Publications

Journals Papers

• Frances Heredia-Negrón, Eduardo L. Tosado-Rodríguez, Joshua Meléndez-Berrios, Brenda Nieves, Claudia P. Amaya-Ardila and Abiel Roche-Lima. Assessing the Impact of AI Education on Hispanic Healthcare Professionals’ Perceptions and Knowledge Educ. Sci. 2024, 14(4), 339; https://doi.org/10.3390/educsci14040339.
• Roche-Lima A, Rosado-Quiñones AM, Feliu-Maldonado RA, Figueroa-Gispert MDM, Díaz-Rivera J, Díaz-González RG, Carrasquillo-Carrion K, Nieves BG, Colón-Lorenzo EE, Serrano AE. Antimalarial Drug Combination Predictions Using the Machine Learning Synergy Predictor (MLSyPred©) tool. Acta Parasitol. 2024 Jan 2. doi: 10.1007/s11686-023-00765-z. Epub ahead of print. PMID: 38165555.
• Yang G, González P, Moneró M, Carrasquillo K, Renta JY, Hernandez-Suarez DF, Botton MR, Melin K, Scott SA, Ruaño G, Roche-Lima A, Alarcon C, Ritchie MD, Perera MA, Duconge J. Discovery of Ancestry-specific Variants Associated with Clopidogrel Response among Caribbean Hispanics. medRxiv [Preprint]. 2023 Oct 2:2023.09.29.23296372. doi: 10.1101/2023.09.29.23296372. PMID: 37873439; PMCID: PMC10593031.
• Velev J, LeBien J, Roche-Lima A. Unsupervised machine learning method for indirect estimation of reference intervals for chronic kidney disease in the Puerto Rican population. Sci Rep. 2023 Oct 11;13(1):17198. doi: 10.1038/s41598-023-43830-3. PMID: 37821500; PMCID: PMC10567761
• Monero-Paredes M, Feliu-Maldonado R, Carrasquillo-Carrion K, Gonzalez P, Rogozin IB, Roche-Lima A, Duconge J. Non-Random Enrichment of Single-Nucleotide Polymorphisms Associated with Clopidogrel Resistance within Risk Loci Linked to the Severity of Underlying Cardiovascular Diseases: The Role of Admixture. Genes (Basel). 2023 Sep 17;14(9):1813. doi: 10.3390/genes14091813. PMID: 37761953; PMCID: PMC10531115.
• Alvare G, Roche-Lima A, Fristensky B. BioLegato: a programmable, object-oriented graphic user interface. BMC Bioinformatics. 2023 Aug 21;24(1):316. doi: 10.1186/s12859-023-05436-4. PMID: 37605108; PMCID: PMC10441721.
• Rebello BC, Ramirez ARG, Heredia-Negron F, Roche-Lima A. A machine learning-based approach to epileptic seizure prediction using electro-encephalographic signals. J Eng Res (Ponta Grossa). 2022;2(8):10.22533/at.ed.317282219056. doi: 10.22533/at.ed.317282219056. PMID: 35711293; PMCID: PMC9199360.
• Heredia FL, Roche-Lima A, Parés-Matos EI. A novel artificial intelligence-based approach for identification of deoxynucleotide aptamers. PLoS Comput Biol. 2021 Aug 3;17(8):e1009247. doi: 10.1371/journal.pcbi.1009247. PMID: 34343165; PMCID: PMC8362955.
• Hernandez-Suarez DF, Ranka S, Kim Y, Latib A, Wiley J, Lopez-Candales A, Pinto DS, Gonzalez MC, Ramakrishna H, Sanina C, Nieves-Rodriguez BG, Rodriguez-Maldonado J, Feliu Maldonado R, Rodriguez-Ruiz IJ, da Luz Sant'Ana I, Wiley KA, Cox-Alomar P, Villablanca PA, Roche-Lima A. Machine-Learning-Based In-Hospital Mortality Prediction for Transcatheter Mitral Valve Repair in the United States. Cardiovasc Revasc Med. 2021 Jan;22:22-28. doi: 10.1016/j.carrev.2020.06.017. Epub 2020 Jun 15. PMID: 32591310; PMCID: PMC7736498.
• Zenón-Meléndez CN, Carrasquillo Carrión K, Cantres Rosario Y, Roche Lima A, Meléndez LM. Inhibition of Cathepsin B and SAPC Secreted by HIV-Infected Macrophages Reverses Common and Unique Apoptosis Pathways. J Proteome Res. 2022 Feb 4;21(2):301-312. doi: 10.1021/acs.jproteome.1c00187. Epub 2022 Jan 7. PMID: 34994563; PMCID: PMC9169015.
• Borges-Vélez G, Rosado-Philippi J, Cantres-Rosario YM, Carrasquillo-Carrion K, Roche-Lima A, Pérez-Vargas J, González-Martínez A, Correa-Rivas MS, Meléndez LM. Zika virus infection of the placenta alters extracellular matrix proteome. J Mol Histol. 2022 Apr;53(2):199-214. doi: 10.1007/s10735-021-09994-w. Epub 2021 Jul 15. PMID: 34264436; PMCID: PMC8760362.
• Gonzalez-Cordero AF, Duconge-Soler J, Franqui-Rivera H, Feliu-Maldonado R, Roche-Lima A, Almodovar-Rivera I. Insight on the Genetics of Atrial Fibrillation in Puerto Rican Hispanics. Stroke Res Treat. 2021 Jan 7;2021:8819896. doi: 10.1155/2021/8819896. PMID: 33505650; PMCID: PMC7810540.
• Borges-Vélez G, Arroyo JA, Cantres-Rosario YM, Rodriguez de Jesus A, Roche-Lima A, Rosado-Philippi J, Rosario-Rodríguez LJ, Correa-Rivas MS, Campos-Rivera M, Meléndez LM. Decreased CSTB, RAGE, and Axl Receptor Are Associated with Zika Infection in the Human Placenta. Cells. 2022 Nov 16;11(22):3627. doi: 10.3390/cells11223627. PMID: 36429055; PMCID: PMC9688057.
• Heredia-Negron F, Alamo-Rodriguez N, Oyola-Velazquez L, Nieves B, Carrasquillo K, Hochheiser H, Fristensky B, Daluz-Santana I, Fernandez-Repollet E, Roche-Lima A. Evaluation of AIML + HDR-A Course to Enhance Data Science Workforce Capacity for Hispanic Biomedical Researchers. Int J Environ Res Public Health. 2023 Feb 3;20(3):2726. doi: 10.3390/ijerph20032726. PMID: 36768092; PMCID: PMC9914971.
• Awad CS, Deng Y, Kwagyan J, Roche-Lima A, Tchounwou PB, Wang Q, Idris MY. Summary of Year-One Effort of the RCMI Consortium to Enhance Research Capacity and Diversity with Data Science. Int J Environ Res Public Health. 2022 Dec 24;20(1):279. doi: 10.3390/ijerph20010279. PMID: 36612607; PMCID: PMC9819075.
• Bykova A, Saura A, Glazko GV, Roche-Lima A, Yurchenko V, Rogozin IB. The 29-nucleotide deletion in SARS-CoV: truncated versions of ORF8 are under purifying selection. BMC Genomics. 2023 Jul 10;24(1):387. doi: 10.1186/s12864-023-09482-3. PMID: 37430204; PMCID: PMC10332002.
• Martínez-Matías N, Chorna N, González-Crespo S, Villanueva L, Montes-Rodríguez I, Melendez-Aponte LM, Roche-Lima A, Carrasquillo-Carrión K, Santiago-Cartagena E, Rymond BC, Babu M, Stagljar I, Rodríguez-Medina JR. Toward the discovery of biological functions associated with the mechanosensor Mtl1p of Saccharomyces cerevisiae via integrative multi-OMICs analysis. Sci Rep. 2021 Apr 1;11(1):7411. doi: 10.1038/s41598-021-86671-8. PMID: 33795741; PMCID: PMC8016984.
• Tchounwou PB, Malouhi M, Ofili EO, Fernández-Repollet E, Sarpong DF, Yanagihara R, Aguilera RJ, Ayón C, Chen X, Dasmahapatra A, Gao S, Hinton CV, Holt R, Kolesnichenko V, Powell MD, Merchant F, Redda KK, Roche-Lima A, Shikuma CM, Stevens JJ, Torres JA, Trotter RT, Wachira J, Wang P, Wells KJ, White J, Wu Y. Research Infrastructure Core Facilities at Research Centers in Minority Institutions: Part I-Research Resources Management, Operation, and Best Practices. Int J Environ Res Public Health. 2022 Dec 17;19(24):16979. doi: 10.3390/ijerph192416979. PMID: 36554864; PMCID: PMC9779820.
• Rabelo-Fernández RJ, Santiago-Sánchez GS, Sharma RK, Roche-Lima A, Carrion KC, Rivera RAN, Quiñones-Díaz BI, Rajasekaran S, Siddiqui J, Miles W, Rivera YS, Valiyeva F, Vivas-Mejia PE. Reduced RBPMS Levels Promote Cell Proliferation and Decrease Cisplatin Sensitivity in Ovarian Cancer Cells. Int J Mol Sci. 2022 Jan 4;23(1):535. doi: 10.3390/ijms23010535. PMID: 35008958; PMCID: PMC8745614.
• Rogozin IB, Roche-Lima A, Tyryshkin K, Carrasquillo-Carrión K, Lada AG, Poliakov LY, Schwartz E, Saura A, Yurchenko V, Cooper DN, Panchenko AR, Pavlov YI. DNA Methylation, Deamination, and Translesion Synthesis Combine to Generate Footprint Mutations in Cancer Driver Genes in B-Cell Derived Lymphomas and Other Cancers. Front Genet. 2021 May 19;12:671866. doi: 10.3389/fgene.2021.671866. PMID: 34093666; PMCID: PMC8170131.
• Roche-Lima A, Roman-Santiago A, Roberto Feliu-Maldonado R, Jovaniel Rodriguez-Maldonado R, Nieves-Rodriguez BG, Carrasquillo-Carrion K, Ramos C.M., da Luz Sant’Ana I, Massey S.E., Duconge J. . Machine Learning Algorithm for Predicting Warfarin Dose in Caribbean Hispanics Using Pharmacogenetic Data. Front Pharmacol 2020. PMID: 32038238 PMCID: PMC6987072 DOI: 10.3389/fphar.2019.01550
• Hernandez-Suarez DF, Villablanca PA, Kim Y, Wiley J, Sanina C, Roche-Lima A. Reply: Leveraging Machine Learning to Generate Prediction Models for Structural Valve Interventions. PMID: 31648770 PMCID: PMC7011192 (available on 2020-10-28) DOI: 10.1016/j.jcin.2019.09.001
• Hernandez-Suarez DF, Kim Y, Villablanca P, Gupta T, Wiley J, Nieves-Rodriguez BG, Rodriguez-Maldonado J, Feliu Maldonado R, da Luz Sant'Ana I, Sanina C, Cox-Alomar P, Ramakrishna H, Lopez-Candales A, O'Neill WW, Pinto DS, Latib A, Roche-Lima A. Machine Learning Prediction Models for In-Hospital Mortality After Transcatheter Aortic Valve Replacement. JACC Cardiovasc Interv. 2019 Jul 22;12(14):1328-1338. doi: 10.1016/j.jcin.2019.06.013. PMID: 31320027
• Gómez-Moreno R, Martínez-Ramírez R, Roche-Lima A, Carrasquillo-Carrión K, Pérez-Santiago J, Baerga-Ortiz A. Hotspots of Sequence Variability in Gut Microbial Genes Encoding Pro-Inflammatory Factors Revealed by Oligotyping. Front Genet. 2019 Jul 9;10:631. doi: 10.3389/fgene.2019.00631. eCollection 2019. PMID: 31354787
• Graydon JS, Claudio K, Baker S, Kocherla M, Ferreira M, Roche-Lima A, Rodríguez-Maldonado J, Duconge J, Ruaño G. Ethnogeographic prevalence and implications of the 677C>T and 1298A>C MTHFR polymorphisms in US primary care populations. Biomark Med. 2019 Jun;13(8):649-661. doi: 10.2217/bmm-2018-0392. Epub 2019 Jun 3. PMID: 31157538
• Hernandez-Suarez DF, Lopez-Menendez F, Roche-Lima A, Lopez-Candales A. Assessment of Mitral Annular Plane Systolic Excursion in Patients With Left Ventricular Diastolic Dysfunction. Cardiol Res. 2019 Apr;10(2):83-88. doi: 10.14740/cr837. Epub 2019 Apr 11. PMID: 31019637
• Hernandez-Suarez DF, Ranka S, Villablanca P, Yordan-Lopez N, González-Sepúlveda L, Wiley J, Sanina C, Roche-Lima A, Nieves-Rodriguez BG, Thomas S, Cox-Alomar P, Lopez-Candales A, Ramakrishna H. Racial/Ethnic Disparities in Patients Undergoing Transcatheter Aortic Valve Replacement: Insights from the Healthcare Cost and Utilization Project's National Inpatient Sample. Cardiovasc Revasc Med. 2019 Jul;20(7):546-552. doi: 10.1016/j.carrev.2019.04.005. Epub 2019 Apr 9. PMID: 30987828
• Rogozin IB, Roche-Lima A, Lada AG, Belinky F, Sidorenko IA, Glazko GV, Babenko VN, Cooper DN, Pavlov YI. Nucleotide Weight Matrices Reveal Ubiquitous Mutational Footprints of AID/APOBEC Deaminases in Human Cancer Genomes. Cancers (Basel). 2019 Feb 12;11(2). pii: E211. doi: 10.3390/cancers11020211. PMID: 30759888
• Vélez-Segarra, V., Carrasquillo-Carrión, K., Santini-González, J. J., Ramos-Valerio, Y. A., Vázquez-Quiñones, L. E., Roche-Lima, A., Rodriguez-Medina, J.R., Parés-Matos, E. I. (2019). Modelling and molecular docking studies of the cytoplasmic domain of Wsc-family, full-length Ras2p, and therapeutic antifungal compounds. Computational Biology and Chemistry, 78, 338-352. doi:10.1016/j.compbiolchem.2019.01.001
• Claudio-Campos, K.I., González-Santiago, P., Renta, J.Y., Roche-Lima, A., Rodriguez Maldonado, J., Carrasquillo-Carrión, K., Gaedigk, A., Duconge, J. CYP2C9*61, a rare missense variant in exon 9, identified in a Puerto Rican patient with low warfarin dose requirements: A Case Report. Pharmacogenomics, 2018.
• Roche-Lima, A., Carrasquillo-Carrion, K., Gomez-Moreno, R., Cruz, J.M., Velazquez-Morales, D., Rogozin, I.B., Baerga-Ortiz, A. (2018) The presence of genotoxic and/or pro-inflammatory bacterial genes in gut metagenomic databases and their possible link with inflammatory bowel diseases, Frontiers in Genetics, Vol 9, pp116, doi: 10.3389/fgene.2018.00116.
• Manfredi, B, Morales-Ortíz, J., Díaz-Díaz, L.M., Hernandez-Matias, L., Barreto-Vázquez, D., Menéndez-Pérez, J., Rodríguez-Cordero, J.A., Villalobos-Santos, J.C., Santiago-Rivera, E., Rivera-Dompenciel, A., Lozada-Delgado, E.L., Kuchibhotla, M., Carrasquillo-Carrión, K., Roche-Lima, A., Washington, A.V. (2018). Characterization of monoclonal antibodies to mouse TLT-1 suggests that TLT-1 plays a role in wound healing. Monoclonal Antibodies in Immunodiagnosis and Immunotherapy. Vol. 37, No. 2. 
• Ordoñez, P., Schwarz, N., Figueroa Jiménez, A., García Lebrón, L., Roche Lima, A.; Learning stochastic finite-state transducer to predict individual patient outcomes. Published at Journal of Health and Technology (2016). 6:239. doi:10.1007/s12553-016-0146-2. First published online: October 17, 2016. 
• Roche Lima, A. (2016). Implementation and comparison of kernel-based learning methods to predict metabolic networks. Network Modeling Analysis in Health Informatics and Bioinformatics. 5: 26. doi:10.1007/s13721-016-0134-5.
• Roche-Lima, A.; Domaratzki, M., Fristensky, B. (2014). Metabolic Network Prediction Through Pairwise Rational Kernels. BMC Bioinformatics 2014, 15:318. doi:10.1186/1471-2105-15-318. (1380 visits in 3 months). 
• Roche-Lima, A.; Domaratzki, M., Fristensky, B. (2014). Pairwise Rational Kernels Obtained by Automaton Operations. Submitted to CIAA'2014. International Conference of Implementation and Application of Automata. Febrero 2014. Volume 8587, 2014, pp 332-345.
• Auriemma WS, Berger AC, Bar-Ad V, Boland PM, Cohen SJ, S CM, Roche-Lima A, Morris GJ. Locally Advanced Pancreatic Cancer. PMID: 22846869 DOI: 10.1053/j.seminoncol.2012.05.015
• Alvare GG, Roche-Lima A, Fristensky B. BioPCD - A Language for GUI Development Requiring a Minimal Skill Set. PMID: 27818582 PMCID: PMC5096648
• Roche-Lima A, Thulasiram RK. Bioinformatics Algorithm Based on a Parallel Implementation of a Machine Learning Approach Using Transducers. PMID: 27795731 PMCID: PMC5082745 DOI: 10.1088/1742-6596/341/1/012034

      A final list of all publications can be seen here.

Books

• Aponte-Caraballo, F.M., Heredia-Negrón, F., Nieves-Rodriguez, B.G., Roche-Lima, A., Death Prediction by Race in Colorectal Cancer Patients Using Machine Learning Approaches. In: Maier, A.K., Schnabel, J.A., Tiwari, P., Stegle, O. (eds) Machine Learning for Multimodal Healthcare Data. ML4MHD 2023. Lecture Notes in Computer Science, vol 14315. Springer, Cham. https://doi.org/10.1007/978-3-031-47679-2_1. 2023.
• Gabriel-Antunes, J,  Sales, A. B. D., Roche-Lima, A. Usability Evaluation of Educational Serious Games. Advances in Intelligent Systems and Computing Information Technology and Systems (WorldCIST). 2022: 381-389. 2022. doi:10.1007/978-3-031-04826-5_38.
• Palmeira, E. G. Q., Roche-Lima, A., & Sales, A. B. D. Users Preferences Regarding Types of Help: Different Contexts Comparison. Advances in Intelligent Systems and Computing Information Technology and Systems (ICITS 2020), 307–314. doi:10.1007/978-3-030-40690-5_30.