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Inferring Developmental Stage Composition from Gene Expression in Human Malaria

Regina Joice, Vagheesh Narasimhan, Jacqui Montgomery, Amar Bir Sidhu, Keunyoung Oh, Evan Meyer, Willythssa Pierre-Louis, Karl Seydel, Danny Milner, Kim Williamson, Roger Wiegand, Daouda Ndiaye (+6 others)
<span title="2013-12-12">2013</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
Here, we present a method for estimating relative amounts of Plasmodium falciparum asexual and sexual stages from gene expression measurements.  ...  We illustrate its use in vitro in inferring changes in stage distribution following stress and drug treatment and in vivo in identifying immature and mature sexual stage carriers within patient cohorts  ...  Acknowledgments We would like to thank the patients and their families in Malawi and Sengal for their participation in this project.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1003392">doi:10.1371/journal.pcbi.1003392</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24348235">pmid:24348235</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3861035/">pmcid:PMC3861035</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5lkprwcqwvbo7nwwy2jj62dlri">fatcat:5lkprwcqwvbo7nwwy2jj62dlri</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190501200926/https://dash.harvard.edu/bitstream/handle/1/11879228/3861035.pdf;jsessionid=B99F4CE22BE11666A14F6E51742B1D49?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/5d/73/5d734ed187ff4510a725135777490bf984d7df69.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1003392"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3861035" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Immunogenetic response to a malaria-like parasite in a wild primate [article]

Amber Eliza Trujillo, Christina Marie Bergey
<span title="2020-11-24">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We identified colobus genes with expression strongly correlated with parasitemia, including many implicated in human malaria and suggestive of common genetic architecture of disease response.  ...  For instance, the expression of ACKR1 (alias DARC) gene, previously linked to resistance in humans, was found to be positively correlated with parasitemia.  ...  Proportion of Hepatocystis reads inferred to be in each parasite 592 developmental stage via deconvolution.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.11.24.396317">doi:10.1101/2020.11.24.396317</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gvcbulvuqjd2fgmkpp6xokpahy">fatcat:gvcbulvuqjd2fgmkpp6xokpahy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210427075326/https://www.biorxiv.org/content/biorxiv/early/2020/11/24/2020.11.24.396317.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/1b/64/1b64dd5bc06e74c4613e78f9760ebfc7b967d101.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.11.24.396317"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Plasmodium vivax transcriptomes reveal stage-specific chloroquine response and differential regulation of male and female gametocytes

Adam Kim, Jean Popovici, Didier Menard, David Serre
<span title="2019-01-22">2019</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a4wan6l5o5dfzn767kyz7jqevi" style="color: black;">Nature Communications</a> </i> &nbsp;
Finally, we analyze gene expression changes induced by chloroquine and show that this antimalarial drug efficiently eliminates most P. vivax parasite stages but, in contrast to P. falciparum, does not  ...  Here, we characterize the transcriptomes of P. vivax parasites from 26 malaria patients.  ...  Acknowledgements The authors would like to thank all patients and healthcare workers involved in this study and the staff of the Malaria Molecular Epidemiology Unit at the Institut Pasteur in Cambodia  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41467-019-08312-z">doi:10.1038/s41467-019-08312-z</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30670687">pmid:30670687</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6342968/">pmcid:PMC6342968</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rl7ohh3t6bastpxnjc7iyuas7i">fatcat:rl7ohh3t6bastpxnjc7iyuas7i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191030100603/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6342968&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/02/d4/02d4967ee908f9ea2fd567581acf5c985670ff20.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41467-019-08312-z"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> nature.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6342968" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Host and Parasite Transcriptomic Changes upon Successive Plasmodium falciparum Infections in Early Childhood

Katie R. Bradwell, Drissa Coulibaly, Abdoulaye K. Koné, Matthew B. Laurens, Ahmadou Dembélé, Youssouf Tolo, Karim Traoré, Amadou Niangaly, Andrea A. Berry, Bourema Kouriba, Christopher V. Plowe, Ogobara K. Doumbo (+6 others)
<span title="2020-07-07">2020</span> <i title="American Society for Microbiology"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/mktoulxoszhmliyz2vp2sfjn6a" style="color: black;">mSystems</a> </i> &nbsp;
Here, we describe methods to analyze the host and parasite gene expression profiles generated simultaneously from blood samples collected from five consecutive symptomatic P. falciparum infections in three  ...  While limited by the modest sample size, our analyses suggest that host gene expression profiles primarily clustered by individual, while the parasite gene expression profiles seemed to differentiate early  ...  Beyond testing for gene expression differences, we leveraged the RNA-seq data to determine the relative proportions of WBC subsets and parasite developmental stages in each sample using gene expression  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1128/msystems.00116-20">doi:10.1128/msystems.00116-20</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32636334">pmid:32636334</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/d24lop7spfgsph2wgpyznc2m74">fatcat:d24lop7spfgsph2wgpyznc2m74</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200713220554/https://msystems.asm.org/content/msys/5/4/e00116-20.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/15/ac/15ac1a4e78d34b9b2c0337dc60027baa90e46385.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1128/msystems.00116-20"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> asm.org </button> </a>

Plasmodium falciparum transcription in different clinical presentations of malaria associates with circulation time of infected erythrocytes

Richard Thomson Luque
<span title="2021-07-30">2021</span> <i title="Zenodo"> Zenodo </i> &nbsp;
transcriptomes of parasites obtained from malaria cases of differing clinical severity across multiple studies.  ...  Following Plasmodium falciparum infection, individuals can remain asymptomatic, present with mild fever in uncomplicated malaria cases, or show one or more severe malaria symptoms.  ...  We are grateful to Terrie Taylor for facilitating the collaboration with the Blantyre Malaria Project, Blantyre, Malawi.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.5582346">doi:10.5281/zenodo.5582346</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cgeraryornfh5el5irkpsvzosm">fatcat:cgeraryornfh5el5irkpsvzosm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20211027201655/https://zenodo.org/record/5582347/files/s41467-021-25062-z.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/70/3f/703f7722398928389924f870b0fb661a883a2802.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.5582346"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> zenodo.org </button> </a>

Transcriptomic Studies of Malaria: a Paradigm for Investigation of Systemic Host-Pathogen Interactions

Hyun Jae Lee, Athina Georgiadou, Thomas D. Otto, Michael Levin, Lachlan J. Coin, David J. Conway, Aubrey J. Cunnington
<span title="2018-04-25">2018</span> <i title="American Society for Microbiology"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6degphsfcjfjnhtermmfa2ndre" style="color: black;">Microbiology and Molecular Biology Reviews</a> </i> &nbsp;
natural and experimental infections in humans.  ...  We illustrate lessons learned from transcriptomic studies of malaria and how these lessons may guide studies of host-pathogen interactions in other infectious diseases.  ...  A similar sequence of gene expression dynamics was inferred in humans by mapping sequential mouse data onto patterns of gene expression from a crosssectional study of subjects with uncomplicated malaria  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1128/mmbr.00071-17">doi:10.1128/mmbr.00071-17</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29695497">pmid:29695497</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5968457/">pmcid:PMC5968457</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/m2bw5jlov5aqzei6c5obdlhjyq">fatcat:m2bw5jlov5aqzei6c5obdlhjyq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190430033211/https://mmbr.asm.org/content/mmbr/82/2/e00071-17.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d5/92/d592725a0612e5355e009e63151198f26b2e4a79.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1128/mmbr.00071-17"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> asm.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5968457" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Clinical expression and antigenic profiles of a Plasmodium vivax vaccine candidate: merozoite surface protein 7 (PvMSP-7)

Chew Weng Cheng, Somchai Jongwutiwes, Chaturong Putaporntip, Andrew P. Jackson
<span title="2019-06-13">2019</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/52kcjpkb45hmrlgxcm4joetsym" style="color: black;">Malaria Journal</a> </i> &nbsp;
Methods: Merozoite surface protein 7 gene expression was profiled using RNA-seq data from blood samples isolated from ten human patients with vivax malaria.  ...  This may reflect developmental regulation, and potentially functional differentiation, within the gene family.  ...  We extend our appreciation to the staff of the Bureau of Vector Borne Disease, Department of Disease Control, Ministry of Public Health, Thailand, for assistance in field work. 1  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12936-019-2826-7">doi:10.1186/s12936-019-2826-7</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/h5ksk75rufbipoq65layuf5mhm">fatcat:h5ksk75rufbipoq65layuf5mhm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200213003332/https://malariajournal.biomedcentral.com/track/pdf/10.1186/s12936-019-2826-7" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/64/af/64af824d020ef827024ed027685b952750ed2378.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12936-019-2826-7"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a>

The Malaria Cell Atlas: Single parasite transcriptomes across the complete Plasmodium life cycle

Virginia M. Howick, Andrew J. C. Russell, Tallulah Andrews, Haynes Heaton, Adam J. Reid, Kedar Natarajan, Hellen Butungi, Tom Metcalf, Lisa H. Verzier, Julian C. Rayner, Matthew Berriman, Jeremy K. Herren (+4 others)
<span title="2019-08-22">2019</span> <i title="American Association for the Advancement of Science (AAAS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/qirzh7firjdsjhg4tutxtir6ey" style="color: black;">Science</a> </i> &nbsp;
We then used our atlas to precisely define developmental stages of single cells from three different human malaria parasite species, including parasites isolated directly from infected individuals.  ...  The Malaria Cell Atlas provides both a comprehensive view of gene usage in a eukaryotic parasite and an open-access reference dataset for the study of malaria parasites.  ...  We then used our atlas to precisely define developmental stages of single cells from three different human malaria parasite species, including parasites isolated directly from infected individuals.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1126/science.aaw2619">doi:10.1126/science.aaw2619</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31439762">pmid:31439762</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7056351/">pmcid:PMC7056351</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jxl4pjv5cnbmxdiz5jkibx4ioi">fatcat:jxl4pjv5cnbmxdiz5jkibx4ioi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200504011903/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC7056351&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ef/69/ef692bdc6b717724d299443fbeff3f165527372b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1126/science.aaw2619"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> sciencemag.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7056351" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Cyclical regression covariates remove the major confounding effect of cyclical developmental gene expression with strain-specific drug response in the malaria parasite Plasmodium falciparum

Gabriel J. Foster, Mackenzie A. C. Sievert, Katrina Button-Simons, Katelyn M. Vendrely, Jeanne Romero-Severson, Michael T. Ferdig
<span title="2022-03-05">2022</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
Analysis of differential gene expression in the clinical data samples that vary broadly for developmental stage resulted in the detection of far fewer transcripts in fewer functional categories while,  ...  Background The cyclical nature of gene expression in the intraerythrocytic development cycle (IDC) of the malaria parasite, Plasmodium falciparum, confounds the accurate detection of specific transcriptional  ...  Cyclical regression covariates have been applied to a range of biological data with cyclical covariance, including diarrheal severity, transmission of malaria, and seasonal changes in human gene expression  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12864-021-08281-y">doi:10.1186/s12864-021-08281-y</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/35247977">pmid:35247977</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8897900/">pmcid:PMC8897900</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6rx63ptqrvc7ddxgekrfgvdjmm">fatcat:6rx63ptqrvc7ddxgekrfgvdjmm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220421042514/https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/s12864-021-08281-y.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e7/c9/e7c9cb9a8e715ab4cd656721744411cfc87f07c8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12864-021-08281-y"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8897900" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

In vivo gene expression analyses provide unique insights on P. vivax gametocytogenesis and chloroquine response [article]

Adam Kim, Jean Popovici, Didier Menard, David Serre
<span title="2018-06-08">2018</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
However, few studies have targeted P. vivax, the cause of one third of all human malaria cases outside Africa, due to the lack of in vitro culture system and the difficulties associated with studying clinical  ...  Gene expression deconvolution analysis reveals that most parasite mRNAs derive from trophozoites and that the asynchronicity of P. vivax infections is unlikely to confound gene expression studies.  ...  (A) The top panel displays the stage composition determined by microscopy (A) 457 while the bottom panel shows the stage composition inferred from gene expression 458 deconvolution of the same infections  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/342196">doi:10.1101/342196</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ef7guhai75fv3nfoqigsmjr6uq">fatcat:ef7guhai75fv3nfoqigsmjr6uq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190504190326/https://www.biorxiv.org/content/biorxiv/early/2018/06/08/342196.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/1a/2f/1a2f039828186bba72e44416e1b325de05540651.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/342196"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

A single-cell atlas of Plasmodium falciparum transmission through the mosquito

Eliana Real, Virginia M. Howick, Farah A. Dahalan, Kathrin Witmer, Juliana Cudini, Clare Andradi-Brown, Joshua Blight, Mira S. Davidson, Sunil Kumar Dogga, Adam J. Reid, Jake Baum, Mara K. N. Lawniczak
<span title="2021-05-27">2021</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a4wan6l5o5dfzn767kyz7jqevi" style="color: black;">Nature Communications</a> </i> &nbsp;
Additionally, we identify both conserved and non-conserved gene usage between human and rodent parasites, which point to both essential mechanisms in malaria transmission and species-specific adaptations  ...  Here we use single-cell transcriptomics to illuminate gene usage across the transmission cycle of the most virulent agent of human malaria - Plasmodium falciparum.  ...  The Facility for Imaging by Light Microscopy (FILM) at Imperial College London is part supported by funding from the Wellcome Trust (grant 104931/Z/14/Z) and BBSRC (grant BB/L015129/1).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41467-021-23434-z">doi:10.1038/s41467-021-23434-z</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34045457">pmid:34045457</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8159942/">pmcid:PMC8159942</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jufsv557tfh57drfxonm4esmim">fatcat:jufsv557tfh57drfxonm4esmim</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210718162549/https://www.nature.com/articles/s41467-021-23434-z.pdf?error=cookies_not_supported&amp;code=b95e39ba-247a-4709-a156-bafdcd508d02" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/77/dc/77dc87a321d726cc1b2506caac4153274d81ee4f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41467-021-23434-z"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> nature.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8159942" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Recent Progress in Functional Genomic Research in Plasmodium falciparum

Jianbing Mu, Karl B. Seydel, Adam Bates, Xin-Zhuan Su
<span title="2010-06-01">2010</span> <i title="Bentham Science Publishers Ltd."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/mqegkl27nzckpogkyj47kjwblu" style="color: black;">Current Genomics</a> </i> &nbsp;
In addition, the Plasmodium falciparum genome sequence provides the basis for the development of various microarrays to monitor gene expression and to detect nucleotide substitution and deletion/amplification  ...  In this brief review, we will highlight some recent advances and studies in characterizing gene function and related phenotype in P. falciparum that were made possible by the genome sequence, particularly  ...  Gene functions can also be predicted by monitoring the dynamic of mRNA or protein expression in combination with related phenotypes or developmental stages.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2174/138920210791233081">doi:10.2174/138920210791233081</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21119892">pmid:21119892</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2930667/">pmcid:PMC2930667</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/igqtoyfrpvfqxd5ggq7buo3y4q">fatcat:igqtoyfrpvfqxd5ggq7buo3y4q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190309054845/http://pdfs.semanticscholar.org/ff4c/d6b45e2b0c42b2326e984f319f4cf4b40d30.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ff/4c/ff4cd6b45e2b0c42b2326e984f319f4cf4b40d30.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2174/138920210791233081"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2930667" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Hierarchical transcriptional control regulates Plasmodium falciparum sexual differentiation [article]

Riette van Biljon, Roelof van Wyk, Heather Painter, Lindsey Orchard, Janette Reader, Jandeli Niemand, Manuel Llinas, Lyn-Marie Birkholtz
<span title="2019-05-09">2019</span> <i title="Cold Spring Harbor Laboratory"> biorxiv/medrxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
As anticipated, the gametocyte-associated transcriptome is significantly different from that of the asexual blood cycle, and a dynamic shift in gene expression characterizes early, intermediate and late-stage  ...  Although malaria is characterized by cyclic waves of infection by asexual parasites, only sexual gametocyte forms of the malaria parasite can be transmitted between the infected human and the mosquito  ...  Nascent RNA sequencing reveals mechanisms of gene regulation in the human malaria parasite Plasmodium falciparum. Nucleic Acids Res. 2017;1-16. 39.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/633222">doi:10.1101/633222</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/p5ycs45kxzcvbj26he2rw27uwu">fatcat:p5ycs45kxzcvbj26he2rw27uwu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201107045206/https://assets.researchsquare.com/files/rs-3600/v1/manuscript.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/2a/70/2a70f974bcc8ca13b61764d5c9fadd5932f1e4e3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/633222"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Malaria parasite transmission stages: an update

Shahid M. Khan, Andrew P. Waters
<span title="">2004</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/plpwnlpq5vechgqsnaxfmqf4wm" style="color: black;">Trends in Parasitology</a> </i> &nbsp;
analyze in vivo gene expression in liver stages (Figure 2 ).  ...  The beauty of the genetic orthology in the genes expressed in the transmission stages of Plasmodium is that genes identified in one species as being significantly expressed in a particular mosquito stage  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.pt.2004.10.001">doi:10.1016/j.pt.2004.10.001</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15522667">pmid:15522667</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5ish23j4ebhqvahewlctn7nup4">fatcat:5ish23j4ebhqvahewlctn7nup4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809051347/http://izt.ciens.ucv.ve/ecologia/Archivos/ECOLOGIA_DE%20_POBLACIONES_Hasta%202004/ECOL_POBLAC_Hasta%202004_(H-N)/Khan%20y%20Waters%202004.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b1/33/b1337fdba10c8242e2df3b8e547e598ab66b3892.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.pt.2004.10.001"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Predicting malaria interactome classifications from time-course transcriptomic data along the intraerythrocytic developmental cycle

Antonina Mitrofanova, Samantha Kleinberg, Jane Carlton, Simon Kasif, Bud Mishra
<span title="">2010</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/7zekrk5bkbglxhzdjmkpl6hksq" style="color: black;">Artificial Intelligence in Medicine</a> </i> &nbsp;
We propose an automated method for predicting functions for the malaria parasite, which capitalizes on the importance of the intraerythrocytic developmental cycle data and expression changes during its  ...  We conclude that analyzing time-course gene expression profiles in separate phases leads to much higher prediction accuracy when compared with Pearson correlation coefficients computed across the time  ...  Marco Antoniotti and Andrew Sundstrom) for many useful discussions, and Naoki Nariai of Boston University for his patience and help in answering many questions about the software usage and statistical  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.artmed.2010.04.013">doi:10.1016/j.artmed.2010.04.013</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20580212">pmid:20580212</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/adlsekgamjc3lf6u7tr6tfswf4">fatcat:adlsekgamjc3lf6u7tr6tfswf4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170706073713/http://www.cs.nyu.edu/mishra/PUBLICATIONS/09.Malaria-AIIM.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/bc/e7/bce7a8d6cd12091fccbedc117660a53c829a1057.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.artmed.2010.04.013"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>
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