Results 151 to 160 of about 557,186 (345)

FANTASIA leverages language models to decode the functional dark proteome across the animal tree of life

Communications Biology
Protein functional annotation is crucial in biology, but many protein-coding genes remain uncharacterized, especially in non-model organisms. FANTASIA (Functional ANnoTAtion based on embedding space SImilArity) integrates protein language models for ...
Gemma I. Martínez-Redondo, Francisco M. Perez-Canales, Belén Carbonetto, José M. Fernández, Israel Barrios-Núñez, Marçal Vázquez-Valls, Ildefonso Cases, Ana M. Rojas, Rosa Fernández   +8 more
doaj   +1 more source

Ontology-based domain modelling for consistent content change management [PDF]

, 2010
Ontology-based modelling of multi-formatted software application content is a challenging area in content management. When the number of software content unit is huge and in continuous process of change, content change management is important.
Abgaz, Yalemisew, Javed, Muhammad, Pahl, Claus   +2 more
core   +1 more source

JGI Plant Gene Atlas: An updateable transcriptome resource to improve structural annotations and functional gene descriptions across the plant kingdom [PDF]

, 2022
Avinash Sreedasyam, Christopher Plott, Md Shakhawat Hossain, John T. Lovell, Jane Grimwood, Jerry Jenkins, Christopher Daum, Kerrie Barry, Joseph W. Carlson, Shengqiang Shu, Jeremy Phillips, Mojgan Amirebrahimi, Matthew Zane, Mei Wang, David Goodstein, Fabian B. Haas, Manuel Hiß, Pierre‐François Perroud, Sara Jawdy, Rongbin Hu, Jenifer Johnson, Janette Kropat, Sean D. Gallaher, Anna Lipzen, Ryan Tillman, Eugene V. Shakirov, Xiaoyu Weng, Ivone Torres‐Jerez, Brock Weers, Daniel Conde, Marilia R. Pappas, Lifeng Liu, Andrew Muchlinski, Hui Jiang, Christine Shyu, Pu Huang, José Sebastián, Carol Laiben, Alyssa Medlin, Sankalpi Carey, Alyssa A. Carrell, Mariano Perales, Kankshita Swaminathan, Isabel Allona, Dário Grattapaglia, Elizabeth Cooper, Dorothea Tholl, John P. Vogel, David J. Weston, Xiaohan Yang, Thomas P. Brutnell, Elizabeth A. Kellogg, Ivan Baxter, Michael K. Udvardi, Yuhong Tang, Todd C. Mockler, Thomas Juenger, John E. Mullet, Stefan A. Rensing, Gerald A. Tuskan, Sabeeha Merchant, Gary Stacey, Jeremy Schmutz   +62 more
openalex   +1 more source

In vitro models of cancer‐associated fibroblast heterogeneity uncover subtype‐specific effects of CRISPR perturbations

Molecular Oncology, EarlyView.
Development of therapies targeting cancer‐associated fibroblasts (CAFs) necessitates preclinical model systems that faithfully represent CAF–tumor biology. We established an in vitro coculture system of patient‐derived pancreatic CAFs and tumor cell lines and demonstrated its recapitulation of primary CAF–tumor biology with single‐cell transcriptomics ...
Elysia Saputra, Shamsudheen Karuthedath Vellarikkal, Lixia Li, Hong Sun, Khoa Nguyen, Amber Montano, Suchitra Natarajan, Federica Piccioni, Alex Michael Tamburino, Xin Yu, Aleksandra Katarzyna Olow   +10 more
wiley   +1 more source

Effect of chemotherapy on passenger mutations in metastatic colorectal cancer

Molecular Oncology, EarlyView.
Changes in passenger mutation load and predicted immunotherapy response after chemotherapy treatment. Tumor cells rich with passenger mutations have increased sensitivity to chemotherapy. Correlation of passenger mutations with neoantigen load suggests highly mutated clones promote a more effective response to immunotherapy, and therefore, first‐line ...
Marium T. Siddiqui, Matthew A. Cottam, Muhammad Bilal Mirza, Keeli B. Lewis, Kristen K. Ciombor, Mary Kay Washington, Kamran Idrees   +6 more
wiley   +1 more source

Modelling Discourse-related terminology in OntoLingAnnot’s ontologies [PDF]

, 2010
Recently, computational linguists have shown great interest in discourse annotation in an attempt to capture the internal relations in texts. With this aim, we have formalized the linguistic knowledge associated to discourse into different linguistic ...
Aguado de Cea, G., Pareja-Lora, A.
core   +1 more source

Facilitating functional annotation of chicken microarray data

BMC Bioinformatics, 2009
Background Modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays.
Gresham Cathy R, Kumar Ranjit, Buza Teresia J, Burgess Shane C, McCarthy Fiona M   +4 more
doaj   +1 more source

Dual targeting of RET and SRC synergizes in RET fusion‐positive cancer cells

Molecular Oncology, EarlyView.
Despite the strong activity of selective RET tyrosine kinase inhibitors (TKIs), resistance of RET fusion‐positive (RET+) lung cancer and thyroid cancer frequently occurs and is mainly driven by RET‐independent bypass mechanisms. Son et al. show that SRC TKIs significantly inhibit PAK and AKT survival signaling and enhance the efficacy of RET TKIs in ...
Juhyeon Son, Lily L. Remsing Rix, Bin Fang, Eric A. Welsh, Nicole V. Bremer, Valentina Foglizzo, Paola Roa, Nickole Sigcha‐Coello, Yi Liao, Eric B. Haura, Alexander Drilon, John M. Koomen, Emiliano Cocco, Uwe Rix   +13 more
wiley   +1 more source

ez-CAZy a reference annotation database for linking glycoside hydrolase sequence to enzymatic activity

Scientific Reports
Glycoside Hydrolases (GH) are carbohydrate-active enzymes that play a critical role in the degradation of carbohydrates, impacting ecosystem function, human health, and biotechnological applications.
Daniel S. Erdody, Nicholas G. Griffin, Renaud Berlemont   +2 more
doaj   +1 more source

Partitioning heritability by functional annotation using genome-wide association summary statistics

, 2015
Hilary K. Finucane, Brendan Bulik‐Sullivan, Alexander Gusev, Gosia Trynka, Yakir Reshef, Po‐Ru Loh, Verneri Anttila, Han Xu, Chongzhi Zang, Kyle Kai-How Farh, Stephan Ripke, Felix R. Day, Shaun Purcell, Eli A. Stahl, Sara Lindström, John R. B. Perry, Yukinori Okada, Soumya Raychaudhuri, Mark J. Daly, Hon‐Cheong So, Benjamin M. Neale, Alkes L. Price   +21 more
openalex   +2 more sources