Publications

2025

Peer-Reviewed Publications

• Exploring the Molecularity of Spices: The Gustatory Perspective.  Thomas, S. S., Bhayani, H. S., & Crasto, C. J. Eur Food Res Tech. (2025): DOI:10.1007/s00217-025-04862-3
• Hepatic transcriptome profiling unveils candidate genes in cattle with liver abscesses under the influence of beef genetics in dairy cattle. Felizari, L. D., Bowman, S. M., Crasto, C. J., Sarturi, J. O., Woerner, D. R., Johnson, B. J. PLOS One, 20(6), e0324209. (2025)
• Cross-study transcriptomic investigation of Alzheimer’s brain tissue discoveries and limitations.  Tsurukawa, F. K., Mao, Y., Sanchez-Villalobos, C., Khanna, N., Crasto, C. J., Lawrence, J., and Pal, R. Nature: Scientific Reports, 15:16041. (2025)
• Effects of innate immune activation by Toll-like receptor agonists on ethanol consumption and preference in FVB/NJ x C57BL/6J hybrid mice. Brent R. Kisby, Isabel Castro-Piedras, Sambantham Shanmugam, Igor Ponomarev. bioRxiv 2025.05.06.652465; doi: https://doi.org/10.1101/2025.05.06.652465
• Differential Effects of Human Immunodeficiency Virus Nef Variants on Pulmonary Vascular Endothelial Cell Dysfunction. Garcia AK, Lujea NC, Baig J, Heath E, Nguyen MT, Rodriguez M, Campbell P, Castro Piedras I, Suarez Martinez E, Almodovar S. Infectious Disease Reports. 2025; 17(3):65. https://doi.org/10.3390/idr17030065
• Intron Retention: A Reemerging Paradigm in RNA Biology and Post-Transcriptional Gene Regulation. Porras-Tobias AL, Caldera A, Castro-Piedras I. Genes. 2025; 16(8):986. https://doi.org/10.3390/genes16080986
• Assessing the Performance of Environmental DNA Metabarcoding in Fish Diversity Surveys of the Texas Gulf Coast. Knauss, Madelyn, et al. Estuaries and Coasts 48.6 (2025): 177.
• TIAM1 drives prostatic branching phenotype and is a potential therapeutic target for benign prostatic hyperplasia."  Khedmatgozar, Hamed, et alJCI insight 10.12 (2025): e188062.
• Deciphering crop-specific rhizobacteriome assembly in cotton, sorghum, and soybean under hot semi-arid field conditions in Texas.  Abdelrahman, Mostafa, et al. Environmental Microbiome 20.1 (2025): 105.
• Fun-Sized Library Prep: Miniaturization is a valid method for per-sample cost reduction in targeted sequencing of angiosperm DNA. Bullock, Madison R., et al.  bioRxiv (2025): 2025-09.
• Molecular Characterization of Fusarium Isolates from Upland Cotton Roots in Uzbekistan and Whole-Genome Comparison with Isolates from the United States. Jobe, Timothy O., et al.  Phytopathology 115.1 (2025): 54-65.

Conference Papers

• Two-dimensional Molecular Fingerprints in Molecules Exhibiting the Sweet Flavor. Albers, C., Manam, S., Bhatta, S., & Crasto, C. J.  International Journal of BioLife Sciences. 4(2):154-160. (2025) --Conference paper

Talks and Presentations

• Connecting the Dots: The Beginning of the Journey to Uncover DVL3’s Role in Cancer Through Biotechnology” TC3R Seminar– School of Veterinary Medicine – Amarillo. Isabel Castro-Piedras, April 24, 2025.
• Two-dimensional Molecular Fingerprints in Molecules Exhibiting the Sweet Flavor. 8th International Conference on Nutritional, Environmental and Agricultural Sciences, Istanbul, Turkey.  Chiquito Crasto May 18, 2025. 
• Molecular Fingerprinting for Environmental Organic Toxins. One Health Innovation Symposium, Texas Tech University Innovation Hub, Lubbock, Texas, USA. Chiquito Crasto May 2, 2025
• Sophrosine Code: Interactive Sonification of Genetic Data for Music Therapy. (Shared talk with Dr. Hideki Isoda, School of Music, TTU).  Texas Tech University.  Lubbock, Texas, USA. Chiquito Crasto April 11, 2025.
• Exploring the Molecularity of Spices – A Computational Approach.  11th Annual World Congress on Food and Nutrition–2024.  Singapore. Chiquito Crasto November 13, 2024. 
• Bioinformatics Stream in the MS Program in Interdisciplinary Studies. Program in Interdisciplinary Studies, Texas Tech University. Chiquito Crasto October 29-30, 2024.
• A chromosome-scale reference genome of Moroccan Argane (Argania spinosa). El Idrissi, H., Iraqi, D., Khoulassa, S., Fokar, M., Badaoui, B., Moussadek, R., & Mentag, R. (2025).
• Effect of inbred mouse strain on the transcriptomic response to exercise training. Massett, Michael, Hyoseon Kim, and Mohamed Fokar. Physiology 40.S1 (2025): 1726.

Book Chapters

• Exploring the Conformational Odorant Space in the Olfactory Receptor Binding Region.   Lokubandara, A., Mandla, V. & Crasto, C.  In: Computational Intelligence Methods for Bioinformatics and Biostatistics.  Eds. Vettoretti, M., Tavazzi, E., Longato, E., Baruzzo, G. & Bellato, M., pp: 101-116/ Padova, Italy (2025).

Posters

• -Endogenous tagging using CRISPR/CAS9 to purify native proteins from human cells. Akinniyi K.O, Sheikh Alard A., Cuello L.G, Castro-Piedras, 2025 Graduate Poster Competition TTU – Lubbock
• -Pan-cancer analysis of the oncogenic role and immunological function of DVL3 in multiple tumors. Sheikh Alard A., Akinniyi K., Castro-Piedras, 2025 Graduate Poster Competition TTU – Lubbock
• KCNIP1 at the Convergence of Retinoic Acid Receptor Regulation, Ion Channel Dysfunction, and Alzheimer’s Disease: A Bioinformatics Study. Nishtha Khanna, Fernando Tsurukawa, Cesar Augusto Sanchez-Villalobos, Isabel Castro, Chanda Bose, Chiquito Crasto, Ranadip Pal, and J. Josh Lawrence. 

Book

• Biopython for Beginners. Crasto, C. J. (2025). Sentia Publishers, Lakeway, Texas.Biopython for Beginners. 

2024

Peer-Reviewed Publication

• Human Olfactory Receptor Comparative Sequence Assessments from the Genome. (Review) Marenco, L. N., & Crasto, C. J., Open Acc Biostat Bioinform. 3(5). OABB.000571. (2024). DOI: 10.31031/OABB.2024.03.000571
• Diversity Within Olfactory Receptor Gene Families: A Case Study of Humans, Mice, Rats, and Elephants. Inan, F. A., Gopaldas, R., Marenco, L. N, & Crasto, C. J. JOJ Wildlife and Biodiversity.  5(1): 555654. (2024)
  

Conference Abstracts

• Exploring the Molecularity of Spices- The Olfactory Perspective. Thomas, S.S. & Crasto. C.J. The Obesity Research Institute-One Health: Metabolic Health. Author Name: Sona Sara Thomas. April 2024
• Far Peripheral Vision as an Early Biomarker for Neurodegenerative Disorders. Bidiwala, E.S. & Chiquito Crasto. Promoting Cross-Disciplinary Faculty Collaborations in One Health Research Conference. Lubbock, Texas. April 2024. Poster

Talks and Presentations

• Exploring the Molecularity of Spices – A Computational Approach.  11th Annual World Congress on Food and Nutrition–2024.  Singapore. November 13, 2024.
• Bioinformatics Stream in the MS Program In Interdisciplinary Studies. Program in Interdisciplinary Studies, Texas Tech University. October 29-30, 2024.
• Exploring Metabolic Diversity: A Non-Targeted Metabolomics Study of Cleome     gynandra and Cleome hassleriana. 30th edition of the International Symposium on Electro- and Liquid Phase Separation Techniques (ITP), Sept. 29 to Oct. 3rd, 2024. Fort Worth, Texas, USA.
• Sarah Metwally, Mona Goli, Fang Chen, Mohamed Fokar, Yehia Mechref. Proteomic Insights into Fusarium Oxysporum Adaptation and Host Interaction: A Study of Cotton Root Influence on Pathogen Protein Expression. 30th edition of the International Symposium on Electro- and Liquid Phase Separation Techniques (ITP), Sept. 29 to Oct. 3rd, 2024.  Fort Worth, Texas, USA.
• Fang Chen, Arpita Marick, Sarah Metwally, Yehia Mechref. Understanding Protein Accumulation in Cleome Seeds Using NanoLC-MS/MS-Based Proteomics. 30th edition of the International Symposium on Electro- and Liquid Phase Separation Techniques (ITP), Sept. 29 to Oct. 3rd, 2024.  Fort Worth, Texas, USA

2023

Peer-reviewed Publications

• Exploring the Molecularity of Specific Olfactory and Gustatory Perceptive Phenotypes:  Computational Approach. Crasto, C. J., Bhayani, H., Thomas, S. S., Thilakarathne, R., and Perera, N. Biomed J Sci & Tech Res 53(5), 2023.
• Exploring the Odorant-Determined, Molecular Basis for Olfactory Perception.  Thikalakaratne, R., Perera, N., and Crasto, C. J. Biomed J Sci & Tech Res. 52(2), (2023)
• Exploring the Molecularity of Odor and Taste Perceptions of “Brown”: A Computational Approach. Bhayani, H.S., Thilakarathne, R., Perera, N., & Crasto, C. J.  Conference Paper.  International Conference on New Trends in Applied Sciences. Konya, Turkey–E-conference. pp.98-102. (2023)

Talks and Presentations

• Exploring the Molecularity of Odor and Taste Perceptions of “Brown”: A Computational Approach. International Conference on New Trends in Applied Sciences. December 1, 2023, Konya, Turkey–E-conference (Speaker and Session Chair)
• Exploring Odorant Conformational Space in the Olfactory Receptor Binding Region.  CIBB 2023. Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics. September 8, 2023, Padova, Italy.
• Using OBS Studio for Dynamic Presentations and Teaching. Transforming the Teaching and Learning Environment.  February 15, 2023.  (Virtual Conference)
• Services and Collaborative Research at TTU CBG’s Bioinformatics Core. Traumatic Brain Injury Mini-Symposium, Texas Tech University. February 9, 2023, Lubbock, Texas

2022

2021

Peer-reviewed Publications

• Machine Learning Ideations to Map Odorant Activity in Olfactory-Receptor Odorant Interactions. Crasto, C.J., Thilakarathne, R., Perera, N., and Lokubandara, A.H., 2021, September.  In CHEMICAL SENSES (Vol. 46). 

Talks and Presentations

• Machine Learning Ideations to Map Odorant Activity in Receptor Odorant Interactions. Association of Chemoreception Sciences. 2021. (Virtual Meeting).

2020

Peer-reviewed Publications

• Elucidating Olfactory Receptor-Odorant Interactions: Leveraging Drug-Design Ideations. Crasto, C. J., Lokubandara, A., Mandla, V., and Buzatu, D. Biophysical Journal, 116(3), p. 53a. (2020)
• Odorant perspectives and computational drug-design notions to elucidate olfactory-receptor (OR) odorant interactions. Crasto, C., Lokubandara, A., & Mandla, V. (2020, February).  In CHEMICAL SENSES 45(2), 155. (2020)
• User as a bitter tastant: Immersive experience within the binding region of a bitter taste receptor. Dang, T., Lokubandara, A., Nguyen, N. N. V., Lai, P. C., Nguyen, V. T., and Crasto, C. J. Proceedings of 32nd European Modeling & Simulation Systems/17th International Multidisciplinary Modeling & Simulation Multiconference. (2020) 2274-0079. 
• PIACAN: Pathway Integration and Analysis of Cancer Networks. Quintana, A., Vinh, N., Dang, T., and Crasto, C. J.  Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies. (2020) 3:246-252.       – also published in BIOINFORMATICS. (2020)

 

Talks and Presentations

• User as a bitter tastant: Immersive experience within the binding region of a bitter taste receptor. Joint-Presenter.  32nd European Modeling and Simulation Symposium/ 17th International Multidisciplinary Modeling and Simulation Multiconference.  Stockholm, Sweden, September 2020 (Virtual Meeting)
• Odorant Roles in Olfactory Receptor Odorant Interactions: A Novel Perspective. International Society of Olfaction and Taste/Association of Chemoreception Sciences joint meeting, Portland, Oregon. August 2020 (Virtual Meeting)
• PIACAN: Pathway Integration and Analysis of Cancer Networks.  BIOSTEC 2020. 13th International Joint Conference on Biomedical Engineering Systems and Technologies. Valletta, Malta, February 2020.

2019

Peer-reviewed publications

• Root endophytic fungus Piriformospora indica improves drought stress adaptation in barley by metabolic and proteomic reprogramming. MR Ghaffari, M Mirzaei, M Ghabooli, B Khatabi, Y Wu, M Zabet-Moghaddam, G Mohammadi-Nejad, P Haynes, MR Hajirezaei, M Sepehri, GH Salekdeh. Environmental and experimental botany 157, 197-210, 2019
• Elucidating Olfactory Receptor-Odorant Interactions: Leveraging Drug-Design Ideations. CJ Crasto, A Lokubandara, V Mandla, D Buzatu. Biophysical Journal 116 (3), 53a-54a , 2019
• Integrated Transcriptomics, Proteomics, and Glycomics Reveals the Association between Up-regulation of Sialylated N-glycans/Integrin and Breast Cancer Brain Metastasis. Wenjing Peng, Rui Zhu, Shiyue Zhou, Parvin Mirzaei & Yehia Mechref. Scientific Reports volume 9, Article number: 17361, 2019

Talks and Presentations

• Developing Multidisciplinary Education in Computer Applications, Department of University Studies, Texas Tech University, October 2019.

Mentions

• The Editors would like to thank those listed below who have given their valuable help over the last year, between 1st October 2017 and 30th September 2018, in the review of.  M Albers, M Aoki, R Apfelbach, A Arzi, E Beckett, M Behrens, M Bensafi, ... Crasto, C.J., et al.Chemical Senses 44 (1), 69-70, 2019

2018

Peer-reviewed publications

• Magnetic carbon nanocomposites as a MALDI co-matrix enhancing MS-based glycomics. YM Alireza Banazadeh, Seth Williamson, Masoud Zabet, Ahmed Hussien. Analytical and Bioanalytical Chemistry 410 (28), 7395–7404, 2018
• Distribution and development of molecularly distinct perineuronal nets in visual thalamus. F Sabbagh, Ubadah, A Monavarfeshani, K Su, M Zabet-Moghadam, J Cole, E Carnival, J Su, M Mirzaei, V Gupta, GH Salekdeh, M IA. Journal of Neurochemistry, 2018
• Sm-p80-based schistosomiasis vaccine: a double-blind pre-clinical trial in baboons demonstrates comprehensive prophylactic and parasite-transmission-blocking efficacy. W Zhang, AJ Molehin, JU Rojo, J Sudduth, PK Ganapathy, E Kim, et al.  Annals of the New York Academy of Sciences 1425 (1), 38, 2018.

Talks and Presentations

• Fang Chen, Arpita Marick, Sarah Metwally, Yehia Mechref. Understanding Protein Accumulation in Cleome Seeds Using NanoLC-MS/MS-Based Proteomics. 30th edition of the International Symposium on Electro- and Liquid Phase Separation Techniques (ITP), Sept. 29 to Oct. 3rd, 2024.  Fort Worth, Texas, USA.
• Rabia, A. H., Yacout, D. M., Shaheen, S. F., Mohamed, A. A., and Fawzy, E. A. (2018).
  Towards Sustainable Production of Potato under Climate Change Conditions. Journal of Current Applied Science and Technology. 18 (3).

2017

Peer-reviewed publications

• Recent advances in mass spectrometric analysis of glycoproteins. Alireza Banazadeh, Lucas Veillon, Kerry M. Wooding, Masoud Zabet‐Moghaddam, Yehia Mechref.  Electrophoresis 38 (1), 162-189, 2017
• Quantitative proteomic analysis of human testis reveals system-wide molecular and cellular pathways associated with non-obstructive azoospermia. M Alikhani, M Mirzaei, M Sabbaghian, P Parsamatin, R Karamzadeh, S Adib, N Sodeifi, M Gilani, M Zabet-Moghaddam, L Parker, Y Wu, V Gupta, P Haynes, H Gourabi, H Baharvand, G Salekdeh. Journal of proteomics 162, 141-154, 2017
• Nanospray liquid chromatography/tandem mass spectrometry analysis of steroids from gray whale blubber M Hayden, R Bhawal, J Escobedo, C Harmon, TM O'Hara, D Klein, S San‐Francisco, M Zabet‐Moghaddam, C Godard‐Codding. Rapid Communications in Mass Spectrometry 31 (13), 1088-1094, 2017

Talks and Presentations

• Bioinformatics Education.  Biology Student Group.  South Plains College, South Plains, Texas.  April 12, 2017.
• Bioinformatics Research. Honors Program.  Texas Tech University, Lubbock, TX.  March 6, 2017.
• E-Education in Bioinformatics. New Mexico Bioinformatics, Science and Technology (NMBIST) Symposium,  New Mexico. March 2017.

 

2016

Peer-reviewed Publications

• Novel Paradigm for Odorant-Olfactory Receptor Interactions. Lai, P. C., and Crasto, C. J.  MOJ Proteomics and Bioinformatics. (2016); 4(3):1-6.  Opinion.
• ORDB, HORDE, ODORactor, and other online knowledge resources of olfactory receptor-odorant interactions. Marenco, L. N., Wang, R., McDougal, R., Olender, T., Twik, M. Bruford, E., Liu, X., Zhang, J., Lancet, D., Shepherd, G. M., and Crasto, C. J.  Database. (2016); pii, baw132.

2015

Peer-reviewed Publications

• Substituted 2-(Dimethylamino)biphenyl-2'-carboxaldehyde as Substrates for Studying n→π Interactions and as a Promising Framework for Tracing the Bürgi-Dunitz Trajectory. Breton, G. W. and Crasto, C. J. (2015) J. Org. Chem. 80(15):7375-84

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005