Marcos Pérez Losada

RESEARCH: 
I am an evolutionary and computational biologist working on applied issues in translational medicine. My research focuses on the molecular and epidemiological dynamics of microbes related to human illnesses and how these microbes interact with their hosts during health and disease. Towards this goal, I use a systems biology approach to integrate genomic, metagenomic and metatranscriptomic data from microbial communities (bacterial, viral and fungal microbiotas), including pathogens, with transcriptomic, clinical and demographic data from their human hosts. I have a broad background in biology with an emphasis on molecular and computational biology, and specific training and expertise in next-generation sequencing technologies and bioinformatics. My current research focuses in two areas: molecular epidemiology of HIV and systems biology of host-microbe interactions in pediatric asthma. My long-term goals are to establish a network of partners with different expertise to understand the evolutionary and ecological dynamics of human microbial pathogens, improve on current strategies for monitoring and controlling HIV transmission, and develop more efficient treatments and classifications for asthma. Such integrative systems biology is readily transferable to other emerging and respiratory diseases such as HCV or bronchiolitis, respectively, and the comparison could lead to valuable horizontal insights.

PUBLICATIONS: 

SCI Journals

2023

• Marcos Pérez-Losada and Keith A. Crandall. Spatial diversity of the skin bacteriome. Frontiers in Microbiology (in press).
• Tyson Dawson, Liang Chen, Barry Kreiswirth, Michael Zody, Samantha Fennessey, Marcos Pérez-Losada, Keith A. Crandall, Barun Mathema, Ali Rahnavard. Integrating multi-omics and clinical data to identify associates of epidemiological health outcomes: the early COVID-19 pandemic in New Jersey. Cell Host and Microbe (in press).
• Gisela Loretan, Federico Giri, Juan Manuel Cabrera, Florencia Coronel, Pablo Agustín Collins, Marcos Pérez-Losada, Eva Carolina Rueda. Phylogeography reveals complex historical processes and different evolutionary significant units in Aegla scamosa freshwater crabs. Hydrobiologia 850: 3627–3644.
• Ignacio Ramos-Tapia, Katiuska Reynaldos, Marcos Pérez-Losada, Eduardo Castro-Nallar. Characterization of the upper respiratory tract microbiota in Chilean asthmatic children reveals compositional, functional and structural changes. Frontiers in Allergy 4:1223306.
• Ryohei Shibata, Zhaozhong Zhu, Michihito Kyo, Tadao Ooka, Robert J. Freishtat, Jonathan M. Mansbach, Marcos Pérez-Losada, Carlos A. Camargo Jr. and Kohei Hasegawa. Nasopharyngeal fungal subtypes of infant bronchiolitis and disease severity risk. eBioMedicine 95:104742.
• Suzanne L. Groah, Amanda K. Rounds, Bruce Sprague and Marcos Pérez-Losada. Intravesical Lactobacillus rhamnosus GG alters urobiome composition and diversity among people with neurogenic lower urinary tract dysfunction. Topics in Spinal Cord Injury Rehabilitation 29 (3): 44–57.
• Zhaozhong Zhu, Robert J. Freishtat, Brennan Harmon, Andrea Hahn, Stephen J. Teach, Marcos Pérez-Losada, Kohei Hasegawa and Carlos A. Camargo. Nasal airway microRNA profiling of infants with severe bronchiolitis and risk of childhood asthma: A multicenter prospective study. European Respiratory Journal 62(2): 2300502.
• Marcos Pérez-Losada, Eduardo Castro-Nallar, José Laerte Boechat, Luis Delgado, Tiago Azenha Rama, Valentín Berrios-Farías and Manuela Oliveira. Nasal bacteriomes of patients with asthma and allergic rhinitis show unique composition, structure, function and interactions. Microorganisms 11, 683.
• Ryohei Shibata, Zhaozhong Zhu, Tadao Ooka, Robert J. Freishtat, Jonathan M. Mansbach, Marcos Pérez-Losada, Ignacio Ramos-Tapia, Stephen J. Teach, Carlos A. Camargo Jr. and Kohei Hasegawa. Immunoglobulin E-virus phenotypes of infant bronchiolitis and risk of childhood asthma. Frontiers in Immunology 14:1187065.
• Ana Pereira, Marta C. Soares, Teresa Santos, Ana Poças, Marcos Pérez-Losada, Amy Apprill, Paul C. Sikkel and Raquel Xavier. Reef location and client diversity influence the skin microbiome of the Caribbean cleaner goby Elacatinus evelynae. Microbial Ecology 85: 372–382.
• Marcos Pérez-Losada, Eduardo Castro-Nallar, José Laerte Boechat, Luis Delgado, Tiago Azenha Rama, Valentín Berrios-Farías and Manuela Oliveira. The oral bacteriomes of patients with allergic rhinitis and asthma differ from that of healthy controls. Frontiers in Microbiology 14:1197135.

2022

• Sergio Guajardo-Leiva, Jaime Alarcón, Florence Gutzwiller, Jorge Gallardo-Cerda, Ian S. Acuña-Rodríguez, Marco Molina-Montenegro, Keith A. Crandall, Marcos Pérez-Losadaand Eduardo Castro-Nallar. Source and acquisition of rhizosphere microbes in Antarctic vascular plants. Frontiers in Microbiology 13:916210.
• Zhaozhong Zhu, Carlos A. Camargo Jr., Yoshihiko Raita, Robert J. Freishtat, Michimasa Fujiogi, Andrea Hahn, Jonathan M. Mansbach, Jonathan M. Spergel, Marcos Pérez-Losada and Kohei Hasegawa. Nasopharyngeal airway dual-transcriptome of infants with severe bronchiolitis and risk of childhood asthma: A multicenter prospective study. The Journal of Allergy and Clinical Immunology 150(4):806-816.
• Daniela Rosado, Ignacio Ramos-Tapia, Keith A. Crandall, Marcos Pérez-Losada and Jorge Domínguez. Grapevine treatment with bagasse vermicompost changes the microbiome of Albariño must and wine and improves wine quality. OENO One, 56(3), 219–230.
• Daniela Rosado, Marta Lores, Ignacio Ramos-Tapia, Keith A. Crandall, Marcos Pérez-Losada and Jorge Domínguez. Integrated fertilization with bagasse vermicompost changes the microbiome of red grapevine Mencía must and improves wine quality. Fermentation 8(8), 357.
• Manuel Aira, Marcos Pérez-Losada, Keith A. Crandall and Jorge Domínguez. Host taxonomy determines the composition, structure, and diversity of the earthworm gut microbiome under homogenous feeding conditions. FEMS Microbiology Ecology 98 (9), fiac093.
• Michimasa Fujiogi, Yoshihiko Raita, Marcos Pérez-Losada, Robert J. Freishtat, Juan Celedón, Jonathan M. Mansbach, Pedro A. Piedra, Zhaozhong Zhu, Carlos A. Camargo Jr., and Kohei Hasegawa. Integrated relationship of nasopharyngeal airway host response and microbiome with bronchiolitis severity: dual-transcriptomic profiling. Nature Communications 13, 4970.
• Manuel Aira, Marcos Pérez-Losada, Keith A. Crandall and Jorge Domínguez. Composition, structure and diversity of soil bacterial communities before, during and after transit through the gut of the earthworm Aporrectodea caliginosa. Microorganisms 10(5), 1025.
• Gracelyn Hill, Marcos Pérez-Losada, Elena Delgado, Sonia Benito, Vanessa Montero, Horacio Gil, Mónica Sánchez, Javier Enrique Cañada-García, Elena Garcia Bodas, Keith A Crandall and Michael M Thomson. The origin, epidemiology and phylodynamics of HIV-1 CRF47_BF. Frontiers in Microbiology 13, 863123.
• Marcos Pérez-Losada, Dhatri Badri Narayanan, Allison R. Kolbe, Ignacio Ramos-Tapia, Eduardo Castro-Nallar, Keith A. Crandall and Jorge Domínguez. Comparative analysis of metagenomics and metataxonomics for the characterization of vermicompost microbiomes. Frontiers in Microbiology 13, 854423.
• Daniela Rosado, Marcos Pérez-Losada, Ricardo Severino, Raquel Xavier. Monitoring disease and antibiotic treatment in the skin microbiota of farmed seabass fingerlings. Microbial Ecology 83(3):789-797.
• James P. Bernot; Pavel Avdeyev; Anton Zamyatin; Niklas Dreyer; Nikita Alexeev; Marcos Pérez-Losada; Keith A Crandall. Chromosome-level genome assembly, annotation and phylogenomics of the gooseneck barnacle Pollicipes pollicipes. GIGA Science 12;11.
• Yoshihiko Raita, Marcos Pérez-Losada, Robert J. Freishtat, Andrea Hahn, Eduardo Castro-Nallar, Ignacio Ramos-Tapia, Nathaniel Stearrett, Yury A. Bochkov, James E. Gern, Zhaozhong Zhu, Carlos A. Camargo, Jr. and Kohei Hasegawa. Nasopharyngeal metatranscriptome profiles of infants with bronchiolitis and risk of childhood asthma: a multicentre prospective study. European Respiratory Journal 60(1): 2102293.

2021

• Daniela Rosado, Marcos Pérez-Losada, Manuel Aira, Jorge Domínguez. Bacterial succession during vermicomposting of silver wattle (Acacia dealbata Link). Microorganisms 10, 65
• Benny K. K. Chan, Andy S. Gale, Niklas Dreyer, Henrik Glenner, Christine Ewers-Saucedo, Marcos Pérez-Losada, Gregory A. Kolbasov, Keith A. Crandall and Jens T. Høeg. The evolutionary diversity of barnacles with an updated classification of fossil and living forms. Zoological Journal of the Linnean Society 193(3), 789-846.
• David T.J. Broderick, David W. Waite, Robyn L. Marsh, Carlos A. Camargo, Paul Cardenas, Anne B. Chang, William O.C. Cookson, Leah Cuthbertson, Wenkui Dai, Mark L. Everard, Alain Gervaix, J. Kirk Harris, Kohei Hasegawa, Lucas R. Hoffman, Soo-Jong Hong, Laurence Josset, Matthew S. Kelly, Bong-Soo Kim, Yong Kong, Shuai C Li, Jonathan M. Mansbach, Asuncion Mejias, George A. O’Toole, Laura Paalanen, Marcos Pérez-Losada, Melinda M. Pettigrew, Maxime Pichon, Octavio Ramilo, Lasse Ruokolainen, Olga Sakwinska, Patrick C. Seed, Christopher J. van der Gast, DPhil Brandie D. Wagner, Hana Yi, Edith T. Zemanick, Yuejie Zheng, Naveen Pillarisetti, Mike Taylor. Bacterial signatures of paediatric respiratory disease: an individual participant data meta-analysis. Frontiers in Microbiology 12, 4018.
• Ali Rahnavard, Tyson Dawson, Rebecca Clement, Nathaniel Stearrett, Marcos Pérez-Losada, Keith A. Crandall. Epidemiological associations with genomic variation in SARS-CoV-2. Scientific Reports 11, 23023.
• Jorge Domínguez, Manuel Aira, Keith A. Crandall, Marcos Pérez-Losada. Earthworms drastically change fungal and bacterial communities during vermicomposting of sewage sludge. Scientific Reports 11, 15556.
• Susana Seixas, Allison R. Kolbe, Silvia Gomes, Maria Sucena, Catarina Sousa, Luís Vaz Rodrigues, Gilberto Teixeira, Paula Pinto, Tiago Tavares de Abreu, Cristina Bárbara, Júlio Semedo, Leonor Mota, Ana Sofia Carvalho, Rune Matthiesen, Patrícia Isabel Marques and Marcos Pérez-Losada. Comparative analysis of the bronchoalveolar microbiome in Portuguese patients with different chronic lung disorders. Scientific Reports 11, 15042.
• Daniela Rosado, Raquel Xavier, Jo Cable, Ricardo Severino, Marcos Pérez-Losada. Longitudinal sampling of external mucosae in farmed European seabass reveals the impact of water temperature on bacterial dynamics. ISME Communications 1, 28.
• Matthew L. Bendall, Keylie M. Gibson, Margaret C. Steiner, Uzma Rentia, Marcos Pérez-Losada and Keith A. Crandall. HAPHPIPE: Haplotype reconstruction and phylodynamics for deep sequencing of intra-host viral populations. Molecular Biology and Evolution 38:1677-1690.
• Catherine Forster, Michael H. Hsieh, Marcos Pérez-Losada, Ljuba Caldovic, Hans Pohl, Inger Ljungberg, Bruce Sprague, Crystal Stroud and Suzanne Groah. A single intravesical instillation of Lactobacillus rhamnosus GG is safe in children and adults with neuropathic bladder: A phase Ia clinical trial. The Journal of Spinal Cord Medicine 44:62-69.
• Daniela Rosado; Marcos Pérez-Losada; Ana Pereira; Ricardo Severino; Raquel Xavier. Effects of aging on the skin and gill microbiota of farmed seabass and seabream. Animal Microbiome 3:10.
• Nathaniel Stearrett, Tyson Dawson, Gholamali Rahnavard, Prathyusha Bachali, Matthew Lewis Bendall, Chen Zeng, Roberto Caricchio, Marcos Pérez-Losada, Amrie C Grammer, Peter E Lipsky and Keith A Crandall. Expression of Human Endogenous Retroviruses in Systemic Lupus Erythematosus: Multiomic Integration with Gene Expression. Frontiers in Immunology, section Microbial Immunology 12, Article 661437.
• Yoshihiko Raita, Marcos Pérez-Losada, Robert J. Freishtat, Brennan Harmon, Tina V. Hartert, Jonathan M. Mansbach, Pedro A. Piedra, Zhaozhong Zhu, Carlos A. Camargo, Jr., and Kohei Hasegawa. Integrated-omics endotyping of infants with respiratory syncytial virus bronchiolitis and risk of childhood asthma. Nature Communications 12: 3601.
• Elena Delgado, Aurora Fernández-García, Marcos Pérez-Losada, María Moreno-Lorenzo, Ismael Fernández-Miranda, Sonia Benito, Vanesa Montero, Horacio Gil, Silvia Hernáez, Josefa Muñoz, Miren Z. Zubero-Sulibarria, Elena García-Bodas, Mónica Sánchez, Jorge del Romero, Carmen Rodríguez, Luis Elorduy, Elena Bereciartua, Esther Culebras, Icíar Rodríguez-Avial, María Luisa Giménez-Alarcón, Carmen Martín-Salas, Carmen Gómez-González, José J García-Irure, Gema Cenzual, Ana Martínez-Sapiña, María Maiques-Camarero, Lucía Pérez-Álvarez, and Michael M Thomson. Identification of CRF89_BF, a new member of an HIV-1 circulating BF intersubtype recombinant form family widely spread in South America. Scientific Reports 11(1):11442.
• Bianca L. Zimmermann, Ivanice Buzzato, Sandro Santos, Federico Giri, Franco T. de Mello, Keith A. Crandall, Marcos Pérez-Losada and Marlise L. Bartholomei-Santos. Entangled Aeglidae (Decapoda, Anomura): Additional evidence for cryptic species. Zoologica scripta 50 (4), 473-484.

2020

• Juan Carlos Nogues, Marcos Pérez-Losada, Diego Preciado. A review of otitis media microbiome studies: What do they tell us? Laryngoscope Investigative Otolaryngology 5: 936–940.
• Kyle Salka, Maria Arroyo, Elizabeth Chorvinsky, Karima Abutaleb, Geovanny F. Perez, Seth Wolf, Xilei Xuchen, Jered Weinstock, Maria J. Gutierrez, Marcos Pérez-Losada, Dinesh Pillai, Gustavo Nino. Innate IFN-lambda responses in the human infant airway epithelium and clinical regulatory factors during viral respiratory infections in early life. Clinical & Experimental Allergy 50 (9): 1044–1054.
• Anton Eliseev, Dimitry Novik, Pavel Avdeyev, Keylie M. Gibson, Matthew L. Bendall, Marcos Pérez-Losada, Nikita Alexeev and Keith A. Crandall. Evaluation of haplotype callers for next-generation sequencing of viruses. Infection Genetics and Evolution 82, 104277.
• Marcos Pérez-Losada, Miguel Arenas, Juan Carlos Galán, Mª Alma Bracho, Julia Hillung, Neris García-González and Fernando González-Candelas. High-Throughput Sequencing (HTS) for the analysis of viral populations. Infection Genetics and Evolution 80, 104208.
• Matthieu J. Miossec, Sandro Valenzuela, Marcos Pérez-Losada, W. Evan Johnson, Keith A. Crandall, Eduardo Castro-Nallar. Evaluation of computational methods for human microbiome analysis using simulated data. PeerJ 8:e9688.
• Allison R. Kolbe, Matthew L. Bendall, Alexander T. Pearson, Doru Paul, Douglas F. Nixon, Marcos Pérez-Losada and Keith A. Crandall. Human endogenous retrovirus expression is associated with head and neck cancer and differential survival. Viruses 12, 956.
• Keylie M Gibson, Kamwing Jair, Amanda D Castel, Matthew L Bendall, Brittany Wilbourn, Jeanne A Jordan, Keith A Crandall, Marcos Pérez-Losada and the DC Cohort Executive Committee. A cross-sectional study to characterize local HIV-1 dynamics in Washington, DC using next-generation sequencing. Scientific Reports 10, 1989.
• Raquel Xavier; Ana Pereira; Andres Pagan; Gina C. Hendrick; Matthew D. Nicholson; Daniela Rosado; Marta C. Soares; Marcos Pérez-Losada; Paul C. Sikkel. The effects of environment and ontogeny on the skin microbiome of two Stegastes damselfishes (Pomacentridae) from the eastern Caribbean Sea. Marine Biology 167, 102.
• Michimasa Fujiogi, Carlos A. Camargo Jr., Jimmy Bernot, Robert J Freishtat, Brennan Harmon, Jonathan Mansbach, Eduardo Castro-Nallar, Marcos Pérez-Losada and Kohei Hasegawa. In infants with severe bronchiolitis: dual-transcriptomic profiling of nasopharyngeal microbiome and host response. Pediatric Research 88: 144–146.
• Keylie M. Gibson, Margaret C. Steiner, Uzma Rentia, Matthew L. Bendall, Marcos Pérez-Losada and Keith A. Crandall. Validation of variant assembly using HAPHPIPE with next generation sequence data from viruses. Viruses 12 (7), 758.
• María Gómez-Brandón, Manuel Aira, Natielo Santana, Marcos Pérez-Losada and Jorge Dominguez. Temporal dynamics of bacterial communities in a pilot-scale vermireactor fed with distilled grape marc. Microorganisms 8, 642.
• Hans G. Pohl, Suzanne L. Groah, Marcos Pérez-Losada, Inger Ljungberg, Bruce M. Sprague, Neel Chandal, Ljubica Caldovic and Michael Hsieh. The urine microbiome of healthy men and women differs by urine collection method. International Neurourology Journal 24(1): 41-51.
• Marcos Pérez-Losada, Kelly M. Crandall and Keith A. Crandall. Testing the “grandma hypothesis”: a project-based learning approach to genomics by characterizing skin microbiome diversity. Journal of Microbiology & Biology Education 21(1): 21.1.7.
• Gisela Loretán, Rueda, Eva Carolina, Cabrera, Juan Manuel, Pérez-Losada, Marcos, Collins, Pablo Agustín, Giri, Federico. Geographical isolation and restricted gene flow drive Aegla singularis (Decapoda. Anomura. Aeglidae) speciation in southern South America. Biological Journal of Linnean Society 129(1): 177–189.

2019

• Matthew L. Bendall, Miguel de Mulder Rougvi, Aarón Lecanda-Sánchez, Marcos Pérez-Losada, Mario A. Ostrowski, R. Brad Jones, Lubbertus C. Mulder, Gustavo Reyes-Terán, Keith A. Crandall, Christopher E. Ormsby and Douglas F. Nixon. Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression. PLoS Computational Biology 15(9): e1006453.
• Suchitra Hourigan, Michelle Ahn, Keylie Gibson, Marcos Pérez-Losada, Grace Felix, Melissa Weidner, Ian Leibowitz, John Niederhuber, Cynthia L. Sears, Keith A. Crandall, Maria Oliva-Hemker. Fecal transplant in children with Clostridioides difficile gives sustained reduction in antimicrobial resistance and pathogenic burden. Open Forum Infectious Diseases 6(10), ofz379.
• Daniela Rosado, Raquel Xavier, Ricardo Severino, Fernando Tavares, Jo Cable, Marcos Pérez-Losada. Effects of disease, antibiotic treatment and recovery trajectory on the microbiome of farmed seabass (Dicentrarchus labrax). Scientific Reports 9: 18946.
• Keylie M. Gibson, Margaret C. Steiner, Seble Kassaye, Frank Maldarelli, Zehava Grossman, Marcos Pérez-Losada, Keith A Crandall. A 28-year history of HIV-1 drug resistance and transmission in Washington, DC. Frontiers in Microbiology 10:369.
• Maria Gómez-Brandón, Manuel Aira, Allison R. Kolbe, Nariane de Andrade, Marcos Pérez-Losada, Jorge Domínguez. Rapid bacterial community changes during vermicomposting of grape marc derived from red winemaking. Microorganisms 7, 473.
• Allison R. Kolbe, Eduardo Castro-Nallar, Diego Preciado, Marcos Pérez-Losada. Altered middle ear microbiome in children with chronic otitis media with effusion and respiratory illnesses. Frontiers Cellular and Infection Microbiology 9:339.
• Jorge Domínguez, Manuel Aira, Allison R. Kolbe, María Gómez-Brandón and Marcos Pérez-Losada. Changes in the composition and function of bacterial communities during vermicomposting may explain beneficial properties of vermicompost. Scientific Reports 9(1):9657.
• Allison R. Kolbe, Manuel Aira, María Gómez-Brandón, Marcos Pérez-Losada, and Jorge Domínguez. Bacterial succession and functional diversity during vermicomposting of the white grape marc Vitis vinifera v. Albariño. Scientific Reports 16;9(1):7472.
• Christine Ewers-Saucedo, Christopher L. Owen, Marcos Pérez-Losada, Jens T. Høeg, Henrik Glenner, Benny Kwok Kan Chan & Keith A. Crandall. Towards a Barnacle Tree of life: Integrating diverse phylogenetic efforts into a comprehensive hypothesis of thecostracan evolution. Peer J. 7:e7387.
• Manuel Aira, Marcos Pérez-Losada and Jorge Domínguez. Microbiome dynamics during cast ageing in the earthworm Aporrectodea caliginosa. Applied Soil Ecology 139: 56-63.
• Kamwing Jair, Chase D. McCann, Harrison Reed, Amanda D. Castel, Marcos Pérez-Losada, Brittany Wilbourn, Alan E. Greenberg, Jeanne A. Jordan and the DC Cohort Executive Committee. Validation of publicly-available software used in analyzing NGS data for HIV-1 drug resistance mutations and transmission networks in a Washington, DC, Cohort. PLoS One 14(4): e0214820.
• Farnaz Bozorgi, Masoumeh Malek, Manuel Aira, Marcos Pérez-Losada, Jorge Dominguez. Multigene phylogeny reveals a new Iranian earthworm genus (Lumbricidae: Philomontanus) with three new species. PLoS One 14(1): e0208904.
• Raquel Xavier, Renata Mazzei, Marcos Pérez-Losada, Daniela Rosado, Joana Santos, Ana Veríssimo, Marta C Soares. A risky business? Habitat and social behaviour impact skin and gut microbiomes in Caribbean cleaning gobies. Frontiers in Microbiology 10:716.
• Keylie M. Gibson, Margaret C. Steiner, Seble Kassaye, Frank Maldarelli, Zehava Grossman, Marcos Pérez-Losada, Keith A. Crandall. A 28 year history of HIV-1 drug resistance and transmission in Washington, DC. Frontiers in Microbiology 10:369.
• Daniela Rosado, Marcos Pérez-Losada, Ricardo Severino, Jo Cable, Raquel Xavier. Characterization of the skin and gill microbiomes of the farmed seabass (Dicentrarchus labrax) and seabream (Sparus aurata). Aquaculture 500: 57-64.

2018

• Luis M. Mejía-Ortiz, Marilú López-Mejía, Juan Carlos Tejeda-Mazariegos, Oscar Frausto-Martínez, Keith A. Crandall, Marcos Pérez-Losada, Jair Gaspar Valladarez. Los camarones de agua dulce de la subfamilia Palaemoninae en la Península de Yucatán (México, Guatemala y Belice). Teoría y Praxis 25: 115-130.
• Carlos G. Jara, Marcos Pérez-Losada, and Keith A. Crandall. Aegla chilota, new species of anomuran freshwater crab from Chiloé Island, western Patagonia. Nauplius 26: e2018029.
• Val Stéphanie, Marian Poley, Anna, Krueger, Gustavo Nino, Kristy Brown, Marcos Perez-Losada, Heather Gordish-Dressman, Diego Preciado. Characterization of mucoid and serous middle ear effusions from patients with chronic otitis media: implication of different biological mechanisms? Pediatric Research 84(2):296-305.
• Pérez-Losada Marcos, Robert J. Graham, Madeline Coquillette, Amenah Jafarey, Eduardo Castro-Nallar, Manuel Aira, Claire Hoptay, Robert J. Freishtat, Jonathan M. Mansbach. Tracheal Microbiota in Patients With a Tracheostomy Before, During and After an Acute Respiratory Infection. Pediatric Infectious Disease Journal 37(11): e269–e271.
• Pérez-Losada, Marcos, Kayla J Authelet, Claire E. Hoptay, Christine Kwak, Keith A. Crandall; Robert J. Freishtat. Pediatric asthma comprises different phenotypic clusters with unique nasal microbiotas. Microbiome 6:179.
• *Emma Nally, Suzanne L. Groah, Marcos Pérez-Losada, Ljubica Caldovic, Inger Ljungberg, Neel J. Chandel, Bruce Sprague, Michael H. Hsieh, Hans G. Pohl. Identification of Burkholderia fungorum in the urine of an individual with spinal cord injury and augmentation cystoplasty using 16S sequencing: copathogen or innocent bystander? Spinal Cord Series and Cases 4: 85.
• Bianca Zimmermann, Marcelo Crivellaro, Marlise Bartholomei-Santos, Keith A. Crandall, Marcos Pérez-Losada, Federico Giri, Pablo Collins, Sandro Santos, Caroline Hauschild. Phylogeography reveals an unexpectedly low genetic diversity in a widely distributed species: the case of the freshwater crab Aegla platensis (Decapoda: Anomura). Biological Journal of the Linnean Society 123 (3): 578–592.
• Hahn, Andrea, Stephanie Warnken, Marcos Pérez-Losada, Robert J Freishtat, Keith A Crandall. Microbial diversity within the airway microbiome in chronic pediatric lung diseases. Infection, Genetics and Evolution 63: 316-325.
• Houzet L., M. Pérez-Losada, G. Matusali, C. Deleage, N. Dereuddre-Bosquet, A. P. Satie, F. Aubry, E. Becker, B. Jégou, R. Le Grand, B. F. Keele, K. A. Crandall and N. Dejucq-Rainsford. Seminal SIV in chronically-infected cynomolgus macaques is dominated by virus originating from multiple genital organs. Journal of Virology 92 (14) e00133-18.
• Pérez-Losada, Marcos, Miguel Arenas and Eduardo Castro-Nallar. Microbial sequence typing in the genomic era. Infection, Genetics and Evolution 63: 346-359.
• Kohei Hasegawa, Marcos Pérez-Losada, Claire E. Hoptay, Samuel Epstein, Jonathan M. Mansbach, Stephen J. Teach, Pedro A. Piedra, Carlos A. Camargo, Jr., and Robert J. Freishtat. RSV bronchiolitis versus rhinovirus: Difference in nasal airway microRNA profiles and NFκB signaling. Pediatric Research 83(3): 606-614.
• Arenas, Miguel, Natalia M. Araujo, Catarina Branco, Nadine Castelhano, Eduardo Castro-Nallar and Marcos Pérez-Losada. Mutation and recombination in pathogen evolution: Relevance, methods and controversies. Infection, Genetics and Evolution 63: 295-306.
• Regina Wetzer, Niel L. Bruce and Marcos Pérez-Losada. Relationships of the Sphaeromatidae genera (Peracarida: Isopoda) inferred from 18S rDNA and 16S rDNA genes. Arthropod Phylogeny and Systematics 76(1): 1-30.
• Aira, Manuel, Marcos Pérez-Losada, Jorge Domínguez. Diversity, structure and sources of bacterial communities of earthworm cocoons. Scientific Reports 8: 6632.
• Noguera, José C., Manuel Aira, Marcos Pérez-Losada, Jorge Domínguez, Alberto Velando. Glucocorticoids modulate gastrointestinal microbiome in a wild young bird. Royal Society open science 5: 171743.
• Raquel Xavier, Joanne Cable, Camino Gestal, Marcos Pérez-Losada, David James Harris, Rita Freitas, Daniela Rosado, Ana Verissimo, Ricardo Severino. Phylogenetic analysis of Apicomplexan parasites infecting commercially valuable species from the Northeast Atlantic reveals new and high levels of species diversity. Parasites & Vectors 11: 63.
• Jorge Domínguez, Manuel Aira, Pablo G. Porto, Darío J. Díaz Cosín, Marcos Pérez-Losada. Multigene phylogeny reveals two new isolated and relic earthworm genera (Oligochaeta: Lumbricidae). Zoological Journal of the Linnean Society 18: 258–274.

2017

• Crivellaro, M. S., Bianca L. Zimmermann, Marlise L. Bartholomei-Santos, Keith A. Crandall, Marcos Pérez-Losada, Georgina Bond-Buckup and Sandro Santos. Looks can be deceiving: species delimitation reveals hidden diversity in the freshwater crab Aegla longirostri (Decapoda: Anomura). Zoological Journal of the Linnean Society 182: 24-37.
• Pérez-Losada, M., Amanda D. Castel, Brittany Lewis, M. Kharfen, C. P. Cartwright, B. Huang, T. Maxwell, A. Greenberg and Keith A. Crandall, on behalf of the DC Cohort Executive Committee. Characterization of HIV diversity, phylodynamics and drug resistance in Washington, DC. PLoS One 12(9): e0185644.
• Perez-Losada, M., Robert J Graham, Madeline Coquillette, Amenah Jafarey, Eduardo Castro-Nallar, Manuel Aira, Robert J Freishtat, Jonathan M Mansbach. The temporal dynamics of the tracheal microbiome in tracheostomised patients with and without lower respiratory infections. PLoS One 12(8): e0182520.
• Perez, Geovanny F., Marcos Pérez-Losada, Natalia Isaza, Mary C. Rose, Anamaris M. Colberg-Poley, Gustavo Nino. Nasopharyngeal Microbiome in Premature Infants and Stability during Rhinovirus Infection. Journal of Investigative Medicine 65: 984-990.    
• Krueger A., Val S., Pérez-Losada M., Panchapakesan K., Devaney J., Duah V., DeMasson C., Poley M., Rose M., Preciado D. The Relationship of the Middle Ear Effusion Microbiome to Secretory Mucin Production in Pediatric Patients with Chronic Otitis Media. The Pediatric Infectious Disease Journal 36: 635-640.    
• Pérez-Losada Marcos, Lamia Alamri, Keith A. Crandall and Robert J. Freishtat. Nasopharyngeal microbiome diversity changes over time in children with asthma. PLoS One 12(1): e0170543.    

2016

• Jörg, Römbke; Manuel Aira; Thierry Backeljau; Karin Breugelmans; Jorge Dominguez; Elisabeth Funke; Nadin Graf; Mehrdad Hajibabaei; Marcos Perez-Losada; Pablo G Porto; Rüdiger Schmelz; Joaquin Vierna; Anton Vizcaino; Markus Pfenninger. DNA barcoding of earthworms (Eisenia fetida/andrei) from 28 ecotoxicological test laboratories. Applied Soil Ecology 104: 3–11.
• Groah Suzanne, Marcos Perez-Losada, Ljuba Caldovic, Inger Ljungberg, Bruce Sprague, Eduardo Castro-Nallar, Neel Shah, Michael Hsieh, Hans Pohl. Redefining healthy urine: a cross-sectional exploratory metagenomic study of people at low- and high-risk for urinary tract infection. The Journal of Urology 196: 579-587.
• Hahn A., Sanyal A, Perez G, Colberg-Poley AM, Campos J, Rose M, Pérez-Losada M. Different Next Generation Sequencing platforms produce different microbial profiles and diversity in cystic fibrosis sputum. Journal of Microbiological Methods 130: 95–99.
• Val Stephanie, Marian Poley, Kristy Brown, Rachel Choi, Stephanie Jeong, AnaMaris Colberg-Poley, Mary C. Rose, Karuna C. Panchapakesan, Joe C. Devaney, Marcos Perez-Losada, Diego Preciado. Proteomic characterization of middle ear fluid reveals neutrophil extracellular traps as a predominant innate immune response in chronic otitis media. PLoS One 11(4): e0152865.    
• Pérez-Losada Marcos, Keith A. Crandall and Robert J. Freishtat. Two sampling methods yield distinct microbial signatures in the nasopharynges of asthmatic children. Microbiome 4:25.    
• Pérez-Losada Marcos, Keith A. Crandall, Robert J. Freishtat. Comparison of two commercial DNA extraction kits for the analysis of nasopharyngeal bacterial communities. AIMS Microbiology 2(2): 108-119.    
• Hilton Sarah K., Eduardo Castro-Nallar, Marcos Pérez-Losada, Ian Toma, Timothy A. McCaffrey, Eric P. Hoffman, Marc O. Siegel, Gary L. Simon, W. Evan Johnson and Keith A. Crandall. Metataxonomic and metagenomic approaches versus culture-based techniques for clinical pathology. Frontiers Microbiology 7: 484.

2015

• Aira Manuel, Jessica Olcina, Marcos Pérez-Losada, Jorge Domínguez. Characterization of the bacterial communities of casts from Eisenia andrei fed with different substrates. Applied Soil Ecology 98: 103-111.    
• Sandro Santos, Georgina Bond-Buckup, Ludwig Buckup, Marlise Ladvocat Bartholomei-Santos, Marcos Pérez-Losada, Carlos G. Jara, and Keith A. Crandall. Three new species of Aeglidae (Aegla leach, 1820) from the Paraná state, Brazil. Journal of Crustacean Biology 35(6): 839–849.    
• Delgado, E., María Teresa Cuevas, Francisco Domínguez, Yolanda Vega, Marina Cabello, Aurora Fernández-García, Marcos Pérez-Losada, María Ángeles Castro, Vanessa Montero, Mónica Sánchez, Ana Mariño, Hortensia Álvarez, Patricia Ordóñez, Antonio Ocampo, Celia Miralles, Sonia Pérez-Castro, María José López-Álvarez, Raúl Rodríguez, Matilde Trigo, Julio Diz-Arén, Carmen Hinojosa, Pablo Bachiller, Silvia Hernáez Crespo, Ramón Cisterna, Eugenio Garduño, Lucía Pérez-Álvarez, Michael M Thomson. Phylogeny and Phylogeography of a Recent HIV-1 Subtype F Outbreak among Men Who Have Sex with Men in Spain Deriving from a Cluster with a Wide Geographic Circulation in Western Europe. PLoS One 10(11): e0143325.    
• Aira Manuel, Seth Bybee, Marcos Pérez-Losada, Jorge Dominguez. Feeding on microbiomes: effects of detritivory on the taxonomic and phylogenetic bacterial composition of animal manures. FEMS Microbiology Ecology 91: 2015, fiv117.    
• Castro-Nallar, E., Matthew L. Bendall, Marcos Pérez-Losada, Sarven Sabuncyan, Emily G. Severance, Faith B. Dickerson, Jennifer R. Schroeder, Robert H. Yolken, Keith A. Crandall. Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls. Peer J 3: e1140.    
• Castro-Nallar, E., Ying Shen, Robert J. Freishtat, Marcos Pérez-Losada, Solaiappan Manimaran, Gang Liu, Avrum Spira, W. Evan Johnson, and Keith A. Crandall. Integrating Metagenomics and Host Gene Expression to Characterize Asthma-Associated Microbial Communities. BMC Medical Genomics 8: 50.    
• Pérez-Losada, M., Eduardo Castro-Nallar, Matthew Bendall, Robert J. Freishtat, Keith A. Crandall. Dual transcriptomic profiling of host and microbiota during health and disease in pediatric asthma. PLoS One 10(6): e0131819.    
• Pérez-Losada, M., M. Arenas, J. C. Galán, F. Palero; F. Gonzalez-Candelas. Recombination in viruses: Mechanisms, methods of study, and evolutionary consequence. Infection, Genetics and Evolution 30: 296-307.    
• Pérez-Losada, M., J. W. Breinholt, M. Aira, J. Domínguez. An updated multilocus phylogeny of the Lumbricidae (Annelida: Clitellata: Oligochaeta) earthworms. Journal of Phylogenetics and Evolutionary Biology 3: 1.    
• Dominguez J., M. Aira, J. W. Breinholt, M. Stojanovic, S. W. James, M. Pérez-Losada. Underground evolution: new roots for the old tree of lumbricid earthworms. Molecular Phylogenetics and Evolution 83: 7-19.    

2014

• Toma I., Marc O. Siegel, John Keiser, Anna Yakovleva, Alvin Kim, Lionel Davenport, Joseph Devaney, Eric P. Hoffman, Rami Alsubai, Keith A. Crandall, Eduardo Castro-Nallar, Marcos Pérez-Losada, Sarah Hilton, Lakhmir S. Chawla, Timothy A. McCaffrey, and Gary L. Simon. Single-Molecule Long Read 16S Sequencing to Characterize the Lung Microbiome from Mechanically Ventilated Patients with Suspected Pneumonia. Journal of Clinical Microbiology 52: 3913-3921.    
• Pérez-Losada M., Jens T. Høeg, Noa Simon-Blecher, Yair Achituv, Diana Jones, Keith A. Crandall. Molecular phylogeny, systematics and morphological evolution of the acorn barnacles (Thoracica: Sessilia: Balanomorpha). Molecular Phylogenetics and Evolution 81: 147-158.    

2013

• Pérez-Losada, M., P. Cabezas, E. Castro-Nallar, K. A. Crandall. Pathogen typing in the genomics era: MLST and the future of molecular epidemiology. Infection, Genetics and Evolution 16: 38-53.    
• Santos S., C. G. Jara, M. Ladvocat Bartholomei-Santos, M. Pérez-Losada and K. A. Crandall. New species and records of the genus Aegla Leach, 1820 (Crustacea, Anomura, Aeglidae) from the West-Central region of Rio Grande do Sul, Brazil. Nauplius 21(2): 211-223.    
• Faria J, Pérez‐Losada M., Cabezas P., Alexandrino P., Froufe E. Multiplexing of novel microsatellite loci for the vulnerable slipper lobster Scyllarus arctus (Linnaeus, 1758). Journal of Experimental Zoology 9999A: 1–5.    
• Faria J., E. Froufe, F. Tuya, P. Alexandrino and M. Pérez-Losada. Panmixia in the endangered slipper lobster Scyllarides latus from the Northeastern Atlantic and Western Mediterranean. Journal of Crustacean Biology 33: 557-566.    
• Castellanos-Martínez, S., M. Pérez-Losada and C. Gestal. Molecular phylogenetic analysis of the coccidian cephalopod parasites Aggregata octopiana and Aggregata eberthi from the NE Atlantic coast using 18S rRNA sequences. European Journal of Parasitology 49: 373-380.    
• Wetzer, R., M. Pérez-Losada and N. L. Bruce. Phylogenetic relationships of the family Sphaeromatidae Latreille, 1825 (Crustacea: Peracarida: Isopoda) within Sphaeromatidea based on 18S-rDNA molecular data. Zootaxa 3599: 161–177.    
• Xavier R., Severino R., Pérez-Losada M., Cable J., Harris D.J. First record of Sphaerospora dicentrarchi (Myxosporea, Sphaerosporidae) in Dicentrarchus punctatus. Bulletin of the European Association of Fish Pathologists 33: 21-24.    

2012

• Pérez-Losada, M., R. Bloch, J. W. Breinholt, M. Pfenninger and J. Domínguez. Taxonomic assessment of Lumbricidae (Oligochaeta) earthworm genera using DNA barcodes. European Journal of Soil Biology 48: 41-47.    
• Barber, B., J. Xu, M. Pérez-Losada, C. G. Jara and K. A. Crandall. Conflicting evolutionary patterns due to mitochondrial introgression and multilocus phylogeography of the Patagonian freshwater crab Aegla neuquensis. PLoS One 7: e37105.    
• Andonov, A., M. B. Coulthart, M. Pérez-Losada, K. A. Crandall, D. Posada, R. Padmore, A. Giulivi, J. J. Oger, A. A. Peters, G. A. Dekaban. Insights into origins of Human T-cell Lymphotropic Virus Type 1 based on new strains from aboriginal people of Canada. Infection, Genetics and Evolution 12: 1822-1830.    
• Pérez-Losada, M., J. T. Høeg and K. A. Crandall. Deep phylogeny and character evolution in Thecostraca (Crustacea: Maxillopoda). Integrative and Comparative Biology 52: 430-442.    
• Pérez-Losada, M., J. T. Høeg, K. A. Crandall and Y. Achituv. Molecular phylogeny and character evolution of the chthamaloid barnacles (Cirripedia: Thoracica). Molecular Phylogenetics and Evolution 65: 329-334.    
• Santos, S., G. Bond-Buckup, L. Buckup, M. Pérez-Losada, M. Finley, K. A. Crandall. Three new species of Aegla (ANOMURA) freshwater crabs from the upper Uruguay River hydrographic basin in Brazil. Journal of Crustacean Biology 32: 529-540.    
• Castro-Nallar, E., K. A. Crandall and M. Pérez-Losada. Genetic diversity and molecular epidemiology of HIV transmission. Future Virology 7: 1-14.    
• Castro-Nallar, E., M. Pérez-Losada, G. F. Burton and K. A. Crandall. The evolution of HIV: Inferences using phylogenetics. Molecular Phylogenetics and Evolution 62: 777-792.    

2011

• Pérez-Losada, M., D. V. Jobes, F. Sinangil, K. A. Crandall, M. Arenas, D. Posada, and P. W. Berman. Phylodynamics of HIV-1 from a Phase III AIDS Vaccine Trial in Bangkok, Thailand. PLoS One 6: e16902.    
• Barber, B. R., P. J. Unmack, M. Pérez-Losada, J. B. Johnson and K.A. Crandall. Different processes lead to identical patterns: a test of codivergence and the role of sea-level and climate changes in shaping a southern temperate species assemblage. BMC Evolutionary Biology 11: 343.
• Pérez-Losada, M., J. W. Breinholt, P. G. Porto, M. Aira and J. Dominguez. An earthworm riddle: systematics and phylogeography of the Spanish lumbricid Postandrilus. PLoS One 6 e28153.    
• Tazi L, Imamichi H, Hirschfeld S, Metcalf JA, Orsega S, Pérez-Losada M, Posada D, Clifford Lane H and Crandall KA. HIV-1 infected monozygotic twins: a tale of two outcomes. BMC Evolutionary Biology 11: 62.    

2010

• Pérez-Losada, M., David V. Jobes, Faruk Sinangil, Keith A. Crandall, David Posada, and Phillip W. Berman. Phylodynamics of gp120 sequences from a Phase 3 HIV-1 vaccine trial in North America. Molecular Biology and Evolution 27: 417-425.    
• Nuñez, J. J., M. T. González and M. Pérez-Losada. Testing species boundaries between Sebastes capensis and S. oculatus (Teleostei: Scorpaenidae) through mitochondrial DNA sequences. Revista de Biología Marina y Oceanografía 45: S1 565-573.    
• Toon, A., M. Pérez-Losada, C. E. Schweitzer, R. M. Feldman, M. Carlson and K. A. Crandall. Gondwanan radiation of the southern hemisphere crayfish (Decapoda: Parastacidae): Evidence from fossils and molecules. Journal of Biogeography 37: 2275-2290.    
• Santos S, Bond-Buckup G, Pérez-Losada M., Jara CG, Crandall KA and Buckup L. New records and description of a new species of Aeglidae (Crustacea: Anomura) from river basins in Southern Brazil. Nauplius 18: 79-86.    
• Guerra, A., A. Roura, A. F. González, S. Pascual, Y. Cherel and M. Pérez-Losada. Morphological and genetic evidence that Octopus vulgaris Cuvier, 1797 inhabits Amsterdam and Saint Paul Islands (Southern Indian Ocean). ICES Journal of Marine Science 67: 1401-1407.    
• Bond-Buckup, G., C. G. Jara, L. Buckup, M. Pérez-Losada, A. A. P. Bueno, K. A. Crandall and S. Santos. New species and new records of endemic freshwater crabs from the Atlantic forest in southern Brazil (Anomura, Aeglidae). Journal of Crustacean Biology 30: 495-502.    
• Bond-Buckup, G, C. G. Jara, L. Buckup, A. A. P. Bueno, M. Pérez-Losada and K. A. Crandall. Description of a new species of Aeglidae, and new records of related species from river basins in Argentina (Crustacea, Anomura). Zootaxa 2343: 18-30.    
• Tazi, T., M. Pérez-Losada, W. Gu, L. Xue, K. A. Crandall and R. P. Viscidi. Population Dynamics of Neisseria gonorrhoeae in Shanghai, China: A Comparative Study. BMC Infectious Diseases 10: 13.
• Domínguez, J. and M. Pérez-Losada. Eisenia fetida (Savigny, 1826) y Eisenia andrei Bouché, 1972 son dos especies diferentes de lombrices de tierra. Acta Zoologica Mexicana (n. s.) 2: 321-331.

2009

• Xu, J., M. Pérez-Losada, C. G. Jara and K. A. Crandall. Pleistocene glaciation leaves deep signature on the freshwater crab Aegla alacalufi in Chilean Patagonia. Molecular Ecology 18: 904-918.    
• Høeg, J. T., M. Perez-Losada, Henrik Glenner, Gregory A Kolbasov and Keith A. Crandall. Evolution of morphology, ontogeny and life cycles within the Crustacea Thecostraca. Arthropod Systematics and Phylogeny 67: 199-217.    
• Santos, S., G. Bond-Buckup, M. Pérez-Losada, M. Ladvocat Bartholomei-Santos and L. Buckup. Aegla manuinflata, a new species of freshwater anomuran (Decapoda: Anomura: Aeglidae) from the Ibicuí River basin, Rio Grande do Sul, Brazil, determined by morphological and molecular characters. Zootaxa 2088: 31-40.    
• Pérez-Losada, M., D. Posada, D. V. Jobes, F. Sinangil, P. W. Berman and K. A. Crandall. Ethnic differences in the adaptation rate of HIV gp120 from a vaccine trail. Retrovirology 6: 67.    
• Pérez-Losada, M., M. Ricoy, J. Marshall and J. Domínguez. Phylogenetic assessment of the earthworm Aporrectodea caliginosa species complex (Oligochaeta, Lumbricidae) based on mitochondrial and nuclear DNA sequences. Molecular Phylogenetics and Evolution 52: 293-302.    
• Pérez-Losada, M., G. Bond-Buckup, C. G. Jara and K. A. Crandall. Conservation assessment of southern South American freshwater ecoregions on the basis of the distribution and genetic diversity of crabs from the genus Aegla. Conservation Biology 23: 692-702.     
• Pérez-Losada, M., Jens T. Høeg and Keith A. Crandall. Remarkable convergent evolution in specialized parasitic Thecostraca (Crustacea). BMC Biology 7: 15.    
• Høeg, J. T., Y. Achituv, B. K.K. Chan, K. Chan, P. Gram Jensen and M. Pérez-Losada. Cypris Morphology in the barnacles Ibla and Paralepas (Crustacea: Cirripedia Thoracica) - Implications for Cirripede Evolution. Journal of Morphology 270: 241-255.   

2008

• Pérez-Losada, M., M. Harp, J. T. Høeg, Y. Achituv, D. Jones, H. Watanabe and K. A. Crandall. The tempo and mode of barnacle evolution. Molecular Phylogenetics and Evolution 46: 328–346.    
• Weaver, K. F., M. Pérez-Losada, R. P. Guralnick, A. Nelson, S. Blatt and K. A. Crandall. Assessing the conservation status of the land snail Oreohelix peripherica wasatchensis (Family Oreohelicidae). Conservation Genetics 9: 907-916.    
• Carvajal-Rodríguez, A., D. Posada, M. Pérez-Losada, E. Keller, E. J. Abrams, K. A. Crandall and R. P. Viscidi. Disease progression and evolution of the HIV-1 env gene in 24 infected infants. Infection Genetics and Evolution 8: 110-120.    
• Bond-Buckup, G., C. G. Jara, M. Pérez-Losada, L. Buckup and K. A. Crandall. An assessment of global diversity of the freshwater ‘crab’ Aeglidae (Decapoda: Anomura). Hydrobiologia 595: 267–273.    

2007

• Porter, M. L., K. Dittmar de la Cruz and M. Pérez-Losada. How long does evolution of the troglomorphic form take? Estimating divergence times in Astyanax mexicanus. Acta Carsologica 36: 173-182.    
• Pérez-Losada, M., K. A. Crandall, M. C. Bash, M. Dan, J. Zenilman and R. P. Viscidi. Distinguishing importation from diversification of quinolone-resistant Neisseria gonorrhoeae by molecular evolutionary analysis. BMC Evolutionary Biology 7: 84-94.    
• Pérez-Losada, M., K. A. Crandall, J. Zenilman and R. P Viscidi. Temporal trends in gonococcal population genetics in a high prevalence urban community. Infection, Genetics and Evolution 7: 271-278.    
• Pérez-Losada, M., M. J. Nolte, K. A. Crandall, and P. W. Shaw. Testing hypotheses of population structuring in the NE Atlantic Ocean and Mediterranean Sea using the common cuttlefish Sepia officinalis. Molecular Ecology 16: 2667-2679. 
• Pérez-Losada, M., M. L. Porter, L. Tazi, and K. A. Crandall. New methods for inferring population dynamics from microbial sequences. Infection, Genetics and Evolution 7: 24-43.

2006

• Pérez-Losada, M., E. B. Browne, A. Madsen, T. Wirth, R. P. Viscidi and K. A. Crandall. Population genetics of microbial pathogens estimated from Multilocus Sequence Typing (MLST) data. Infection, Genetics and Evolution 6: 97-112.
• Daniels, S. R., N. Cumberlidge, M. Pérez-Losada and K. A. Crandall. Evolution of Afrotropical freshwater crab lineages obscured by morphological convergence. Molecular Phylogenetics and Evolution 40: 227-235.
• Jobes, D. V., M. Daoust, V. T. Nguyen, A. Padua, F. Sinangil, M. Pérez-Losada, K. A. Crandall, T. Oliphant, D. Posada, A. Rambaut, J. Fuchs, and P. W. Berman. Longitudinal population analysis of dual infection with recombination in two strains of HIV-1 subtype B in an individual from a Phase 3 HIV vaccine efficacy trial. AIDS 22: 968-978.    
• Pérez-Losada, M., R. G. Christensen, D. A. McClellan, Byron Adams, R. P. Viscidi, and K. A. Crandall. Phylogenetic codivergence of polyomaviruses and their hosts. Journal of Virology 80: 5663-5669.
• Crandall, K. A., M. Pérez-Losada, R. G. Christensen, D. A. McClellan and R. P. Viscidi. Phylogenomics and molecular evolution of Polyomaviruses. Advances in Experimental Medicine and Biology 577: 46-59. Review. 

2005

• Pérez-Losada, M., J. Eiroa, S. Mato and J. Domínguez. Phylogenetic species delimitation of the earthworms Eisenia fetida (Savigny, 1826) and Eisenia andrei Bouché, 1972 (Oligochaeta, Lumbricidae) based on mitochondrial and nuclear DNA sequences. Pedobiologia 49: 317-324.    
• Pérez-Losada M., G. Bond-Buckup, C. Jara and K. A. Crandall. Molecular systematics and biogeography of the southern South American freshwater “crabs” Aegla (Decapoda: Anomura: Aeglidae) using multiple heuristic tree search approaches. Systematic Biology 53: 767-780
• Martínez, P., M. Pérez-Losada, A. Guerra and A. Sanjuan. First genetic validation and diagnosis of the short-finned squid species of the genus Illex (Cephalopoda: Ommastrephidae). Marine Biology 148: 97-108.    
• Porter, M. L., M. Pérez-Losada and K.A. Crandall. Model based multi-locus estimation of Decapod phylogeny and divergence times. Molecular Phylogenetics and Evolution 37: 355-369.    
• Pérez-Losada, M., Raphael P. Viscidi, and Keith A. Crandall. Population Genetics of Neisseria gonorrhoeae in a High Prevalence Community Using a Hyper-Variable Outer Membrane porB and Thirteen Slow-Evolving Housekeeping Genes. Molecular Biology and Evolution 22: 1887-1902.    
• Shull, H. C., M. Pérez-Losada, D. Blair, K. Sewell, E. A. Sinclair, S. Lawler, M. Ponniah and K. A. Crandall. Phylogeny and biogeography of the freshwater crayfish Euastacus (Decapoda: Parastacidae) based on nuclear and mitochondrial DNA. Molecular Phylogenetics and Evolution 37: 249-263.    

2004

• Pérez-Losada M., J. T. Høeg and K. A. Crandall. Unraveling the evolutionary radiation of the thoracican barnacles using molecular and morphological evidence: a comparison of several divergence time estimation approaches. Systematic Biology 53: 244-264.
• Pérez-Losada M., G. Bond-Buckup, C. Jara and K. A. Crandall. Molecular systematics and biogeography of the southern South American freshwater “crabs” Aegla (Decapoda: Anomura: Aeglidae) using multiple heuristic tree search approaches. Systematic Biology 53: 767-780.  

2003

• Jara C. G., M. Pérez-Losada and K. A. Crandall. Aegla occidentalis (Crustacea: Decapoda: Aeglidae), a new species of freshwater anomuran crab from the Nahuelbuta Coastal Range, Chile. Proceeding of the Biological Society of Washington 116: 954-963.    
• Pérez-Losada M., A. Guerra and A. Sanjuan. Allozyme divergence supporting the taxonomic separation of Octopus mimus and O. maya from Octopus vulgaris (Cephalopoda: Octopoda). Bulletin of Marine Science 71: 653-664.    
• Pérez-Losada M., A. Guerra, G. R. Carvalho, A. Sanjuan and P. W. Shaw. Extensive population subdivision of the cuttlefish Sepia officinalis (Mollusca: Cephalopoda) around the Iberian Peninsula indicated by microsatellite DNA variation. Heredity 89: 417-424.    
• Pérez-Losada M., C. Jara, G. Bond-Buckup and K. A. Crandall. Phylogenetic relationships among the species of Aegla (ANOMURA: AEGLIDAE) freshwater crabs from Chile. Journal of Crustacean Biology 22: 304-313.    
• Pérez-Losada M., J. T. Høeg, G. A. Kolbasov and K. A. Crandall. Reanalysis of the relationships among the Cirripedia and the Ascothoracida and the phylogenetic position of the Facetotecta (Maxillopoda: Thecostraca) using 18S rDNA sequences. Journal of Crustacean Biology 22: 661-669.    
• Pérez-Losada M., C. Jara, G. Bond-Buckup, M. Porter and K. A. Crandall. Phylogenetic position of the freshwater anomuran Aeglidae. Journal of Crustacean Biology 22: 670-676.    

2002

• Pérez-Losada M., C. Jara, G. Bond-Buckup and K. A. Crandall. Conservation phylogenetics of Chilean freshwater crabs Aegla (ANOMURA, AEGLIDAE): assigning priorities for aquatic habitat protection. Biological Conservation 105: 345-353.    

2001

• Guerra A., M. Pérez-Losada, F. Rocha and A. Sanjuan. Species differentiation of Sepia officinalis and Sepia hierredda (Cephalopoda: Sepiidae) based on morphological and allozyme analyses. Journal Marine Biology Association U.K. 81: 271-281.    

2000

• Shaw P. W. and M. Pérez-Losada. Polymorphic microsatellites in the common cuttlefish Sepia officinalis. Molecular Ecology 9: 237-238.    

1999

• Pérez-Losada M., A. Guerra and A. Sanjuan. Allozyme differentiation in the cuttlefish Sepia officinalis (Mollusca: Cephalopoda) from the NE Atlantic and Mediterranean. Heredity 83: 280-289.    

1997

• Sanjuan A., M. Pérez-Losada and E. Rolán. Allozyme evidence for cryptic speciation in sympatric populations of the marine pollution indicator Nassarius spp. (MOLLUSCA: GASTROPODA). Journal Marine Biology Association U. K. 77: 773-784.    
• Sanjuan A., M. Pérez-Losada and A. Guerra. Genetic differentiation in three Sepia species (Mollusca: Cephalopoda) from Galician waters (north-west Iberian Peninsula). Marine Biology 126: 253-259.    

1996

• Pérez-Losada M., A. Guerra and A. Sanjuan. Allozyme electrophoretic technique and phylogenetic relationships in three species of Sepia (Cephalopoda: Sepiidae). Comparative Biochemical Physiology 114B: 11-18.

* Awarded Editors’ Choice

Book Series

2011

• Pérez-Losada, M., J. Xu, C. Jara and K. Crandall. Comparing phylogeographic patterns across the Patagonian Andes in two freshwater crabs of the genus Aegla (Decapoda: Aeglidae). Phylogeography and Population Genetics in Crustacea. Crustacean Issues 19: 291-303. 
• Froufe, E., P. Cabezas, P. Alexandrino, and M. Pérez-Losada. Comparative phylogeography of three achelate lobster species from Macaronesia (North East Atlantic). Phylogeography and Population Genetics in Crustacea. Crustacean Issues 19: 157-173. 

Book Chapters

2019

• Luis M. Mejía-Ortíz, Jesús E. Cupul-Pool, Marilú López-Mejía, Alfredo G. Baez-Meléndres, Juan C. Tejeda Mazariegos, Jair G. Valladarez, Keith A. Crandall, Marcos Pérez-Losada and Oscar Frausto-Martínez. The Habitat Types of Freshwater Prawns (Palaemonidae: Macrobrachium) with Abbreviated Larval Development in Mesoamerica (Mexico, Guatemala and Belize), pp. 1-11. In: Crustacea. IntechOpen (www.intechopen.com).

2018

• Juan Carlos Tejeda-Mazariegos, Luis M. Mejía-Ortíz, Marilú López-Mejía, Keith A. Crandall, Marcos Pérez-Losada and Oscar Frausto-Martínez. Freshwater Crustaceans Decapods: An Important Resource of Guatemala, pp. 169-179. In: Biological Resources of Water.

2017

• Pérez-Losada Marcos, Miguel Arenas and Eduardo Castro-Nallar. Multilocus sequence typing of pathogens: methods, analyses and applications, pp. 383-404. In: Genetics and evolution of infectious diseases (M. Tibayrenc, Ed). Elsevier Inc.

2014

• Pérez-Losada, M. Mandibulata. Chapter 28. In: Tree of Life. (Rafael Zardoya and P. Vargas-Gómez, Eds.). Sinauer Associates.

2012

• Pérez-Losada, M. Mandibulados. In: El árbol de la vida: sistemática y evolución de los seres vivos, chapter 27 (Rafael Zardoya and P. Vargas-Gómez, Eds.). Museo de Ciencias Naturales, CSIC, Madrid, Spain.

2011

• Pérez-Losada, M., M. L. Porter, R. P. Viscidi, and K. A. Crandall. Multilocus sequence typing of pathogens. In: Genetics and evolution of infectious diseases, pp. 503-521 (M. Tibayrenc, Ed). Elsevier Inc.

2009

• Crandall, K. A., M. L. Porter, M. Pérez-Losada. Crabs, shrimps and lobsters (Decapoda). In: The Timetree of Life, pp. 293-297 (S. Blair Hedges and Sudhir Kumar, Eds.). Oxford University Press, Oxford.
• Pérez-Losada, M., J. T. Høeg and K. A. Crandall. Stalked and acorn barnacles (Thoracica). In: The Timetree of Life, pp. 298-301 (S. Blair Hedges and Sudhir Kumar, Eds.). Oxford University Press, Oxford.
• Breinholt, J., M. Pérez-Losada and K. A. Crandall. The timing of the diversification of the freshwater crayfishes. In: Decapoda crustacean phylogenetics, pp. 335-347 (J. W. Martin, K. A. Crandall and D. L. Felder, Eds.). CRC Press, Taylor and Francis Group.

2008

• Crandall, K. A. and M. Pérez-Losada. Epidemiological and evolutionary dynamics of pathogens. In: Evolutionary biology of bacterial and fungal pathogens, pp. 21-30 (Baquero et al., Eds.). American Society of Microbioly Press, Washington, D. C.
• Pérez-Losada, M., M. L. Porter and K. A. Crandall. Methods for analyzing viral evolution. In: Plant Virus Evolution, pp. 165-204 (M. J. Roossinck, Ed.). Springer-Verlag Berlin Heidelberg.

2005

• Sinclair E. A., M. Pérez-Losada and K. A. Crandall. Molecular phylogenetics for conservation biology. In Phylogeny and conservation, pp. 19-56 (Purvis, A., T. Brooks, and J. Gittleman, Eds.). Cambridge University Press, Cambridge, UK.

Non-SCI Journals

2010

• Domínguez, J. and M. Pérez-Losada. Eisenia fetida (Savigny, 1826) y Eisenia andrei Bouché, 1972 son dos especies diferentes de lombrices de tierra. Acta Zoologica Mexicana (n. s.) 2: 321-331.

2004

• Pérez-Losada M. and K. A. Crandall. Can taxonomic richness be used as a surrogate for phylogenetic distinctness indices for ranking areas for conservation? Animal Biodiversity and Conservation 26.1: 77-84.

Conference Proceedings

2016

• Perez-Losada, M., Goldstein, A., Alamri, L., Crandall, K.A., Freishtat, R.J. Nasopharynx microbiome composition varies over time in pediatric asthma. Journal of Investigative Medicine. 64: 815.

2015

• Groah, S., Perez-Losada, M., Caldovic, L., Ljungberg, I., Sprague, B., Castro-Nallar, E., Shah, N., Hsieh, M., Pohl, H. All asymptomatic bacteriuria, all the time. Journal of Urology. 193: E225.
• Perez, G.F., Perez-Losada, M., Pancham, K., Huseni, S., Colberg-Poley, A., Nino, G. Characterization of nasal airway microbiota during rhinovirus infection in full term and in premature infants. Journal of Investigative Medicine. 63: 574.
• Perez-Losada, M., Mansell, D., Nallar, E.C., Johnson, W.E., Crandall, K.A., Freishtat, R.J. PathoScope: integrating microbiome characterization and host gene expression in pediatric asthma. Journal of Investigative Medicine. 63: 575.
• Groah, S., Perez-Losada, M., Caldovic, L., Ljungberg, I., Sprague, B., Castro-Nallar, E., Shah, N., Hsieh, M., Pohl, H. Pyuria and asymptomatic bacteriuria is associated with novel and specific urine microbiomes. Journal of Urology. 193: E226.

2008

• Høeg, J., H. Glenner, M.J. Grygier, Y. Fujita, M. Pérez-Losada and K.A. Crandall. Metamorphosis in crustacean Y-larvae. A parasitic solution to an old zoological riddle. Journal of Morphology 269: 1471

• Martínez, P., M. Pérez-Losada, A. Guerra and A. Sanjuan. First genetic validation and diagnosis of the short-finned squid species of the genus Illex (Cephalopoda: Ommastrephidae). Marine Biology 148: 97-108.    
• Porter, M. L., M. Pérez-Losada and K.A. Crandall. Model based multi-locus estimation of Decapod phylogeny and divergence times. Molecular Phylogenetics and Evolution 37: 355-369.    
• Pérez-Losada, M., Raphael P. Viscidi, and Keith A. Crandall. Population Genetics of Neisseria gonorrhoeae in a High Prevalence Community Using a Hyper-Variable Outer Membrane porB and Thirteen Slow-Evolving Housekeeping Genes. Molecular Biology and Evolution 22: 1887-1902.    
• Shull, H. C., M. Pérez-Losada, D. Blair, K. Sewell, E. A. Sinclair, S. Lawler, M. Ponniah and K. A. Crandall. Phylogeny and biogeography of the freshwater crayfish Euastacus (Decapoda: Parastacidae) based on nuclear and mitochondrial DNA. Molecular Phylogenetics and Evolution 37: 249-263.