Dr. Victor Hugo Tierrafria Pulido
Investigador Posdoctoral SECIHTI
Doctorado, Doctor en Ciencias, 2019
* Indica publicación con otra institución de adscripción
Total de publicaciones: 17
- Tipo
- Fecha
Artículo
1 - Lally,P., Gomez-Romero,L., Tierrafria,V.H., Aquino,P., Rioualen,C., Zhang,X., Kim,S., Baniulyte,G., Plitnick,J., Smith,C., Babu,M., Collado-Vides,J., Wade,J.T., Galagan,J.E. (2025). Predictive biophysical neural network modeling of a compendium of in vivo transcription factor DNA binding profiles for Escherichia coli.
Nature Communications,
16 (1).
*
Artículo
2 - Lara,P., Gama-Castro,S., Salgado,H., Rioualen,C., Tierrafria,V.H., Muniz-Rascado,L.J., Bonavides-Martinez,C., Collado-Vides,J. (2024). Flexible gold standards for transcription factor regulatory interactions in Escherichia coli K-12: architecture of evidence types.
Frontiers in Genetics,
15.
*
Revisión
3 - Karp,P.D., Paley,S., Caspi,R., Kothari,A., Krummenacker,M., Midford,P.E., Moore,L.R., Subhraveti,P., Gama-Castro,S., Tierrafria,V.H., Lara,P., Muniz-Rascado,L., Bonavides-Martinez,C., Santos-Zavaleta,A., Mackie,A., Sun,G., hn-Horst,T.A., Choi,H., Covert,M.W., Collado-Vides,J., Paulsen,I. (2023). The EcoCyc Database (2023).
Ecosal Plus,
11 (1).
*
Revisión
4 - Femerling,G., Gama-Castro,S., Lara,P., Ledezma-Tejeida,D., Tierrafria,V.H., Muniz-Rascado,L., Bonavides-Martinez,C., Collado-Vides,J. (2022). Sensory Systems and Transcriptional Regulation in Escherichia coli.
Frontiers in Bioengineering and Biotechnology,
10.
*
Artículo
5 - Tierrafria,V.H., Rioualen,C., Salgado,H., Lara,P., Gama-Castro,S., Lally,P., Gomez-Romero,L., Pena-Loredo,P., Lopez-Almazo,A.G., Alarcon-Carranza,G., Betancourt-Figueroa,F., Alquicira-Hernandez,S., Polanco-Morelos,J.E., Garcia-Sotelo,J., Gaytan-Nunez,E., Mendez-Cruz,C.F., Muniz,L.J., Bonavides-Martinez,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).
*
Artículo
6 - Diaz-Rodriguez,M., Lithgow-Serrano,O., Guadarrama-Garcia,F., Tierrafria,V.H., Gama-Castro,S, Solano-Lira,H, Salgado,H, Rinaldi,F, Mendez-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 (BBA) - Gene Regulatory Mechanisms,
1864 (11-12).
*
Article
7 - Keseler,I.M., Gama-Castro,S., Mackie,A., Billington,R., Bonavides-Martinez,C., Caspi,R., Kothari,A., Krummenacker,M., Midford,P.E., Muniz-Rascado,L., Ong,W.K., Paley,S., Santos-Zavaleta,A., Subhraveti,P., Tierrafria,V.H, Wolfe,A.J, Collado-Vides,J, Paulsen,I.T, Karp,P.D (2021). The EcoCyc Database in 2021.
Frontiers in Microbiology,
12.
*
Artículo
8 - Centeno-Leija,S., Tapia-Cabrera,S., Guzman-Trampe,S., Esquivel,B., Esturau-Escofet,N., Tierrafria,V.H., Rodriguez-Sanoja,R., Zarate-Romero,A., Stojanoff,V., Rudino-Pinera,E., Sanchez,S., Serrano-Posada,H. (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.
Artículo
9 - Lithgow-Serrano,O., Gama-Castro,S., Ishida-Gutierrez,C., Mejia-Almonte,C., Tierrafria,V.H., Martinez-Luna,S., Santos-Zavaleta,A., Velazquez-Ramirez,D., Collado-Vides,J. (2019). Similarity corpus on microbial transcriptional regulation.
Journal of Biomedical Semantics,
10 (1).
*
Artículo
10 - Tierrafria,V.H., Mejia-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.
*
Artículo
11 - Santos-Zavaleta,A., Sanchez-Perez,M., Salgado,H., Velazquez-Ramirez,D.A., Gama-Castro,S., Tierrafria,V.H., Busby,S.J.W, Aquino,P, Fang,X, Palsson,B.O, Galagan,J.E, Collado-Vides,J (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).
*
Artículo
12 - Romero-Rodriguez,A., Ruiz-Villafan,B., Tierrafria,V.H., Rodriguez-Sanoja,R., Sanchez,S. (2016). Carbon Catabolite Regulation of Secondary Metabolite Formation and Morphological Differentiation in Streptomyces coelicolor.
Applied Biochemistry and Biotechnology,
180 (6),
1152-1166.
*
Artículo
13 - Romero-Rodriguez,A., Rocha,D., Ruiz-Villafan,B., Tierrafria,V., Rodriguez-Sanoja,R., Segura-Gonzalez,D., Sanchez,S. (2016). Transcriptomic analysis of a classical model of carbon catabolite regulation in Streptomyces coelicolor.
BMC Microbiology,
16 (1),
77.
Artículo
14 - Tierrafria,V.H., Licona-Cassani,C., Maldonado-Carmona,N., Romero-Rodriguez,A., Centeno-Leija,S., Marcellin,E., Rodriguez-Sanoja,R., Ruiz-Villafan,B., Nielsen,L.K., Sanchez,S. (2016). Deletion of the hypothetical protein SCO2127 of Streptomyces coelicolor allowed identification of a new regulator of actinorhodin production.
Applied Microbiology and Biotechnology,
100 (21),
9229-9237 [Correction 104 (8) 3687].
*
Artículo
15 - Tierrafria,V.H., Ramos-Aboites,H.E., Gosset,G., Barona-Gomez,F. (2011). Disruption of the siderophore-binding desE receptor gene in Streptomyces coelicolor A3(2) results in impaired growth in spite of multiple iron-siderophore transport systems.
Microbial Biotechnology,
4 (2),
275-285.
Preprint
16 - Lara,P., Gama-Castro,S., Salgado,H., Rioualen,C., Muniz-Rascado,L.J., Garcia-Sotelo,J.S., Tierrafria,V.H., Collado-Vides,J. (2023). A Gold Standard for Transcription Factor-Gene Regulatory Interactions in Escherichia coli K-12: Architecture of the Evidence Types.
bioRxiv,
Preprint posted April 30.
*
17 - Tierrafria Pulido, Victor Hugo (2010). Determinacion de la especificidad de los transportadores de ferroxaminas B y E en Streptomyces coelicolor mediante ingenieria genetica : repercusion en el proceso biotecnologico de purificacion de desferroxamina B (desferal) .
Instituto de Biotecnologia,
Maestria en Ciencias Bioquimicas,
UNAM.
Asesor: Barona Gomez, Francisco
Artículo
18 - Lally,P., Gomez-Romero,L., Tierrafria,V.H., Aquino,P., Rioualen,C., Zhang,X., Kim,S., Baniulyte,G., Plitnick,J., Smith,C., Babu,M., Collado-Vides,J., Wade,J.T., Galagan,J.E.. Predictive biophysical neural network modeling of a compendium of in vivo transcription factor DNA binding profiles for Escherichia coli.
Nature Communications,
16 (1).
*
Artículo
19 - Lara,P., Gama-Castro,S., Salgado,H., Rioualen,C., Tierrafria,V.H., Muniz-Rascado,L.J., Bonavides-Martinez,C., Collado-Vides,J.. Flexible gold standards for transcription factor regulatory interactions in Escherichia coli K-12: architecture of evidence types.
Frontiers in Genetics,
15.
*
Revisión
20 - Karp,P.D., Paley,S., Caspi,R., Kothari,A., Krummenacker,M., Midford,P.E., Moore,L.R., Subhraveti,P., Gama-Castro,S., Tierrafria,V.H., Lara,P., Muniz-Rascado,L., Bonavides-Martinez,C., Santos-Zavaleta,A., Mackie,A., Sun,G., hn-Horst,T.A., Choi,H., Covert,M.W., Collado-Vides,J., Paulsen,I.. The EcoCyc Database (2023).
Ecosal Plus,
11 (1).
*
Preprint
21 - Lara,P., Gama-Castro,S., Salgado,H., Rioualen,C., Muniz-Rascado,L.J., Garcia-Sotelo,J.S., Tierrafria,V.H., Collado-Vides,J.. A Gold Standard for Transcription Factor-Gene Regulatory Interactions in Escherichia coli K-12: Architecture of the Evidence Types.
bioRxiv,
Preprint posted April 30.
*
Revisión
22 - Femerling,G., Gama-Castro,S., Lara,P., Ledezma-Tejeida,D., Tierrafria,V.H., Muniz-Rascado,L., Bonavides-Martinez,C., Collado-Vides,J.. Sensory Systems and Transcriptional Regulation in Escherichia coli.
Frontiers in Bioengineering and Biotechnology,
10.
*
Artículo
23 - Tierrafria,V.H., Rioualen,C., Salgado,H., Lara,P., Gama-Castro,S., Lally,P., Gomez-Romero,L., Pena-Loredo,P., Lopez-Almazo,A.G., Alarcon-Carranza,G., Betancourt-Figueroa,F., Alquicira-Hernandez,S., Polanco-Morelos,J.E., Garcia-Sotelo,J., Gaytan-Nunez,E., Mendez-Cruz,C.F., Muniz,L.J., Bonavides-Martinez,C., Moreno-Hagelsieb,G., Galagan,J.E., Wade,J.T., Collado-Vides,J.. RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12.
Microbial Genomics,
8 (5).
*
Artículo
24 - Diaz-Rodriguez,M., Lithgow-Serrano,O., Guadarrama-Garcia,F., Tierrafria,V.H., Gama-Castro,S, Solano-Lira,H, Salgado,H, Rinaldi,F, Mendez-Cruz,C.F., Collado-Vides,J. Lisen&Curate: A platform to facilitate gathering textual evidence for curation of regulation of transcription initiation in bacteria.
Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms,
1864 (11-12).
*
Article
25 - Keseler,I.M., Gama-Castro,S., Mackie,A., Billington,R., Bonavides-Martinez,C., Caspi,R., Kothari,A., Krummenacker,M., Midford,P.E., Muniz-Rascado,L., Ong,W.K., Paley,S., Santos-Zavaleta,A., Subhraveti,P., Tierrafria,V.H, Wolfe,A.J, Collado-Vides,J, Paulsen,I.T, Karp,P.D. The EcoCyc Database in 2021.
Frontiers in Microbiology,
12.
*
Artículo
26 - Centeno-Leija,S., Tapia-Cabrera,S., Guzman-Trampe,S., Esquivel,B., Esturau-Escofet,N., Tierrafria,V.H., Rodriguez-Sanoja,R., Zarate-Romero,A., Stojanoff,V., Rudino-Pinera,E., Sanchez,S., Serrano-Posada,H.. 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.
Artículo
27 - Lithgow-Serrano,O., Gama-Castro,S., Ishida-Gutierrez,C., Mejia-Almonte,C., Tierrafria,V.H., Martinez-Luna,S., Santos-Zavaleta,A., Velazquez-Ramirez,D., Collado-Vides,J.. Similarity corpus on microbial transcriptional regulation.
Journal of Biomedical Semantics,
10 (1).
*
Artículo
28 - Tierrafria,V.H., Mejia-Almonte,C., Camacho-Zaragoza,J.M., Salgado,H., Alquicira,K., Ishida,C., Gama-Castro,S., Collado-Vides,J.. MCO: Towards an ontology and unified vocabulary for a framework-based annotation of microbial growth conditions.
Bioinformatics,
35 (5),
856-864.
*
Artículo
29 - Santos-Zavaleta,A., Sanchez-Perez,M., Salgado,H., Velazquez-Ramirez,D.A., Gama-Castro,S., Tierrafria,V.H., Busby,S.J.W, Aquino,P, Fang,X, Palsson,B.O, Galagan,J.E, Collado-Vides,J. 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).
*
Artículo
30 - Romero-Rodriguez,A., Ruiz-Villafan,B., Tierrafria,V.H., Rodriguez-Sanoja,R., Sanchez,S.. Carbon Catabolite Regulation of Secondary Metabolite Formation and Morphological Differentiation in Streptomyces coelicolor.
Applied Biochemistry and Biotechnology,
180 (6),
1152-1166.
*
Artículo
31 - Romero-Rodriguez,A., Rocha,D., Ruiz-Villafan,B., Tierrafria,V., Rodriguez-Sanoja,R., Segura-Gonzalez,D., Sanchez,S.. Transcriptomic analysis of a classical model of carbon catabolite regulation in Streptomyces coelicolor.
BMC Microbiology,
16 (1),
77.
Artículo
32 - Tierrafria,V.H., Licona-Cassani,C., Maldonado-Carmona,N., Romero-Rodriguez,A., Centeno-Leija,S., Marcellin,E., Rodriguez-Sanoja,R., Ruiz-Villafan,B., Nielsen,L.K., Sanchez,S.. Deletion of the hypothetical protein SCO2127 of Streptomyces coelicolor allowed identification of a new regulator of actinorhodin production.
Applied Microbiology and Biotechnology,
100 (21),
9229-9237 [Correction 104 (8) 3687].
*
Artículo
33 - Tierrafria,V.H., Ramos-Aboites,H.E., Gosset,G., Barona-Gomez,F.. Disruption of the siderophore-binding desE receptor gene in Streptomyces coelicolor A3(2) results in impaired growth in spite of multiple iron-siderophore transport systems.
Microbial Biotechnology,
4 (2),
275-285.
34 - Tierrafria Pulido, Victor Hugo. Determinacion de la especificidad de los transportadores de ferroxaminas B y E en Streptomyces coelicolor mediante ingenieria genetica : repercusion en el proceso biotecnologico de purificacion de desferroxamina B (desferal) .
Instituto de Biotecnologia,
Maestria en Ciencias Bioquimicas,
UNAM.
Asesor: Barona Gomez, Francisco