Alejandro Ochoa

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Herpes simplex virus 1 (HSV-1) causes a chronic, lifelong infection in >60% of adults. Multiple recent vaccine trials have failed, with viral diversity likely contributing to these failures. To understand HSV-1 diversity better, we comprehensively compared 20 newly sequenced viral genomes from China, Japan, Kenya, and South Korea with six previously(More)
Lysine acetylation is a ubiquitous post-translational modification in many organisms including the malaria parasite Plasmodium falciparum, yet the full extent of acetylation across the parasite proteome remains unresolved. Moreover, the functional significance of acetylation or how specific acetyl-lysine sites are regulated is largely unknown. Here we(More)
The rotamer approximation states that protein side-chain conformations can be described well using a finite set of rotational isomers. This approximation is often applied in the context of computational protein design and structure prediction to reduce the complexity of structural sampling. It is an effective way of reducing the structure space to the most(More)
The integration of new wireless technologies with vehicle computing systems has opened the doors for new fields of applications such as intelligent transportation systems. Vehicular ad hoc networks emerge as the technical basis in solutions aiming to improve road safety and efficiency as well as driving comfort. This paper discusses different factors that(More)
Motivation: Protein domain prediction is one of the most powerful approaches for sequence-based function prediction. Although domain instances are typically predicted independently of each other, newer approaches have demonstrated improved performance by rewarding domain pairs that frequently co-occur within sequences. However, most of these approaches have(More)
Pfam 30 (16,306 HMMs) provides the PfamA.full.uniprot file that corresponds to UniProt 2016_02 (46,974,580 proteins). This file was used to obtain dPUC2’s observed family pair counts, CODD’s list of certified domain pairs [1], and DAMA’s domain information and observed architectures [2]. We used the HMMER 3.1b2 version of hmmscan to predict domains (this(More)
Identifying domains in protein sequences is an important step in protein structural and functional annotation. Existing domain recognition methods typically evaluate each domain prediction independently of the rest. However, the majority of proteins are multidomain, and pairwise domain co-occurrences are highly specific and non-transitive. Here, we(More)
E-values have been the dominant statistic for protein sequence analysis for the past two decades: from identifying statistically significant local sequence alignments to evaluating matches to hidden Markov models describing protein domain families. Here we formally show that for "stratified" multiple hypothesis testing problems-that is, those in which(More)