Seq2scFv: a toolkit for the comprehensive analysis of display libraries from long-read sequencing platforms

Autor: Marianne Bachmann Salvy, Luca Santuari, Emanuel Schmid-Siegert, Nikolaos Lykoskoufis, Ioannis Xenarios, Bulak Arpat

Publikováno v: mAbs, Vol 16, Iss 1 (2024)

Antibodies have emerged as the leading class of biotherapeutics, yet traditional screening methods face significant time and resource challenges in identifying lead candidates. Integrating high-throughput sequencing with computational approaches mark

Externí odkaz: https://doaj.org/article/f85acb18d6bb4dca8286f8f0fd6b6991

Reference mouse strain assemblies for BALB/c Nude and NOD/SCID mouse models

Autor: Emanuel Schmid-Siegert, Mengting Qin, Huan Tian, Bulak Arpat, Bonnie Chen, Ioannis Xenarios

Mouse xenograft models play a vital role in tumor studies for research as well as for screening of drugs for the pharmaceutical industry. In particular, models with compromised immunity are favorable to increase the success of transplantation, such a

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::d0dfda480644b107382fe5783d4d9190
https://doi.org/10.1101/2023.03.16.532783

A neuron-specific deletion of the microRNA-processing enzyme DICER induces severe but transient obesity in mice.

Autor: Géraldine M Mang, Sylvain Pradervand, Ngoc-Hien Du, Alaaddin Bulak Arpat, Frédéric Preitner, Leonore Wigger, David Gatfield, Paul Franken

Publikováno v: PLoS ONE, Vol 10, Iss 1, p e0116760 (2015)

MicroRNAs (miRNAs) are small, non-coding RNA molecules that regulate gene expression post-transcriptionally. MiRNAs are implicated in various biological processes associated with obesity, including adipocyte differentiation and lipid metabolism. We u

Externí odkaz: https://doaj.org/article/0e94556c72db4a1cb73c3446bcd3647a

Guidelines for Genome-Scale Analysis of Biological Rhythms

Autor: Achim Kramer, Karl Kornacker, Justin Blau, Susan S. Golden, Samuel S. C. Rund, Michael H. Hastings, Han Wang, Joanna C. Chiu, Pierre Baldi, Andrew J. Millar, David Gatfield, Tanya L. Leise, Christy Hoffmann, María Teresa Camacho Olmedo, Scott Sherrill-Mix, Derk-Jan Dijk, Debra J. Skene, Jason P. DeBruyne, Hanspeter Herzel, Charles J. Weitz, Gad Asher, Jiajia Li, Katja A. Lamia, Francis J. Doyle, John B. Hogenesch, Tomasz Zielinski, Stacey L. Harmer, Xiaodong Li, Jacob J. Hughey, Christian I. Hong, Zheng Chen, Michael Rosbash, Jennifer J. Loros, Maria S. Robles, Jennifer M. Hurley, Jerome S. Menet, Scott A. Lewis, Karyn A. Esser, Juergen Cox, M. Fernanda Ceriani, Ying-Hui Fu, Joseph S. Takahashi, Ying Xu, Hiroki R. Ueda, Giles E. Duffield, Garret A. FitzGerald, Michael E. Hughes, Deborah Bell-Pedersen, Carl Hirschie Johnson, Marc D. Ruben, Felix Naef, Paul de Goede, Amita Sehgal, Horacio O. de la Iglesia, Akhilesh B. Reddy, Alaaddin Bulak Arpat, Todd C. Mockler, Emi Nagoshi, Dmitri A. Nusinow, Luciano DiTacchio, Gang Wu, Lauren J. Francey, John Harer, Steve A. Kay, Charissa de Bekker, Aziz Sancar, Ron C. Anafi, Katherine C. Abruzzi, Seung Hee Yoo, Kai-Florian Storch, Nobuya Koike, Daniel B. Forger, Erik D. Herzog, Andrew C. Liu, Louis J. Ptáček, Carla B. Green, Michael W. Young, Michael N. Nitabach, Eric E. Zhang, Jay C. Dunlap, Alexander M. Crowell, Tami A. Martino, Frédéric Gachon, Ravi Allada, Pål O. Westermark, Till Roenneberg, Martha Merrow, Herman Wijnen, Kristin Eckel-Mahan, Steve Brown, Jeff Haspel, Paolo Sassone-Corsi, David A. Rand

Publikováno v: Journal of Biological Rhythms, vol. 32, no. 5, pp. 380-393
CONICET Digital (CONICET)
Consejo Nacional de Investigaciones Científicas y Técnicas
instacron:CONICET
Journal of biological rhythms, 32(5), 380-393. SAGE Publications Inc.
Journal of Biological Rhythms
Hughes, M E, Abruzzi, K C, Allada, R, Anafi, R, Arpat, A B, Asher, G, Baldi, P, de Bekker, C, Bell-Pedersen, D, Blau, J, Brown, S, Ceriani, M F, Chen, Z, Chiu, J C, Cox, J, Crowell, A M, DeBruyne, J P, Dijk, D-J, DiTacchio, L, Doyle, F J, Duffield, G E, Dunlap, J C, Eckel-Mahan, K, Esser, K A, FitzGerald, G A, Forger, D B, Francey, L J, Fu, Y-H, Gachon, F, Gatfield, D, de Goede, P, Golden, S S, Green, C, Harer, J, Harmer, S, Haspel, J, Hastings, M H, Herzel, H, Herzog, E D, Hoffmann, C, Hong, C, Hughey, J J, Hurley, J M, de la Iglesia, H O, Johnson, C, Kay, S A, Koike, N, Kornacker, K, Kramer, A, Lamia, K, Leise, T, Lewis, S A, Li, J, Li, X, Liu, A C, Loros, J J, Martino, T A, Menet, J S, Merrow, M, Millar, A J, Mockler, T, Naef, F, Nagoshi, E, Nitabach, M N, Olmedo, M, Nusinow, D A, Ptáček, L J, Rand, D, Reddy, A B, Robles, M S, Roenneberg, T, Rosbash, M, Ruben, M D, Rund, S S C, Sancar, A, Sassone-Corsi, P, Sehgal, A, Sherrill-Mix, S, Skene, D J, Storch, K-F, Takahashi, J S, Ueda, H R, Wang, H, Weitz, C, Westermark, P O, Wijnen, H, Xu, Y, Wu, G, Yoo, S-H, Young, M, Zhang, E E, Zielinski, T & Hogenesch, J B 2017, ' Guidelines for Genome-Scale Analysis of Biological Rhythms ', Journal of biological rhythms, vol. 32, no. 5, 748730417728663, pp. 380-393 . https://doi.org/10.1177/0748730417728663
Hughes, ME; Abruzzi, KC; Allada, R; Anafi, R; Arpat, AB; Asher, G; et al.(2017). Guidelines for Genome-Scale Analysis of Biological Rhythms. Journal of Biological Rhythms, 32(5), 380-393. doi: 10.1177/0748730417728663. UC Irvine: Retrieved from: http://www.escholarship.org/uc/item/2dq117tj
Journal of biological rhythms, 32(5): 380-393

Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs of the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout the day. These m

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::98132f5b6879e2975b22c568261f17f7
https://doi.org/10.1177/0748730417728663

Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing

Autor: Angélica Liechti, René Dreos, Mara De Matos, Peggy Janich, David Gatfield, Alaaddin Bulak Arpat

Translation initiation is the major regulatory step defining the rate of protein production from an mRNA. Meanwhile, the impact of non-uniform ribosomal elongation rates is largely unknown. Using a modified ribosome profiling protocol based on footpr

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::f2ed8cf131e472b21f17b43ea5bdfa87
https://doi.org/10.1101/710061