Yeast and nonyeast fungi: the hidden allies in pulque fermentation Carolina Rocha-Arriaga, Alfredo Cruz-Ramirez. 2022. Elsevier. doi: 10.1016/j.cofs.2022.100878

Construction of the axolotl cell landscape using combinatorial hybridization sequencing at single-cell resolution Fang Ye, Guodong Zhang, Haide Chen, Chengxuan Yu, Lei Yang, Yuting Fu, Jiaqi Li, Sulei Fu, Zhongyi Sun, Lijiang Fei, Qile Guo, Jingjing Wang, Yanyu Xiao, Xinru Wang, Peijing Zhang, Lifeng Ma, Dapeng Ge, Suhong Xu, Juan Caballero-Pérez, Alfredo Cruz-Ramírez, Yincong Zhou, Ming Chen, Ji-Feng Fei, Xiaoping Han, Guoji Guo. 2022. Nature Communications 13.1, 1-18. doi: 10.1016/j.ydbio.2020.08.002

Predicted landscape of RETINOBLASTOMA-RELATED LxCxE-mediated interactions across the Chloroplastida Jesus León-Ruiz, Alfredo Cruz-Ramírez 2022. The Plant Journal. doi: 10.1111/tpj.16012

Cancer in amphibia, a rare phenomenon? Esteban Torres-Dimas, Alfredo Cruz-Ramirez, Rosa M. Bermúdez-Cruz. 2022. Cell Biology International. doi: 10.1002/cbin.11888

Transcriptional analysis of Ceratopteris richardii young sporophyte reveals conservation of stem cell factors in the root apical meristem Alejandro Aragón-Raygoza, Luis Herrera-Estrella, Alfredo Cruz-Ramirez. 2022. Frontiers in Plant Science. doi: 10.3389/fpls.2022.924660

Evidence of requirement for homologous-mediated DNA repair during Ambystoma mexicanum limb regeneration Ulises Omar García-Lepe, Esteban Torres-Dimas, Annie Espinal-Centeno, Alfredo Cruz-Ramírez, Rosa Maria Bermúdez-Cruz. 2022. Developmental Dynamics 251.6, 1035-1053. doi: 10.1002/dvdy.455

RETINOBLASTOMA RELATED (RBR) interaction with key factors of the RNA-directed DNA methylation (RdDM) pathway Jesus Leon-Ruiz, Annie Espinal-Centeno, Ikram Blilou, Ben Scheres, Alfredo. Arteaga-Vazquez, Mario and Cruz-Ramirez. 2022. BioRxiv. doi: 10.1101/2022.01.06

Arabidopsis thaliana PrimPol is a primase and lesion bypass DNA polymerase with the biochemical characteristics to cope with DNA damage in the nucleus, mitochondria, and chloroplast Paola L García-Medel, Antolín Peralta-Castro, Noe Baruch-Torres, Alma Fuentes-Pascacio, José A Pedroza-García, Alfredo Cruz-Ramirez, Luis G Brieba. 2021. Scientific reports. 11.1, 1-14. doi: 10.1038/s41598-021-00151-7

Science forum: vision, challenges and opportunities for a plant cell atlas Suryatapa Ghosh Jha, Alexander T Borowsky, Benjamin J Cole, Noah Fahlgren, Andrew Farmer, Shao-Shan Carol Huang, Purva Karia, Marc Libault, Nicholas J Provart, Selena L Rice, Maite Saura-Sanchez, Pinky Agarwal, Amir H Ahkami, Christopher R Anderton, Steven P Briggs, Jennifer An Brophy, Peter Denolf, Luigi F Di Costanzo, Moises Exposito-Alonso, Stefania Giacomello, Fabio Gomez-Cano, Kerstin Kaufmann, Dae Kwan Ko, Sagar Kumar, Andrey V Malkovskiy, Naomi Nakayama, Toshihiro Obata, Marisa S Otegui, Gergo Palfalvi, Elsa H Quezada-Rodríguez, Rajveer Singh, R Glen Uhrig, Jamie Waese, Klaas Van Wijk, R Clay Wright, David W Ehrhardt, Kenneth D Birnbaum, Seung Y Rhee, Plant Cell Atlas Consortium. 2021. Elife. doi: 10.7554/eLife.66877

Pickle Recruits Retinoblastoma Related 1 to Control Lateral Root Formation in Arabidopsis Stéphanie Robert and László Bako Krisztina Ötvös, Pál Miskolczi, Peter Marhavý, Alfredo Cruz-Ramírez, Eva Benková. 2021. Intl. J. Mol. Sci.. doi: 10.3390/ijms22083862

DNA repair during regeneration in Ambystoma mexicanum. Ulises García-Lepe, Alfredo Cruz-Ramírez, R. Bermúdez-Cruz. 2021. Developmental Dynamics, 250.6, 788-799. doi: 10.1002/dvdy.276

Development and Cell Cycle Activity of the Root Apical Meristem in the Fern Ceratopteris richardii Alejandro Aragón-Raygoza, Alejandra Vasco, Ikram Blilou, Luis Herrera-Estrella, Alfredo Cruz-Ramírez. 2020. Genes, 11.12: 1455. doi: 10.3390/genes11121455

Conservation analysis of core cell cycle regulators and their transcriptional behavior during limb regeneration in Ambystoma mexicanum Annie Espinal-Centeno, Melissa Dipp-Álvarez, Carlos Saldaña, Laszlo Bako, Alfredo Cruz-Ramírez. 202. Mechanisms of Development, 164. doi: 10.1016/j.mod.2020.103651Get

Deep microbial community profiling along the fermentation process of pulque, a biocultural resource of Mexico Carolina Rocha-Arriaga, Annie Espinal-Centeno, Shamayim Martinez-Sánchez, Juan Caballero-Pérez, Luis D Alcaraz, Alfredo Cruz-Ramírez. 2020. Microbiological Research, 241. doi: 10.1016/j.micres.2020.126593

Functional Characterization of the Lin28/let-7 Circuit During Forelimb Regeneration in Ambystoma mexicanum and Its Influence on Metabolic Reprogramming Hugo Varela-Rodríguez, Diana G Abella-Quintana, Annie Espinal-Centeno, Luis Varela-Rodríguez, David Gomez-Zepeda, Juan Caballero-Pérez, Paola L García-Medel, Luis G Brieba, José J Ordaz-Ortiz, Alfredo Cruz-Ramirez. 2020. Frontiers in cell and developmental biology. doi: 10.3389/fcell.2020.562940

Transcriptional and Morpho-Physiological Responses of Marchantia polymorpha upon Phosphate Starvation Félix Rico-Reséndiz, Sergio Alan Cervantes-Pérez, Annie Espinal-Centeno, Melissa Dipp-Álvarez, Araceli Oropeza-Aburto, Enrique Hurtado-Bautista, Andrés Cruz-Hernández, John L Bowman, Kimitsune Ishizaki, Mario A Arteaga-Vázquez, Luis Herrera-Estrella, Alfredo Cruz-Ramírez. 2020. International journal of molecular sciences. doi: 10.3390/ijms21218354

Phosphate Starvation Triggers Transcriptional Changes in the Biosynthesis and Signaling Pathways of Phytohormones in Marchantia polymorpha F Rico-Reséndiz, Z Diaz-Santana, M Dipp-Álvarez, A Cruz-Hernández, J Bowman, L Herrera-Estrella, K Ishizaki, A Artega-Vázquez, M and Cruz-Ramírez. 2020. Proceedings, IECPS. doi: 10.3390/IECPS2020-08729

miRNAs analysis during marigold (Tagetes erecta) flower development A. Cruz-Ramirez, A., Ferrusquilla, N., Aguilar-Ruiz, C., Gonzalez-Marques, M., Arellano-Perusquia, A and Cruz-Hernández. 2020 Acta Hortic. XXX IHC – Proc. International Symposium on Applied Functional Molecular Biology. doi: 10.17660/ActaHortic.2020.1297.81

Multi-organ transcriptomic landscape of Ambystoma velasci metamorphosis J Palacios-Martínez, J Caballero-Pérez, A Espinal-Centeno, G Marquez-Chavoya, H Lomelí, E Salas-Vidal, Schnabel, D, J Chimal-Monroy, A Cruz-Ramírez. 2020 Developmental Biolgy. 466(1-2), 22-35. doi: 10.1016/j.ydbio.2020.08.002

A Phylogenetic Study of the ANT Family Points to a preANT Gene as the Ancestor of Basal and euANT Transcription Factors in Land Plants. Dipp-Álvarez M, Cruz-Ramírez A. 2019.Frontiers in Plant Science. DOI=10.3389/fpls.2019.00017.

Emergent protective organogenesis in date palms: A Morpho-devo-dynamic adaptive strategy during early development." Tingting Xiao, Alejandro Aragón-Raygoza, Juan Caballero-Pérez, Gwendolyn Kirschner, Yanming Deng, Brian Atkinson, Craig Sturrock, Vinicius Lube, Jian You Wang, Gilles Lubineau, Salim Al-Babili, Alfredo Cruz-Ramírez, Malcolm Bennett and Ikram Blilou. 2019, The Plant Cell. In press

CONSTITUTIVE TRIPLE RESPONSE1 and PIN2 act in a coordinate manner to support the indeterminate root growth and meristem cell proliferating activity in Arabidopsis seedlings. Méndez-Bravo A, Ruiz-Herrera LF, Cruz-Ramírez A, Guzman P., Martínez-Trujillo M, Ortiz-Castro R, López-Bucio J.2019. Plant Science. 175-186

Transcriptional profiling of the CAM plant Agave salmiana reveals conservation of a genetic program for regeneration. Sergio Alan Cervantes-Pérez, Annie Espinal-Centeno, Araceli Oropeza-Aburto, Juan Caballero, Francisco Falcon, Alejandro Aragón-Raygoza, Lino Sánchez-Segura, Luis Herrera-Estrella, Andrés Cruz-Hernández, Alfredo Cruz-Ramírez. 2018. Developmental Biology.

The axolotl genome and the evolution of key tissue formation regulators. Sergej Nowoshilow, Siegfried Schloissnig, Ji-Feng Fei, Andreas Dahl, Andy Wing Chun Pang, Martin Pippel, Sylke Winkler, Alex R Hastie, George Robert Young, Juliana Roscito, Francisco Falcon, Dunja Knapp, Sean Powell, Alfredo Cruz-Ramírez, Han Cao, Bianca Habermann, Michael Hiller, Elly M Tanaka, Eugene W Myers. 2018. Nature 554:50-55

Transcriptional landscapes of Axolotl (Ambystoma mexicanum). Juan Caballero, Annie Espinal-Centeno, Francisco Falcon, Luis Fernando García-Ortega, Everardo Curiel-Quesada, Andrés Cruz-Hernandez, László Bakó, Xuemei Chen, Octavio Martínez, Mario Arteaga-Vazquez, Luis Herrera-Estrella, Alfredo Cruz-Ramírez. 2017. Developmental Biology. 433:227-239

XYLEM NAC DOMAIN1, an angiosperm NAC transcription factor, inhibits xylem differentiation through conserved motifs that interact with RETINOBLASTOMA-RELATED. Chengsong Zhao, Theres Lasses, László Bakó, Danyu Kong, Bingyu Zhao, Bidisha Chanda, Aureliano Bombarely, Alfredo Cruz-Ramírez, Ben scheres, Amy M. Brunner, Eric P. Beers. 2017. New Phythologist. 216: 76-89

Phosphate Starvation-Dependent Iron Mobilization Induces CLE14 Expression to Trigger Root Meristem Differentiation through CLV2/PEPR2 Signaling. Dolores Gutierrez Alanis, Lenin Yong, Pedro Jiménez, Funlgencio Alatorre-Cobos, Araceli Oropeza-Aburto, Javier Mora, Federico Sánchez-Rodríguez, Alfredo Cruz-Ramírez, Luis Herrera-Estrella. 2017. Developmental Cell 41:555-570

Computational Modeling of Auxin: A Foundation for Plant Engineering. Alejandro Morales-Tapia and Alfredo Cruz Ramirez. 2016. Front. Plant Sci. (7) 1881. doi: 10.3389/fpls.2016.01881

A phosphate starvation-driven bidirectional promoter as a potential tool for crop improvement and in vitro plant biotechnology. Araceli Oropeza-Aburto, Alfredo Cruz-Ramírez A, Javier Mora-Macías, Luis Herrera-Estrella. 2016. Plant Biotechnol J. Oct 24.doi: 10.1111/pbi.12653. [Epub ahead of print] PubMed PMID: 27775858.

MicroRNAs Sequencing for Understanding the Genetic Regulation of Plant Genomes. Christopher Cedillo, Marcelo Hernández-Salazar, Tania Escobar-Feregrino, Juan Caballero, Mario Arteaga-Vazquez, Alfredo Cruz-Ramírez, Irineo Torres Pacheco, Ramón Gerardo Guevara-Gonzalez, Andres Cruz-Hernandez. 2016. In Plant Genomics.

The Role of microRNAs in Animal Cell Reprogramming. María Concepción Cruz-Santos, Alejandro Aragón-Raygoza, Annie Espinal-Centeno,Mario Arteaga-Vázquez, Andrés Cruz-Hernández, Laszlo Bako, and Alfredo Cruz-Ramírez. 2016. Stem Cells and Development 25.14, 1035-1049.

RETINOBLASTOMA-RELATED protein stimulates cell differentiation in the Arabidopsis root meristem by interacting with cytokinin signaling. Serena Perilli, Jose Manuel Perez-Perez, Riccardo Di Mambro , Cristina Llavata Peris, Sara Díaz-Triviño, Del Marta del Bianco, Emanuela Pierdonati, Laila Moubayidin, Alfredo Cruz-Ramírez, Paolo Costantino, Ben Scheres, Sabrina Sabatini. 2016. Plant Cell 25:4469-78.

Methylome analysis reveals an important role for epigenetic changes in the regulation of the Arabidopsis response to phosphate starvation. Lenin Yong-Villalobos, Sandra Isabel González-Morales, Kazimierz Wrobel, Dolores Gutiérrez-Alanis, Sergio Alan Cervantes-Peréz, Corina Hayano-Kanashiro, Araceli Oropeza-Aburto, Alfredo Cruz-Ramírez, Octavio Martínez, and Luis Herrera-Estrella. 2015. PNAS 112 (52) E7293-E7302; published ahead of print December 14, 2015, doi:10.1073/pnas.1522301112.

Reprogramación celular de embriones de Anthurium andraeanum por fitohormonas para micropropagación masiva. Julieta Mireles-Ordaz, Abraham Arellano-Perusquia, Annie Espinal-Centeno, Lino Sánchez-Segura, Andrés Estrada-Luna, and Luis Alfredo Cruz-Ramírez. 2015. Nova Scientia Vol. 7, núm. 15: 49-67.

Arabidopsis BIRD Zinc Finger Proteins Jointly Stabilize Tissue Boundaries by Confining the Cell Fate Regulator SHORT-ROOT and Contributing to Fate Specification. Yuchen Long, Wouter Smet, Alfredo Cruz-Ramírez, Bas Castelijns, Wim de Jonge, Ari Pekka Mähönen, Benjamin P. Bouchetd, Gabino Sanchez Perez, Anna Akhmanova, Ben Scheres, and Ikram Blilou. 2015. The Plant Cell.

Irreversible fate commitment in the Arabidopsis stomatal lineage requires a FAMA and RETINOBLASTOMA-RELATED module. Juliana L. Matos, Charles Hachez, On Su Lau, Alfredo Cruz-Ramírez, Ben Scheres, Dominique C. Bergman. 2014. eLife 03271.

Plants as Bioreactors for Human Health Nutrients. Chapter 15 in Biosystems Engineering: Biofactories for Food Production in the Century XXI. Cruz-Ramírez Luis Alfredo, García-Ramírez Jesús Agustín, Rico-Resendiz Felix Edgardo, Membrilla-Ochoa Alfonso, Herrada-Alonso Janette, Escobar-Feregrino Tania, Torres-Pacheco Irineo, Guevara-González G. Ramón,Campos-Guillén Juan and Cruz-Hernández Andrés. 2013. Springer International Publishing, 423-54.

A SCARECROW-RETINOBLASTOMA Protein Network Controls Protective Quiescence in the Arabidopsis Root Stem Cell Organizer. Alfredo Cruz-Ramírez, Sara Díaz-Triviño, Guy Wachsman, Yujuan Du, Mario Arteága-Vázquez, Hongtao Zhang, Rene Benjamins, Ikram Blilou, Anne B. Neef, Vicki Chandler and Ben Scheres. 2013. Plos Biology, 11: e1001724.

An attenuated bi-stable circuit involving SCARECROW-RETINOBLASTOMA interaction mediates asymmetric stem cell divisions in Arabidopsis. Alfredo Cruz-Ramírez, Sara Díaz-Triviño, Ikram Blilou, Verónica A. Grieneisen, Athanasius F. M. Marée, Rosangela Sozzani, Christos Zamioudis, Pál Miskolczi, Jeroen Nieuwland, René Benjamins, Pankaj Dhonukshe, Juan Caballero-Pérez, Beatrix Horvath, Ari Pekka Mähonën,Jian Xu, James A.H. Murray, Philip N. Benfey, Laszlo Bako and Ben Scheres. 2012. Cell, 150: 1002-15.

Translational regulation of Arabidopsis XIPOTL1 is modulated by phosphocholine levels via the phylogenetically conserved upstream open reading frame 30. Alatorre-Cobos, Alfredo Cruz-Ramírez, Celine A. Hayden, Claudia-Anahí Pérez Torres, Anne-Laure Chauvin, Enrique Ibarra-Laclette, Erika Alva-Cortés, Richar Jorgensen and Luis Herrera-Estrella. 2012. J. Exp. Bot. 63: 5203-21.

Functional and Transcriptome Analysis Reveals an Aclimatization Strategy for Abiotic Stress Tolerance mediated by Arabidopsis NF-YA Family members. Marco Antonio Leyva-González, Enrique Ibarra-Laclette, Alfredo Cruz-Ramírez and Luis Herrera-Estrella. 2012. PLoS One. 7: e48138.

Functional analysis of the Arabidopsis PLDZ2 promoter reveals an evolutionarily conserved low-Pi-responsive transcriptional enhancer element. Araceli Oropeza-Aburto, Alfredo Cruz-Ramírez, Gustavo J. Acevedo-Hernández, Claudia-Anahí Pérez-Torres, Juan Caballero-Pérez, and Luis Herrera-Estrella. 2012. J Exp Bot, 635: 2189-202.

Effect of Nutrient Availability on Root System Development. Cruz-Ramírez A, Calderón-Vázquez and Herrera-Estrella L. 2009. pp 288–324. Annual Plant Reviews, Volume 37: Root Development. Wiley-Blackwell Publishing.

The genome of Bacillus coahuilensis reveals adaptationsessential for survival in the relic of an ancient marine environment. Alcaraz LD, Olmedo G, Bonilla G, Cerritos R, Hernández G, Cruz A, Ramírez E, Putonti C, Jiménez B, Martínez E, López V, Arvizu JL, Ayala F, Razo F, CaballeroJ, Siefert J, Eguiarte L, Vielle JP, Martínez O, Souza V, Herrera-Estrella A, Herrera-Estrella L. 2008. Proc.Nac. Acad. Sci. (PNAS) 105: 5803-8.

Phosphate Availability Alters Lateral Root Development in Arabidopsis by Modulating Auxin Sensitivity via a Mechanism Involving the TIR1 Auxin Receptor. Claudia-Anahí Pérez-Torres, Jose López-Bucio, Alfredo Cruz-Ramírez, EnriqueIbarra-Laclette, Sunethra Dharmasiri, Mark Estelle and Luis Herrera-Estrella. 2008. The Plant Cell, 20: 3258-72.

Phospholipase DΖ2 plays an important role in extraplastidic galactolipid biosynthesis and Pi recycling in Arabidopsis roots. Alfredo Cruz-Ramírez, Araceli Oropeza-Aburto, Francisco Razo-Hernández, Enrique Ramírez-Chavez, Luis Herrera Estrella. 2006. Proc. Nac. Acad. Sci. (PNAS), 103: 6765–70.

3 Mexican crops of agroalimentary importance. In Advances in Agricultural and Food Biotechnology. Cruz-Ramírez Luís Alfredo, Valdez-Morales Maribel, Chacón-López Martina Alejandra, Rosas-Cárdenas Flor de Fátima and Cruz-Hernández Andrés. 2006. Research Signpost 35-53.

Phosphate Starvation Induces a Determinate Developmental Program inthe Roots of Arabidopsis thaliana. Lenin Sánchez-Calderón, José López-Bucio, Alejandra Chacón-López, Alfredo Cruz-Ramírez, Fernanda Nieto-Jacobo, Joseph G. Dubrovsky and Luis Herrera Estrella. 2005. Plant Cell Physiol, 46: 174-84.

Root architecture. In Plant Architecture and its Manipulation. J. López-Bucio, A. Cruz-Ramírez, A. Pérez-Torres, J. G. Ramírez-Pimentel, L. Sánchez- Calderón and L. Herrera-Estrella. 2005. Annual Plant Reviews, Volume 17. Blackwell Publishing.

The xipotl Mutant of Arabidopsis Reveals a Critical Role for Phospholipid Metabolism in Root System Development and Epidermal Cell Integrity. Alfredo Cruz-Ramírez, Jose López-Bucio, Gabriel Ramírez-Pimentel, Andrés Zurita-Silva, Lenin Sánchez-Calderon, Enrique Ramırez-Chavez, Emmanuel Gonzalez-Ortega, and Luis Herrera-Estrella. 2004. The Plant Cell, 16: 2020–34.

The role of nutrient availability in regulating root architecture. José López-Bucio, Alfredo Cruz-Ramírez and Luis Herrera-Estrella. 2003. Current Opinion in Plant Biology, 6: 280–87.