Enrique Hernández-Lemus

Enrique Hernández-Lemus
Instituto Nacional de Medicina Genómica · Computational Genomics

Phd

About

215
Publications
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Publications

Publications (215)
Article
Breast cancer is a complex phenotype (or better yet, several complex phenotypes) characterized by the interplay of a large number of cellular and biomolecular entities. Biological networks have been successfully used to capture some of the heterogeneity of intricate pathophenotypes, including cancer. Gene coexpression networks, in particular, have...
Article
Full-text available
Retinoblastoma (Rb) is a rare intraocular tumour in early childhood, with an approximate incidence of 1 in 18 000 live births. Experimental studies for Rb are complex due to the challenges associated with obtaining a normal retina to contrast with diseased tissue. In this work, we reanalyse a dataset that contains normal retina samples. We identifi...
Article
Full-text available
Background During the COVID-19 pandemic, the slope of the epidemic curve in Mexico City has been quite unstable. Changes in human activity led to changes in epidemic activity, hampering attempts at economic and general reactivation of the city. Methods We have predicted that where a fraction of the population above a certain threshold returns to t...
Article
Full-text available
Gene co-expression networks have become a usual approach to integrate the vast amounts of information coming from gene expression studies in cancer cohorts. The reprogramming of the gene regulatory control and the molecular pathways depending on such control are central to the characterization of the disease, aiming to unveil the consequences for c...
Article
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Health equity is a rather complex issue. Social context and economical disparities, are known to be determining factors. Cultural and educational constrains however, are also important contributors to the establishment and development of health inequities. As an important starting point for a comprehensive discussion, a detailed analysis of the lit...
Article
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A main goal of Precision Medicine is that of incorporating and integrating the vast corpora on different databases about the molecular and environmental origins of disease, into analytic frameworks, allowing the development of individualized, context-dependent diagnostics, and therapeutic approaches. In this regard, artificial intelligence and mach...
Article
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The function of a protein is strongly dependent on its structure. During evolution, proteins acquire new functions through mutations in the amino-acid sequence. Given the advance in deep mutational scanning, recent findings have found functional change to be position dependent, notwithstanding the chemical properties of mutant and mutated amino aci...
Article
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Cardiovascular diseases are the leading cause of morbidity and mortality worldwide. High blood pressure in particular, continues to increase throughout the global population at an increasingly fast pace. The relationship between arterial hypertension and periodontitis has been recently discussed in the context of its origins and implications. Parti...
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Background: The COVID-19 pandemic has caused an exponential increase in the demand for medical care worldwide. In Mexico, the COVID Medical Units (CMUs) conversion strategy was implemented. Objective: To evaluate the CMU coverage strategy in the Mexico City Metropolitan Area (MCMA) by territory. Materials: The CMU directory was used, as were C...
Chapter
High-throughput genomic technologies have revolutionized the study of cancer. Current research in oncology is now limited more for the capacity of analyzing and interpreting data, rather than the availability of data itself. Integrative approaches to obtain functional information from data are at the core of the disciplines gathered under the syste...
Preprint
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Background Worldwide, it has been observed that there is a strong association between the severity of COVID-19 and with being over 40 years of age, having diabetes mellitus (DM), hypertension and/or obesity. Objective To compare the probability of death caused by COVID-19 in patients with comorbidities during three periods defined for this study a...
Article
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Gene regulatory and signaling phenomena are known to be relevant players underlying the establishment of cellular phenotypes. It is also known that such regulatory programs are disrupted in cancer, leading to the onset and development of malignant phenotypes. Gene co-expression matrices have allowed us to compare and analyze complex phenotypes such...
Preprint
Full-text available
The COVID-19 pandemic has caused an exponential increase in the demand for medical care worldwide. In Mexico, the COVID Medical Units (CMU) conversion strategy was implemented. Objective. To evaluate the CMU coverage strategy in the Mexico City Metropolitan Area (MCMA) by territory. Materials. The CMU directory was used, as were COVID-19 infection...
Article
Full-text available
Periodontitis is a common inflammatory disease of infectious origins that often evolves into a chronic condition. Aside from its importance as a stomatologic ailment, chronic periodontitis has gained relevance since it has been shown that it can develop into a systemic condition characterized by unresolved hyper-inflammation, disruption of the inna...
Article
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Network modeling, from the ecological to the molecular scale has become an essential tool for studying the structure, dynamics and complex behavior of living systems. Graph representations of the relationships between biological components open up a wide variety of methods for discovering the mechanistic and functional properties of biological syst...
Article
Full-text available
Gene co-expression networks (GCNs) have been developed as relevant analytical tools for the study of the gene expression patterns behind complex phenotypes. Determining the association between structure and function in GCNs is a current challenge in biomedical research. Several structural differences between GCNs of breast cancer and healthy phenot...
Article
Full-text available
Breast cancer is a complex, heterogeneous disease at the phenotypic and molecular level. In particular, the transcriptional regulatory programs are known to be significantly affected and such transcriptional alterations are able to capture some of the heterogeneity of the disease, leading to the emergence of breast cancer molecular subtypes. Recent...
Article
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Luminal A is the most common breast cancer molecular subtype in women worldwide. These tumors have characteristic yet heterogeneous alterations at the genomic and transcriptomic level. Gene co-expression networks (GCNs) have contributed to better characterize the cancerous phenotype. We have previously shown an imbalance in the proportion of intra-...
Article
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A random field is the representation of the joint probability distribution for a set of random variables. Markov fields, in particular, have a long standing tradition as the theoretical foundation of many applications in statistical physics and probability. For strictly positive probability densities, a Markov random field is also a Gibbs field, i....
Article
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There has been limited study of Native American whole genome diversity to date, which impairs effective implementation of personalized medicine and a detailed description of its demographic history. Here we report high coverage whole genome sequencing of 76 unrelated individuals, from 27 indigenous groups across Mexico, with more than 97% average N...
Article
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Lung cancer is one of the deadliest, most aggressive cancers. Abrupt changes in gene expression represent an important challenge to understand and fight the disease. Gene co-expression networks (GCNs) have been widely used to study the genomic regulatory landscape of human cancer. Here, based on 1,143 RNA-Seq experiments from the TCGA collaboration...
Article
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Breast cancer is a complex, highly heterogeneous disease at multiple levels ranging from its genetic origins and molecular processes to clinical manifestations. This heterogeneity has given rise to the so-called intrinsic or molecular breast cancer subtypes. Aside from classification, these subtypes have set a basis for differential prognosis and t...
Article
Full-text available
It is known that cancer onset and development arise from complex, multi-factorial phenomena spanning from the molecular, functional, micro-environmental, and cellular up to the tissular and organismal levels. Important advances have been made in the systematic analysis of the molecular (mostly genomic and transcriptomic) within large studies of hig...
Article
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Cardiovascular diseases (CVD) are the leading causes of morbidity and mortality worldwide. The complex etiology of CVD is known to be significantly affected by environmental and social factors. There is, however, a lag in our understanding of how population level components may be related to the onset and severity of CVD, and how some indicators of...
Article
Full-text available
Understanding the spatial and temporal patterns of mortality rates in a highly heterogeneous metropolis, is a matter of public policy interest. In this context, there is no, to the best of our knowledge, previous studies that correlate both spatio-temporal and age-specific mortality rates in Mexico City. Spatio-temporal Kriging modeling was used ov...
Article
Full-text available
Cancer is a set of complex pathologies that has been recognized as a major public health problem worldwide for decades. A myriad of therapeutic strategies is indeed available. However, the wide variability in tumor physiology, response to therapy, added to multi-drug resistance poses enormous challenges in clinical oncology. The last years have wit...
Article
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Assessment of the air quality in metropolitan areas is a major challenge in environmental sciences. Issues related include the distribution of monitoring stations, their spatial range, or missing information. In Mexico City, stations have been located spanning the entire Metropolitan zone for pollutants, such as CO, NO2, O3, SO2, PM2.5, PM10, NO, N...
Article
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Metabolism is loosely defined as the set of physical and chemical interactions associated with the processes responsible for sustaining life. Two evident features arise whenever one looks at metabolism: first, metabolism is conformed as a very complex and intertwined construct of the many associated biomolecular processes. Second, metabolism is cha...
Article
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Clear cell renal carcinoma (ccRC) is a highly heterogeneous and progressively malignant disease. Analyzing ccRC progression in terms of modifications at the molecular and genetic level may help us to develop a broader understanding of its patho-physiology and may give us a glimpse toward improved therapeutics. In this work, by using TCGA data, we s...
Article
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Objectives: There is no consensus on how to evaluate inflammatory activity in Takayasu's arteritis (TAK). Here we compare biochemical tests and three clinical scores, which evaluate inflammatory activity (IA) in TAK, versus quantitative 18F-FDG PET/CT as the gold standard. Methods: This prospective study included patients with TA diagnosed accor...
Article
Full-text available
The origin, stability, and contribution to the formation of noncovalent interactions, such as hydrogen bonds and π − π stacking, have been already widely discussed. However, there are few discussions about the relevance of these weak interactions in DNA performance. In this work, we seek to shed light on the effect of hydrogen bonds and π − π stack...
Article
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Introducción. Como una iniciativa para mejorar la calidad de la atención sanitaria se ha incrementado la tendencia en investigación biomédica centrada en las disparidades en salud y el sexo. Objetivo. Realizar una caracterización de la evidencia científica sobre la disparidad en salud definida como la brecha existente entre la distribución de la sa...
Preprint
Full-text available
During the COVID-19 pandemic, the slope of the epidemic curve in Mexico City has been quite unstable. We have predicted that in the case that a fraction of the population above a certain threshold returns to the public space, the negative tendency of the epidemic curve will revert. Such predictions were based on modeling the reactivation of economi...
Article
Full-text available
Abstract The study of co-expression programs in the context of cancer can help to elucidate the genetic mechanisms that are altered and lead to the disease. The identification of gene co-expression patterns, unique to healthy profiles (and absent in cancer) is an important step in this direction. Networks are a good tool for achieving this as they...
Article
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PurposeExpression microarrays are powerful technology that allows large-scale analysis of RNA profiles in a tissue; these platforms include underexploited detection scores outputs. We developed an algorithm using the detection score, to generate a detection profile of shared elements in retinoblastoma as well as to determine its transcriptomic size...
Article
Full-text available
Background: Cardiovascular diseases are the leading causes of mortality worldwide. One reason behind this lethality lies in the fact that often cardiovascular illnesses develop into systemic failure due to the multiple connections to organismal metabolism. This in turn is associated with co-morbidities and multimorbidity. The prevalence of coexisti...
Article
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At the end of December of 2019, a new type of coronavirus, now called COVID-19 started spreading in Wuhan, China and later throughout the world. Due to the global emergency state the World Health Organization declared and the need to know more about the danger Mexico is in, we worked on analyzing the risk of the COVID-19 importation to Mexico throu...
Article
Full-text available
Breast carcinomas are characterized by anomalous gene regulatory programs. As is well-known, gene expression programs are able to shape phenotypes. Hence, the understanding of gene co-expression may shed light on the underlying mechanisms behind the transcriptional regulatory programs affecting tumor development and evolution. For instance, in brea...
Article
Full-text available
Follicle-stimulating hormone exists as different major glycoforms defined by distinct glycosylation patterns of the hormone-specific β-subunit. It has been documented that variations in glycosylation confer differential biological effects to the glycoforms when multiple in vitro biochemical readings are analyzed. We here applied Next Generation Seq...
Article
Full-text available
Breast cancer is a disease that exhibits heterogeneity that goes from the genomic to the clinical levels. This heterogeneity is thought to be captured (at least partially) by the so-called breast cancer molecular subtypes. These molecular subtypes were initially defined based on the unsupervised clustering of gene expression and its correlate with...
Article
Full-text available
Here, we introduce a class of Tensor Markov Fields intended as probabilistic graphical models from random variables spanned over multiplexed contexts. These fields are an extension of Markov Random Fields for tensor-valued random variables. By extending the results of Dobruschin, Hammersley and Clifford to such tensor valued fields, we proved that...
Article
Full-text available
Cancer is the quintessential complex disease. As technologies evolve faster each day, we are able to quantify the different layers of biological elements that contribute to the emergence and development of malignancies. In this multi-omics context, the use of integrative approaches is mandatory in order to gain further insights on oncological pheno...
Poster
Follicle-stimulating hormone exists as different major glycoforms defined by distinct glycosylation patterns of the hormone-specific β-subunit. It has been documented that variations in glycosylation confer differential biological effects to the glycoforms when multiple in vitro biochemical readings are analyzed. We here applied Next Generation Seq...
Article
Full-text available
Background: Around the world, there is a significant difference in the proportion of women with access to leadership in healthcare with respect to men. This article studies gender imbalance and wage gap in managerial, executive, and directive job positions at the Mexican National Institutes of Health. Methods: Cohort data were described using a...
Preprint
Full-text available
Background Understanding the spatial and temporal patterns of mortality rates in a highly inhomogeneous metropolis, is a matter of public policy interest. In this context, there is no previous study that correlates both spatio-temporal and age-specific mortality rates in Mexico City. Methods Spatio-temporal kriging modelling was used over six age-s...
Article
Full-text available
Metabolic deregulation is an emergent hallmark of cancer. Altered patterns of metabolic pathways result in exacerbated synthesis of macromolecules, increased proliferation, and resistance to treatment via alteration of drug processing. In addition, molecular heterogeneity creates a barrier to therapeutic options. In breast cancer, this broad variat...
Preprint
Full-text available
Background Understanding the spatial and temporal patterns of mortality rates in a highly inhomogeneous metropolis, is a matter of public policy interest. In this context, there is no previous study that correlates both spatio-temporal and age-specific mortality rates in Mexico City. Methods Spatio-temporal kriging modelling was used over six age-s...
Preprint
Full-text available
Background Understanding the spatial and temporal patterns of mortality rates in a highly inhomogeneous metropolis, is a matter of public policy interest. In this context, there is no previous study that correlates both spatio-temporal and age-specific mortality rates in Mexico City. Methods Spatio-temporal kriging modelling was used over six age-s...
Chapter
Breast cancer has been a major public health problem worldwide for decades. Many therapeutic strategies are indeed available. However, the broad variability in tumor physiology and response to therapy as well as multidrug resistance pose enormous challenges in clinical oncology. In recent times, we have witnessed a fast-paced development of novel e...
Article
Full-text available
Analysis of gene regulatory networks allows the identification of master transcriptional factors that control specific groups of genes. In this work, we inferred a gene regulatory network from a large dataset of breast cancer samples to identify the master transcriptional factors that control the genes within signal transduction pathways. The focus...
Article
Full-text available
Cancer is a complex disease at many different levels. The molecular phenomenology of cancer is also quite rich. The mutational and genomic origins of cancer and their downstream effects on processes such as the reprogramming of the gene regulatory control and the molecular pathways depending on such control have been recognized as central to the ch...
Conference Paper
Introduction: Retinoblastoma (Rb) is an intraocular malignant tumour of early childhood, considered the most robust clinical model of genetic predisposition to develop cancer. Previous transcriptomic studies in Rb are based on differential analysis of expression data, ignoring the detection scores that can be obtained from high throughput technolog...