Core promoterome of barley embryo

Authors: Simon Pavlu, Sarvesh Nikumbh, Martin Kovacik, Tadaichi An, Boris Lenhard, Hana Simkova, Pavla Navratilova

Source: Computational and Structural Biotechnology Journal, Vol 23, Iss , Pp 264-277 (2024)

Subject Terms: Core promoter, Cap Analysis of Gene Expression, Morex, Initiator, TOR-signaling, Hordeum vulgare, Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2001037023004798; https://doaj.org/toc/2001-0370

Access URL: https://doaj.org/article/786a595c6397481d967d6119e74adb95

Widespread 3′UTR capped RNAs derive from G-rich regions in proximity to AGO2 binding sites

Authors: Nejc Haberman, Holly Digby, Rupert Faraway, Rebecca Cheung, Anob M. Chakrabarti, Andrew M. Jobbins, Callum Parr, Kayoko Yasuzawa, Takeya Kasukawa, Chi Wai Yip, Masaki Kato, Hazuki Takahashi, Piero Carninci, Santiago Vernia, Jernej Ule, Christopher R. Sibley, Aida Martinez-Sanchez, Boris Lenhard

Source: BMC Biology, Vol 22, Iss 1, Pp 1-23 (2024)

Subject Terms: 3′UTR, CAGE, Capping, AGO2, UPF1, 3′UTR-derived RNA, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1741-7007

Access URL: https://doaj.org/article/ad037dcdd70a4cf1aefd83bb7b5773ce

Interferon-gamma rescues dendritic cell calcineurin-dependent responses to Aspergillus fumigatus via Stat3 to Stat1 switching

Authors: Amit Adlakha, Thomas J. Williams, Xinxin Shou, Anna K. Reed, Boris Lenhard, Darius Armstrong-James

Source: iScience, Vol 28, Iss 2, Pp 111535- (2025)

Subject Terms: Pathophysiology, Microbiology, Transcriptomics, Science

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2589004224027627; https://doaj.org/toc/2589-0042

Access URL: https://doaj.org/article/5816beef59fb49dfa785c0b1f0e56fcc

Roles for the long non-coding RNA Pax6os1/PAX6-AS1 in pancreatic beta cell function

Authors: Livia Lopez-Noriega, Rebecca Callingham, Aida Martinez-Sánchez, Sameena Nawaz, Grazia Pizza, Nejc Haberman, Nevena Cvetesic, Marie-Sophie Nguyen-Tu, Boris Lenhard, Piero Marchetti, Lorenzo Piemonti, Eelco de Koning, A.M. James Shapiro, Paul R. Johnson, Isabelle Leclerc, Benoit Hastoy, Benoit R. Gauthier, Timothy J. Pullen, Guy A. Rutter

Source: iScience, Vol 28, Iss 1, Pp 111518- (2025)

Subject Terms: Cell biology, Cellular physiology, Molecular biology, Science

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2589004224027457; https://doaj.org/toc/2589-0042

Access URL: https://doaj.org/article/f195e6b6021d48928eb2e93138f9e0d3

A deep learning method for replicate-based analysis of chromosome conformation contacts using Siamese neural networks

Authors: Ediem Al-jibury, James W. D. King, Ya Guo, Boris Lenhard, Amanda G. Fisher, Matthias Merkenschlager, Daniel Rueckert

Source: Nature Communications, Vol 14, Iss 1, Pp 1-13 (2023)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/d7dda5f518cd4ccaa907111a9072e516

Integrative genomic analyses in adipocytes implicate DNA methylation in human obesity and diabetes

Authors: Liam McAllan, Damir Baranasic, Sergio Villicaña, Scarlett Brown, Weihua Zhang, Benjamin Lehne, Marco Adamo, Andrew Jenkinson, Mohamed Elkalaawy, Borzoueh Mohammadi, Majid Hashemi, Nadia Fernandes, Nathalie Lambie, Richard Williams, Colette Christiansen, Youwen Yang, Liudmila Zudina, Vasiliki Lagou, Sili Tan, Juan Castillo-Fernandez, James W. D. King, Richie Soong, Paul Elliott, James Scott, Inga Prokopenko, Inês Cebola, Marie Loh, Boris Lenhard, Rachel L. Batterham, Jordana T. Bell, John C. Chambers, Jaspal S. Kooner, William R. Scott

Source: Nature Communications, Vol 14, Iss 1, Pp 1-20 (2023)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/ea82019d0abe4ca49fb6dbbbe87cd979

Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation.

Authors: Sarvesh Nikumbh, Boris Lenhard

Source: PLoS Computational Biology, Vol 19, Iss 11, p e1011491 (2023)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011491&type=printable; https://doaj.org/toc/1553-734X; https://doaj.org/toc/1553-7358

Access URL: https://doaj.org/article/34b9f53529054f9b899bfcfef82cf886

Identification of downstream effectors of retinoic acid specifying the zebrafish pancreas by integrative genomics

Authors: Ana R. López-Pérez, Piotr J. Balwierz, Boris Lenhard, Ferenc Muller, Fiona C. Wardle, Isabelle Manfroid, Marianne L. Voz, Bernard Peers

Source: Scientific Reports, Vol 11, Iss 1, Pp 1-16 (2021)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/850bfa32b31943dd9ae0d3bdc4010ac4

Neuronal genes deregulated in Cornelia de Lange Syndrome respond to removal and re-expression of cohesin

Authors: Felix D. Weiss, Lesly Calderon, Yi-Fang Wang, Radina Georgieva, Ya Guo, Nevena Cvetesic, Maninder Kaur, Gopuraja Dharmalingam, Ian D. Krantz, Boris Lenhard, Amanda G. Fisher, Matthias Merkenschlager

Source: Nature Communications, Vol 12, Iss 1, Pp 1-13 (2021)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/afef53aab6c24336822425f4c1c3c8be

The order and logic of CD4 versus CD8 lineage choice and differentiation in mouse thymus

Authors: Mohammad M. Karimi, Ya Guo, Xiaokai Cui, Husayn A. Pallikonda, Veronika Horková, Yi-Fang Wang, Sara Ruiz Gil, Gustavo Rodriguez-Esteban, Irene Robles-Rebollo, Ludovica Bruno, Radina Georgieva, Bhavik Patel, James Elliott, Marian H. Dore, Danielle Dauphars, Michael S. Krangel, Boris Lenhard, Holger Heyn, Amanda G. Fisher, Ondřej Štěpánek, Matthias Merkenschlager

Source: Nature Communications, Vol 12, Iss 1, Pp 1-14 (2021)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/ce6d54e4a05749d99545339b720e286a

TBPL2/TFIIA complex establishes the maternal transcriptome through oocyte-specific promoter usage

Authors: Changwei Yu, Nevena Cvetesic, Vincent Hisler, Kapil Gupta, Tao Ye, Emese Gazdag, Luc Negroni, Petra Hajkova, Imre Berger, Boris Lenhard, Ferenc Müller, Stéphane D. Vincent, László Tora

Source: Nature Communications, Vol 11, Iss 1, Pp 1-13 (2020)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/17a2545846504f2fb6572d460793c1a3

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

Authors: 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

Source: Nature Communications, Vol 11, Iss 1, Pp 1-14 (2020)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/3ee35708eeee438bbb6649cdd0169ea5

Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing

Authors: Chirag Nepal, Yavor Hadzhiev, Piotr Balwierz, Estefanía Tarifeño-Saldivia, Ryan Cardenas, Joseph W. Wragg, Ana-Maria Suzuki, Piero Carninci, Bernard Peers, Boris Lenhard, Jesper B. Andersen, Ferenc Müller

Source: Nature Communications, Vol 11, Iss 1, Pp 1-16 (2020)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/1ccdccedb09b4f3faf2cec376a66c412

Widespread conservation and lineage-specific diversification of genome-wide DNA methylation patterns across arthropods.

Authors: Samuel H Lewis, Laura Ross, Stevie A Bain, Eleni Pahita, Stephen A Smith, Richard Cordaux, Eric A Miska, Boris Lenhard, Francis M Jiggins, Peter Sarkies

Source: PLoS Genetics, Vol 16, Iss 6, p e1008864 (2020)

Subject Terms: Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1553-7390; https://doaj.org/toc/1553-7404

Access URL: https://doaj.org/article/7951cbc5c39449c3908f02bb355e6640

Distinct core promoter codes drive transcription initiation at key developmental transitions in a marine chordate

Authors: Gemma B. Danks, Pavla Navratilova, Boris Lenhard, Eric M. Thompson

Source: BMC Genomics, Vol 19, Iss 1, Pp 1-12 (2018)

Subject Terms: Core promoter, DNA methylation, Histone modification, MZT, Oogenesis, Operons, Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12864-018-4504-5; https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/f234b7dbf5fd41e3900e0ffb7c86ab13

Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation

Authors: Nathan Harmston, Elizabeth Ing-Simmons, Ge Tan, Malcolm Perry, Matthias Merkenschlager, Boris Lenhard

Source: Nature Communications, Vol 8, Iss 1, Pp 1-13 (2017)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/1b04c3b1a6a64b378ed9795e790183ff

Ancestrally Duplicated Conserved Noncoding Element Suggests Dual Regulatory Roles of HOTAIR in cis and trans

Authors: Chirag Nepal, Andrzej Taranta, Yavor Hadzhiev, Sachin Pundhir, Piotr Mydel, Boris Lenhard, Ferenc Müller, Jesper B. Andersen

Source: iScience, Vol 23, Iss 4, Pp - (2020)

Subject Terms: Science

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2589004220301929; https://doaj.org/toc/2589-0042

Access URL: https://doaj.org/article/b7e405ff8faf4bdeb530e90665aa9585

CNEr: A toolkit for exploring extreme noncoding conservation.

Authors: Ge Tan, Dimitris Polychronopoulos, Boris Lenhard

Source: PLoS Computational Biology, Vol 15, Iss 8, p e1006940 (2019)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1553-734X; https://doaj.org/toc/1553-7358

Access URL: https://doaj.org/article/10ff80d9eb5540f6b0feb76a8946642c

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

Authors: 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

Source: Nature Communications, Vol 12, Iss 1, Pp 1-1 (2021)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/1c6594919e4a4dec9114c20da2fa808b

Feedforward regulation of Myc coordinates lineage-specific with housekeeping gene expression during B cell progenitor cell differentiation.

Authors: Isabel Ferreirós-Vidal, Thomas Carroll, Tianyi Zhang, Vincenzo Lagani, Ricardo N Ramirez, Elizabeth Ing-Simmons, Alicia G Gómez-Valadés, Lee Cooper, Ziwei Liang, Georgios Papoutsoglou, Gopuraja Dharmalingam, Ya Guo, Sonia Tarazona, Sunjay J Fernandes, Peri Noori, Gilad Silberberg, Amanda G Fisher, Ioannis Tsamardinos, Ali Mortazavi, Boris Lenhard, Ana Conesa, Jesper Tegner, Matthias Merkenschlager, David Gomez-Cabrero

Source: PLoS Biology, Vol 17, Iss 4, p e2006506 (2019)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1544-9173; https://doaj.org/toc/1545-7885

Access URL: https://doaj.org/article/9bf45eded0be40789c3b6f117e693ee1