Splice_sim: a nucleotide conversion-enabled RNA-seq simulation and evaluation framework

Authors: Niko Popitsch, Tobias Neumann, Arndt von Haeseler, Stefan L. Ameres

Source: Genome Biology, Vol 25, Iss 1, Pp 1-19 (2024)

Subject Terms: Nucleotide conversion sequencing, Metabolic RNA labeling, SLAMseq, RNA-BS-seq, 3′ end sequencing, Spliced read mapping, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/82b79117ed5b4c5591dea76d334124af

Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases

Authors: Alistair T. Pagnamenta, Carme Camps, Edoardo Giacopuzzi, John M. Taylor, Mona Hashim, Eduardo Calpena, Pamela J. Kaisaki, Akiko Hashimoto, Jing Yu, Edward Sanders, Ron Schwessinger, Jim R. Hughes, Gerton Lunter, Helene Dreau, Matteo Ferla, Lukas Lange, Yesim Kesim, Vassilis Ragoussis, Dimitrios V. Vavoulis, Holger Allroggen, Olaf Ansorge, Christian Babbs, Siddharth Banka, Benito Baños-Piñero, David Beeson, Tal Ben-Ami, David L. Bennett, Celeste Bento, Edward Blair, Charlotte Brasch-Andersen, Katherine R. Bull, Holger Cario, Deirdre Cilliers, Valerio Conti, E. Graham Davies, Fatima Dhalla, Beatriz Diez Dacal, Yin Dong, James E. Dunford, Renzo Guerrini, Adrian L. Harris, Jane Hartley, Georg Hollander, Kassim Javaid, Maureen Kane, Deirdre Kelly, Dominic Kelly, Samantha J. L. Knight, Alexandra Y. Kreins, Erika M. Kvikstad, Craig B. Langman, Tracy Lester, Kate E. Lines, Simon R. Lord, Xin Lu, Sahar Mansour, Adnan Manzur, Reza Maroofian, Brian Marsden, Joanne Mason, Simon J. McGowan, Davide Mei, Hana Mlcochova, Yoshiko Murakami, Andrea H. Németh, Steven Okoli, Elizabeth Ormondroyd, Lilian Bomme Ousager, Jacqueline Palace, Smita Y. Patel, Melissa M. Pentony, Chris Pugh, Aboulfazl Rad, Archana Ramesh, Simone G. Riva, Irene Roberts, Noémi Roy, Outi Salminen, Kyleen D. Schilling, Caroline Scott, Arjune Sen, Conrad Smith, Mark Stevenson, Rajesh V. Thakker, Stephen R. F. Twigg, Holm H. Uhlig, Richard van Wijk, Barbara Vona, Steven Wall, Jing Wang, Hugh Watkins, Jaroslav Zak, Anna H. Schuh, Usha Kini, Andrew O. M. Wilkie, Niko Popitsch, Jenny C. Taylor

Source: Genome Medicine, Vol 15, Iss 1, Pp 1-25 (2023)

Subject Terms: Genome sequencing, Rare diseases, Structural variant, Splice site variant, Non-coding, Diagnostic yield, Medicine, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1756-994X

Access URL: https://doaj.org/article/c9f00f4d0c70402d8c69f3f7e4981fbc

The identification of protein and RNA interactors of the splicing factor Caper in the adult Drosophila nervous system

Authors: M. Brandon Titus, Adeline W. Chang, Niko Popitsch, Christopher C. Ebmeier, Jeremy M. Bono, Eugenia C. Olesnicky

Source: Frontiers in Molecular Neuroscience, Vol 16 (2023)

Subject Terms: alternative splicing, RNA-binding proteins, caper, RBM39, Drosophila, tissue specific function, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fnmol.2023.1114857/full; https://doaj.org/toc/1662-5099

Access URL: https://doaj.org/article/5dd07272bdad45079db99203363d36f7

Targeting foam cell formation in inflammatory brain diseases by the histone modifier MS‐275

Authors: Bettina Zierfuss, Isabelle Weinhofer, Agnieszka Buda, Niko Popitsch, Lena Hess, Verena Moos, Simon Hametner, Stephan Kemp, Wolfgang Köhler, Sonja Forss‐Petter, Christian Seiser, Johannes Berger

Source: Annals of Clinical and Translational Neurology, Vol 7, Iss 11, Pp 2161-2177 (2020)

Subject Terms: Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571, Neurology. Diseases of the nervous system, RC346-429

File Description: electronic resource

Relation: https://doaj.org/toc/2328-9503

Access URL: https://doaj.org/article/40f371d81c5841558e4739b6c421dc16

Sequencing of human genomes with nanopore technology

Authors: Rory Bowden, Robert W. Davies, Andreas Heger, Alistair T. Pagnamenta, Mariateresa de Cesare, Laura E. Oikkonen, Duncan Parkes, Colin Freeman, Fatima Dhalla, Smita Y. Patel, Niko Popitsch, Camilla L. C. Ip, Hannah E. Roberts, Silvia Salatino, Helen Lockstone, Gerton Lunter, Jenny C. Taylor, David Buck, Michael A. Simpson, Peter Donnelly

Source: Nature Communications, Vol 10, Iss 1, Pp 1-9 (2019)

Subject Terms: Science

File Description: electronic resource

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

Access URL: https://doaj.org/article/2580fae944954c8fb4376bb048722780

CD371 cell surface expression: a unique feature of DUX4-rearranged acute lymphoblastic leukemia

Authors: Dagmar Schinnerl, Ester Mejstrikova, Angela Schumich, Marketa Zaliova, Klaus Fortschegger, Karin Nebral, Andishe Attarbaschi, Karel Fiser, Maximilian O. Kauer, Niko Popitsch, Sabrina Haslinger, Andrea Inthal, Barbara Buldini, Giuseppe Basso, Jean-Pierre Bourquin, Giuseppe Gaipa, Monika Brüggemann, Tamar Feuerstein, Margarita Maurer-Granofszky, Renate Panzer-Grümayer, Jan Trka, Georg Mann, Oskar A. Haas, Ondrej Hrusak, Michael N. Dworzak, Sabine Strehl

Source: Haematologica, Vol 104, Iss 8 (2019)

Subject Terms: Diseases of the blood and blood-forming organs, RC633-647.5

File Description: electronic resource

Relation: https://haematologica.org/article/view/9023; https://doaj.org/toc/0390-6078; https://doaj.org/toc/1592-8721

Access URL: https://doaj.org/article/343859e0df1048019cf722f1f412616e

Classical and Non-classical Presentations of Complement Factor I Deficiency: Two Contrasting Cases Diagnosed via Genetic and Genomic Methods

Authors: Adrian M. Shields, Alistair T. Pagnamenta, Andrew J. Pollard, OxClinWGS, Jenny C. Taylor, Holger Allroggen, Smita Y. Patel, Samantha J. L. Knight, Niko Popitsch, Carme Camps, Melissa M. Pentony, Erika M. Kvikstad, Lukas Lange, Mona Hashim, Steve Harris, Mark Tilley, Dimitris Vavoulis, Pamela Kaisaki, Vassilis Ragoussis, Matteo Feral

Source: Frontiers in Immunology, Vol 10 (2019)

Subject Terms: complement factor I, primary immunodeficiency, genomic medicine, pneumococcal infection, neuroinflammation, complement deficiency, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fimmu.2019.01150/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/b00ed76bf8364c97a638ff44d5f2c49e

Targeted Next-Generation Sequencing of Plasma DNA from Cancer Patients: Factors Influencing Consistency with Tumour DNA and Prospective Investigation of Its Utility for Diagnosis.

Authors: Pamela J Kaisaki, Anthony Cutts, Niko Popitsch, Carme Camps, Melissa M Pentony, Gareth Wilson, Suzanne Page, Kulvinder Kaur, Dimitris Vavoulis, Shirley Henderson, Avinash Gupta, Mark R Middleton, Ioannis Karydis, Denis C Talbot, Anna Schuh, Jenny C Taylor

Source: PLoS ONE, Vol 11, Iss 9, p e0162809 (2016)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC5023174?pdf=render; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/c84931d42bd34e6883e57ececea2c9cd

Correction: The Borrelia burgdorferi RelA/SpoT Homolog and Stringent Response Regulate Survival in the Tick Vector and Global Gene Expression during Starvation.

Authors: Dan Drecktrah, Meghan Lybecker, Niko Popitsch, Philipp Rescheneder, Laura S Hall, D Scott Samuels

Source: PLoS Pathogens, Vol 11, Iss 10, p e1005242 (2015)

Subject Terms: Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC4608782?pdf=render; https://doaj.org/toc/1553-7366; https://doaj.org/toc/1553-7374

Access URL: https://doaj.org/article/0cf65ca7bf5e4e5c8ea91561336a0f0e

The Borrelia burgdorferi RelA/SpoT Homolog and Stringent Response Regulate Survival in the Tick Vector and Global Gene Expression during Starvation.

Authors: Dan Drecktrah, Meghan Lybecker, Niko Popitsch, Philipp Rescheneder, Laura S Hall, D Scott Samuels

Source: PLoS Pathogens, Vol 11, Iss 9, p e1005160 (2015)

Subject Terms: Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC4570706?pdf=render; https://doaj.org/toc/1553-7366; https://doaj.org/toc/1553-7374

Access URL: https://doaj.org/article/d344ca90bc184fbe905167c941f495a8

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METIS: a flexible foundation for the unified management of multimedia assets.

Authors: Ross King¹, Niko Popitsch¹, Utz Westermann²

Source: Multimedia Tools & Applications; Jun2007, Vol. 33 Issue 3, p325-349, 25p