9 documents found, page 1 of 1
Design and proof of concept for targeted phage-based COVID-19 vaccination strat...
Staquicini, Daniela I.; Tang, Fenny H.F.; Markosian, Christopher; Yao, Virginia J.; Staquicini, Fernanda I.; Dodero-Rojas, EstebanMade available in DSpace on 2022-04-28T19:41:58Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-07-27; Development of effective vaccines against coronavirus disease 2019 (COVID-19) is a global imperative. Rapid immunization of the entire human population against a widespread, continually evolving, and highly pathogenic virus is an unprecedented challenge, and different vaccine approaches are being pursue...
Chromosome Modeling on Downsampled Hi-C Maps Enhances the Compartmentalization ...
Oliveira Junior, Antonio B.; Estrada, Cynthia Perez; Aiden, Erez Lieberman; Contessoto, Vinícius G. [UNESP]; Onuchic, José N.Made available in DSpace on 2022-04-29T08:31:58Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-08-12; The human genome is organized within a nucleus where chromosomes fold into an ensemble of different conformations. Chromosome conformation capture techniques such as Hi-C provide information about the genome architecture by creating a 2D heat map. Initially, Hi-C map experiments were performed in human ...
Examining the Ensembles of Amyloid-β Monomer Variants and Their Propensities to...
Sanches, Murilo N. [UNESP]; Knapp, Kaitlin; Oliveira, Antonio B.; Wolynes, Peter G.; Onuchic, José N.; Leite, Vitor B. P. [UNESP]Made available in DSpace on 2022-04-29T08:38:36Z (GMT). No. of bitstreams: 0 Previous issue date: 2022-01-13; The amyloid-β (Aβ) monomer, an intrinsically disordered peptide, is produced by the cleavage of the amyloid precursor protein, leading to Aβ-40 and Aβ-42 as major products. These two isoforms generate pathological aggregates, whose accumulation correlates with Alzheimer’s disease (AD). Experiments have ...
The Nucleome Data Bank: Web-based resources to simulate and analyze the three-d...
Contessoto, Vinícius G. [UNESP]; Cheng, Ryan R.; Hajitaheri, Arya; Dodero-Rojas, Esteban; Mello, Matheus F.; Lieberman-Aiden, Erez; Wolynes, Peter G.Made available in DSpace on 2021-06-25T10:15:21Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-01-08; Welch Foundation; National Science Foundation; We introduce the Nucleome Data Bank (NDB), a web-based platform to simulate and analyze the three-dimensional (3D) organization of genomes. The NDB enables physics-based simulation of chromosomal structural dynamics through the MEGABASE + MiChroM computatio...
A Scalable Computational Approach for Simulating Complexes of Multiple Chromosomes
Oliveira Junior, Antonio B.; Contessoto, Vinícius G. [UNESP]; Mello, Matheus F.; Onuchic, José N.Made available in DSpace on 2021-06-25T10:45:52Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-03-19; Significant efforts have been recently made to obtain the three-dimensional (3D) structure of the genome with the goal of understanding how structures may affect gene regulation and expression. Chromosome conformational capture techniques such as Hi-C, have been key in uncovering the quantitative inform...
Exploring Energy Landscapes of Intrinsically Disordered Proteins: Insights into...
Oliveira Junior, Antonio B.; Lin, Xingcheng [UNESP]; Kulkarni, Prakash; Onuchic, José N.; Roy, Susmita; Leite, Vitor B. P. [UNESP]Made available in DSpace on 2021-06-25T10:59:11Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-01-01; Intrinsically disordered proteins (IDPs) lack a rigid three-dimensional structure and populate a polymorphic ensemble of conformations. Because of the lack of a reference conformation, their energy landscape representation in terms of reaction coordinates presents a daunting challenge. Here, our newly d...
Improving the thermostability of xylanase a from bacillus subtilis by combining...
Ngo, Khoa; Da Silva, Fernando Bruno [UNESP]; Leite, Vitor B. P.; Contessoto, Vinícius G.; Onuchic, José N.Made available in DSpace on 2021-06-25T11:00:21Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-05-06; The rational improvement of the enzyme catalytic activity is one of the most significant challenges in biotechnology. Most conventional strategies used to engineer enzymes involve selecting mutations to increase their thermostability. Determining good criteria for choosing these substitutions continues ...
3D genomics across the tree of life reveals condensin II as a determinant of ar...
Hoencamp, Claire; Dudchenko, Olga; Elbatsh, Ahmed M.O.; Brahmachari, Sumitabha; Raaijmakers, Jonne A.; van Schaik, Tom; Cacciatore, Ángela SedeñoMade available in DSpace on 2021-06-25T10:31:27Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-05-28; National Science Foundation; National Institutes of Health; Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP); U.S. Department of Agriculture; Ministry of Education, Culture, Sports, Science and Technology; European Research Council; Ministerio de Economía y Competitividad; Welch Foundation;...
Modeling Chikungunya control strategies and Mayaro potential outbreak in the ci...
Dodero-Rojas, Esteban; Ferreira, Luiza G.; Leite, Vitor B.P. [UNESP]; Onuchic, José N.; Contessoto, Vinícius G.Made available in DSpace on 2020-12-12T01:13:38Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-01-01; Mosquito-borne diseases have become a significant health issue in many regions around the world. For tropical countries, diseases such as Dengue, Zika, and Chikungunya, became epidemic in the last decades. Health surveillance reports during this period were crucial in providing scientific-based informat...