20 papers · ranked by Valyu relevance
Cecilia H Deng, Sushma Naithani, Sunita Kumari, Irene Cobo-Simón + 10 more
'Elsa H Quezada-Rodríguez' 'Maria Skrabisova' 'Nick Gladman' 'Melanie J Correll' 'Akeem Babatunde Sikiru' 'Olusola O Afuwape' 'Annarita Marrano' 'Ines Rebollo' 'Wentao Zhang' 'Sook Jung'] Title: Abstract Large-scale genotype and phenotype data have been increasingly generated to identify genetic markers, understand…
Daniel S Thayer, Shahzad Mumtaz, Muhammad A Elmessary, Ieuan Scanlon + 19 more
The prototype library was launched in November 2020 with an initial collection of 308 phenotypes. Over the pilot phase of the project, this grew to 330 phenotypes via user submissions. This was followed by the official launch of the production Phenotype Library in October 2021. As of the submission of this manuscript…
Nicolas Matentzoglu, Susan M Bello, Ray Stefancsik, Sarah M Alghamdi + 43 more
'Anna V Anagnostopoulos' 'James P Balhoff' 'Meghan A Balk' 'Yvonne M Bradford' 'Yasemin Bridges' 'Tiffany J Callahan' 'Harry Caufield' 'Alayne Cuzick' 'Leigh C Carmody' 'Anita R Caron' 'Vinicius de Souza' 'Stacia R Engel' 'Petra Fey' 'Malcolm Fisher' 'Sarah Gehrke' 'Christian Grove' 'Peter Hansen' 'Nomi L Harris'…
Yasemin Bridges, Vinicius de Souza, Katherina G Cortes, Melissa Haendel + 10 more
Computational approaches to support rare disease diagnosis are challenging to build, requiring the integration of complex data types such as ontologies, gene-to-phenotype associations, and cross-species data into variant and gene prioritisation algorithms (VGPAs). However, the performance of VGPAs has been difficult to…
Nicolas Matentzoglu, Susan M Bello, Ray Stefancsik, Sarah M. Alghamdi + 42 more
Phenotypic data are critical for understanding biological mechanisms and consequences of genomic variation, and are pivotal for clinical use cases such as disease diagnostics and treatment development. For over a century, vast quantities of phenotype data have been collected in many different contexts covering a…
Sarah M. Alghamdi, Paul N. Schofield, Robert Hoehndorf
Computing phenotypic similarity has been shown to be useful in identification of new disease genes and for rare disease diagnostic support. Genotype–phenotype data from orthologous genes in model organisms can compensate for lack of human data to greatly increase genome coverage. Work over the past decade has…
Vincent Gardeux, Roel P.J. Bevers, Fabrice P.A. David, Emily Rosschaert + 2 more
Genome-wide association studies have advanced our understanding of complex traits, but studying how a GWAS variant can affect a specific trait in the human population remains challenging due to environmental variability. Drosophila melanogaster is in this regard an excellent model organism for studying the relationship…
Fernando Zhapa-Camacho, Robert Hoehndorf
1 Computer, Electrical and Mathematical Sciences & Engineering Division, King Abdullah University of Science and Technology, 4700 KAUST, 23955, Thuwal, Saudi Arabia, 2 KAUST Center of Excellence for Smart Health (KCSH), King Abdullah University of Science and Technology, 4700 King Abdullah University of Science and…
Markus S. Ladewig, Julius O. B. Jacobsen, Alex H. Wagner, Daniel Danis + 15 more
'Daniel Danis' 'Baha El Kassaby' 'Michael Gargano' 'Tudor Groza' 'Michael Baudis' 'Robin Steinhaus' 'Dominik Seelow' 'Nikolaos E. Bechrakis' 'Christopher J. Mungall' 'Paul N. Schofield' 'Olivier Elemento' 'Lindsay Smith' 'Julie A. McMurry' 'Monica Munoz‐Torres' 'Melissa A. Haendel' 'Peter N. Robinson'] Title: Abstract…
Daniel Danis, Michael J Bamshad, Yasemin Bridges, Pilar Cacheiro + 28 more
'Leigh C Carmody' 'Jessica X Chong' 'Ben Coleman' 'Raymond Dalgleish' 'Peter J Freeman' 'Adam S L Graefe' 'Tudor Groza' 'Julius O B Jacobsen' 'Adam Klocperk' 'Maaike Kusters' 'Markus S Ladewig' 'Anthony J Marcello' 'Teresa Mattina' 'Christopher J Mungall' 'Monica C Munoz-Torres' 'Justin T Reese' 'Filip Rehburg'…
Y. G. Liu, Xiong Xiong, Yong Liao, Mingli Qin + 17 more
Yangfan Liu1,2† , Xiong Xiong1,3\† , Yong Liao1,3, Mingli Qin1,3 , Zhen Huang 6 , Shilin Zhu1,3, Lilin Yin1,3, Yuhua Fu1,3 , Haohao Zhang 7 , Jingya Xu1,3, Dong Yin1,3, Xin Huang1,3 , Yuan Quan 8 , Xuan Li 9 , Tengfei Jiang1,3, Wanneng Yang3,10 , Xiaohui Yuan2,11, Laurent Frantz4,5\, Xinyun Li1,3\ , Xiaolei Liu1,3\…
Jacob S. Zelko, Sarah Gasman, Shenita R. Freeman, Dong Yun Lee + 3 more
'Jaan Altosaar' 'Azza Shoaibi' 'Gowtham Rao'] Abstract—Health informatics can inform decisions that practitioners, patients, policymakers, and researchers need to make about health and disease. Health informatics is built upon patient health data leading to the need to codify patient health information. Such…
Nicholas C Wan, Monika E Grabowska, Vern Eric Kerchberger, Wei-Qi Wei
The Phenome-Wide Association Study (PheWAS), akin to an inverted genome-wide association study (GWAS), is a burgeoning biomedical informatics method that can leverage longitudinal electronic health records (EHRs) data to simultaneously investigate numerous phenotypic traits.1 PheWAS has the capacity to either replicate…
Mengdi Liu, Zhangyang Gao, Hong Chang, Stan Z. Li + 2 more
'Xinlin Chen'] Discovering the genotype-phenotype relationship is crucial for genetic engineering, which will facilitate advances in fields such as crop breeding, conservation biology, and personalized medicine. Current research usually focuses on single species and small datasets due to limitations in phenotypic data…
Weiqi Zhai, Xiaodi Huang, Nan Shen, Shanfeng Zhu
By utilizing the Human Phenotype Ontology (HPO), recent approaches to prioritizing disease-causing genes for patients become popular. However, these approaches do not comprehensively use information about phenotypes of diseases and patients. We present a new method called Phen2Disease that calculates similarity scores…
Caiwan Sun, Yi Xin, Sarah Zeng, Sudeep D. Sunthankar + 6 more
Phenotype-genotype associations underpin precision medicine by enabling disease prevention, early diagnosis, risk stratification, therapeutic target discovery, and personalized treatment. However, the rapid growth of scientific evidence has made manual curation of these associations increasingly labor-intensive…
Authors not listed
Synthetic cells emulate fundamental biological behaviors, such as growth, metabolism, and evolution, under non-equilibrium conditions, but have lacked genotype-driven selection, which is essential for Darwinian evolution. Here, we introduce short DNA sequences as genotypes into fuel-dependent, peptide-RNA-based…
Authors not listed
As the volume and diversity of bioactivity data in ChEMBL continues to grow, ensuring that assay metadata is standardized, interoperable, and machine-readable is critical for effective use in cheminformatics and ML applications. In this work, we present recent efforts to enhance the quality and granularity of bioassay…
Helle W. van den Maagdenberg, Martin Šícho, David Alencar Araripe, Sohvi Luukkonen + 9 more
Building reliable and robust quantitative structure-property relationship (QSPR) models is a challenging task. First, the experimental data needs to be obtained, analyzed and curated. Second, the number of available methods is continuously growing and evaluating different algorithms and methodologies can be arduous.…
Frédéric Burdet, Pierre-Marie Allard, Louis-Felix Nothias, Olivier Kirchhoffer + 16 more
Plants have a complex chemo-diversity and represent a reservoir of potential new therapeutic agents. Within a Swiss research project, six scientific research groups from different disciplines are collaborating to investigate a collection of more than 17’000 unique dried plant extracts. It aims to find new bioactive…