Computational Genomics

The Program of Computational Genomics is focused, in the field of bioinformatics, on the challenge of accelerating access to genomic knowledge, in particular on the regulation of microbial gene expression. The backbone of our work is the design and expansion of the RegulonDB database, with knowledge of the genetic regulation in Escherichia coli K-12 extracted by curators, both from classical experiments and from High-Throughput (HT) post-genomic methods. We work with algorithms for the identification of binding sites, promoters and transcription units, as well as co-regulation, and for the processing of data from HT methods, such as ChIP-seq, among others. We work in an ontology and a controlled vocabulary of microbial growth conditions, and in an ontology of microbial genetic regulation. An important aspect is the use of Natural language processing (NLP) to enrich knowledge extraction strategies that shall allow us to expand the biocuration to other bacteria such as Salmonella, and other few more bacteria. We have supported integrative concepts such as regulatory phrases and, more recently, the genetic-metabolic sensory-response units (GENSOR Units), which pose a lot of new questions. We are investigating the formalism of S-systems by Michael Savageau for the modeling, initially, of GENSOR Units; extending it to complete circuits and, if possible, to an integral modeling of the cell at the molecular level. This with a novel approach of computational algebraic geometry.

All this way of seeing and conceiving scientific knowledge has its application with similar strategies in a project that seeks to break the separation between texts for laymen and texts for experts with the Conogasi Project (

Recently, Dr. Sohail was incorporated into the program. Her interest research is focused in human genomics, using computational and statistical approaches to investigate the genetic architecture and evolution of complex traits and disease, and the impact of human demographic history on trait variation and disease incidence. For instance, a new project is using deep learning and large genomics datasets to predict complex diseases such as Type 2 Diabetes in humans.

Access our projects here and here if you want to know more details.

Tools and resources for COVID-19

Group Staff

Pedro Julio Collado VidesResearcherEmeritus 3139877
Mashaal Sohail ResearcherAssociate 3132063
Carlos Francisco Méndez CruzResearcherAssistant 3132063
César Augusto Bonavides MartínezLaboratory TechnicianLaboratory 3132063
Ma. del Socorro Gama CastroLaboratory TechnicianLaboratory 3132063
Heladia Salgado OsorioLaboratory TechnicianLaboratory 3132063
Shirley Alquicira HernándezLaboratory TechnicianLaboratory 3132063
Amara Shaukat Postdoctoral 3132063
Paloma Lara FigueroaPostdoctoral 3132063
Martin Jair Díaz RodríguezSupport 3132063
Francisco de Jesus Guadarrama GarcíaSupport 3132063
Jose Daniel Gutierrez NietoSupport 3132063
Luis José Muñíz RascadoSupport 3132063
Pablo Emilio Peña LoredoSupport 3132063
Victor Hugo Tierrafria PulidoSupport 3132063

Group Publications

2023Kun, E., Javan, E.M., Smith, O., Gulamali, F., de la Fuente, J., Flynn, B.I., Vajrala, K., Trutner, Z., Jayakumar, P., Tucker-Drob, E.M., Sohail, M., Singh, T., Narasimhan, V.M.. (2023). "The genetic architecture and evolution of the human skeletal form.". Science. 381(6655):8009-8009. [doi:10.1126/science.adf8009]37471560
2023Anna C. F. Lewis, Santiago J. Molina, Paul S. Appelbaum, Bege Dauda, Agustin Fuentes, Stephanie M. Fullerton, Nanibaa A. Garrison, NayanikaGhosh, Robert C. Green, Evelynn M. Hammonds, Janina M. Jeff, David S.Jones, Eimear E. Kenny, Peter Kraft, Madelyn Mauro, Anil P. S. Ori, Aaron Panofsky, Mashaal Sohail, Benjamin M. Neale, Danielle S. Allen. (2023). "An Ethical Framework for Research Using Genetic Ancestry". Johns Hopkins University Press. ():-. [doi:]
2023Collado-Vides, Julio. (2023). "Regulatory promoter architectures in the hands of thermodynamic modelling.". NATURE REVIEWS GENETICS. ():-. [doi:10.1038/s41576-023-00578-w]36747003
2023Dauda, B., Molina, S.J., Allen, D.S., Fuentes, A., Ghosh, N., Mauro, M., Neale, B.M., Panofsky, A., Sohail, M., Zhang, S.R., Lewis, A.C.F.. (2023). "Ancestry: How researchers use it and what they mean by it.". Frontiers in Genetics. 14():-. [doi:10.3389/fgene.2023.1044555]36755575
2022Tierrafría, V.H., Rioualen, C., Salgado, H., Lara, P., Gama-Castro, S., Lally, P., Gómez-Romero, L., Peña-Loredo, P., López-Almazo, A.G., Alarcón-Carranza, G., Betancourt-Figueroa, F., Alquicira-Hernández, S., Polanco-Morelos, J.E., García-Sotelo, J., Gaytan-Nuñez, E., Méndez-Cruz, C.F., Muñiz, L.J., Bonavides-Martínez, C., Moreno-Hagelsieb, G., Galagan, J.E., Wade, J.T., Collado-Vides, J.. (2022). "RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12.". Microbial genomics. 8(5):-. [doi:10.1099/mgen.0.000833]35584008
2022Méndez Cruz, Carlos Francisco, Arroyo Fernández, Ignacio. (2022). "Análisis automático de unidades morfológicas: segmentación y agrupamiento en español, maya y náhuatl". Ámbitos Morfológicos. Descripciones y métodos. México: UNAM. ISBN 978-607-30-5946-6. ():-.
2022Lewis ACF, Molina SJ, Appelbaum PS, Dauda B, Di Rienzo A, Fuentes A, Fullerton SM, Garrison NA, Ghosh N, Hammonds EM, Jones DS, Kenny EE, Kraft P, Lee SS, Mauro M, Novembre J, Panofsky A, Sohail M, Neale BM, Allen DS. (2022). "Getting genetic ancestry right for science and society.". Science. 376(6590):250-252. [doi:10.1126/science.abm7530]35420968
2022Ortega-Del Vecchyo, D., Berg, J., Sohail, M.. (2022). "Editorial: Genetic Architecture and Evolution of Complex Traits and Diseases in Diverse Human Populations.". Frontiers in Genetics. 13():-. [doi:10.3389/fgene.2022.869056]35368673
2022Collado-Vides J, Gaudet P, de Lorenzo V. (2022). "Missing Links Between Gene Function and Physiology in Genomics.". FRONT PHYSIOL. 13():815874-815874. [doi:10.3389/fphys.2022.815874]35295568
2022Femerling, G., Gama-Castro, S., Lara, P., Ledezma-Tejeida, D., Tierrafría, V.H., Muñiz-Rascado, L., Bonavides-Martínez, C., Collado-Vides, J.. (2022). "Sensory Systems and Transcriptional Regulation in Escherichia coli .". Frontiers in bioengineering and biotechnology. 10():-. [doi:10.3389/fbioe.2022.823240]35237580
2022Jiménez-Kaufmann, A., Chong, A.Y., Cortés, A., Quinto-Cortés, C.D., Fernandez-Valverde, S.L., Ferreyra-Reyes, L., Cruz-Hervert, L.P., Medina-Muñoz, S.G., Sohail, M., Palma-Martinez, M.J., Delgado-Sánchez, G., Mongua-Rodríguez, N., Mentzer, A.J., Hill, A.V.S., Moreno-Macías, H., Huerta-Chagoya, A., Aguilar-Salinas, C.A., Torres, M., Kim, H.L., Kalsi, N., Schuster, S.C., Tusié-Luna, T., Del-Vecchyo, D.O., García-García, L., Moreno-Estrada, A.. (2022). "Imputation Performance in Latin American Populations: Improving Rare Variants Representation With the Inclusion of Native American Genomes.". Frontiers in Genetics. 12():-. [doi:10.3389/fgene.2021.719791]35046991
2021D'Elia, D., Bonavides-Martínez, C., Bongcam-Rudloff, E., Barreto-Hernandez, E., Efthimiadou, A., Papakonstantinou, E., Vlachakis, E., Klucar, L.. (2021). "The EMBnet International Conference 2020: Bioinformatics Approaches to Precision Research". EMBnet.journal. 26():1006-. [doi:10.14806/ej.26.A.1006]
2021Keseler, I.M., Gama-Castro, S., Mackie, A., Billington, R., Bonavides-Martínez, C., Caspi, R., Kothari, A., Krummenacker, M., Midford, P.E., Muñiz-Rascado, L., Ong, W.K., Paley, S., Santos-Zavaleta, A., Subhraveti, P., Tierrafría, V.H., Wolfe, A.J., Collado-Vides, J., Paulsen, I.T., Karp, P.D.. (2021). "The EcoCyc Database in 2021.". Frontiers in Microbiology. 12():-. [doi:10.3389/fmicb.2021.711077]34394059
2021Arroyo-Fernández, Ignacio, Carrasco-Ruiz, Mauricio, Méndez, C.. (2021). "Procesamiento de lenguaje natural en la conservación de la herencia cultural: una red semántica del Popol Vuh". Patrimonio digital. Métodos computacionales y medios interactivos para estudiar y divulgar el patrimonio cultural. ():25-34.
2021Díaz-Rodríguez, M., Lithgow-Serrano, O., Guadarrama-García, F., Tierrafría, V.H., Gama-Castro, S., Solano-Lira, H., Salgado, H., Rinaldi, F., Méndez-Cruz, C.F., Collado-Vides, J.. (2021). "Lisen&Curate: A platform to facilitate gathering textual evidence for curation of regulation of transcription initiation in bacteria.". BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS. 1864(11-12):-. [doi:10.1016/j.bbagrm.2021.194753]34461312
2021Lithgow-Serrano, O., Gama-Castro, S., Ishida-Gutiérrez, Collado-Vides, J.. (2021). "L-Regulon: A novel “soft-curation” approach supported by a semantic enriched reading for RegulonDB literature". bioRxiv. ():-. [doi:]
2021Lithgow-Serrano O, Cornelius J, Kanjirangat V, Méndez-Cruz CF, Rinaldi F. (2021). "Improving classification of low-resource COVID-19 literature by using Named Entity Recognition.". Genomics & informatics. 19(3):-. [doi:10.5808/gi.21018]34638169
2021Sohail, M., Izarraras-Gomez, A., Ortega-Del Vecchyo, D.. (2021). "Populations, Traits, and Their Spatial Structure in Humans.". Genome Biology And Evolution. 13(12):-. [doi:10.1093/gbe/evab272]34894236
2020Mejía-Almonte, C., Busby, S.J.W., Wade, J.T., van Helden, J., Arkin, A.P., Stormo, G.D., Eilbeck, K., Palsson, B.O., Galagan, J.E., Collado-Vides, J.. (2020). "Redefining fundamental concepts of transcription initiation in bacteria". NATURE REVIEWS GENETICS. 21(11):699-714. [doi:10.1038/s41576-020-0254-8][]32665585
2020Villaseñor-Altamirano AB, Moretto M, Maldonado M, Zayas-Del Moral A, Munguía-Reyes A, Romero Y, García-Sotelo JS, Aguilar LA, Aldana-Assad O, Engelen K, Selman M, Collado-Vides J, Balderas-Martínez YI, Medina-Rivera A. (2020). "PulmonDB: a curated lung disease gene expression database.". SCIENTIFIC REPORTS. 10(1):514-514. [doi:10.1038/s41598-019-56339-5]31949184
2020Méndez-Cruz, C.F., Blanchet, A., Godínez, A., Arroyo-Fernández, I., Gama-Castro, S., Martínez-Luna, S.B., González-Colín, C., Collado-Vides, J.. (2020). "Knowledge extraction for assisted curation of summaries of bacterial transcription factor properties.". DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. 2020():-. [doi:10.1093/database/baaa109]33306798
2020Jiménez-Jacinto V., Gómez-Romero, L., Méndez-Cruz CF. (2020). "Pattern Recognition Applied to the Analysis of Genomic Data and Its Association to Diseases". Pattern Recognition Techniques Applied to Biomedical Problems. ():31-61.
2020Chávez, J., Barberena-Jonas, C., Sotelo-Fonseca, J.E., Alquicira-Hernández, J., Salgado, H., Collado-Torres, L., Reyes, A.. (2020). "Programmatic access to bacterial regulatory networks with regutools.". Bioinformatics. 36(16):4532-4534. [doi:10.1093/bioinformatics/btaa575]32573705
2019Centeno-Leija, Sara, Tapia-Cabrera, Silvana, Guzman-Trampe, Silvia, Esquivel, Baldomero, Esturau-Escofet, Nuria, Tierrafria, Victor H., Rodriguez-Sanoja, Romina, Zarate-Romero, Andres, Stojanoff, Vivian, Rudino-Pinera, Enrique, Sanchez, Sergio, Serrano-Posada, Hugo. (2019). "The structure of (E)-biformene synthase provides insights into the biosynthesis of bacterial bicyclic labdane-related diterpenoids". JOURNAL OF STRUCTURAL BIOLOGY. 207(1):29-39. [doi:10.1016/j.jsb.2019.04.010]30981884
2019Tierrafría, V.H., Mejía-Almonte, C., Camacho-Zaragoza, J.M., Salgado, H., Alquicira, K., Ishida, C., Gama-Castro, S., Collado-Vides, J.. (2019). "MCO: towards an ontology and unified vocabulary for a framework-based annotation of microbial growth conditions.". Bioinformatics. 35(5):856-864. [doi:10.1093/bioinformatics/bty689]30137210
2019Lithgow-Serrano, O., Collado-Vides, J.. (2019). "In the pursuit of semantic similarity for literature on microbial transcriptional regulation". JOURNAL OF INTELLIGENT & FUZZY SYSTEMS. 36(5):4777-4786. [doi:10.3233/JIFS-179026]
2019Santos-Zavaleta, A., Salgado, H., Gama-Castro, S., Sánchez-Pérez, M., Gómez-Romero, L., Ledezma-Tejeida, D., García-Sotelo, J.S., Alquicira-Hernández, K., Muñiz-Rascado, L.J., Peña-Loredo, P., Ishida-Gutiérrez, C., Velázquez-Ramírez, D.A., Del Moral-Chávez, V., Bonavides-Martínez, C., Méndez-Cruz, C.F., Galagan, J., Collado-Vides, J.. (2019). "RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12". Nucleic Acids Research. 47(D1):212-220. [doi:10.1093/nar/gky1077]30395280
2019Arroyo Fernández, Ignacio, Méndez, C., Sierra, Gerardo, Sidorov, Grigori, Torres-Moreno, Juan-Manuel. (2019). "Unsupervised Sentence Representations as Word Information Series: Revisiting TF--IDF". COMPUTER SPEECH AND LANGUAGE. 56():107-129. [doi:10.1016/j.csl.2019.01.005]
2019Giner-Lamia, J., Vinuesa, P., Betancor, L., Silva, C., Bisio, J., Soleto, L., Chabalgoity, J.A., Puente, J.L., Soncini, F.C., García-Vescovi, E., Flores, G., Pedraza, J., Yim, L., García, C., Astocondor, L., Ochoa, T., Hinostroza, N., Graciela Pucciarelli, M., Hernández-Alvarez, A., Del Moral, V., García-Del Portillo, F.. (2019). "Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256". Bmc Genomics. 20(1):99-99. [doi:10.1186/s12864-018-5352-z]30704413
2019Lithgow-Serrano, O., Gama-Castro, S., Ishida-Gutiérrez, C., Mejía-Almonte, C., Tierrafría, V.H., Martínez-Luna, S., Santos-Zavaleta, A., Velázquez-Ramírez, D., Collado-Vides, J.. (2019). "Similarity corpus on microbial transcriptional regulation.". JOURNAL OF BIOMEDICAL SEMANTICS. 10(1):-. [doi:10.1186/s13326-019-0200-x]31118102
2019Santos-Zavaleta, A., Pérez-Rueda, E., Sánchez-Pérez, M., Velázquez-Ramírez, D.A., Collado-Vides, J.. (2019). "Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes.". Bmc Genomics. 20(1):-. [doi:10.1186/s12864-019-5619-z]30991941
2019Arroyo Fernández, Ignacio, Curiel, Arturo, Méndez, C.. (2019). "Language features in extractive summarization: Humans Vs. Machines". KNOWLEDGE-BASED SYSTEMS. 180():1-11. [doi:10.1016/j.knosys.2019.05.014]
2019Rioualen, C., Charbonnier-Khamvongsa, L., Collado-Vides, J., van Helden, J.. (2019). "Integrating Bacterial ChIP-seq and RNA-seq Data With SnakeChunks.". Current Protocols in Bioinformatics. 66(1):-. [doi:10.1002/cpbi.72]30786165
2019Ledezma-Tejeida D, Altamirano-Pacheco L, Fajardo V, Collado-Vides J. (2019). "Limits to a classic paradigm: most transcription factors in E. coli regulate genes involved in multiple biological processes.". Nucleic Acids Research. 47(13):6656-6667. [doi:10.1093/nar/gkz525]31194874
2018Villasenor-Altamirano, A. B., Balderas-Martinez, Y. I., Moretto, M., Zayas-Del Moral, A., Maldonado, M., Munguia-Reyes, A., Garcia-Sotelo, J. S., Aguilar Bautista, L. A., Ramirez-Navarro, L., Santillan, O., Engelen, K., Selman, M., Medina-Rivera, A., Collado-Vides, J.. (2018). "PulmonDB: A Gene Expression Lung Diseases". AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE. 197():-.
2018Balderas-Martinez, Y. I., Moreno-Quiroga, B., Negreros, M., Ledezma-Tejeida, D., Pardo, A., Collado-Vides, J., Selman, M.. (2018). "Proof of Concept of Eukaryotic Genetic Sensory Response Units in TGF-beta Signaling in Idiopathic Pulmonary Fibrosis". AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE. 197():-.
2018Santos-Zavaleta, Alberto, Sanchez-Perez, Mishael, Salgado, Heladia, Velazquez-Ramirez, David A., Gama-Castro, Socorro, Tierrafria, Victor H., Busby, Stephen J. W., Aquino, Patricia, Fang, Xin, Palsson, Bernhard O., Galagan, James E., Collado-Vides, Julio. (2018). "A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0". BMC BIOLOGY. 16(1):91-91. [doi:10.1186/s12915-018-0555-y]30115066
2018Salgado, H., Martínez-Flores, I., Bustamante, V.H., Alquicira-Hernández, K., García-Sotelo, J.S., García-Alonso, D., Collado-Vides, J.. (2018). "Using RegulonDB, the Escherichia coli K-12 Gene Regulatory Transcriptional Network Database.". Current Protocols in Bioinformatics. 61(1):1321-13230. [doi:10.1002/cpbi.43]30040192
2018Gomez-Romero, Laura, Palacios-Flores, Kim, Reyes, Jose, Garcia, Delfino, Boege, Margareta, Davila, Guillermo, Flores, Margarita, Schatz, Michael C., Palacios, Rafael. (2018). "Precise detection of de novo single nucleotide variants in human genomes". PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 115(21):5516-5521. [doi:10.1073/pnas.1802244115]29735690
2017Ledezma-Tejeida D, Ishida C, Collado-Vides J. (2017). "Genome-wide mapping of transcriptional regulation and metabolism describes information-processing units in Escherichia coli". Frontiers in Microbiology. 8(AUG):1466-1466. [doi:10.3389/fmicb.2017.01466]28824593
2017Perez-Morales, Deyanira, Banda, Maria M., Elizabeth Chau, N. Y., Salgado, Heladia, Martinez-Flores, Irma, Antonio Ibarra, J., Ilyas, Bushra, Coombes, Brian K., Bustamante, Victor H.. (2017). "The transcriptional regulator SsrB is involved in a molecular switch controlling virulence lifestyles of Salmonella". PLOS PATHOGENS. 13(7):-. [doi:10.1371/journal.ppat.1006497]28704543
2017De Las Rivas J, Bonavides-Martínez C, Campos-Laborie FJ. (2017). "Bioinformatics in Latin America and SoIBio impact, a tale of spin-off and expansion around genomes and protein structures.". BRIEFINGS IN BIOINFORMATICS. 20(2):390-397. [doi:10.1093/bib/bbx064]28981567
2017Balderas-Martínez YI, Rinaldi F, Contreras G, Solano-Lira H, Sánchez-Pérez M, Collado-Vides J, Selman M, Pardo A. (2017). "Improving biocuration of microRNAs in diseases: a case study in idiopathic pulmonary fibrosis". DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. 2017():-. [doi:10.1093/database/bax030]28605770
2017Pannier L, Merino E, Marchal K, Collado-Vides J. (2017). "Effect of genomic distance on coexpression of coregulated genes in E. coli". Plos One. 12(4):-. [doi:10.1371/journal.pone.0174887]28419102
2017Rinaldi F, Lithgow O, Gama-Castro S, Solano H, Lopez A, Muñiz Rascado LJ, Ishida-Gutiérrez C, Méndez-Cruz CF, Collado-Vides J. (2017). "Strategies towards digital and semi-automated curation in RegulonDB". DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. 2017(1):-. [doi:10.1093/database/bax012]28365731
2017Méndez-Cruz CF, Gama-Castro S, Mejía-Almonte C, Castillo-Villalba MP, Muñiz-Rascado LJ, Collado-Vides J. (2017). "First steps in automatic summarization of transcription factor properties for RegulonDB: classification of sentences about structural domains and regulated processes". DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. 2017():-. [doi:10.1093/database/bax070]29220462
2017Castillo-Villalba MP, Gomez-Romero, Laura, Collado-Vides, Julio. (2017). "Genetic-metabolic networks can be modeled as toric varities". arXiv. ():-. [doi:arXiv:1708.05384v1]
2017Keseler, I.M., Mackie, A., Santos-Zavaleta, A., Billington, R., Bonavides-Martínez, C., Caspi, R., Fulcher, C., Gama-Castro, S., Kothari, A., Krummenacker, M., Latendresse, M., Muñiz-Rascado, L., Ong, Q., Paley, S., Peralta-Gil, M., Subhraveti, P., Velázquez-Ramírez, D.A., Weaver, D., Collado-Vides, J., Paulsen, I., Karp, P.D.. (2017). "The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.". Nucleic Acids Research. 45(D1):543-550. [doi:10.1093/nar/gkw1003]27899573
2016Mendez-Cruz, Carlos-Francisco, Medina-Urrea, Alfonso, Sierra, Gerardo. (2016). "Unsupervised morphological segmentation based on affixality measurements". PATTERN RECOGNITION LETTERS. 84():127-133. [doi:10.1016/j.patrec.2016.09.001]
2016Martínez-Flores I, Pérez-Morales D, Sánchez-Pérez M, Paredes CC, Collado-Vides J, Salgado H, Bustamante VH. (2016). "In Silico clustering of Salmonella global gene expression data reveals novel genes co-regulated with the SPI-1 virulence genes through HilD". SCIENTIFIC REPORTS. 6():37858-37858. [doi:10.1038/srep37858]27886269
2016Wang, Qinghua, Abdul, Shabbir S., Almeida, Lara, Ananiadou, Sophia, Balderas-Martinez, Yalbi I., Batista-Navarro, Riza, Campos, David, Chilton, Lucy, Chou, Hui-Jou, Contreras, Gabriela, Cooper, Laurel, Dai, Hong-Jie, Ferrell, Barbra, Fluck, Juliane, Gama-Castro, Socorro, George, Nancy, Gkoutos, Georgios, Irin, Afroza K., Jensen, Lars J., Jimenez, Silvia, Jue, Toni R., Keseler, Ingrid, Madan, Sumit, Matos, Sergio, McQuilton, Peter, Milacic, Marija, Mort, Matthew, Natarajan, Jeyakumar, Pafilis, Evangelos, Pereira, Emiliano, Rao, Shruti, Rinaldi, Fabio, Rothfels, Karen, Salgado, David, Silva, Raquel M., Singh, Onkar, Stefancsik, Raymund, Su, Chu-Hsien, Subramani, Suresh, Tadepally, Hamsa D., Tsaprouni, Loukia, Vasilevsky, Nicole, Wang, Xiaodong, Chatr-Aryamontri, Andrew, Laulederkind, Stanley J. F., Matis-Mitchell, Sherri, McEntyre, Johanna, Orchard, Sandra, Pundir, Sangya, Rodriguez-Esteban, Raul, Van Auken, Kimberly, Lu, Zhiyong, Schaeffer, Mary, Wu, Cathy H., Hirschman, Lynette, Arighi, Cecilia N.. (2016). "Overview of the interactive task in BioCreative V". DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. 2016():-. [doi:10.1093/database/baw119]27589961
2016Moretto, M., Sonego, P., Dierckxsens, N., Brilli, M., Bianco, L., Ledezma-Tejeida, D., Gama-Castro, S., Galardini, M., Romualdi, C., Laukens, K., Collado-Vides, J., Meysman, P., Engelen, K.. (2016). "COLOMBOS v3.0: Leveraging gene expression compendia for cross-species analyses". Nucleic Acids Research. 44(D1):620-623. [doi:10.1093/nar/gkv1251]26586805
2016Gama-Castro, S., Salgado, H., Santos-Zavaleta, A., Ledezma-Tejeida, D., Muñiz-Rascado, L., García-Sotelo, J.S., Alquicira-Hernández, K., Martínez-Flores, I., Pannier, L., Castro-Mondragón, J.A., Medina-Rivera, A., Solano-Lira, H., Bonavides-Martínez, C., Pérez-Rueda, E., Alquicira-Hernández, S., Porrón-Sotelo, L., López-Fuentes, A., Hernández-Koutoucheva, A., Del Moral-Chavez, V., Rinaldi, F., Collado-Vides, J.. (2016). "RegulonDB version 9.0: High-level integration of gene regulation, coexpression, motif clustering and beyond". Nucleic Acids Research. 44(D1):133-143. [doi:10.1093/nar/gkv1156]26527724
2015Alvarez-Vasquez, Fernando J., Freyre-Gonzalez, Julio A., Balderas-Martinez, Yalbi I., Delgado-Carrillo, Monica I., Collado-Vides, Julio. (2015). "Mathematical modeling of the apo and holo transcriptional regulation in Escherichia coli". Molecular Biosystems. 11(4):994-1003. [doi:10.1039/c4mb00561a]25683745
2014Meysman, Pieter, Collado-Vides, Julio, Morett, Enrique, Viola, Roberto, Engelen, Kristof, Laukens, Kris. (2014). "Structural properties of prokaryotic promoter regions correlate with functional features". Plos One. 9(2):-. [doi:10.1371/journal.pone.0088717]24516674
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2013Weiss, V., Medina-Rivera, A, Huerta, AM, Santos-Zavaleta, A, Salgado, H, Morett, E., Collado-Vides, J. (2013). "Evidence classification of high-throughput protocols and confidence integration in RegulonDB". DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. 2013():-. [doi:10.1093/database/bas059]23327937
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2013Salgado, H., Peralta, M., Gama, M., Santos, A., Muñíz, L., Garcia, J., Weiss, V., Solano, H., Martínez, I., Medina, A., Salgado, G., Alquicira, S., Alquicira, K., López, A., Porrón, L., Huerta, A., Bonavides, C., Balderas, Y., Pannier, L., Olvera, M., Labastida, A., Jiménez-Jacinto, V., Vega-Alvarado, L., del Moral, V., Hernández, A., Morett, E., Collado, P.. (2013). "RegulonDB v8.0: Omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more". Nucleic Acids Research. 41(D1):203-213. [doi:10.1093/nar/gks1201]23203884
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2005Espinosa, V., Gonzalez, A.D., Vasconcelos, A.T., Huerta, A., Collado, P.. (2005). "Comparative studies of transcriptional regulation mechanisms in a group of eight gamma-proteobacterial genomes". Journal Of Molecular Biology. 354(1):184-199. [doi:10.1016/j.jmb.2005.09.037]16236313
2005Janga, SC, Collado-Vides, J, Moreno-Hagelsieb, G. (2005). "Nebulon: A system for the inference of functional relationships of gene products from the rearrangement of predicted operons". Nucleic Acids Research. 33(8):2521-2530. [doi:10.1093/nar/gki545]15867197
2005Guia, M.H., Perez, A.G., Angarica, V.E., Vasconcelos, A.T., Collado Vides, Pedro Julio. (2005). "Complementing computationally predicted regulatory sites in Tractor_DB using a pattern matching approach". In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation. 5(2):209-219. 15972018
2005Menchaca, R., Janga, S., Collado, P.. (2005). "The network of transcriptional interactions imposes linear constrains in the genome". OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY. 9(2):139-145. [doi:10.1089/omi.2005.9.139]15969646
2005Ibarra-Junquera, V, Torres, LA, Rosu, HC, Arguello, G, Collado-Vides, J. (2005). "Nonlinear software sensor for monitoring genetic regulation processes with noise and modeling errors". PHYSICAL REVIEW E. 72(1):11919-11919. [doi:10.1103/PhysRevE.72.011919]16090013
2005Gonzalez, A.D., Espinosa, V., Vasconcelos, A.T., Perez-Rueda, E., Collado, P.. (2005). "TRACTOR_DB: A database of regulatory networks in gamma-proteobacterial genomes". Nucleic Acids Research. 33(DATABASE ISS.):98-102. [doi:10.1093/nar/gki054]15608293
2005Keseler, I.M., Collado, P., Gama, M., Ingraham, J., Paley, S., Paulsen, I.T., Peralta, M., Karp, P.D.. (2005). "EcoCyc: A comprehensive database resource for Escherichia coli". Nucleic Acids Research. 33(DATABASE ISS.):334-337. [doi:10.1093/nar/gki108]15608210
2005Resendis, O., Freyre, J., Menchaca, R., Gutiérrez, R., Martínez, A., Ávila, C., Collado, P.. (2005). "Modular analysis of the transcriptional regulatory network of E. coli". TRENDS IN GENETICS. 21(1):16-20. [doi:10.1016/j.tig.2004.11.010]15680508
2004Resendis-Antonio, O, Collado-Vides, J. (2004). "The growth of random networks as a diffusion process". PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS. 342(3-4):551-560. [doi:10.1016/j.physa.2004.05.037]
2004Oviedo, N.A., Salgado, H., Collado, P., Guarneros, G.. (2004). "Distribution of minigenes in the bacteriophage lambda chromosome". Gene. 329(1-2):115-124. [doi:10.1016/j.gene.2003.12.031]15033534
2004Salgado, H., Gama, M., Martínez, A., Díaz, E., Sánchez, E., Peralta, M., García, D., Jiménez, V., Santos, A., Bonavides, C., Collado, P.. (2004). "RegulonDB (version 4.0): Transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12". Nucleic Acids Research. 32(DATABASE ISS.):303-306. [doi:10.1093/nar/gkh140]14681419
2004Karp, PD, Arnaud, M, Collado-Vides, J, Ingraham, J, Paulsen, IT, Saier, MH. (2004). "The E. coli EcoCyc database: No longer just a metabolic pathway database". Asm News. 70(1):25-30.
2004Perez-Rueda, E., Collado, P., Segovia, L.. (2004). "Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea". COMPUTATIONAL BIOLOGY AND CHEMISTRY. 28(5-6):341-350. [doi:10.1016/j.compbiolchem.2004.09.004]15556475
2004Medrano, L., Moreno, G., Vinuesa, P., Christen, J.A., Collado, P.. (2004). "Successful lateral transfer requires codon usage compatibility between foreign genes and recipient genomes". MOLECULAR BIOLOGY AND EVOLUTION. 21(10):1884-1894. [doi:10.1093/molbev/msh202]15240837
2003Perret, X., Kobayashi, H., Collado Vides, Pedro Julio. (2003). "Regulation of expression of symbiotic genes in Rhizobium sp. NGR234". INDIAN JOURNAL OF EXPERIMENTAL BIOLOGY. 41(10):1101-1113. 15242276
2003González, V., Bustos, V., Ramírez, M., Medrano, L., Salgado, H., Hernández, I., Hernández, J., Quintero, V., Moreno, G., Girard, M., Rodríguez, O., Flores, M., Cevallos, M., Collado, P., Romero, D., Dávila, J.. (2003). "The mosaic structure of the symbiotic plasmid of Rhizobium etli CFN42 and its relation to other symbiotic genome compartments.". Genome Biology. 4(6):-. [doi:10.1186/gb-2003-4-6-r36]12801410
2003Martínez, A., Salgado, H., Gama, M., Gutiérrez, R., Jiménez, V., Collado, P.. (2003). "Environmental Conditions and Transcriptional Regulation in Escherichia coli: A Physiological Integrative Approach". BIOTECHNOLOGY AND BIOENGINEERING. 84(7):743-749. [doi:10.1002/bit.10846]14708114
2003Jauregui, R, Abreu-Goodger, C, Moreno-Hagelsieb, G, Collado-Vides, J, Merino, E. (2003). "Conservation of DNA curvature signals in regulatory regions of prokaryotic genes". Nucleic Acids Research. 31(23):6770-6777. [doi:10.1093/nar/gkg882]14627810
2003Gutiérrez, R., Rosenblueth, D.A., Loza, J., Huerta, A., Glasner, J.D., Blattner, F.R., Collado, P.. (2003). "Regulatory network of Escherichia coli: Consistency between literature knowledge and microarray profiles". GENOME RESEARCH. 13(11):2435-2443. [doi:10.1101/gr.1387003]14597655
2003Huerta, AM, Collado-Vides, J. (2003). "Sigma70 promoters in Escherichia coli: Specific transcription in dense regions of overlapping promoter-like signals". Journal Of Molecular Biology. 333(2):261-278. [doi:10.1016/j.jmb.2003.07.017]14529615
2003Martinez-Antonio, A, Collado-Vides, J. (2003). "Identifying global regulators in transcriptional regulatory networks in bacteria". Current Opinion In Microbiology. 6(5):482-489. [doi:10.1016/j.mib.2003.09.002]14572541
2003Collado Vides, Pedro Julio, Medrano Soto, Luis Arturo, Tusié-Luna, M.T.. (2003). "With the finished human genome in hand, what next?". Genome Biology. 4(7):328-328. [doi:10.1186/gb-2003-4-7-328]12844356
2002Karp, PD, Riley, M, Saier, M, Paulsen, IT, Collado-Vides, J, Paley, SM, Pellegrini-Toole, A, Bonavides, C, Gama-Castro, S. (2002). "The EcoCyc database". Nucleic Acids Research. 30(1):56-58. [doi:10.1093/nar/30.1.56]11752253
2002Collado Vides, Pedro Julio, Moreno Hagelsieb, Gabriel, Pérez Rueda, Ernesto, Salgado Osorio, Heladia, Huerta Moreno, Araceli, Gutiérrez Ríos, Rosa María, Rosenblueth, David A., Christen, Andrés, Benítez Bellón, Esperanza, Medrano Soto, Luis Arturo, Gama Castro, Ma. del Socorro, Santos Zavaleta, Alberto, Bonavides Martínez, César Augusto, DíPeredo, Edgar, Sánchez Solano, Erika Fabiola, Millá, Dulce María. (2002). "Genomics of Gene Regulation: The view from Escherichia coli". Gene Regulation and Metabolism, Post-Genomic Computational Approaches. ():103-128.
2002de Daruvar, A, Collado-Vides, J, Valencia, A. (2002). "Analysis of the cellular functions of Escherichia coli operons and their conservation in Bacillus Subtilis". Journal Of Molecular Evolution. 55(2):211-221. [doi:10.1007/s00239-002-2317-1]12107597
2002Collado-Vides, J., Moreno-Hagelsieb, G., Medrano-Soto, A.. (2002). "Microbial computational genomics of gene regulation". PURE AND APPLIED CHEMISTRY. 74(6):899-905. [doi:10.1351/pac200274060899]
2002Huerta, AM, Glasner, JD, Gutierrez-Rios, RM, Blattner, FR, Collado-Vides, J. (2002). "GETools: gene expression tool for analysis of transcriptome experiments in E. coli". TRENDS IN GENETICS. 18(4):217-218. [doi:10.1016/S0168-9525(01)02620-8]
2002Degrave, W.M., Vargas, R., Alvarez, F., Collado Vides, Pedro Julio, Nunez, L., Ramirez, J.L., Grau, O.. (2002). "Towards a bioinformatics network for Latin America and the Caribbean (LACBioNet).". Applied Bioinformatics. 1(1):53-56. 15130857
2002Moreno Hagelsieb, Gabriel, Collado Vides, Pedro Julio. (2002). "A powerful non-homology method for the prediction of operons in prokaryotes.". Bioinformatics. 18 Suppl 1():329-336. [doi:10.1093/bioinformatics/18.suppl_1.s329]12169563
2002Benítez Bellón, Esperanza, Moreno Hagelsieb, Gabriel, Collado Vides, Pedro Julio. (2002). "Evaluation of thresholds for the detection of binding sites for regulatory proteins in Escherichia coli K12 DNA.". Genome Biology. 3(3):-. 11897025
2002Moreno Hagelsieb, Gabriel, Collado Vides, Pedro Julio. (2002). "Operon conservation from the point of view of Escherichia coli, and inference of functional interdependence of gene products from genome context". In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation. 2(2):87-95. 12066843
2002Collado-Vides, J, Moreno-Hagelsieb, G, Medrano-Soto, A. (2002). "Microbial computational genomics of gene regulation". PURE AND APPLIED CHEMISTRY. 74(6):899-905. [doi:10.1351/pac200274060899]
2001Moreno-Hagelsieb, G, Trevino, V, Pérez-Rueda, E, Smith, TF, Collado-Vides, J. (2001). "Transcription unit conservation in the three domains of life: A perspective from Escherichia coli". TRENDS IN GENETICS. 17(4):175-177. [doi:10.1016/S0168-9525(01)02241-7]11275307
2001Pérez-Rueda, E, Collado-Vides, J. (2001). "Common history at the origin of the position - Function correlation in transcriptional regulators in archaea and bacteria". Journal Of Molecular Evolution. 53(3):172-179. [doi:10.1007/s002390010207]11523004
2001Tan, K., Moreno, G., Collado, P., Stormo, G.D.. (2001). "A comparative genomics approach to prediction of new members of regulons". GENOME RESEARCH. 11(4):566-584. [doi:10.1101/gr.149301]11282972
2001Salgado, H, Santos-Zavaleta, A, Gama-Castro, S, Millen-Zarate, D, Diaz-Peredo, E, Sanchez-Solano, F, Pérez-Rueda, E, Bonavides-Martinez, C, Collado-Vides, J. (2001). "RegulonDB (version 3.2): Transcriptional regulation and operon organization in Escherichia coli K-12". Nucleic Acids Research. 29(1):72-74. [doi:10.1093/nar/29.1.72]11125053
2001Ramirez-Santos, J, Collado-Vides, J, Garcia-Varela, M, Gomez-Eichelmann, MC. (2001). "Conserved regulatory elements of the promoter sequence of the gene rpoH of enteric bacteria". Nucleic Acids Research. 29(2):380-386. [doi:10.1093/nar/29.2.380]11139607
2000Salgado, H, Santos-Zavaleta, A, Gama-Castro, S, Millan-Zarate, D, Blattner, FR, Collado-Vides, J. (2000). "RegulonDB (version 3.0): Transcriptional regulation and operon organization in Escherichia coli K-12". Nucleic Acids Research. 28(1):65-67. [doi:10.1093/nar/28.1.65]10592182
2000Strainic, MG, Sullivan, JJ, Collado-Vides, J, deHaseth, PL. (2000). "Promoter interference in a bacteriophage lambda control region: Effects of a range of interpromoter distances". Journal Of Bacteriology. 182(1):216-220. [doi:10.1128/JB.182.1.216-220.2000]10613884
2000Perez-Rueda, Ernesto, Collado-Vides, Julio. (2000). "The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12". Nucleic Acids Research. 28(8):1838-1847. [doi:10.1093/nar/28.8.1838]10734204
2000van Heiden, Jacques, Rios, Alma. F., Collado-Vides, Julio. (2000). "Discovering regulatory elements in non-coding sequences by analysis of spaced dyads". Nucleic Acids Research. 28(8):1808-1818. [doi:10.1093/nar/28.8.1808]10734201
2000Salgado, H., Moreno, G., Smith, T.F., Collado, P.. (2000). "Operons in Escherichia coli: Genomic analyses and predictions". PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 97(12):6652-6657. [doi:10.1073/pnas.110147297]10823905
2000van Helden, J., Andre, B., Collado, P.. (2000). "A web site for the computational analysis of yeast regulatory sequences". Yeast. 16(2):177-187. 3.0.CO;2-9">[doi:10.1002/(SICI)1097-0061(20000130)16:23.0.CO;2-9]10641039
1999Collado Vides, Pedro Julio, Hofestadt, R., Mavrovouniotis, M., Michal, G.. (1999). "Modeling and simulation of gene regulation and metabolic pathways". Biosystems. 49(1):79-82. [doi:10.1016/S0303-2647(98)00081-1]10091975
1999Salgado, H, Santos, A, Garza-Ramos, U, van Helden, J, Diaz, E, Collado-Vides, J. (1999). "RegulonDB (version 2.0): A database on transcriptional regulation in Escherichia coli". Nucleic Acids Research. 27(1):59-60. [doi:10.1093/nar/27.1.59]9847141
1998Thieffry, D, Salgado, H, Huerta, AM, Collado-Vides, J. (1998). "Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12". Bioinformatics. 14(5):391-400. [doi:10.1093/bioinformatics/14.5.391]9682052
1998Pérez, E., Gralla, J.D., Collado, P.. (1998). "Genomic position analyses and the transcription machinery". Journal Of Molecular Biology. 275(2):165-170. [doi:10.1006/jmbi.1997.1465]9466899
1998Thieffry, D., Huerta, A., Pérez, E., Collado, P.. (1998). "From specific gene regulation to genomic networks: A global analysis of transcriptional regulation in Escherichia coli". Bioessays. 20(5):433-440. 3.0.CO;2-2">[doi:10.1002/(SICI)1521-1878(199805)20:53.0.CO;2-2]9670816
1998van Helden, J., Andre, B., Collado, P.. (1998). "Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies". Journal Of Molecular Biology. 281(5):827-842. [doi:10.1006/jmbi.1998.1947]9719638
1998Collado-Vides, J, Gutierrez-Rios, RM, Bel-Enguix, G. (1998). "Networks of transcriptional regulation encoded in a grammatical model". Biosystems. 47(1-2):103-118. [doi:10.1016/S0303-2647(98)00016-1]9715754
1998Huerta, AM, Salgado, H, Thieffry, D, Collado-Vides, J. (1998). "RegulonDB: A database on transcriptional regulation in Escherichia coli". Nucleic Acids Research. 26(1):55-59. [doi:10.1093/nar/26.1.55]9399800
1997Thieffry Jacot-Descombes, Denis Louis, Rosenblueth, D.A., Huerta Moreno, Araceli, Salgado Osorio, Heladia, Collado Vides, Pedro Julio. (1997). "Definite-clause grammars for the analysis of CIS-regulatory regions in E. coli.". Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. ():441-452. 9390313
1997Blattner, FR, Plunkett, G, Bloch, CA, Perna, NT, Burland, V, Riley, M, ColladoVides, J, Glasner, JD, Rode, CK, Mayhew, GF, Gregor, J, Davis, NW, Kirkpatrick, HA, Goeden, MA, Rose, DJ, Mau, B, Shao, Y. (1997). "The complete genome sequence of Escherichia coli K-12". Science. 277(5331):1453-1462. [doi:10.1126/science.277.5331.1453]9278503
1997Collado-Vides, J, Huerta, AM, Klose, K. (1997). "Three models of gene regulation in E. coli". LECTURE NOTES IN COMPUTER SCIENCE. 1278():72-78.
1996Hofestadt, R., Mavrovouniotis, M., Collado, P., Loffler, M.. (1996). "Modeling and simulation of metabolic pathways, gene regulation and cell differentiation. International Conference and Research Center for Computer Science, Schloss Dagstuhl, Saarland, Germany, 22-27 October, 1995". Bioessays. 18(4):333-335. [doi:10.1002/bies.950180412]8967902
1996ColladoVides, J. (1996). "Towards a unified grammatical model of s70 and s54 bacterial promoters". Biochimie. 78(5):351-363. [doi:10.1016/0300-9084(96)84767-5]8905154
1996Rosenblueth, DA, Thieffry, D, Huerta, AM, Salgado, H, ColladoVides, J. (1996). "Syntactic recognition of regulatory regions in Escherichia coli". COMPUTER APPLICATIONS IN THE BIOSCIENCES. 12(5):415-422. [doi:10.1093/bioinformatics/12.5.415]8996790
1993COLLADOVIDES, J. (1993). "A linguistic representation of the regulation of transcription initiation. II. Distinctive features of sigma 70 promoters and their regulatory binding sites". Biosystems. 29(2-3):105-128. [doi:10.1016/0303-2647(93)90087-S]8374063
1993Collado, P.. (1993). "The elements for a classification of units of genetic information with a combinatorial component". JOURNAL OF THEORETICAL BIOLOGY. 163(4):527-548. [doi:10.1006/jtbi.1993.1136]8246512
1993COLLADOVIDES, J. (1993). "A linguistic representation of the regulation of transcription initiation. I. An ordered array of complex symbols with distinctive features". Biosystems. 29(2-3):87-104. [doi:10.1016/0303-2647(93)90086-R]8374070
1992COLLADOVIDES, J. (1992). "Grammatical model of the regulation of gene expression". PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 89(20):9405-9409. [doi:10.1073/pnas.89.20.9405]1409648