diff --git a/data/members.yml b/data/members.yml index 15b63a8..1034f69 100644 --- a/data/members.yml +++ b/data/members.yml @@ -53,12 +53,6 @@ current: mail: "yael.a.1406 (at) gmail.com" website: "https://resendislab.inmegen.gob.mx" twitter: "inmegen" - name: "Gabriela Montserrat Torres Fernández" - function: "M.Sc. student" - image: "Gabriela .jpg" - mail: "gabrielatofdz (at) gmail.com" - website: "https://resendislab.inmegen.gob.mx" - twitter: "inmegen" - name: "Mayavi Peña" function: "Bsc. student" image: "Mayavi.jpg" diff --git a/docs/404.html b/docs/404.html new file mode 100644 index 0000000..e69de29 diff --git a/index.html b/index.html deleted file mode 100644 index 670f312..0000000 --- a/index.html +++ /dev/null @@ -1,99 +0,0 @@ - - - - - - - - - Webpage of the Resendis Lab - - - - - - - - -
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RESENDIS ANTONIO LAB


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Blending Biology and Computation to understand human diseases.

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Who we are

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Welcome to the webpage of the Human Systems Biology group in the National Institute for Genomic Medicine at Mexico City, INMEGEN. Our group is interdisciplinary and have the objective to develop a systems biology framework to analyze mainly human diseases and metabolic phenotype in microorganisms through the use of computational models and high-throughput technologies. -Currently, our laboratory focuses on the analysis of metabolic alterations in cancer cells by the implementation of genome scale metabolic reconstructions and assess the predictions in terms of experimental data at different scales.

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Latest News

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Biological Physics Mexico City 2017

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from 17-05-2017 to 19-05-2017


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Frontiers at the interface of Physics, Math and Biology. This conference (the second in a series) is intended as an international, multidisciplinary scientific forum to discuss the latest developments in biological physics (including proteins, peptides and enzymes, among many other topics). -The conference is expected to boost a new paradigm of interdisciplinary approaches converging into specific problems in biological physics. Hence, the conference audience is broad: We aim to attract the attention of biologists as well as biochemists, organic chemists, engineers, computational scientists, physicists, and mathematicians.

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Latest Publication

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"Gestaltomics": Systems Biology Schemes for the Study of Neuropsychiatric Diseases.

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Frontiers In Physiology 2017

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Nora A Gutierrez Najera, Osbaldo Resendis-Antonio and Humberto Nicolini

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The integration of different sources of biological information about what defines a behavioral phenotype is difficult to unify in an entity that reflects the arithmetic sum of its individual parts. In this sense, the challenge of Systems Biology for understanding the “psychiatric phenotype” is to provide an improved vision of the shape of the phenotype as it is visualized by “Gestalt” psychology, whose fundamental axiom is that the observed phenotype (behavior or mental disorder) will be the result of the integrative composition of every part.

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- - - - - - diff --git a/index.xml b/index.xml deleted file mode 100644 index 72893c0..0000000 --- a/index.xml +++ /dev/null @@ -1,327 +0,0 @@ - - - - Webpage of the Resendis Lab - https://resendislab.github.io/ - Recent content on Webpage of the Resendis Lab - Hugo -- gohugo.io - en-us - Thu, 29 Jun 2017 12:53:05 -0500 - - - - - - Graduate student positions - https://resendislab.github.io/positions/students/ - Thu, 29 Jun 2017 12:53:05 -0500 - - https://resendislab.github.io/positions/students/ - We extend an invitation to undergrads and grad students with interest to continue his/her academic education through a Master&rsquo;s or Doctoral degree in one of these academic programs: biological (http://pcbiol.posgrado.unam.mx), biochemical (http://www.mdcbq.posgrado.unam.mx/) or Biomedical (http://www.pdcb.unam.mx/)) Sciences at UNAM. We encourage candidates with an academic background in biology, biology physics, biophysics, genome sciences, applied mathematics and computational sciences. The students incorporated to one of these programs will be guided to develop a systems biology description in one of these areas: - - - - Postdoctoral position - https://resendislab.github.io/positions/postdocs/ - Thu, 29 Jun 2017 12:52:56 -0500 - - https://resendislab.github.io/positions/postdocs/ - We always are looking for researchers with interest to contribute in Systems Biology to understand human diseases. If you are interested in any of the general areas of research described before and would like to carry out post-doctoral or research stays in Systems Biology of the Microbiome, or develop systems paradigms in precision medicine, send your curriculum vitae, a brief statement of your research interests, and the names of 2-3 references to oresendis [at] inmegen. - - - - "Gestaltomics": Systems Biology Schemes for the Study of Neuropsychiatric Diseases. - https://resendislab.github.io/pubs/pm28536537/ - Fri, 26 May 2017 00:00:00 +0000 - - https://resendislab.github.io/pubs/pm28536537/ - The integration of different sources of biological information about what defines a behavioral phenotype is difficult to unify in an entity that reflects the arithmetic sum of its individual parts. In this sense, the challenge of Systems Biology for understanding the &ldquo;psychiatric phenotype&rdquo; is to provide an improved vision of the shape of the phenotype as it is visualized by &ldquo;Gestalt&rdquo; psychology, whose fundamental axiom is that the observed phenotype (behavior or mental disorder) will be the result of the integrative composition of every part. - - - - Biological Physics Mexico City 2017 - https://resendislab.github.io/events/biological_physics/ - Wed, 17 May 2017 00:00:00 +0000 - - https://resendislab.github.io/events/biological_physics/ - Frontiers at the interface of Physics, Math and Biology. This conference (the second in a series) is intended as an international, multidisciplinary scientific forum to discuss the latest developments in biological physics (including proteins, peptides and enzymes, among many other topics). -The conference is expected to boost a new paradigm of interdisciplinary approaches converging into specific problems in biological physics. Hence, the conference audience is broad: We aim to attract the attention of biologists as well as biochemists, organic chemists, engineers, computational scientists, physicists, and mathematicians. - - - - Natural selection drove metabolic specialization of the chromatophore in Paulinella chromatophora. - https://resendislab.github.io/pubs/pm28410570/ - Sun, 16 Apr 2017 00:00:00 +0000 - - https://resendislab.github.io/pubs/pm28410570/ - Genome degradation of host-restricted mutualistic endosymbionts has been attributed to inactivating mutations and genetic drift while genes coding for host-relevant functions are conserved by purifying selection. Unlike their free-living relatives, the metabolism of mutualistic endosymbionts and endosymbiont-originated organelles is specialized in the production of metabolites which are released to the host. This specialization suggests that natural selection crafted these metabolic adaptations. In this work, we analyzed the evolution of the metabolism of the chromatophore of Paulinella chromatophora by in silico modeling. - - - - Personalized Prediction of Proliferation Rates and Metabolic Liabilities in Cancer Biopsies. - https://resendislab.github.io/pubs/pm28082911/ - Sat, 14 Jan 2017 00:00:00 +0000 - - https://resendislab.github.io/pubs/pm28082911/ - Cancer is a heterogeneous disease and its genetic and metabolic mechanism may manifest differently in each patient. This creates a demand for studies that can characterize phenotypic traits of cancer on a per-sample basis. Combining two large data sets, the NCI60 cancer cell line panel, and The Cancer Genome Atlas, we used a linear interaction model to predict proliferation rates for more than 12,000 cancer samples across 33 different cancers from The Cancer Genome Atlas. - - - - Host-Microbiome Interaction and Cancer: Potential Application in Precision Medicine. - https://resendislab.github.io/pubs/pm28018236/ - Tue, 27 Dec 2016 00:00:00 +0000 - - https://resendislab.github.io/pubs/pm28018236/ - It has been experimentally shown that host-microbial interaction plays a major role in shaping the wellness or disease of the human body. Microorganisms coexisting in human tissues provide a variety of benefits that contribute to proper functional activity in the host through the modulation of fundamental processes such as signal transduction, immunity and metabolism. The unbalance of this microbial profile, or dysbiosis, has been correlated with the genesis and evolution of complex diseases such as cancer. - - - - Hola!!! - https://resendislab.github.io/posts/test/ - Tue, 06 Dec 2016 09:19:57 -0600 - - https://resendislab.github.io/posts/test/ - <h2 id="this-is-an-example-post">This is an example post</h2> - -<p>Please substitute all text below &ldquo;+++&rdquo; with your own!</p> - -<p>This is my text now grrrr :)</p> - - - - In silico study of metabolic reprogramming during epithelial-mesenchymal transition - https://resendislab.github.io/projects/emt/ - Tue, 06 Dec 2016 00:00:00 +0000 - - https://resendislab.github.io/projects/emt/ - An epithelial-mesenchymal transition (EMT) is a biologic process that allows a polarized epithelial cell, which normally interacts with basement membrane via its basal surface, to undergo multiple biochemical changes that enable it to assume a mesenchymal cell phenotype, which includes enhanced migratory capacity, invasiveness, elevated resistance to apoptosis, and greatly increased production of ECM components. EMT induces invasive properties in epithelial tumors and promotes metastasis. Although EMT-mediated cellular and molecular changes are well understood, very little is known about EMT-induced metabolic changes. - - - - Integrating transcriptomic and metabolomic to understand hepatocellular carcinoma in a rat model - https://resendislab.github.io/projects/hepato/ - Tue, 06 Dec 2016 00:00:00 +0000 - - https://resendislab.github.io/projects/hepato/ - Hepatocellular carcinoma (HCC) is now the third leading cause of cancer deaths worldwide, with over 500,000 people affected. It occurs predominantly in patients with underlying chronic liver disease and cirrhosis. Despite this, knowledge about the metabolic states of this disease is limited. Using a rat model that recreates some of the most important characteristics of HCC, including cirrhosis, we aim to understand the metabolic state when compared to healthy liver. To this end we will integrate transcriptomic and metabolic data in a systems biology framework that point us changes in reactions. - - - - Metabolic heterogeneity in cancer and its applications in Personalized Medicine - https://resendislab.github.io/projects/prolif/ - Tue, 06 Dec 2016 00:00:00 +0000 - - https://resendislab.github.io/projects/prolif/ - Cancer is a very heterogeneous disease and tumors can differ greatly across and within different cancer types. Consequently, cancer is not a single disease but thousands. One property shared by all cancers is the ability to sustain chronic uncontrolled proliferation which raises the question how different cancers alter their metabolism in order to achieve consistent proliferation. -In this project we combine large-scale genomic data from DNA and RNA sequencing as well as proteomics and metabolomics to understand the connection between variations in the genotype and cancer metabolism. - - - - The impact of the microRNAs in the metabolic reprogramming of the MCF-7 cells during the spheroids development - https://resendislab.github.io/projects/spheroids/ - Tue, 06 Dec 2016 00:00:00 +0000 - - https://resendislab.github.io/projects/spheroids/ - Alterations in the metabolism are a common property in cancer cells, so that, many efforts have been directed to develop models to understand the mechanism by which cancer cells behave differently compared to normal tissues. In recent years, it has been reported that microRNAs (miRNAs) are involved in the regulation of all biological process, and there are evidences that shown its dysregulation play an important role in the development and progression of cancer. - - - - Who we are - https://resendislab.github.io/about/we/ - Mon, 05 Dec 2016 14:48:16 -0600 - - https://resendislab.github.io/about/we/ - Welcome to the webpage of the Human Systems Biology group in the National Institute for Genomic Medicine at Mexico City, INMEGEN. Our group is interdisciplinary and have the objective to develop a systems biology framework to analyze mainly human diseases and metabolic phenotype in microorganisms through the use of computational models and high-throughput technologies. -Currently, our laboratory focuses on the analysis of metabolic alterations in cancer cells by the implementation of genome scale metabolic reconstructions and assess the predictions in terms of experimental data at different scales. - - - - Evolution of Centrality Measurements for the Detection of Essential Proteins in Biological Networks. - https://resendislab.github.io/pubs/pm27616995/ - Tue, 13 Sep 2016 00:00:00 +0000 - - https://resendislab.github.io/pubs/pm27616995/ - - - - - 2nd International Summer Symposium on Systems Biology - https://resendislab.github.io/events/is3b/ - Tue, 02 Aug 2016 00:00:00 +0000 - - https://resendislab.github.io/events/is3b/ - With great pleasure we are hereby announcing the 2nd International Summer Symposium on Systems Biology (IS3B) taking place in Mexico City, Mexico from August 2nd - 4th 2016. The IS3B 2016 is organized by The Human Systems Biology Laboratory (HSBL), RAI-UNAM &amp; INMEGEN. -The IS3B is currently the largest symposium on Systems Biology in Mexico and Latin America, and strives to unite leading researchers and students in an informal setting with the aim to present current research in Systems Biology and Systems Medicine. - - - - The space of enzyme regulation in HeLa cells can be inferred from its intracellular metabolome. - https://resendislab.github.io/pubs/pm27335086/ - Fri, 24 Jun 2016 00:00:00 +0000 - - https://resendislab.github.io/pubs/pm27335086/ - During the transition from a healthy state to a cancerous one, cells alter their metabolism to increase proliferation. The underlying metabolic alterations may be caused by a variety of different regulatory events on the transcriptional or post-transcriptional level whose identification contributes to the rational design of therapeutic targets. We present a mechanistic strategy capable of inferring enzymatic regulation from intracellular metabolome measurements that is independent of the actual mechanism of regulation. - - - - 1st International Summer Symposium on Systems Biology - https://resendislab.github.io/events/is3b_2014/ - Mon, 04 Aug 2014 00:00:00 +0000 - - https://resendislab.github.io/events/is3b_2014/ - Those are the proceedings for the 1st edition of the “International Summer Symposium on Systems Biology: From networks to phenotypes in human diseases”. The meeting took place at the National Institute of Genomic Medicine (INMEGEN) in Mexico City from August 4-6, 2014. This event was the first of a series of meetings to encourage the development of the systems biology in Mexico and the development of this area to tackle basic and applied research in medical and biomedical fields. - - - - Modeling metabolism: a window toward a comprehensive interpretation of networks in cancer. - https://resendislab.github.io/pubs/pm24747697/ - Tue, 22 Apr 2014 00:00:00 +0000 - - https://resendislab.github.io/pubs/pm24747697/ - Given the multi-factorial nature of cancer, uncovering its metabolic alterations and evaluating their implications is a major challenge in biomedical sciences that will help in the optimal design of personalized treatments. The advance of high-throughput technologies opens an invaluable opportunity to monitor the activity at diverse biological levels and elucidate how cancer originates, evolves and responds under drug treatments. To this end, researchers are confronted with two fundamental questions: how to interpret high-throughput data and how this information can contribute to the development of personalized treatment in patients. - - - - Encyclopedia of Systems Biology - https://resendislab.github.io/pubs/encyclopedia/ - Sat, 01 Jun 2013 00:00:00 +0000 - - https://resendislab.github.io/pubs/encyclopedia/ - The Encyclopedia of Systems Biology is conceived as a comprehensive reference work covering all aspects of systems biology, in particular the investigation of living matter involving a tight coupling of biological experimentation, mathematical modeling and computational analysis and simulation. The main goal of the Encyclopedia is to provide a complete reference of established knowledge in systems biology – a ‘one-stop shop’ for someone seeking information on key concepts of systems biology. - - - - Systems biology of cancer: moving toward the integrative study of the metabolic alterations in cancer cells. - https://resendislab.github.io/pubs/pm23316163/ - Tue, 15 Jan 2013 00:00:00 +0000 - - https://resendislab.github.io/pubs/pm23316163/ - One of the main objectives in systems biology is to understand the biological mechanisms that give rise to the phenotype of a microorganism by using high-throughput technologies (HTs) and genome-scale mathematical modeling. The computational modeling of genome-scale metabolic reconstructions is one systemic and quantitative strategy for characterizing the metabolic phenotype associated with human diseases and potentially for designing drugs with optimal clinical effects. The purpose of this short review is to describe how computational modeling, including the specific case of constraint-based modeling, can be used to explore, characterize, and predict the metabolic capacities that distinguish the metabolic phenotype of cancer cell lines. - - - - Symbiotic Endophytes - https://resendislab.github.io/pubs/symbiotic_endophytes/ - Tue, 01 Jan 2013 00:00:00 +0000 - - https://resendislab.github.io/pubs/symbiotic_endophytes/ - This Soil Biology volume examines our current understanding of the mechanisms involved in the beneficial effects transferred to plants by endophytes such as rhizobial, actinorhizal, arbuscular mycorrhizal symbionts and yeasts. Topics presented include how symbiosis starts on the molecular level; chemical signaling in mycorrhizal symbiosis; genomic and functional diversity of endophytes; nitrogen fixation; nutrient uptake and cycling; as well as plant protection against various stress conditions. Further, the use of beneficial microorganisms as biopesticides is discussed, particularly the application of Plant Growth Promoter Rhizobacteria (PGPR) in agriculture with the aim to increase yields. - - - - Functional modules, structural topology, and optimal activity in metabolic networks. - https://resendislab.github.io/pubs/pm23071431/ - Wed, 17 Oct 2012 00:00:00 +0000 - - https://resendislab.github.io/pubs/pm23071431/ - Modular organization in biological networks has been suggested as a natural mechanism by which a cell coordinates its metabolic strategies for evolving and responding to environmental perturbations. To understand how this occurs, there is a need for developing computational schemes that contribute to integration of genomic-scale information and assist investigators in formulating biological hypotheses in a quantitative and systematic fashion. In this work, we combined metabolome data and constraint-based modeling to elucidate the relationships among structural modules, functional organization, and the optimal metabolic phenotype of Rhizobium etli, a bacterium that fixes nitrogen in symbiosis with Phaseolus vulgaris. - - - - Systems biology of bacterial nitrogen fixation: high-throughput technology and its integrative description with constraint-based modeling. - https://resendislab.github.io/pubs/pm21801415/ - Tue, 02 Aug 2011 00:00:00 +0000 - - https://resendislab.github.io/pubs/pm21801415/ - Bacterial nitrogen fixation is the biological process by which atmospheric nitrogen is uptaken by bacteroids located in plant root nodules and converted into ammonium through the enzymatic activity of nitrogenase. In practice, this biological process serves as a natural form of fertilization and its optimization has significant implications in sustainable agricultural programs. Currently, the advent of high-throughput technology supplies with valuable data that contribute to understanding the metabolic activity during bacterial nitrogen fixation. - - - - Proteomic patterns of cervical cancer cell lines, a network perspective. - https://resendislab.github.io/pubs/pm21696634/ - Fri, 24 Jun 2011 00:00:00 +0000 - - https://resendislab.github.io/pubs/pm21696634/ - Cervical cancer is a major mortality factor in the female population. This neoplastic is an excellent model for studying the mechanisms involved in cancer maintenance, because the Human Papilloma Virus (HPV) is the etiology factor in most cases. With the purpose of characterizing the effects of malignant transformation in cellular activity, proteomic studies constitute a reliable way to monitor the biological alterations induced by this disease. In this contextual scheme, a systemic description that enables the identification of the common events between cell lines of different origins, is required to distinguish the essence of carcinogenesis. - - - - Modeling core metabolism in cancer cells: surveying the topology underlying the Warburg effect. - https://resendislab.github.io/pubs/pm20811631/ - Fri, 03 Sep 2010 00:00:00 +0000 - - https://resendislab.github.io/pubs/pm20811631/ - Alterations on glucose consumption and biosynthetic activity of amino acids, lipids and nucleotides are metabolic changes for sustaining cell proliferation in cancer cells. Irrevocable evidence of this fact is the Warburg effect which establishes that cancer cells prefers glycolysis over oxidative phosphorylation to generate ATP. Regulatory action over metabolic enzymes has opened a new window for designing more effective anti-cancer treatments. This enterprise is not trivial and the development of computational models that contribute to identifying potential enzymes for breaking the robustness of cancer cells is a priority. - - - - Filling kinetic gaps: dynamic modeling of metabolism where detailed kinetic information is lacking. - https://resendislab.github.io/pubs/pm19305506/ - Tue, 24 Mar 2009 00:00:00 +0000 - - https://resendislab.github.io/pubs/pm19305506/ - Integrative analysis between dynamical modeling of metabolic networks and data obtained from high throughput technology represents a worthy effort toward a holistic understanding of the link among phenotype and dynamical response. Even though the theoretical foundation for modeling metabolic network has been extensively treated elsewhere, the lack of kinetic information has limited the analysis in most of the cases. To overcome this constraint, we present and illustrate a new statistical approach that has two purposes: integrate high throughput data and survey the general dynamical mechanisms emerging for a slightly perturbed metabolic network. - - - - Regulation by transcription factors in bacteria: beyond description. - https://resendislab.github.io/pubs/pm19076632/ - Wed, 17 Dec 2008 00:00:00 +0000 - - https://resendislab.github.io/pubs/pm19076632/ - Transcription is an essential step in gene expression and its understanding has been one of the major interests in molecular and cellular biology. By precisely tuning gene expression, transcriptional regulation determines the molecular machinery for developmental plasticity, homeostasis and adaptation. In this review, we transmit the main ideas or concepts behind regulation by transcription factors and give just enough examples to sustain these main ideas, thus avoiding a classical ennumeration of facts. - - - - Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli. - https://resendislab.github.io/pubs/pm17922569/ - Wed, 10 Oct 2007 00:00:00 +0000 - - https://resendislab.github.io/pubs/pm17922569/ - Rhizobiaceas are bacteria that fix nitrogen during symbiosis with plants. This symbiotic relationship is crucial for the nitrogen cycle, and understanding symbiotic mechanisms is a scientific challenge with direct applications in agronomy and plant development. Rhizobium etli is a bacteria which provides legumes with ammonia (among other chemical compounds), thereby stimulating plant growth. A genome-scale approach, integrating the biochemical information available for R. etli, constitutes an important step toward understanding the symbiotic relationship and its possible improvement. - - - - Identification of regulatory network topological units coordinating the genome-wide transcriptional response to glucose in Escherichia coli. - https://resendislab.github.io/pubs/pm17559662/ - Fri, 15 Jun 2007 00:00:00 +0000 - - https://resendislab.github.io/pubs/pm17559662/ - Glucose is the preferred carbon and energy source for Escherichia coli. A complex regulatory network coordinates gene expression, transport and enzyme activities in response to the presence of this sugar. To determine the extent of the cellular response to glucose, we applied an approach combining global transcriptome and regulatory network analyses. - - - - Robustness and evolvability in genetic regulatory networks. - https://resendislab.github.io/pubs/pm17188715/ - Tue, 26 Dec 2006 00:00:00 +0000 - - https://resendislab.github.io/pubs/pm17188715/ - Living organisms are robust to a great variety of genetic changes. Gene regulation networks and metabolic pathways self-organize and reaccommodate to make the organism perform with stability and reliability under many point mutations, gene duplications and gene deletions. At the same time, living organisms are evolvable, which means that these kind of genetic perturbations can eventually make the organism acquire new functions and adapt to new environments. It is still an open problem to determine how robustness and evolvability blend together at the genetic level to produce stable organisms that yet can change and evolve. - - - - Modular analysis of the transcriptional regulatory network of E. coli. - https://resendislab.github.io/pubs/pm15680508/ - Tue, 01 Feb 2005 00:00:00 +0000 - - https://resendislab.github.io/pubs/pm15680508/ - The transcriptional network of Escherichia coli is currently the best-understood regulatory network of a single cell. Motivated by statistical evidence, suggesting a hierarchical modular architecture in this network, we identified eight modules with well-defined physiological functions. These modules were identified by a clustering approach, using the shortest path to trace regulatory relationships across genes in the network. We report the type (feed forward and bifan) and distribution of motifs between and within modules. - - - - Contact - https://resendislab.github.io/about/contact/ - Mon, 01 Jan 1900 00:00:00 +0000 - - https://resendislab.github.io/about/contact/ - Directions -Osbaldo Resendis-Antonio, PhD -Laboratory in Systems Biology and Human Diseases -Associated Professor -Instituto Nacional de Medicina Genomica – INMEGEN -Periferico Sur 4809, Arenal Tepepan, Tlalpan, 14610 Mexico City, CDMX -Phone: +52 55 5350 1900 - Ext.1198 - - - - - - https://resendislab.github.io/members/dummy/ - Mon, 01 Jan 0001 00:00:00 +0000 - - https://resendislab.github.io/members/dummy/ - This is a dummy page. 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