Julio Collado‐Vides - Publications, H-index & Citations

Julio Collado‐Vides

programa de genomica computacional

51H指数

193论文数

2.2W被引数

收录论文 67

发表时间

Fine-tuned GPT-based foundation models effectively reconstruct bacterial transcriptional regulatory networks from literature 基于GPT的微调基础模型能够有效从文献中重构细菌转录调控网络

Frontiers in Artificial Intelligence

IF4.7

2026-04-13

OAAI

JR José Romero-Vilchis; MB Maximiliano Barajas-Sánchez; KA Karyme-Ivette Azpeitia-García; AP Ali-Berenice Posada-Reyes; JC Julio Collado-Vides; CM Carlos-Francisco Méndez-Cruz

RegulonDB v12.0: a comprehensive resource of transcriptional regulation in E. coli K-12 RegulonDB v12.0: 大肠杆菌K-12中转录调控的综合资源

NUCLEIC ACIDS RESEARCH

IF13.1

2023-11-16

OAAI

Salgado, Heladia; Gama-Castro, Socorro; Lara, Paloma; Mejia-Almonte, Citlalli; Alarcon-Carranza, Gabriel; Lopez-Almazo, Andres G.; Betancourt-Figueroa, Felipe; Pena-Loredo, Pablo; Alquicira-Hernandez, Shirley; Ledezma-Tejeida, Daniela; Arizmendi-Zagal, Lizeth; Mendez-Hernandez, Francisco; Diaz-Gomez, Ana K.; Ochoa-Praxedis, Elizabeth; Muniz-Rascado, Luis J.; Garcia-Sotelo, Jair S.; Flores-Gallegos, Fanny A.; Gomez, Laura; Bonavides-Martinez, Cesar; del Moral-Chavez, Victor M.; Hernandez-Alvarez, Alfredo J.; Santos-Zavaleta, Alberto; Capella-Gutierrez, Salvador; Gelpi, Josep Lluis; Collado-Vides, Julio

Regulatory promoter architectures in the hands of thermodynamic modelling

NATURE REVIEWS GENETICS

IF52

2023-02-06

PREAI

Collado-Vides, Julio

RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12

MICROBIAL GENOMICS

IF4

2022-05-27

OAAI

Tierrafria, Victor H.; Rioualen, Claire; Salgado, Heladia; Lara, Paloma; Gama-Castro, Socorro; Lally, Patrick; Gomez-Romero, Laura; Pena-Loredo, Pablo; Lopez-Almazo, Andres G.; Alarcon-Carranza, Gabriel; Betancourt-Figueroa, Felipe; Alquicira-Hernandez, Shirley; Polanco-Morelos, J. Enrique; Garcia-Sotelo, Jair; Gaytan-Nunez, Estefani; Mendez-Cruz, Carlos-Francisco; Muniz, Luis J.; Bonavides-Martinez, Cesar; Moreno-Hagelsieb, Gabriel; Galagan, James E.; Wade, Joseph T.; Collado-Vides, Julio

Missing Links Between Gene Function and Physiology in Genomics

FRONTIERS IN PHYSIOLOGY

IF3.4

2022-02-28

OAAI

Collado-Vides, Julio; Gaudet, Pascale; de Lorenzo, Victor

The EcoCyc Database in 2021

FRONTIERS IN MICROBIOLOGY

IF4.5

2021-07-28

157

OAAI

Keseler, Ingrid M.; Gama-Castro, Socorro; Mackie, Amanda; Billington, Richard; Bonavides-Martinez, Cesar; Caspi, Ron; Kothari, Anamika; Krummenacker, Markus; Midford, Peter E.; Muniz-Rascado, Luis; Ong, Wai Kit; Paley, Suzanne; Santos-Zavaleta, Alberto; Subhraveti, Pallavi; Tierrafria, Victor H.; Wolfe, Alan J.; Collado-Vides, Julio; Paulsen, Ian T.; Karp, Peter D.

Knowledge extraction for assisted curation o f summaries of bacterial transcription factor prorerties

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION

IF3.6

2020-12-11

OAAI

Mendez-Cruz, Carlos-Francisco; Blanchet, Antonio; Godinez, Alan; Arroyo-Fernandez, Ignacio; Gama-Castro, Socorro; Berenice Martinez-Luna, Sara; Gonzalez-Colin, Cristian; Collado-Vides, Julio

Redefining fundamental concepts of transcription initiation in bacteria 重新定义细菌转录起始的基本概念

NATURE REVIEWS GENETICS

IF52

2020-07-14

OAAI

Mejia-Almonte, Citlalli; Busby, Stephen J. W.; Wade, Joseph T.; van Helden, Jacques; Arkin, Adam P.; Stormo, Gary D.; Eilbeck, Karen; Palsson, Bernhard O.; Galagan, James E.; Collado-Vides, Julio

PulmonDB: a curated lung disease gene expression database

SCIENTIFIC REPORTS

IF3.9

2020-01-16

OAAI

Villasenor-Altamirano, Ana B.; Moretto, Marco; Maldonado, Mariel; Zayas-Del Moral, Alejandra; Munguia-Reyes, Adrian; Romero, Yair; Garcia-Sotelo, Jair S.; Aguilar, Luis A.; Aldana-Assad, Oscar; Engelen, Kristof; Selman, Moises; Collado-Vides, Julio; Balderas-Martinez, Yalbi, I; Medina-Rivera, Alejandra

Limits to a classic paradigm: most transcription factors in E. coli regulate genes involved in multiple biological processes

NUCLEIC ACIDS RESEARCH

IF13.1

2019-06-13

OAAI

Ledezma-Tejeida, Daniela; Altamirano-Pacheco, Luis; Fajardo, Vicente; Collado-Vides, Julio

Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes

BMC GENOMICS

IF3.7

2019-04-16

OAAI

Santos-Zavaleta, A.; Perez-Rueda, E.; Sanchez-Perez, M.; Velazquez-Ramirez, D. A.; Collado-Vides, J.

RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12

NUCLEIC ACIDS RESEARCH

IF13.1

2018-11-05

280

OAAI

Santos-Zavaleta, Alberto; Salgado, Heladia; Gama-Castro, Socorro; Sanchez-Perez, Mishael; Gomez-Romero, Laura; Ledezma-Tejeida, Daniela; Santiago Garcia-Sotelo, Jair; Alquicira-Hernandez, Kevin; Jose Muniz-Rascado, Luis; Pena-Loredo, Pablo; Ishida-Gutierrez, Cecilia; Velazquez-Ramirez, David A.; Del Moral-Chavez, Victor; Bonavides-Martinez, Cesar; Mendez-Cruz, Carlos-Francisco; Galagan, James; Collado-Vides, Julio

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

IF3.6

2017-09-26

OAAI

Mendez-Cruz, Carlos-Francisco; Gama-Castro, Socorro; Mejia-Almonte, Citlalli; Castillo-Villalba, Marco-Polo; Muniz-Rascado, Luis-Jose; Collado-Vides, Julio

Genome-Wide Mapping of Transcriptional Regulation and Metabolism Describes Information-Processing Units in Escherichia coli

FRONTIERS IN MICROBIOLOGY

IF4.5

2017-08-03

OAAI

Ledezma-Tejeida, Daniela; Ishida, Cecilia; Collado-Vides, Julio

Improving biocuration of microRNAs in diseases: a case study in idiopathic pulmonary fibrosis

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION

IF3.6

2017-04-22

OAAI

Itzel Balderas-Martinez, Yalbi; Rinaldi, Fabio; Contreras, Gabriela; Solano-Lira, Hilda; Sanchez-Perez, Mishael; Collado-Vides, Julio; Selman, Moises; Pardo, Annie

Strategies towards digital and semi-automated curation in RegulonDB (vol 2017, bax012, 2017)

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION

IF3.6

2017-04-17

OAAI

Rinaldi, Fabio; Lithgow, Oscar; Gama-Castro, Socorro; Solano, Hilda; Lopez-Fuentes, Alejandra; Muniz Rascado, Luis Jose; Ishida-Gutierrez, Cecilia; Mendez-Cruz, Carlos-Francisco; Collado-Vides, Julio

Strategies towards digital and semi-automated curation in RegulonDB

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION

IF3.6

2017-03-18

OAAI

Rinaldi, Fabio; Lithgow, Oscar; Gama-Castro, Socorro; Solano, Hilda; Lopez, Alejandra; Rascado, Luis Jose Muniz; Ishida-Gutierrez, Cecilia; Mendez-Cruz, Carlos-Francisco; Collado-Vides, Julio

The EcoCyc database: reflecting new knowledge about Escherichia coli K-12

NUCLEIC ACIDS RESEARCH

IF13.1

2016-11-28

466

OAAI

Keseler, Ingrid M.; Mackie, Amanda; Santos-Zavaleta, Alberto; Billington, Richard; Bonavides-Martinez, Cesar; Caspi, Ron; Fulcher, Carol; Gama-Castro, Socorro; Kothari, Anamika; Krummenacker, Markus; Latendresse, Mario; Muniz-Rascado, Luis; Ong, Quang; Paley, Suzanne; Peralta-Gil, Martin; Subhraveti, Pallavi; Velazquez-Ramirez, David A.; Weaver, Daniel; Collado-Vides, Julio; Paulsen, Ian; Karp, Peter D.

In silico clustering of Salmonella global gene expression data reveals novel genes co-regulated with the SPI-1 virulence genes through HilD

SCIENTIFIC REPORTS

IF3.9

2016-11-25

OAAI

Martinez-Flores, Irma; Perez-Morales, Deyanira; Sanchez-Perez, Mishael; Paredes, Claudia C.; Collado-Vides, Julio; Salgado, Heladia; Bustamante, Victor H.

COLOMBOS v3.0: leveraging gene expression compendia for cross- species analyses

NUCLEIC ACIDS RESEARCH

IF13.1

2015-11-19

OAAI

Moretto, Marco; Sonego, Paolo; Dierckxsens, Nicolas; Brilli, Matteo; Bianco, Luca; Ledezma-Tejeida, Daniela; Gama-Castro, Socorro; Galardini, Marco; Romualdi, Chiara; Laukens', Kris; Collado-Vides, Julio; Meysman, Pieter; Engelen, Kristof

研究方向