David Fernandez-Baca
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Explore the profile of David Fernandez-Baca including associated specialties, affiliations and a list of published articles.
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187
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Recent Articles
1.
Ranjan A, Fahad M, Fernandez-Baca D, Tripathi S, Deepak A
IEEE/ACM Trans Comput Biol Bioinform
. 2022 May;
20(2):1188-1199.
PMID: 35536815
This paper advances the self-attention mechanism in the standard transformer network specific to the modeling of the protein sequences. We introduce a novel context-window based scaled self-attention mechanism for processing...
2.
Fernandez-Baca D, Liu L
Algorithms Mol Biol
. 2021 Dec;
16(1):22.
PMID: 34863219
Background: A semi-labeled tree is a tree where all leaves as well as, possibly, some internal nodes are labeled with taxa. Semi-labeled trees encompass ordinary phylogenetic trees and taxonomies. Suppose...
3.
Parvini G, Braught K, Fernandez-Baca D
IEEE/ACM Trans Comput Biol Bioinform
. 2021 Nov;
19(6):3307-3316.
PMID: 34784284
Suppose we aim to build a phylogeny for a set of taxa X using information from a collection of loci, where each locus offers information for only a fraction of...
4.
Ranjan A, Fernandez-Baca D, Tripathi S, Deepak A
IEEE/ACM Trans Comput Biol Bioinform
. 2021 Jun;
19(5):2685-2696.
PMID: 34185646
This paper explores the use of variants of tf-idf-based descriptors, namely length-normalized-tf-idf and log-normalized-tf-idf, combined with a segmentation technique, for efficient modeling of variable-length protein sequences. The proposed solution, ProtVecGen-Ensemble,...
5.
Otyama P, Kulkarni R, Chamberlin K, Ozias-Akins P, Chu Y, Lincoln L, et al.
G3 (Bethesda)
. 2020 Sep;
10(11):4013-4026.
PMID: 32887672
Cultivated peanut () is an important oil, food, and feed crop worldwide. The USDA peanut germplasm collection currently contains 8,982 accessions. In the 1990s, 812 accessions were selected as a...
6.
Yadav A, Fernandez-Baca D, Cannon S
Evol Bioinform Online
. 2020 Jul;
16:1176934320939943.
PMID: 32694909
Protein domains can be regarded as sections of protein sequences capable of folding independently and performing specific functions. In addition to amino-acid level changes, protein sequences can also evolve through...
7.
Stai J, Yadav A, Sinou C, Bruneau A, Doyle J, Fernandez-Baca D, et al.
Front Plant Sci
. 2019 May;
10:345.
PMID: 31105714
Based on evolutionary, phylogenomic, and synteny analyses of genome sequences for more than a dozen diverse legume species as well as analysis of chromosome counts across the legume family, we...
8.
Ranjan A, Fahad M, Fernandez-Baca D, Deepak A, Tripathi S
IEEE/ACM Trans Comput Biol Bioinform
. 2019 Apr;
17(5):1648-1659.
PMID: 30998479
The order of amino acids in a protein sequence enables the protein to acquire a conformation suitable for performing functions, thereby motivating the need to analyze these sequences for predicting...
9.
Deng Y, Fernandez-Baca D
Algorithms Mol Biol
. 2017 Mar;
12:7.
PMID: 28331536
Background: Semi-labeled trees generalize ordinary phylogenetic trees, allowing internal nodes to be labeled by higher-order taxa. Taxonomies are examples of semi-labeled trees. Suppose we are given collection [Formula: see text]...
10.
McMahon M, Deepak A, Fernandez-Baca D, Boss D, Sanderson M
PLoS One
. 2015 Feb;
10(2):e0117987.
PMID: 25679219
Comprehensively sampled phylogenetic trees provide the most compelling foundations for strong inferences in comparative evolutionary biology. Mismatches are common, however, between the taxa for which comparative data are available and...