Zobrazeno 1 - 10
of 44
pro vyhledávání: '"Newaz, Khalique"'
Identification of human genes involved in the aging process is critical due to the incidence of many diseases with age. A state-of-the-art approach for this purpose infers a weighted dynamic aging-specific subnetwork by mapping gene expression (GE) l
Externí odkaz:
http://arxiv.org/abs/2205.13088
Autor:
Newaz, Khalique, Piland, Jacob, Clark, Patricia L., Emrich, Scott J., Li, Jun, Milenkovic, Tijana
Protein structural classification (PSC) is a supervised problem of assigning proteins into pre-defined structural (e.g., CATH or SCOPe) classes based on the proteins' sequence or 3D structural features. We recently proposed PSC approaches that model
Externí odkaz:
http://arxiv.org/abs/2105.07079
This study focuses on the task of supervised prediction of aging-related genes from -omics data. Unlike gene expression methods for this task that capture aging-specific information but ignore interactions between genes (i.e., their protein products)
Externí odkaz:
http://arxiv.org/abs/2005.03659
As proteins with similar structures often have similar functions, analysis of protein structures can help predict protein functions and is thus important. We consider the problem of protein structure classification, which computationally classifies t
Externí odkaz:
http://arxiv.org/abs/1910.02594
Autor:
Newaz, Khalique, Wright, Gabriel, Piland, Jacob, Li, Jun, Clark, Patricia, Emrich, Scott, Milenkovic, Tijana
Most amino acids are encoded by multiple synonymous codons. For an amino acid, some of its synonymous codons are used much more rarely than others. Analyses of positions of such rare codons in protein sequences revealed that rare codons can impact co
Externí odkaz:
http://arxiv.org/abs/1907.03351
Autor:
Newaz, Khalique, Milenkovic, Tijana
Gene expression (GE) data capture valuable condition-specific information ("condition" can mean a biological process, disease stage, age, patient, etc.) However, GE analyses ignore physical interactions between gene products, i.e., proteins. Since pr
Externí odkaz:
http://arxiv.org/abs/1807.05637
Autor:
Newaz, Khalique, Ghalehnovi, Mahboobeh, Rahnama, Arash, Antsaklis, Panos J., Milenkovic, Tijana
Experimental determination of protein function is resource-consuming. As an alternative, computational prediction of protein function has received attention. In this context, protein structural classification (PSC) can help, by allowing for determini
Externí odkaz:
http://arxiv.org/abs/1804.04725
Network approach integrates 3D structural and sequence data to improve protein structural comparison
Autor:
Faisal, Fazle E., Chaney, Julie L., Newaz, Khalique, Li, Jun, Emrich, Scott J., Clark, Patricia L., Milenkovic, Tijana
Initial protein structural comparisons were sequence-based. Since amino acids that are distant in the sequence can be close in the 3-dimensional (3D) structure, 3D contact approaches can complement sequence approaches. Traditional 3D contact approach
Externí odkaz:
http://arxiv.org/abs/1605.07247
Publikováno v:
BMC Bioinformatics. 10/25/2021 Supplement 4, Vol. 22, p1-26. 26p.
Autor:
Faisal, Fazle E.1,2,3, Newaz, Khalique1,2,3, Chaney, Julie L.4, Li, Jun5, Emrich, Scott J.1, Clark, Patricia L.3,4,6, Milenković, Tijana1,2,3 tmilenko@nd.edu
Publikováno v:
Scientific Reports. 8/10/2020, Vol. 10 Issue 1, p1-5. 5p.