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Hire Dr. Sergio Andrés C.

Italy

USD 60 /hr

Experienced Researcher in Bioinformatics, Microbiome Profiling, and Omics Data Analysis

Profile Summary

I am a Postdoctoral Researcher at the University of Trento, specializing in bioinformatics, computational metagenomics, and microbiome research. My work focuses on analyzing microbial communities in humans and animals, integrating metabarcoding and metagenomics sequencing, RNA-Seq, and multi-omics datasets. I have extensive experience in data preprocessing, statistical analysis, metagenomic assembly, functional profiling, and visualization using tools such as R, Python, Snakemake, and Nextflow. I have contributed to multiple research projects involving parasite-microbiome interactions, host-pathogen dynamics, and environmental microbiomes, including the development of pipelines for metagenomic assembly, binning, taxonomic and functional classification, and longitudinal microbiome analysis. I offer consulting services in: -Bioinformatics and data analysis for microbiome, metagenomics, and RNA-Seq datasets -Development and optimization of computational pipelines -Statistical modeling and visualization of complex biological data -Scientific writing, manuscript editing, and grant support With a strong academic background and practical experience, I provide high-quality, reproducible, and efficient solutions for research projects and industry needs.

Subject Matter Expertise

• ☆ Computational Biology
• ☆ Biostatistics
• ☆ Bioinformatics
• ☆ Gene & Protein Expression Analysis
• ☆ Systems Biology
• ☆ Python
• ☆ R
• ☆ Human Biology
• ☆ Infectious Disease
• ☆ Antibiotic Resistance Research
• ☆ Zoonoses

Services

• Writing
• Research
• Consulting
• Data & AI

Writing Medical Writing, Technical Writing

Research Meta-Research, Feasibility Study, Technology Scouting, Gray Literature Search, Scientific and Technical Research, Systematic Literature Review

Consulting Scientific and Technical Consulting

Data & AI Predictive Modeling, Statistical Analysis, Algorithm Design-ML, Data Visualization, Big Data Analytics, Text Mining & Analytics, Data Mining, Data Cleaning

Work Experience

Postdoctorate Researcher

University of Trento

January 2025 - Present

PhD Student

Universidad Del Rosario

August 2019 - Present

Researcher

Centro de Atención e Investigación Médica (CAIMED)

July 2019 - May 2020

Education

Maestría en Informática Biomédica

Universidad El Bosque

January 2019 - Present

PhD

Universidad del Rosario

January 2021 - December 2024

Epidemiólogo

Universidad del Rosario

January 2012 - December 2014

Bacteriólogo (Ciencias de la Salud)

Universidad-Colegio Mayor de Cundinamarca

July 2006 - December 2011

Certifications

• Bioinformatics for Biologist, Analysing and Interpreting Genomics Datasets

  Future Learn Wellcome Connecting Science

  January 2024 - Present

Publications

JOURNAL ARTICLE

Marteles, Diana, Mart́ınez, Maŕıa Victoria, Fernández, Antonio, Riera, Cristina, Fisa, Roser, Roca-Geronès, Xavier, Chavez-Fisa, Sarah, Castañeda, Sergio, Raḿırez, Juan David, Davis, Janine Elizabeth, et al.(2024). Assessment of the exposure to Phlebotomus perniciosus and the presence of anti-Leishmania infantum antibodies in stray cats in an endemic region of Spain, and their potential correlation with environmental factors. Veterinary Quarterly. 44. (1). p. 1--8. Taylor \& Francis

Castaneda, Sergio, Adeniyi-Ipadeola, Grace, Wu, Yifan, Suarez-Reyes, Charlie, Jain, Antrix, Ramirez Gonzalez, Juan David, Weatherhead, Jill(2024). Characterizing Excretory-Secretory Products Proteome Across Larval Development Stages in Ascaris suum. bioRxiv. p. 2024--07. Cold Spring Harbor Laboratory

Medina, Julián Esteban, Castañeda, Sergio, Camargo, Milena, Garcia-Corredor, Diego J, Muñoz, Marina, Raḿırez, Juan David(2024). Exploring viral diversity and metagenomics in livestock: insights into disease emergence and spillover risks in cattle. Veterinary Research Communications. p. 1--21. Springer Netherlands Dordrecht

Patiño, Luz Helena, Ballesteros, Nathalia, Muñoz, Marina, Raḿırez, Angie Lorena, Castañeda, Sergio, Galeano, Luis Alejandro, Hidalgo, Arsenio, Paniz-Mondolfi, Alberto, Raḿırez, Juan David(2024). Global and genetic diversity of SARS-CoV-2 in wastewater. Heliyon. 10. (5). Elsevier

Medina, Julián Esteban, Castañeda, Sergio, Páez-Triana, Luisa, Camargo, Milena, Garcia-Corredor, Diego J, Gómez, Marcela, Luna, Nicolas, Raḿırez, Angie L, Pulido-Medelĺın, Mart́ın, Muñoz, Marina, et al.(2024). High prevalence of Enterovirus E, Bovine Kobuvirus, and Astrovirus revealed by viral metagenomics in fecal samples from cattle in Central Colombia. Infection, Genetics and Evolution. 117. p. 105543. Elsevier

Gómez, Marcela, Mart́ınez, David, Páez-Triana, Luisa, Luna, Nicolás, Raḿırez, Angie, Medina, Julián, Cruz-Saavedra, Lissa, Hernández, Carolina, Castañeda, Sergio, Bohórquez Melo, Ramiro, et al.(2024). Influence of dengue virus serotypes on the abundance of Aedes aegypti insect-specific viruses (ISVs). Journal of Virology. 98. (1). p. e01507--23. American Society for Microbiology 1752 N St., NW, Washington, DC

Herrera, Giovanny, Castañeda, Sergio, Arboleda, Juan Camilo, Pérez-Jaramillo, Juan E, Patarroyo, Manuel Alfonso, Raḿırez, Juan David, Muñoz, Marina(2024). Metagenome-assembled genomes (MAGs) suggest an acetate-driven protective role in gut microbiota disrupted by Clostridioides difficile. Microbiological Research. 285. p. 127739. Urban \& Fischer

Castañeda, Sergio, Poveda, Cristina, Suarez-Reyes, Charlie, Wu, Yifan, Haugen, Noah, Patiño, Luz H, Weatherhead, Jill E, Raḿırez, Juan David(2024). Microbiota dynamics during Ascaris suum larval migration: Implications for host microbial communities in a murine model. Microbial Pathogenesis. p. 107122. Academic Press

Castañeda, Sergio, Acosta, Claudia Patricia, Vasquez-A, Luis Reinel, Patiño, Luz H, Mej́ıa, Rojelio, Raḿırez, Juan David(2024). Molecular detection of intestinal parasites in a rural community of Colombia: A one health approach to explore potential environmental--zoonotic transmission. Zoonoses and Public Health.

Raḿırez, Juan David, Castañeda, Sergio, Weatherhead, Jill, Poveda, Cristina(2024). Parasite-microbiota interactions: a pathway to innovative interventions for Chagas disease, leishmaniasis, and ascariasis. Future Microbiology. p. 1--13. Taylor \& Francis

Patiño, Luz Helena, Castañeda, Sergio, Camargo, Milena, Cao, Li Yong, Liggayu, Bernadette, Paniz-Mondolfi, Alberto, Raḿırez, Juan David(2024). Validation of real-time PCR assays for detecting Plasmodium and Babesia DNA species in blood samples. Acta Tropica. 258. p. 107350. Elsevier

Zuluaga, Nathalia, Mart́ınez, David, Hernández, Carolina, Ballesteros, Nathalia, Castañeda, Sergio, Raḿırez, Juan David, Muñoz, Marina(2023). Description of pathogenic bacteria in patients with respiratory symptoms associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Colombia. Annals of clinical microbiology and antimicrobials. 22. (1). p. 56. BioMed Central London

Castañeda, Sergio, Ariza, Gineth, Rincón-Riveros, Andres, Muñoz, Marina, Raḿırez, Juan David(2023). Diet-induced changes in fecal microbiota composition and diversity in dogs (Canis lupus familiaris): A comparative study of BARF-type and commercial diets. Comparative Immunology, Microbiology and Infectious Diseases. 98. p. 102007. Pergamon

Delgado-Noguera, Lourdes A, Hernández-Pereira, Carlos E, Castillo-Castañeda, Adriana C, Patiño, Luz Helena, Castañeda, Sergio, Herrera, Giovanny, Mogollón, Euler, Muñoz, Marina, Duran, Alexander, Loyo, Doris, et al.(2023). Diversity and geographical distribution of Leishmania species and the emergence of Leishmania (Leishmania) infantum and L.(Viannia) panamensis in Central-Western Venezuela. Acta Tropica. 242. p. 106901. Elsevier

Jimenez-Silva, Cinthy, Rivero, Ricardo, Douglas, Jordan, Bouckaert, Remco, Villabona-Arenas, Ch Julian, Atkins, Katherine E, Gastelbondo, Bertha, Calderon, Alfonso, Guzman, Camilo, Echeverri-De la Hoz, Daniel, et al.(2023). Genomic epidemiology of SARS-CoV-2 variants during the first two years of the pandemic in Colombia. Communications Medicine. 3. (1). p. 97. Nature Publishing Group UK London

Castañeda, Sergio, Muñoz, Marina, Hotez, Peter J, Bottazzi, Maria Elena, Paniz-Mondolfi, Alberto E, Jones, Kathryn M, Mejia, Rojelio, Poveda, Cristina, Raḿırez, Juan David(2023). Microbiome Alterations Driven by Trypanosoma cruzi Infection in Two Disjunctive Murine Models. Microbiology Spectrum. p. e00199--23. American Society for Microbiology 1752 N St., NW, Washington, DC

Patiño, Luz Helena, Ballesteros, Nathalia, Muñoz, Marina, Raḿırez, Angie L, Luna, Nicolas, Castañeda, Sergio, Gutierrez-Marin, Reinaldo, Mendoza-Ibarra, Jesús A, Rodriguez, Raúl, Bohada, Diana Patricia, et al.(2023). Mu SARS-CoV-2 (B. 1.621) variant: A genomic snapshot across the Colombian-Venezuelan border. Journal of Medical Virology. 95. (4).

Carrión-Nessi, Fhabián S, Ascanio, Luis C, Pineda-Arapé, Andréına G, Omaña-Ávila, Óscar D, Mendoza-Millán, Daniela L, Romero, Sinibaldo R, Almao-Rivero, Abranny B, Camejo-Ávila, Natasha A, Gebran-Chedid, Karim J, Rodriguez-Saavedra, Carlis M, et al.(2023). New daily persistent headache after SARS-CoV-2 infection in Latin America: a cross-sectional study. BMC Infectious Diseases. 23. (1). p. 877. BioMed Central London

Ballesteros, Nathalia, Castañeda, Sergio, Muñoz, Marina, Flórez, Angel, Pinilla, Juan Carlos, Raḿırez, Juan David(2023). The first report of Dirofilaria repens infection in dogs from Colombia. Parasitology Research. 122. (10). p. 2445--2450. Springer Berlin Heidelberg Berlin/Heidelberg

Hernandez, Matthew M, Banu, Radhika, Shrestha, Paras, Gonzalez-Reiche, Ana S, van de Guchte, Adriana, Farrugia, Keith, Sebra, Robert, Group, Mount Sinai PSP Study, Gitman, Melissa R, Nowak, Michael D, et al.(2022). A robust, highly multiplexed mass spectrometry assay to identify SARS-CoV-2 variants. Microbiology Spectrum. 10. (5). p. e01736--22. American Society for Microbiology

Castañeda, Sergio, Paniz-Mondolfi, Alberto, Raḿırez, Juan David(2022). Detangling the crosstalk between Ascaris, Trichuris and gut microbiota: what́ s next?. Frontiers in Cellular and Infection Microbiology. 12. p. 852900. Frontiers

Patiño, Luz H, Castañeda, Sergio, Muñoz, Marina, Ballesteros, Nathalia, Ramirez, Angie L, Luna, Nicolas, Guerrero-Araya, Enzo, Pérez, Julie, Correa-Cárdenas, Camilo A, Duque, Maria Clara, et al.(2022). Epidemiological dynamics of SARS-CoV-2 variants during social protests in Cali, Colombia. Frontiers in Medicine. 9. p. 863911. Frontiers Media SA

Velásquez-Ortiz, Natalia, Hernández, Carolina, Cantillo-Barraza, Omar, Medina, Manuel, Medina-Alfonso, Mabel, Suescún-Carrero, Sandra, Muñoz, Marina, Vega, Laura, Castañeda, Sergio, Cruz-Saavedra, Lissa, et al.(2022). Estimating the genetic structure of Triatoma dimidiata (Hemiptera: Reduviidae) and the transmission dynamics of Trypanosoma cruzi in Boyacá, eastern Colombia. PLoS Neglected Tropical Diseases. 16. (7). p. e0010534. Public Library of Science San Francisco, CA USA

Botero, Yesica, Raḿırez, Juan David, Serrano-Coll, Héctor, Aleman, Ader, Ballesteros, Nathalia, Martinez, Caty, Muñoz, Marina, Calderon, Alfonso, Patiño, Luz H, Guzman, Camilo, et al.(2022). First report and genome sequencing of SARS-CoV-2 in a cat (Felis catus) in Colombia. Memórias do Instituto Oswaldo Cruz. 117. p. e210375. Instituto Oswaldo Cruz, Minist{\'e}rio da Sa{\'u}de

Luna, Nicolas, Muñoz, Marina, Raḿırez, Angie L, Patiño, Luz H, Castañeda, Sergio, Ballesteros, Nathalia, Raḿırez, Juan David(2022). Genomic Diversity of SARS-CoV-2 Omicron Variant in South American Countries. Viruses. 14. (6). p. 1234. MDPI

Jimenez-Silva, Cinthy, Rivero, Ricardo, Douglas, Jordan, Bouckaert, Remco, Villabona-Arenas, Julian, Atkins, Katherine, Gastelbondo, Bertha, Calderon, Alfonso, Guzman, Camilo, Echeverri-De la Hoz, Daniel, et al.(2022). Genomic epidemiology of circulating SARS-CoV-2 variants during first two years of the pandemic in Colombia. medRxiv. p. 2022--06. Cold Spring Harbor Laboratory Press

Raḿırez, Juan D, Castañeda, Sergio, Ballesteros, Nathalia, Muñoz, Marina, Hernández, Matthew, Banu, Radhika, Shrestha, Paras, Chen, Feng, Shi, Huanzhi, PSP Study Group, et al.(2022). Hotspots for SARS-CoV-2 omicron variant spread: lessons from New York city. Journal of Medical Virology. 94. (7). p. 2911--2914.

Rivero, Ricardo, Garay, Evelin, Botero, Yesica, Serrano-Coll, Héctor, Gastelbondo, Bertha, Muñoz, Marina, Ballesteros, Nathalia, Castañeda, Sergio, Patiño, Luz Helena, Ramirez, Juan David, et al.(2022). Human-to-dog transmission of SARS-CoV-2, Colombia. Scientific Reports. 12. (1). p. 7880. Nature Publishing Group UK London

Ramirez, Angie L, Luna, Nicolas, Patiño, Luz H, Castañeda, Sergio, Muñoz, Marina, Ballesteros, Nathalia, Perez, Julie, Correa-Cárdenas, Camilo A, Duque, Maria Clara, Mendez, Claudia, et al.(2022). Impact of SARS-CoV-2 Mu variant on vaccine effectiveness: A comparative genomics study at the peak of the third wave in Bogota, Colombia. Journal of Medical Virology. 94. (8). p. 3988--3991.

Camargo, Anny, Guerrero-Araya, Enzo, Castañeda, Sergio, Vega, Laura, Cardenas-Alvarez, Maŕıa X, Rodŕıguez, César, Paredes-Sabja, Daniel, Raḿırez, Juan David, Muñoz, Marina(2022). Intra-species diversity of Clostridium perfringens: A diverse genetic repertoire reveals its pathogenic potential. Frontiers in microbiology. 13. p. 952081. Frontiers Media SA

Raḿırez, Juan David, Cao, Liyong, Cruz-Saavedra, Lissa, Hernandez, Carolina, Castañeda, Sergio, Muñoz, Marina, Ballesteros, Nathalia, Banu, Radhika, Shrestha, Paras, Cordon-Cardo, Carlos, et al.(2022). Pan-stage real-time PCR for quantitation of Trypanosoma cruzi parasitic loads in blood samples. International Journal of Infectious Diseases. 122. p. 310--312. Elsevier

Luna, Nicolas, Raḿırez, Angie L, Muñoz, Marina, Ballesteros, Nathalia, Patiño, Luz H, Castañeda, Sergio, Bonilla-Aldana, D Katterine, Paniz-Mondolfi, Alberto, Raḿırez, Juan David(2022). Phylogenomic analysis of the monkeypox virus (MPXV) 2022 outbreak: Emergence of a novel viral lineage?. Travel medicine and infectious disease. 49. p. 102402. Elsevier

Rojas, Manuel, Rodŕıguez, Yhojan, Hernández, Juan Carlos, D́ıaz-Coronado, Juan C, Vergara, José Alejandro Daza, Vélez, Verónica Posada, Mancilla, Jessica Porras, Araujo, Iván, Yepes, Jairo Torres, Ricaurte, Oscar Briceño, et al.(2022). Safety and efficacy of convalescent plasma for severe COVID-19: a randomized, single blinded, parallel, controlled clinical study. BMC Infectious Diseases. 22. (1). p. 575. BioMed Central London

Muñoz, Marina, Patiño, Luz Helena, Ballesteros, Nathalia, Castañeda, Sergio, Luna, Nicolás, Delgado, Lourdes, Hernandez-Pereira, Carlos, Shaban, Maryia V, Muñoz, Shirly Alexandra, Paniz-Mondolfi, Alberto, et al.(2022). Striking lineage diversity of severe acute respiratory syndrome coronavirus 2 from non-human sources. One health. 14. p. 100363. Elsevier

Ballesteros, Nathalia, Castañeda, Sergio, Muñoz, Marina, Patiño, Luz H, Méndez, Claudia, Oliveros, Carolina, Pérez, Julie, Albarraćın, Lorena, Márquez, Elizabeth K, Alvarado, Maŕıa Teresa, et al.(2021). Cluster characterization of SARS-CoV-2 in military personnel deployed to Egypt and subsequent introduction of B. 1.1. 7 and C. 36 lineages to Colombia. Journal of Travel Medicine. 28. (7). p. taab131. Oxford University Press

Hernandez, Matthew M, Banu, Radhika, Shrestha, Paras, Patel, Armi, Chen, Feng, Cao, Liyong, Fabre, Shelcie, Tan, Jessica, Lopez, Heidi, Chiu, Numthip, et al.(2021). Comparison of SARS-CoV-2 detection in Saliva by real-time RT-PCR and RT-PCR/MALDI-TOF Methods. MedRxiv. p. 2021--03. Cold Spring Harbor Laboratory Press

Quiroga, Santiago A, Hernández, Carolina, Castañeda, Sergio, Jimenez, Paula, Vega, Laura, Gomez, Marcela, Martinez, David, Ballesteros, Nathalia, Muñoz, Marina, Cifuentes, Claudia, et al.(2021). Contrasting SARS-CoV-2 RNA copies and clinical symptoms in a large cohort of Colombian patients during the first wave of the COVID-19 pandemic. Annals of Clinical Microbiology and Antimicrobials. 20. p. 1--10. BioMed Central

Hernández, Carolina, Florez, Carolina, Castañeda, Sergio, Ballesteros, Nathalia, Mart́ınez, David, Castillo, Adriana, Muñoz, Marina, Gomez, Sergio, Rico, Angelica, Pardo, Liseth, et al.(2021). Evaluation of the diagnostic performance of nine commercial RT-PCR kits for the detection of SARS-CoV-2 in Colombia. Journal of Medical Virology. 93. (9). p. 5618--5622.

Castañeda, Sergio, Patiño, Luz H, Muñoz, Marina, Ballesteros, Nathalia, Guerrero-Araya, Enzo, Paredes-Sabja, Daniel, Flórez, Carolina, Gomez, Sergio, Raḿırez-Santana, Carolina, Salguero, Gustavo, et al.(2021). Evolution and epidemic spread of SARS-CoV-2 in Colombia: a year into the pandemic. Vaccines. 9. (8). p. 837. MDPI

Rivero, Ricardo, Garay, Evelin, Botero, Yesica, Serrano-Coll, Hector, Gastelbondo, Bertha, Muñoz, Marina, Ballesteros, Nathalia, Castañeda, Sergio, Patiño, Luz, Ramirez, Juan David, et al.(2021). Human-to-dog transmission of SARS-CoV-2 lota variant: should COVID-19 patients avoid close contact with their pets during illness?.

Raḿırez, Juan David, Muñoz, Marina, Ballesteros, Nathalia, Patiño, Luz H, Castañeda, Sergio, Rincón, Carlos A, Mendez, Claudia, Oliveros, Carolina, Perez, Julie, Márquez, Elizabeth K, et al.(2021). Phylogenomic evidence of reinfection and persistence of SARS-CoV-2: first report from Colombia. Vaccines. 9. (3). p. 282. MDPI

Hernandez, Matthew M, Banu, Radhika, Shrestha, Paras, Patel, Armi, Chen, Feng, Cao, Liyong, Fabre, Shelcie, Tan, Jessica, Lopez, Heidi, Chiu, Numthip, et al.(2021). RT-PCR/MALDI-TOF mass spectrometry-based detection of SARS-CoV-2 in saliva specimens. Journal of medical virology. 93. (9). p. 5481--5486.

Patiño, Luz H, Ballesteros, Nathalia, Muñoz, Marina, Castañeda, Sergio, Hernández, Carolina, Gomez, Sergio, Florez, Carolina, Rico, Angelica, Pardo, Liseth, Hernandez-Pereira, Carlos E, et al.(2021). SARS-CoV-2 in transit: characterization of SARS-CoV-2 genomes from Venezuelan migrants in Colombia. International Journal of Infectious Diseases. 110. p. 410--416. Elsevier

Raḿırez, Juan David, Florez, Carolina, Muñoz, Marina, Hernández, Carolina, Castillo, Adriana, Gomez, Sergio, Rico, Angelica, Pardo, Lisseth, Barros, Esther C, Castaneda, Sergio, et al.(2021). The arrival and spread of SARS-CoV-2 in Colombia. Journal of Medical Virology. 93. (2). p. 1158--1163.

Castañeda, Sergio, Muñoz, Marina, Villamizar, Ximena, Hernández, Paula C, Vásquez, Luis Reinel, Tito, Raúl Yhossef, Raḿırez, Juan David(2020). Microbiota characterization in Blastocystis-colonized and Blastocystis-free school-age children from Colombia. Parasites & Vectors. 13. (1). p. 1--12. BioMed Central

Raḿırez, Angie L, Patiño, Luz H, Castañeda, Sergio Andrés, Luna, Nicolas, Ballesteros, Nathalia, Muñoz, Marina, Paniz-Mondolfi, Alberto EEpidemiology, Genomics, and Vaccine. Emerging Viruses in Latin America: Contemporary Virology. p. 213. Springer Nature

BOOK CHAPTER

Raḿırez, Angie L, Patiño, Luz H, Castañeda, Sergio Andrés, Luna, Nicolas, Ballesteros, Nathalia, Muñoz, Marina, Paniz-Mondolfi, Alberto E, Raḿırez, Juan David(2024). COVID-19 in Latin America: Tracking the SARS-CoV-2 Mu (B. 1.621) Variant: Epidemiology, Genomics, and Vaccine Resistance. Emerging Viruses in Latin America: Contemporary Virology. p. 213--224. Springer Nature Switzerland Cham

CONFERENCE PAPER

Tsaousis, Anastasios D, Gentekaki, Eleni, Stensvold, C Rune, Tan, Kevin SW, Dogruman-Al, Funda, Kurt, Ozgur(2021). The 3rd International Blastocystis Conference: coming together virtually. Trends in Parasitology. 37. (9). p. 765--771.