Carter, R. & Mendis, K. N. An Overview of Malaria’s Evolutionary and Historical Impact. Clinical Microbiology Reviews 15, 564–594 (2002).
Gelabert, P., Olalde, I., de-Dios, T., Civit, S. & Lalueza-Fox, C. Weak Impact of Malaria on Ancient Europeans. Scientific Reports 7, 1377 (2017).
Sallares, R., Bouwman, A. & Anderung, C. Examining the Spread of Malaria in Southern Europe During Ancient Times. Medical History 48, 311–328 (2004).
Ashley, E. A., Pyae Phyo, A. & Woodrow, C. J. Malaria’s Impact Explored. The Lancet 391, 1608–1621 (2018).
– The World Health Organization’s World Malaria Report 2021 can be accessed for more information (World Health Organization, 2021).
– An article by Kwiatkowski, D. P. on how malaria has influenced the human genome and its relevance to human genetics is available in Am. J. Hum. Genet. 77, 171–192 (2005). Additional references include: Article, CAS, PubMed, and Plasmodium falciparum in gorillas in their research published in Nature 467, 420–425 (2010). Additional references include: Article, ADS, CAS, PubMed, and Google Scholar reference at Google Scholar.
– Sundararaman, S. A. et al. studied the genomes of hidden chimpanzee Plasmodium species uncovering vital evolutionary events leading to human malaria in Nat. Commun. 7, 11078 (2016). Additional references include: Article, ADS, CAS, and PubMed.- The PubMed Central reference discusses the genomes of cryptic chimpanzee Plasmodium species and their role in the evolution of human malaria.
– Neafsey, D. E. et al. in a Nature Genetics article, found that Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum. The study can be accessed through Article, CAS, PubMed, and PubMed Central.
– Loy, D. E. et al. in the International Journal of Parasitology explore the origins and evolution of Plasmodium falciparum and Plasmodium vivax in a study published in 2017. The article can be found using this link.
– Mu, J. et al. highlight how a host switch led to the emergence of Plasmodium vivax malaria in humans in their research published in Molecular Biology and Evolution in 2005. Access the article through Article, CAS, and PubMed.
– Jongwutiwes, S. et al. found support for ancient population expansion in Plasmodium vivax through mitochondrial genome sequences in a study published in Molecular Biology and Evolution.- Link to the Article
– Link to the CAS
– Link to the PubMed
– Link to the Google Scholar
– Link to the Article
– Link to the ADS
– Link to the CAS
– Link to the PubMed
– Link to the PubMed Central
– Link to the Google Scholar
– Link to the Article
– Link to the CAS
– Link to the PubMed
– Link to the PubMed Central
– Link to the Google Scholar
– Link to the Article
– Link to the ADSPubMed
Google Scholar
Twohig, K. A. et al. Growing evidence of Plasmodium vivax across malaria-endemic Africa. PLoS Negl. Trop. Dis. 13, e0007140 (2019).
Zimmerman, P. A. et al. Emergence of FY*Anull in a Plasmodium vivax-endemic region of Papua New Guinea. Proc. Natl Acad. Sci. USA 96, 13973–13977 (1999).
Gething, P. W. et al. Modelling the global constraints of temperature on transmission of Plasmodium falciparum and P. vivax. Parasit. Vectors 4, 92 (2011)
Mordecai, E. A. et al. Optimal temperature for malaria transmission is significantly lower than previously thought. Ecol. Lett. 16, 22–30 (2013).
Grauer, A. L. & Roberts, C. A. in Ortner’s Identification of Pathological Conditions in Human Skeletal Remains 3rd edn (ed. Buikstra, J. E.) 441–478 (Academic Press, 2019).
Wang, T. et al. Paleoepidemiology of cribra orbitalia: insights from early seventh millennium BP Con Co Ngua, Vietnam. Am. J. Biol. Anthropol. 181, 250–261 (2023).
Smith-Guzmán, N. E. The skeletal manifestation of malaria: an epidemiological approach using documented skeletal collections. Am. J. Phys. Anthropol. 158, 624–635 (2015).
Marciniak, S., Herring, D. A., Sperduti, A., Poinar, H. N. & Prowse, T. L. A multi-faceted anthropological and genomic approach to framing Plasmodium falciparum malaria in Imperial period central-southern Italy (1st–4th c. CE). J. Anthropol. Archaeol. 49, 210–224 (2018).
Rivera, F. & Mirazón Lahr, M. New evidence suggesting a dissociated etiology for cribra orbitalia and porotic hyperostosis. Am. J. Phys. Anthropol. 164, 76–96 (2017).
Walker, P. L., Bathurst, R. R., Richman, R., Gjerdrum, T. & Andrushko, V. A. The causes of porotic hyperostosis and cribra orbitalia: a reappraisal of the iron-deficiency-anemia hypothesis. Am. J. Phys. Anthropol. 139, 109–125 (2009).
Newfield, T. P. Malaria and malaria-like disease in the early Middle Ages. Early Mediev. Eur. 25, 251–300 (2017).
Rodrigues, P. T. et al. Human migration and the spread of malaria parasites to the New World. Sci. Rep. 8, 1993 (2018).
Taylor, J. E. et al. The evolutionary history of Plasmodium vivax as inferred from mitochondrial genomes: parasite genetic diversity in the Americas. Mol. Biol. Evol. 30, 2050–2064 (2013).
– Culleton, R. et al. The origins of African Plasmodium vivax; insights from mitochondrial genome sequencing. PLoS One 6, e29137 (2011).
– Reference to Article
– Reference to ADS
– Reference to CAS
– Reference to PubMed
– Reference to PubMed Central
– Reference to Google Scholar
– van Dorp, L. et al. Plasmodium vivax malaria viewed through the lens of an eradicated European strain. Mol. Biol. Evol. 37, 773–785 (2020).
– Reference to Article
– Reference to PubMed
– Reference to Google Scholar
– Hedrick, P. W. Population genetics of malaria resistance in humans. Heredity 107, 283–304 (2011).
– Reference to CAS
– Reference to PubMed
– Reference to PubMed Central– **Google Scholar reference 31**: Hedrick, P.W. wrote about the population genetics of malaria resistance in humans. The article was published in the journal Heredity in 2011. You can access the article [here](http://scholar.google.com/scholar_lookup?&title=Population%20genetics%20of%20malaria%20resistance%20in%20humans&journal=Heredity&doi=10.1038%2Fhdy.2011.16&volume=107&pages=283-304&publication_year=2011&author=Hedrick%2CPW).
– **Google Scholar reference 32**: Spyrou, M.A. along with other authors discussed ancient pathogen genomics as a tool for infectious disease research in a 2019 article published in Nature Reviews Genetics. You can find the article [here](http://scholar.google.com/scholar_lookup?&title=Ancient%20pathogen%20genomics%20as%20an%20emerging%20tool%20for%20infectious%20disease%20research&journal=Nat.%20Rev.%20Genet.&doi=10.1038%2Fs41576-019-0119-1&volume=20&pages=323-340&publication_year=2019&author=Spyrou%2CMA&author=Bos%2CKI&author=Herbig%2CA&author=Krause%2CJ).
– **Google Scholar reference 33**: Schats, R. presented a critical review of current approaches and future directions in developing an archaeology of malaria in a 2023 article published in the International Journal of Paleopathology. You can access the article [here](http://scholar.google.com/scholar_lookup?&title=Developing%20an%20archaeology%20of%20malaria.%20A%20critical%20review%20of%20current%20approaches%20and%20a%20discussion%20on%20ways%20forward&journal=Int.%20J.%20Paleopathol.&doi=10.1016%2Fj.ijpp.2023.03.002&volume=41&pages=32-42&publication_year=2023&author=Schats%2CR).
– **Google Scholar reference 34**: The study by de-Dios, T. examined the genetic affinities of a European Plasmodium falciparum strain that has been eradicated. The research was published in Microbial Genomics in 2019. You can find more details [here](http://scholar.google.com/scholar_lookup?&title=Genetic%20affinities%20of%20an%20eradicated%20European%20Plasmodium%20falciparum%20strain&journal=Microb.%20Genom.&volume=5&publication_year=2019&author=de-Dios%2CT).
– **Google Scholar reference 35**: Gelabert, P. and team extracted mitochondrial DNA from eradicated European Plasmodium vivax and P. falciparum strains found on slides dating back 70 years from the Ebro Delta in Spain. The study was published in the Proceedings of the National Academy of Sciences of the United States of America in 2016. You can access the article [here](http://scholar.google.com/scholar_lookup?&title=Genetic%20affinities%20of%20an%20eradicated%20European%20Plasmodium%20falciparum%20strain&journal=Microb.%20Genom.&volume=5&publication_year=2019&author=de-Dios%2CT).CAS
PubMed
PubMed Central
Google Scholar
Marciniak, S. et al. Plasmodium falciparum malaria in 1st –2nd century CE southern Italy. Curr. Biol. 26, R1220–R1222 (2016).
MalariaGEN et al. An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples [version 1; peer review: 2 approved]. Wellcome Open Res. 7, 136 (2022).
MalariaGEN et al. An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples [version 2; peer review: 2 approved]. Wellcome Open Res. 6, 42 (2021).
Simons, A., Schön, W. & Shrestha, S. S. Preliminary report on the 1992 campaign of the team of the Institute of Prehistory, University of Cologne. Ancient Nepal 136, 51–75 (1994).
-
Google Scholar
-
Ramsl, P. C. in Iron Age Connectivity in the Carpathian Basin. Proc. Int. Colloquium from Târgu Mureș (eds Berecki, S. et al.) 39–50 (MEGA, 2018).
-
Collis, J. in The European Iron Age Ch. 5 (Routledge, 1997).
-
Villalba-Mouco, V. et al. Genomic transformation and social organization during the Copper Age–Bronze Age transition in southern Iberia. Sci. Adv. 7, eabi7038 (2021).
-
Овчинникова, Н. В. & Хохлов, А. А. Исследование грунтового могильника у с. Гундоровка в лесостепном Поволжье. Тверской археологический сборник 3, 288–299 (1998).
-
Price, R. N. et al. Vivax malaria: neglected and not benign. Am. J. Trop. Med. Hyg. 77, 79–87 (2007).
-
Kumar, S. et al. Distinct genomic architecture of Plasmodium falciparum populations from South Asia. Mol. Biochem. Parasitol. 210, 1–4 (2016).
Yalcindag, E. et al. Multiple independent introductions of Plasmodium falciparum in South America. Proc. Natl Acad. Sci. USA 109, 511–516 (2012).
Siraj, A. S. et al. Altitudinal changes in malaria incidence in highlands of Ethiopia and Colombia. Science 343, 1154–1158 (2014).
Aldenderfer, M. Variation in mortuary practice on the early Tibetan plateau and the high Himalayas. J. Int. Ass. Bon Res. 1, 293–318 (2013).
– Tiwari, D. N. Cave burials from western Nepal, Mustang. Ancient Nepal 85, 1–12 (1984–1985).
– Liu, C.-C. et al. Ancient genomes from the Himalayas illuminate the genetic history of Tibetans and their Tibeto-Burman speaking neighbors. Nat. Commun. 13, 1203 (2022). [Article](https://doi.org/10.1038%2Fs41467-022-28827-2) [ADS](http://adsabs.harvard.edu/cgi-bin/nph-data_query?link_type=ABSTRACT&bibcode=2022NatCo..13.1203L) [CAS](https://www.nature.com/articles/cas-redirect/1:CAS:528:DC%2BB38XmtlCgu78%3D) [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=35260549) [PubMed Central](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8904508) [Google Scholar](http://scholar.google.com/scholar_lookup?&title=Ancient%20genomes%20from%20the%20Himalayas%20illuminate%20the%20genetic%20history%20of%20Tibetans%20and%20their%20Tibeto-Burman%20speaking%20neighbors&journal=Nat.%20Commun.&doi=10.1038%2Fs41467-022-28827-2&volume=13&publication_year=2022&author=Liu%2CC-C)
– Dhimal, M. et al. Spatio-temporal distribution of malaria and its association with climatic factors and vector-control interventions in two high-risk districts of Nepal. Malar. J. 13, 457 (2014). [Article](https://link.springer.com/doi/10.1186/1475-2875-13-457) [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=25421720) [PubMed Central](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4258811) [Google Scholar](http://scholar.google.com/scholar_lookup?&title=Spatio-temporal%20distribution%20of%20malaria%20and%20its%20association%20with%20climatic%20factors%20and%20vector-control%20interventions%20in%20two%20high-risk%20districts%20of%20Nepal&journal=Malar.%20J.&doi=10.1186%2F1475-2875-13-457&volume=13&publication_year=2014&author=Dhimal%2CM)
– Church, W. B. & von Hagen, A. C. in Handbook of South American Archaeology (eds Silverman, H. & Isbell, W. H.) 903–926 (Springer, 2008).
– Koch, A., Brierley, C., Maslin, M. M. & Lewis, S. L. Earth system impacts of the European arrival and Great Dying in the Americas after 1492. Quat. Sci. Rev. 207, 13–36 (2019). [Article](https://doi.org/10.1016%2Fj.quascirev.2018.12.004) [ADS](http://adsabs.harvard.edu/cgi-bin/nph-data_query?link_type=ABSTRACT&bibcode=2019QSRv..207…13K) [Google Scholar](http://scholar.google.com/scholar_lookup?&title=Earth%20system%20impacts%20of%20the%20European%20arrival%20and%20Great%20Dying%20in%20the%20Americas%20after%201492&journal=Quat.%20Sci.%20Rev.&doi=10.1016%2Fj.quascirev.2018.12.004&volume=207&pages=13-36&publication_year=2019&author=Koch%2CA&author=Brierley%2CC&author=Maslin%2CMM&author=Lewis%2CSL)
– Alchon, S. A. C. in A Pest in the Land: New World Epidemics in a Global Perspective 60–82 (Univ. New Mexico Press, 2003).
– Guevara, E. K. et al. Genetic assessment reveals no population substructure and divergentRegional and gender-specific narratives in the Chachapoyas region of northeastern Peru have been documented in the research article published in PLoS One, titled “Genetic assessment reveals no population substructure and divergent regional and sex-specific histories in the Chachapoyas from northeast Peru” (Guevara, E.K., 2020).
Van de Vijver conducted an archaeo-anthropological study in Mechelen, Belgium, focusing on burials from the medieval and post-medieval St. Rombout’s cemetery, spanning the 10th to 18th centuries CE (Van de Vijver, K., 2018).
The motives behind multiple burials in St. Rombout’s cemetery were examined by Van de Vijver in another study, shedding light on burial practices from the tenth to eighteenth centuries A.D. (Van de Vijver, K., 2018).
The formation of the early English gene pool and the impact of the Anglo-Saxon migration were investigated by Gretzinger and his team in a study published in Nature (Gretzinger, J. et al., 2022).
For further information and references related to these studies, readers can refer to the provided links for Google Scholar, PubMed, CAS, and other relevant sources.
Google Scholar
Mayxay, M., Pukrittayakamee, S., Newton, P. N. & White, N. J. Mixed-species malaria infections in humans. Trends Parasitol. 20, 233–240 (2004).
Parker, G. The Army of Flanders and the Spanish Road, 1567–1659: The Logistics of Spanish Victory and Defeat in the Low Countries’ Wars. (Cambridge Univ. Press, 1972).
Piperaki, E. T. & Daikos, G. L. Malaria in Europe: emerging threat or minor nuisance? Clin. Microbiol. Infect. 22, 487–493 (2016).
Hübler, R. et al. HOPS: automated detection and authentication of pathogen DNA in archaeological remains. Genome Biol. 20, 280 (2019).
Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Vågene, Å. J. and colleagues conducted a study where they analyzed Salmonella enterica genomes from victims of a significant sixteenth-century epidemic in Mexico. The research was published in Nature Ecology & Evolution in 2018.
Huson, D. H. and colleagues developed the MEGAN Community Edition, which enables interactive exploration and analysis of large-scale microbiome sequencing data. Their work was published in PLoS Computational Biology in 2016.
Preston, M. D. and colleagues used a barcode of organellar genome polymorphisms to determine the geographic origin of Plasmodium falciparum strains. Their research was published in Nature Communications in 2014.
Morgulis, A., Gertz, E. M., Schäffer, A. A., and Agarwala, R. developed a fast and symmetric DUST implementation for masking low-complexity DNA sequences. This work was published in the Journal of Computational Biology in 2006.
Fu, Q. et al. DNA analysis of an early modern human from Tianyuan Cave, China. Proc. Natl Acad. Sci. USA 110, 2223–2227 (2013).
Pinhasi, R. et al. Optimal ancient DNA yields from the inner ear part of the human petrous bone. PLoS ONE 10, e0129102 (2015).
Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl Acad. Sci. USA 110, 15758–15763 (2013).
Reference 75 is a study by Rohland, N., Glocke, I., Aximu-Petri, A. & Meyer, M. that discusses the extraction of highly degraded DNA from ancient bones, teeth, and sediments for high-throughput sequencing in the Nat. Protoc. journal published in 2018. You can read more about it in an Article or in PubMed or on PubMed Central. More details can also be found on Google Scholar.
Reference 76, authored by Rohland, N., Harney, E., Mallick, S., Nordenfelt, S., and Reich, D., in the Philos. Trans. R. Soc. Lond. B Biol. Sci., talks about the partial uracil–DNA–glycosylase treatment for ancient DNA screening in 2015. Details of this study can be found in an Article, PubMed, PubMed Central, or on Google Scholar.
In reference 77, Meyer, M., & Kircher, M. discusses Illumina sequencing library preparation for highly multiplexed target capture and sequencing in Cold Spring Harb. Protoc.. The study was published in 2010 and more information can be found at https://doi.org/10.1101/pdb.prot5448.
Reference 78 conducted by Gansauge, M.-T. et al. presents single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase. The study can be accessed at CAS, PubMed, or PubMed Central.- [Google Scholar](http://scholar.google.com/scholar_lookup?&title=Single-stranded%20DNA%20library%20preparation%20from%20highly%20degraded%20DNA%20using%20T4%20DNA%20ligase&journal=Nucleic%20Acids%20Res.&volume=45&publication_year=2017&author=Gansauge%2CM-T)
– Gansauge, M.-T., Aximu-Petri, A., Nagel, S. & Meyer, M. published a paper on the manual and automated preparation of single-stranded DNA libraries for sequencing DNA from ancient biological remains and highly degraded sources in the journal Nat. Protoc. in 2020. You can access the [Article](https://doi.org/10.1038%2Fs41596-020-0338-0), [CAS](https://www.nature.com/articles/cas-redirect/1:CAS:528:DC%2BB3cXhtlSht7vF), [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=32612278), and [Google Scholar](http://scholar.google.com/scholar_lookup?&title=Manual%20and%20automated%20preparation%20of%20single-stranded%20DNA%20libraries%20for%20the%20sequencing%20of%20DNA%20from%20ancient%20biological%20remains%20and%20other%20sources%20of%20highly%20degraded%20DNA&journal=Nat.%20Protoc.&doi=10.1038%2Fs41596-020-0338-0&volume=15&pages=2279-2300&publication_year=2020&author=Gansauge%2CM-T&author=Aximu-Petri%2CA&author=Nagel%2CS&author=Meyer%2CM).
– DeAngelis, M. M., Wang, D. G. & Hawkins, T. L. introduced solid-phase reversible immobilization for isolating PCR products in Nucleic Acids Res. in 1995. More details can be found in the [Article](https://doi.org/10.1093%2Fnar%2F23.22.4742), [CAS](https://www.nature.com/articles/cas-redirect/1:CAS:528:DyaK2MXhtVSksLvE), [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=8524672), [PubMed Central](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC307455), and [Google Scholar](http://scholar.google.com/scholar_lookup?&title=Solid-phase%20reversible%20immobilization%20for%20the%20isolation%20of%20PCR%20products&journal=Nucleic%20Acids%20Res.&doi=10.1093%2Fnar%2F23.22.4742&volume=23&pages=4742-4743&publication_year=1995&author=DeAngelis%2CMM&author=Wang%2CDG&author=Hawkins%2CTL).
– Mathieson, I. et al. examined genome-wide selection patterns in 230 ancient Eurasians in the journal Nature in 2015. Reference links include [Article](https://doi.org/10.1038%2Fnature16152), [ADS](http://adsabs.harvard.edu/cgi-bin/nph-data_query?link_type=ABSTRACT&bibcode=2015Natur.528..499M), [CAS](https://www.nature.com/articles/cas-redirect/1:CAS:528:DC%2BC2MXhvVOqs7fF), [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=26595274), and [PubMed Central](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4918750).- Google Scholar reference 81: A study on genome-wide patterns of selection in 230 ancient Eurasians published in Nature in 2015 by Mathieson, C. and others. [Link to Google Scholar](http://scholar.google.com/scholar_lookup?&title=Genome-wide%20patterns%20of%20selection%20in%20230%20ancient%20Eurasians&journal=Nature&doi=10.1038%2Fnature16152&volume=528&pages=499-503&publication_year=2015&author=Mathieson%2CI)
– Google Scholar reference 82: Haak, W. et al. published a study in Nature in 2015 suggesting that massive migration from the steppe contributed to the Indo-European languages in Europe. [Article](https://doi.org/10.1038%2Fnature14317) [ADS](http://adsabs.harvard.edu/cgi-bin/nph-data_query?link_type=ABSTRACT&bibcode=2015Natur.522..207H) [CAS](https://www.nature.com/articles/cas-redirect/1:CAS:528:DC%2BC2MXktVCnsLc%3D) [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=25731166) [PubMed Central](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5048219) [Google Scholar](http://scholar.google.com/scholar_lookup?&title=Massive%20migration%20from%20the%20steppe%20was%20a%20source%20for%20Indo-European%20languages%20in%20Europe&journal=Nature&doi=10.1038%2Fnature14317&volume=522&pages=207-211&publication_year=2015&author=Haak%2CW)
– Google Scholar reference 83: Fellows Yates, J. A. et al. published a study in PeerJ in 2021 on reproducible, portable, and efficient ancient genome reconstruction. [Article](https://doi.org/10.7717%2Fpeerj.10947) [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=33777521) [PubMed Central](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7977378) [Google Scholar](http://scholar.google.com/scholar_lookup?&title=Reproducible%2C%20portable%2C%20and%20efficient%20ancient%20genome%20reconstruction%20with%20nf-core%2Feager&journal=PeerJ&doi=10.7717%2Fpeerj.10947&volume=9&publication_year=2021&author=Fellows%20Yates%2CJA)
– Google Scholar reference 84: Schubert, M., Lindgreen, S., and Orlando, L. conducted a study on rapid adapter trimming and read merging using AdapterRemoval v2 published in BMC Res. Notes in 2016. [Article](https://link.springer.com/doi/10.1186/s13104-016-1900-2) [PubMed](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=26868221) [PubMed Central](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4751634) [Google Scholar](http://scholar.google.com/scholar_lookup?&title=AdapterRemoval%20v2%3A%20rapid%20adapter%20trimming%2C%20identification%2C%20and%20read%20merging&journal=BMC%20Res.%20Notes&doi=10.1186%2Fs13104-016-1900-2&volume=9&publication_year=2016&author=Schubert%2CM&author=Lindgreen%2CS&author=Orlando%2CL)
– Google Scholar reference 85: Chen, S., Zhou, Y., Chen, Y., and Gu, J. worked on an ultra-fast all-in-one FASTQ preprocessor called fastp, published in Bioinformatics in 2018.Article
PubMed
PubMed Central
Google Scholar
Fellows Yates, J. A. et al. Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir. Scientific Data 8, 31 (2021).
DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491–498 (2011).
Bos, K. I. et al. Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis. Nature 514, 494–497 (2014).
Valtueña, A. A. et al. Stone Age Yersinia pestis genomes shed light on the early evolution, diversity, and ecology of plague. Proc. Natl Acad. Sci. USA 119, e2116722119 (2022).
Auburn, S. et al. A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes [version 1; peer review: 2 approved]. Wellcome Open Res 1, 4 (2016).
Jun, G., Wing, M. K., Abecasis, G. R. & Kang, H. M. An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data. Genome Res. 25, 918–925 (2015).
Price, A. L. et al. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38, 904–909 (2006).
Kumar, S., Stecher, G., Peterson, D. & Tamura, K. MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis. Bioinformatics 28, 2685–2686 (2012).
Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49, W293–W296 (2021).
