Octavio Martínez

Octavio Martínez
Center for Research and Advanced Studies of the National Polytechnic Institute | Cinvestav · LANGEBIO - Laboratorio Nacional de Genómica para la Biodiversidad

PhD

About

168
Publications
34,789
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3,315
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Introduction
Currently I lead the Computational Biology lab at Langebio under the motto ‘From Data to Knowledge’. We are interested in the design and application of methods for gaining biological knowledge from the analysis of high-throughput data, mainly from genomics and transcriptomics. We think that biological discovery runs in parallel to the design of efficient methods of data analysis. This is very important now that Biology is flood with quantitative data arising from the new sequencing technologies.
Additional affiliations
January 1996 - present
January 1992 - present
University of Reading
Description
  • I did my PhD there.
January 1990 - present
Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional
Description
  • We are interested in the design of methods for gaining biological knowledge from the analysis of high-throughput data, mainly from genomics, transcriptomics and molecular markers.

Publications

Publications (168)
Article
Full-text available
Background Meiosis is a form of specialized cell division that marks the transition from diploid meiocyte to haploid gamete, and provides an opportunity for genetic reassortment through recombination. Experimental data indicates that, relative to their wild ancestors, cultivated sunflower varieties show a higher recombination rate during meiosis. T...
Article
Full-text available
RNA-seq experiments estimate the number of genes expressed in a transcriptome as well as their relative frequencies. However, an undetermined number of genes can remain unde-tected due to their low expression relative to the sample size (sequence depth). Estimation of the true number of genes expressed in a transcriptome is essential in order to de...
Article
Full-text available
Meiosis is a form of specialized cell division that generates gametes, allowing recombination of alleles and halving the chromosome number. Arabidopsis and maize are the plant models that have been most extensively studied to determine the genes involved in meiosis. Here we present an RNA-seq study in which gene expression in male meiocytes isolate...
Article
Full-text available
The set of all mRNA molecules present in a cell constitute the transcriptome. The transcriptome varies depending on cell type as well as in response to internal and external stimuli during development. Here we present a study of the changes that occur in the transcriptome of chili pepper fruit during development and ripening. RNA-Seq was used to ob...
Article
Full-text available
As maize was domesticated in Mexico around 9,000 years ago, local farmers have selected and maintained seed stocks with particular traits and adapted to local conditions. In the present day, many of these landraces are still cultivated; however, increased urbanization and migration from rural areas implies a risk that this invaluable maize germplas...
Article
Full-text available
Capsicum spp. members are a rich source of specialized compounds due to their secondary metabolism. Some metabolic pathways have suffered modifications during the domestication process and improvement of agricultural traits. Here, we compared non-targeted LC–MS profiles from several areas: wild accessions (C. annuum L. var. glabriusculum), domestic...
Article
Full-text available
Gene expression is the primary molecular phenotype and can be estimated in specific organs or tissues at particular times. Here we analyzed genome-wide inheritance of gene expression in fruits of chili pepper ( Capsicum annuum L.) in reciprocal crosses between a domesticated and a wild accession, estimating this parameter during fruit development....
Article
Full-text available
Chili pepper ( Capsicum annuum ) is one of the most important crops worldwide. Its fruits contain metabolites produced over the maturation process like capsaicinoids and carotenoids. This metabolic process produces internal changes in flavor, color, texture, and aroma in fruits to make them more attractive for seed dispersal organisms. The chiltepi...
Article
Full-text available
The most studied DNA methylation pathway in plants is the RNA Directed DNA Methylation (RdDM), a conserved mechanism that involves the role of noncoding RNAs to control the expansion of the noncoding genome. Genome-wide DNA methylation levels have been reported to correlate with genome size. However, little is known about the catalog of noncoding R...
Article
Full-text available
RNA-Seq experiments allow genome-wide estimation of relative gene expression. Estimation of gene expression at different time points generates time expression profiles of phenomena of interest, as for example fruit development. However, such profiles can be complex to analyze and interpret. We developed a methodology that transforms original RNA-Se...
Article
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Cotton (genus Gossypium) is an important agricultural crop around the world because of its fiber. Gossypium turneri Fryxell is a wild cotton species endemic to the state of Sonora (northwestern Mexico), whose status has been recently raised to endangered in the IUCN Red List. This species has invaluable characteristics that could be useful in the c...
Article
Full-text available
Chili pepper (Capsicum spp.) is an important crop, as well as a model for fruit development studies and domestication. Here, we performed a time-course experiment to estimate standardized gene expression profiles with respect to fruit development for six domesticated and four wild chili pepper ancestors. We sampled the transcriptomes every 10 days...
Article
Full-text available
The MYB transcription factor family is very large and functionally diverse in plants, however, only a few members of this family have been reported and characterized in chili pepper (Capsicum spp.). In the present study, we performed genome-wide analyses of the MYB family in Capsicum annuum, including phylogenetic relationships, conserved domain, g...
Preprint
Full-text available
The most studied DNA methylation pathway in plants is the RNA Directed DNA Methylation (RdDM), a conserved mechanism that involves the role of noncoding RNAs to control the expansion of the noncoding genome. Genome-wide methylation levels have been reported to correlate with genome size. However, little is known about the catalog of noncoding RNAs...
Article
Full-text available
Most of the commercial papaya genotypes show susceptibility to water deficit stress and require high volumes of irrigation water to yield properly. To tackle this problem, we have collected wild native genotypes of Carica papaya that have proved to show better physiological performance under water deficit stress than the commercial cultivar grown i...
Preprint
Full-text available
Background: Open data sharing is instrumental for the advance of biological sciences. Gene expression is the primary molecular phenotype, usually estimated through RNA-Seq experiments. Large scope interpretation of RNA-Seq results is complicated by the extensive gene expression range, as well as by the diversity of biological sources and experiment...
Preprint
Full-text available
The most studied DNA methylation pathway in plants is the RNA Directed DNA Methylation (RdDM), which is a conserved mechanism that involves noncoding-RNAs to control the expansion of intergenic regions. However, little is known about relationship between plant genome size reductions and DNA methylation. Because the compact genome size of the carniv...
Preprint
Full-text available
Chili pepper ( Capsicum spp.) is both an important crop and a model for domestication studies. Here we performed a time course experiment to estimate standardized gene expression profiles across fruit development for six domesticated and four wild chili pepper ancestors. We sampled the transcriptome every 10 days, from flower to fruit at 60 Days Af...
Article
Full-text available
Background: RNA-Seq is the preferred method to explore transcriptomes and to estimate differential gene expression. When an organism has a well-characterized and annotated genome, reads obtained from RNA-Seq experiments can be directly mapped to that genome to estimate the number of transcripts present and relative expression levels of these trans...
Article
Quantification, using an accurate analytical approach, of capsinoids and capsaicinoids was performed on three chili pepper (Capsicum spp.) genotypes: ‘Chiltepín’, ‘Tampiqueño 74’, and ‘Bhut Jolokia’ at various stages of fruit development. The accumulation of capsinoids, in all these peppers started between 10 to 20 days post-anthesis (dpa), increas...
Article
Full-text available
Chili pepper (Capsicum spp.) is one of the most important horticultural crops worldwide, and its unique organoleptic properties and health benefits have been established for centuries. However, there is little knowledge about how metabolites are distributed throughout fruit parts. This work focuses on the use of liquid chromatography coupled with h...
Article
Full-text available
Las especies de Dasylirion se encuentran dentro de las más importantes del desierto chihuahuense en términos ecológicos y económicos. Su uso principal es la elaboración de una bebida alcohólica tradicional llamada sotol. El género comprende 22 especies, no todas aptas para este fin y su identificación es difícil. Herramientas moleculares como el có...
Presentation
Full-text available
In this workshop we give a hands-on introduction to the analysis of genomic diversity with emphasis in crop species using the R platform. This workshop is sponsored by CABANA ( https://www.cabana.online/) ; see Genomic Analysis of Crop Biodiversity Using R ( https://www.ebi.ac.uk/training/events/2019/cabana-workshop-genomic-analysis-crop-biodiversi...
Article
Full-text available
Plants belonging to genus Jatropha has arisen interest because of its high oil content that could be used to produce biodiesel. It is also widely reported that the main fatty acids in Jatropha oilseed are oleic and linoleic acids. However, there are scarce studies related to native species of Jatropha from Northwestern Mexico which are adapted to a...
Poster
Full-text available
El ‘Chiltepín’ es un chile muy popular en México por su intenso color rojo y su característico sabor y picor. Este último atributo es debido a la presencia de unos compuestos pertenecientes a las familias de los capsaicinoides y los capsinoides; sus presencias, así como la distinta relación de sus contenidos perfilan un tipo de picor diferencial. A...
Article
Full-text available
Living cells are highly complex systems comprising a multitude of elements that are engaged in the many convoluted processes observed during the cell cycle. However, not all elements and processes are essential for cell survival and reproduction under steady-state environmental conditions. To distinguish between essential from expendable cell compo...
Data
Supplementary functions. R functions to plot SIs as networks using our package ‘InterPlay’ (included as ‘S1 Binary’) as well as the ‘igraph’ [73] R package. (TXT)
Data
InterPlay R package. Binary file with our R package ‘InterPlay’. The manual for this package is presented as ‘S3 Text’. To install this R [72] package see ‘S1 Text’ or the corresponding R documentation. (GZ)
Data
Additional text and computational examples. Additional details and discussion of the C2E algorithm applied to the cases of the RNA polymerase and streptomycin SIs. Also demonstrates the functions and data of our R [72] package ‘InterPlay’ (included as ‘S1 Binary’) to work with SIs and determine essential structures. Algorithms are exemplified and e...
Data
InterPlay manual. Manual for our R package ‘InterPlay’ (included as ‘S1 Binary’). (PDF)
Preprint
Full-text available
Living cells are highly complex systems comprising a multitude of elements that are engaged in the many convoluted processes observed during the cell cycle. However, not all elements and processes are essential for cell survival and reproduction under steady-state environmental conditions. To distinguish between essential from expendable cell compo...
Chapter
Tissue culture for plant micropropagation is known to be a source of genetic changes termed "somaclonal variation". This protocol is designed to help in the selection of one or more types of molecular marker systems for the optimal detection and measurement of somaclonal variation. Somaclonal variation is influenced by the reproductive biology of t...
Article
Full-text available
Germplasm banks are growing in their importance, number of accessions and amount of characterization data, with a large emphasis on molecular genetic markers. In this work, we offer an integrated view of accessions and marker data in an information theory framework. The basis of this development is the mutual information between accessions and alle...
Data
Scored accessions. Accession names, rarity and divergence for all hexaploid lines. The members of the core subset are marked in the last column. (CSV)
Data
Mathematical proof. Equality between mutual information, average rarity and divergence. (PDF)
Article
Full-text available
Cryogenic storage of vanilla shoot-tips represents the safest biotechnological strategy for the long-term conservation of the vanilla germplasm, but successful cryopreservation depends on its tolerance to both dehydration stress imposed by cryoprotective treatments and thermal stress produced by immersion in liquid nitrogen. In this work, we evalua...
Article
The axolotl (Ambystoma mexicanum) is the vertebrate model system with the highest regeneration capacity. Experimental tools established over the past 100 years have been fundamental to start unraveling the cellular and molecular basis of tissue and limb regeneration. In the absence of a reference genome for the Axolotl, transcriptomic analysis beco...
Article
Full-text available
Establishing a horizontally transmitted mutualism is a critical step for many organisms, particularly when an individual can engage with only one partner over its lifetime. Ant foundresses shed their wings before they start to lay eggs, which makes host choice particularly critical for plant-ants that exclusively colonize myrmecophytes. Volatile or...
Data
Full-text available
Simulation' of data via pseudo-random numbers is a powerful and easy way to show the truthfulness of some statistics laws. Only very basic assumptions need to be accepted by 'faith' to demonstrate some core statistical ideas. Here I show how the law of large numbers and the central limit theorem can be empirically 'demonstrated' by simulation, maki...
Article
Full-text available
Phosphate (Pi) limitation is a constraint for plant growth in many natural and agricultural ecosystems. Plants possess adaptive mechanisms that enable them to cope with conditions of limited Pi supply, including a highly regulated genetic program controlling the expression of genes involved in different metabolic, signaling and development processe...
Presentation
Full-text available
Abstract. We are going to see some of the statistical principles behind the analysis of RNA-seq data. The idea is to understand and discus the basic assumptions and methods for analysis for students familiar only with very basic principles and give a practical example of analysis. We begin by discussing the nature of the data: What do we want and w...
Article
Full-text available
Dasylirion micropterum is described as a new species from high elevations of the Sierra Madre Oriental in the Mexican state of Coahuila. It differs from known species of Dasylirion for having ascending dark green leaves, narrow inflorescences, small fruits with narrow wings and its distribution restricted to the western side of the Sierra Madre Ori...
Research
Full-text available
From the data in ‘The Chili Database’ we identified the mRNA corresponding to the gene for the ascorbate oxidase in Capsicum (Ca-AO) and analyzed its expression pattern during the development of the fruit. We infer that the expression of Ca-AO has significant changes during the development of the chili pepper fruit in the land race ‘Tampiqueño 64’.
Research
Full-text available
I give examples of the use of the resources in ‘ChiliWeb’ ( http://computational.biology.langebio.cinvestav.mx/ChiliWeb/ ), a web interface for the database which contains the results of the RNA-seq experiment presented in ‘Dynamics of the chili pepper transcriptome during fruit development’ (BMC Genomics 2014, 15:143; http://www.biomedcentral.com/...
Research
Full-text available
When Mendel’s laws where ‘rediscovered’ a debate arose about the universal application of these laws to all variable characteristics of living organisms. Two facts confused scientist; the first, that in natural populations almost never a ‘Mendelian’ proportion (as 3:1, 9:3:3:1, etc.) is observed. This was solved by the realization that alleles in p...
Research
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This is the second part of the notes for the Biostatistics course (the part given by me, OMV). In this document, where you see something in bold face it has a web link to a particular resource. We will be using R for demonstrations.
Research
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By years I had been teaching the Biostatistic course in Cinvestav - Irapuato beginning with elementary probability theory and, when that part was understood, I introduced the ‘central’ (or core) concepts needed for statistical inference using practical examples. I think that is the correct approach; however, time limitations had force me to change...
Research
Full-text available
In this tutorial you will learn the principles of the Analysis Of Variance (ANOVA) by example and simulation. The idea is that by carefully following the examples, and performing simulations you will be able to gain a good understanding of the most important method for the analysis of quantitative variables. Here you will find only the very basic A...
Research
Full-text available
The objective of these notes (from a short introductory course at Langebio / Cinvestav) is to give the minimum knowledge to assure that you can follow statistical reasoning and have the ability to apply it to the analysis, interpretation and design of biological experiments. Given the short time to present and explain the ideas, I will follow a pra...
Article
Full-text available
Phosphate (Pi) availability is a significant limiting factor for plant growth and productivity in both natural and agricultural systems. To cope with such limiting conditions, plants have evolved a myriad of developmental and biochemical strategies to enhance the efficiency of Pi acquisition and assimilation to avo