. J. Smith , Tomaž Curk , Jernej Ule
Nature Structural & Molecular Biology,26(10),930-940 (2019-09-30) , Nature Research , info:doi/10.1038/s41594-019-0300-4 , © 2019 The Author(s), under exclusive licence to Springer Nature America, Inc. , none

Widespread use of the “ascidian” mitochondrial genetic code in tunicates

Julien Pichon , Nicholas M. Luscombe , Charles Plessy
F1000Research,8,2072 (2019-12-10) , F1000Research , info:doi/10.12688/f1000research.21551.1 , © 2019 Pichon J et al. , publisher

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RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions

Alessandro Bonetti , Federico Agostini , Ana Maria Suzuki , Kosuke Hashimoto , Giovanni Pascarella , Juliette Gimenez , Leonie Roos , Alex J. Nash , Marco Ghilotti , Christopher J. F. Cameron , Matthew Valentine , Yulia A. Medvedeva , Shuhei Noguchi , Eneritz Agirre , Kaori Kashi , Samudyata , Joachim Luginbühl , Riccardo Cazzoli , Saumya Agrawal , Nicholas M. Luscombe , Mathieu Blanchette , Takeya Kasukawa , Michiel de Hoon , Erik Arner , Boris Lenhard , Charles Plessy , Gonçalo Castelo-Branco , Valerio Orlando , Piero Carninci
Nature Communications,11(1),1018 (2020-02-24) , Nature Research , info:doi/10.1038/s41467-020-14337-6 , © 2020 The Author(s) , publisher

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Nucleosome positioning stability is a modulator of germline mutation rate variation across the human genome

Cai Li , Nicholas M. Luscombe
Nature Communications,11(1),1363 (2020-03-13) , Nature Research , info:doi/10.1038/s41467-020-15185-0 , © 2020 The Author(s) , publisher

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Finding cell-specific expression patterns in the early Ciona embryo with single-cell RNA-seq

Garth R. Ilsley , Ritsuko Suyama , Takeshi Noda , Nori Satoh , Nicholas M. Luscombe
Scientific Reports,10(1),4961 (2020-03-18) , Nature Research , info:doi/10.1038/s41598-020-61591-1 , © 2020 The Author(s)

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How Do You Identify m⁶A Methylation in Transcriptomes at High Resolution? A Comparison of Recent Datasets

Charlotte Capitanchik , Patrick Toolan-Kerr , Nicholas M. Luscombe , Jernej Ule
Frontiers in Genetics,11,398 (2020-05-20) , Frontiers Media S.A. , info:doi/10.3389/fgene.2020.00398 , © 2020 Capitanchik, Toolan-Kerr, Luscombe and Ule. , publisher

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Streamlined Sampling and Cultivation of the Pelagic Cosmopolitan Larvacean, Oikopleura dioica

Aki Masunaga , Andrew W. Liu , Yongkai Tan , Andrew Scott , Nicholas M. Luscombe
Journal of Visualized Experiments,(160),e61279 (2020-06-16) , MyJove Corporation , info:doi/10.3791/61279 , © 2020 JoVE , publisher

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A genome database for a Japanese population of the larvacean Oikopleura dioica

Kai Wang , Ryo Tomura , Wei Chen , Miho Kiyooka , Hinako Ishizaki , Tomoyuki Aizu , Yohei Minakuchi , Masahide Seki , Yutaka Suzuki , Tatsuya Omotezako , Ritsuko Suyama , Aki Masunaga , Charles Plessy , Nicholas M. Luscombe , Christelle Dantec , Patrick Lemaire , Takehiko Itoh , Atsushi Toyoda , Hiroki Nishida , Takeshi A. Onuma
Development, Growth & Differentiation,62(6),450-461 (2020-08-14) , Wiley , Japanese Society of Developmental Biologists , info:doi/10.1111/dgd.12689 , This is the pre-peer reviewed version of the following article: Wang, K, Tomura, R, Chen, W, et al. A genome database for a Japanese population of the larvacean Oikopleura dioica. Develop. Growth Differ. 2020; 62: 450– 461., which has been published in final form at https://doi.org/10.1111/dgd.12689. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. , author

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High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts

Minghao Chia , Cai Li , Sueli Marques , Vicente Pelechano , Nicholas M. Luscombe , Folkert J. van Werven
Genome Biology,22(1),34 (2021-01-14) , BMC , info:doi/10.1186/s13059-020-02245-3 , © 2021 The Author(s). , publisher

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Transcription levels of a noncoding RNA orchestrate opposing regulatory and cell fate outcomes in yeast

Fabien Moretto , N. Ezgi Wood , Minghao Chia , Cai Li , Nicholas M. Luscombe , Folkert J. van Werven
Cell Reports,34(3),108643 (2021-01-19) , Cell Press , info:doi/10.1016/j.celrep.2020.108643 , © 2020 The Author(s). , publisher

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H3S28P Antibody Staining of Okinawan Oikopleura dioica Suggests the Presence of Three Chromosomes

Andrew W. Liu , Yongkai Tan , Aki Masunaga , Aleksandra Bliznina , Charlotte West , Charles Plessy , Nicholas M. Luscombe
F1000Research,9,780 (2021-03-01) , F1000Research , info:doi/10.12688/f1000research.25019.2 , © 2021 Liu AW et al. , publisher

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psiCLIP reveals dynamic RNA binding by DEAH-box helicases before and after exon ligation

Lisa M. Strittmatter , Charlotte Capitanchik , Andrew J. Newman , Martina Hallegger , Christine M. Norman , Sebastian M. Fica , Chris Oubridge , Nicholas M. Luscombe , Jernej Ule , Kiyoshi Nagai
Nature Communications,12(1),1488 (2021-03-05) , Nature Portfolio , info:doi/10.1038/s41467-021-21745-9 , © 2021 The Author(s). , publisher

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Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing

Aleksandra Bliznina , Aki Masunaga , Michael J. Mansfield , Yongkai Tan , Andrew W. Liu , Charlotte West , Tanmay Rustagi , Hsiao-Chiao Chien , Saurabh Kumar , Julien Pichon , Charles Plessy , Nicholas M. Luscombe
BMC Genomics,22(1),222 (2021-03-29) , BMC , info:doi/10.1186/s12864-021-07512-6 , publisher

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Intergenic RNA mainly derives from nascent transcripts of known genes

Federico Agostini , Julian Zagalak , Jan Attig , Jernej Ule , Nicholas M. Luscombe
Genome Biology,22(1),136 (2021-05-05) , BMC , info:doi/10.1186/s13059-021-02350-x , © 2021 The Author(s). , publisher

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TDP-43 condensation properties specify its RNA-binding and regulatory repertoire

Martina Hallegger , Anob M. Chakrabarti , Flora C.Y. Lee , Bo Lim Lee , Aram G. Amalietti , Hana M. Odeh , Katie E. Copley , Jack D. Rubien , Bede Portz , Klara Kuret , Ina Huppertz , Frédérique Rau , Rickie Patani , Nicolas L. Fawzi , James Shorter , Nicholas M. Luscombe , Jernej Ule
Cell,184(18),4680-4696.e22 (2021-09-02) , Elsevier Inc. , info:doi/10.1016/j.cell.2021.07.018 , © 2021 The Author(s) , publisher

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RNA modifications detection by comparative Nanopore direct RNA sequencing

Adrien Leger , Paulo P. Amaral , Luca Pandolfini , Charlotte Capitanchik , Federica Capraro , Valentina Miano , Valentina Migliori , Patrick Toolan-Kerr , Theodora Sideri , Anton J. Enright , Konstantinos Tzelepis , Folkert J. van Werven , Nicholas M. Luscombe , Isaia Barbieri , Jernej Ule , Tomas Fitzgerald , Ewan Birney , Tommaso Leonardi , Tony Kouzarides
Nature Communications,12(1),7198 (2021-10-10) , Nature Portfolio , info:doi/10.1038/s41467-021-27393-3 , © 2021 The Author(s). , publisher

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The cosmopolitan appendicularian Oikopleura dioica reveals hidden genetic diversity around the globe

Aki Masunaga , Michael J. Mansfield , Yongkai Tan , Andrew W. Liu , Aleksandra Bliznina , Paolo Barzaghi , Tamara L. Hodgetts , Alfonso Ferrández-Roldán , Cristian Cañestro , Takeshi A. Onuma , Charles Plessy , Nicholas M. Luscombe
Marine Biology,169(12),157 (2022-11-27) , Springer Nature , info:doi/10.1007/s00227-022-04145-5 , © 2022 The Author(s) , publisher

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