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Additional file 1 of Rapid profiling of Plasmodium parasites from genome sequences to assist malaria control

Jody E. Phelan (6874175)
Anna Turkiewicz (9930419)
Emilia Manko (9930422)
Joseph Thorpe (17374985)
Leen N. Vanheer (10163502)
Marga van de Vegte-Bolmer (359384)
Nguyen Thi Hong Ngoc (16498809)
Nguyen Thi Huong Binh (12062192)
Nguyen Quang Thieu (12178075)
Jesse Gitaka (739283)
Debbie Nolder (357772)
Khalid B. Beshir (12960385)
Jamille G. Dombrowski (8447925)
Silvia Maria Di Santi (4348138)
Teun Bousema (79969)
Colin J. Sutherland (8447931)
Susana Campino (56411)
Taane G. Clark (9901879)

Publication date

November 2023

DOI

10.6084/m9.figshare.24546902.v1

Abstract

Additional file 1: Fig. S1. Schematic highlighting the main steps in the Malaria-Profiler pipeline. Fig. S2. Malaria-Profiler tool

Extracted data

Related items

Additional file 2: Figure S1. of Genome content analysis yields new insights into the relationship between the human malaria parasite Plasmodium falciparum and its anopheline vectors

Sara Oppenheim (3799420)
Jeffrey Rosenfeld (403548)
Rob DeSalle (175611)

February 2017

Flowchart of methods used to identify and annotate gain/loss protein families. (PDF 38Â kb

Additional file 11: of In-depth comparative analysis of malaria parasite genomes reveals protein-coding genes linked to human disease in Plasmodium falciparum genome

Xuewu Liu (457532)
Yuanyuan Wang (20181)
Jiao Liang (5162900)
Luojun Wang (5162903)
Na Qin (774536)
Ya Zhao (807581)
Gang Zhao (161405)

May 2018

Table S6. Identified P. falciparum genes that possibly contribute to cerebral malaria. (XLSX 12Â kb

Additional file 2: of Rapid multiplex gene expression assays for monitoring metabolic resistance in the major malaria vector Anopheles gambiae

Konstantinos Mavridis (6178208)
Nadja Wipf (6178211)
Sandrine Medves (819337)
Ignacio Erquiaga (6178214)
Pie Müller (68677)
John Vontas (154766)

January 2019

Figure S1. Primer and probe design strategy using Detox (A), consisting of RPS7 (normaliser), CYP6P3...

Additional file 2: of In-depth comparative analysis of malaria parasite genomes reveals protein-coding genes linked to human disease in Plasmodium falciparum genome

Xuewu Liu (457532)
Yuanyuan Wang (20181)
Jiao Liang (5162900)
Luojun Wang (5162903)
Na Qin (774536)
Ya Zhao (807581)
Gang Zhao (161405)

May 2018

Figure S1. Clusters composed of members from a single species or six species. a) Clusters comprise P...

Additional file 3: of In-depth comparative analysis of malaria parasite genomes reveals protein-coding genes linked to human disease in Plasmodium falciparum genome

Xuewu Liu (457532)
Yuanyuan Wang (20181)
Jiao Liang (5162900)
Luojun Wang (5162903)
Na Qin (774536)
Ya Zhao (807581)
Gang Zhao (161405)

May 2018

Table S2. Enriched values of all clusters in six Plasmodium species. (XLSX 154Â kb

Additional file 1 of Genomic analysis of single nucleotide polymorphisms in malaria parasite drug targets

Jasmita Gill (12614930)
Amit Sharma (46604)

August 2022

Additional file 1: Table S1. Details of the 20 cytoplasmic and four dual-location Plasmodium aminoac...

Additional file 5: of In-depth comparative analysis of malaria parasite genomes reveals protein-coding genes linked to human disease in Plasmodium falciparum genome

Xuewu Liu (457532)
Yuanyuan Wang (20181)
Jiao Liang (5162900)
Luojun Wang (5162903)
Na Qin (774536)
Ya Zhao (807581)
Gang Zhao (161405)

May 2018

Table S4. The P. berghei genes included in rodent malaria parasite-enriched clusters. (XLSX 20Â kb

Additional file 1: of Schizont transcriptome variation among clinical isolates and laboratory-adapted clones of the malaria parasite Plasmodium falciparum

Sarah Tarr (6067133)
Ofelia DĂaz-Ingelmo (6067136)
Lindsay Stewart (560932)
Suzanne Hocking (6067139)
Lee Murray (3357719)
Craig Duffy (3550022)
Thomas Otto (5241)
Lia Chappell (530631)
Julian Rayner (3988232)
Gordon Awandare (3690160)
David Conway (218340)

December 2018

Masking of P. falciparum genome annotation file to exclude polymorphic regions of genes. (PDF 546â...

Additional file 9: of Schizont transcriptome variation among clinical isolates and laboratory-adapted clones of the malaria parasite Plasmodium falciparum

Sarah Tarr (6067133)
Ofelia DĂaz-Ingelmo (6067136)
Lindsay Stewart (560932)
Suzanne Hocking (6067139)
Lee Murray (3357719)
Craig Duffy (3550022)
Thomas Otto (5241)
Lia Chappell (530631)
Julian Rayner (3988232)
Gordon Awandare (3690160)
David Conway (218340)

December 2018

Sequence annotation file Pf3D7.May2015.NoSplice.LSHTM.gtf (see Additional file 1 for explanatory det...

Additional file 1: of Malaria parasites of long-tailed macaques in Sarawak, Malaysian Borneo: a novel species and demographic and evolutionary histories

Thamayanthi Nada Raja (5085755)
Ting Huey Hu (5085752)
Ramlah Zainudin (615588)
Kim Sung Lee (712746)
Susan L. Perkins (76181)
Balbir Singh (218132)

April 2018

14 internal primers used to sequence the complete mitochondrial genomes of Plasmodium sp. (DOCX 12Â ...

Additional file 2: of Exploration of Plasmodium vivax transmission dynamics and recurrent infections in the Peruvian Amazon using whole genome sequencing

Annie Cowell (5482796)
Hugo Valdivia (3466484)
Danett Bishop (5482793)
Elizabeth Winzeler (56214)

July 2018

Table S2. Sequencing statistics for 69 Plasmodium vivax sequences collected in 3 villages in the Per...

Additional file 1: of Genome-wide identification and characterization of transfer RNA-derived small RNAs in Plasmodium falciparum

Zhensheng Wang (548619)
Chunyan Wei (548617)
Xiao Hao (6211553)
Weiwei Deng (2550691)
Lianhui Zhang (548620)
Zenglei Wang (160548)
Heng Wang (76752)

January 2019

Table S1. Sequences of specific stem-loop reverse transcription primers. Table S2. Sequences of PCR ...

Additional file 1: of Genetic diversity of Plasmodium falciparum isolates from Baka Pygmies and their Bantu neighbours in the north of Gabon

Bertrand Mvé-Ondo (3512009)
Dieudonné Nkoghe (184002)
Céline Arnathau (264001)
Virginie Rougeron (191120)
Ulrich Bisvigou (184038)
Lauriane Mouele (3512012)
Larson Boundenga (749176)
Patrick Durand (72585)
Eric Elguero (271203)
Simone Lemmers (3512000)
Lucrèce Délicat-Loembet (3512003)
Nancy Diamella-Moukodoum (3512006)
Christophe Paupy (184029)
François Renaud (63587)
Franck Prugnolle (21227)
Benjamin Ollomo (201531)

October 2015

Sequences of primers used for genotyping P. falciparum genes. This table shows the primers sequences...

Additional file 9: of In-depth comparative analysis of malaria parasite genomes reveals protein-coding genes linked to human disease in Plasmodium falciparum genome

Xuewu Liu (457532)
Yuanyuan Wang (20181)
Jiao Liang (5162900)
Luojun Wang (5162903)
Na Qin (774536)
Ya Zhao (807581)
Gang Zhao (161405)

May 2018

Table S5. Candidate genes related to virulence of the P. falciparum parasite. (XLSX 31Â kb

Additional file 1: of Prevalence of K13-propeller gene polymorphisms among Plasmodium falciparum parasites isolated from adult symptomatic patients in northern Uganda

Moses Ocan (540836)
Freddie Bwanga (221684)
Alfred Okeng (133434)
Fred Katabazi (3421877)
Edgar Kigozi (724127)
Samuel Kyobe (133439)
Jasper Ogwal-Okeng (518357)
Celestino Obua (375449)

August 2016

Nucleotide sequences of Plasmodium falciparum DNA samples with mutations. This file contains the nuc...

Additional file 2: Figure S1. of Genome content analysis yields new insights into the relationship between the human malaria parasite Plasmodium falciparum and its anopheline vectors

Sara Oppenheim (3799420)
Jeffrey Rosenfeld (403548)
Rob DeSalle (175611)

February 2017

Flowchart of methods used to identify and annotate gain/loss protein families. (PDF 38Â kb

Additional file 11: of In-depth comparative analysis of malaria parasite genomes reveals protein-coding genes linked to human disease in Plasmodium falciparum genome

Xuewu Liu (457532)
Yuanyuan Wang (20181)
Jiao Liang (5162900)
Luojun Wang (5162903)
Na Qin (774536)
Ya Zhao (807581)
Gang Zhao (161405)

May 2018

Table S6. Identified P. falciparum genes that possibly contribute to cerebral malaria. (XLSX 12Â kb

Additional file 2: of Rapid multiplex gene expression assays for monitoring metabolic resistance in the major malaria vector Anopheles gambiae

Konstantinos Mavridis (6178208)
Nadja Wipf (6178211)
Sandrine Medves (819337)
Ignacio Erquiaga (6178214)
Pie Müller (68677)
John Vontas (154766)

January 2019

Figure S1. Primer and probe design strategy using Detox (A), consisting of RPS7 (normaliser), CYP6P3...

Additional file 2: of In-depth comparative analysis of malaria parasite genomes reveals protein-coding genes linked to human disease in Plasmodium falciparum genome

Xuewu Liu (457532)
Yuanyuan Wang (20181)
Jiao Liang (5162900)
Luojun Wang (5162903)
Na Qin (774536)
Ya Zhao (807581)
Gang Zhao (161405)

May 2018

Figure S1. Clusters composed of members from a single species or six species. a) Clusters comprise P...

Additional file 3: of In-depth comparative analysis of malaria parasite genomes reveals protein-coding genes linked to human disease in Plasmodium falciparum genome

Xuewu Liu (457532)
Yuanyuan Wang (20181)
Jiao Liang (5162900)
Luojun Wang (5162903)
Na Qin (774536)
Ya Zhao (807581)
Gang Zhao (161405)

May 2018

Table S2. Enriched values of all clusters in six Plasmodium species. (XLSX 154Â kb

Additional file 1 of Genomic analysis of single nucleotide polymorphisms in malaria parasite drug targets

Jasmita Gill (12614930)
Amit Sharma (46604)

August 2022

Additional file 1: Table S1. Details of the 20 cytoplasmic and four dual-location Plasmodium aminoac...

Additional file 5: of In-depth comparative analysis of malaria parasite genomes reveals protein-coding genes linked to human disease in Plasmodium falciparum genome

Xuewu Liu (457532)
Yuanyuan Wang (20181)
Jiao Liang (5162900)
Luojun Wang (5162903)
Na Qin (774536)
Ya Zhao (807581)
Gang Zhao (161405)

May 2018

Table S4. The P. berghei genes included in rodent malaria parasite-enriched clusters. (XLSX 20Â kb

Additional file 1: of Schizont transcriptome variation among clinical isolates and laboratory-adapted clones of the malaria parasite Plasmodium falciparum

Sarah Tarr (6067133)
Ofelia DĂaz-Ingelmo (6067136)
Lindsay Stewart (560932)
Suzanne Hocking (6067139)
Lee Murray (3357719)
Craig Duffy (3550022)
Thomas Otto (5241)
Lia Chappell (530631)
Julian Rayner (3988232)
Gordon Awandare (3690160)
David Conway (218340)

December 2018

Masking of P. falciparum genome annotation file to exclude polymorphic regions of genes. (PDF 546â...

Additional file 9: of Schizont transcriptome variation among clinical isolates and laboratory-adapted clones of the malaria parasite Plasmodium falciparum

Sarah Tarr (6067133)
Ofelia DĂaz-Ingelmo (6067136)
Lindsay Stewart (560932)
Suzanne Hocking (6067139)
Lee Murray (3357719)
Craig Duffy (3550022)
Thomas Otto (5241)
Lia Chappell (530631)
Julian Rayner (3988232)
Gordon Awandare (3690160)
David Conway (218340)

December 2018

Sequence annotation file Pf3D7.May2015.NoSplice.LSHTM.gtf (see Additional file 1 for explanatory det...

Additional file 1: of Malaria parasites of long-tailed macaques in Sarawak, Malaysian Borneo: a novel species and demographic and evolutionary histories

Thamayanthi Nada Raja (5085755)
Ting Huey Hu (5085752)
Ramlah Zainudin (615588)
Kim Sung Lee (712746)
Susan L. Perkins (76181)
Balbir Singh (218132)

April 2018

14 internal primers used to sequence the complete mitochondrial genomes of Plasmodium sp. (DOCX 12Â ...

Additional file 2: of Exploration of Plasmodium vivax transmission dynamics and recurrent infections in the Peruvian Amazon using whole genome sequencing

Annie Cowell (5482796)
Hugo Valdivia (3466484)
Danett Bishop (5482793)
Elizabeth Winzeler (56214)

July 2018

Table S2. Sequencing statistics for 69 Plasmodium vivax sequences collected in 3 villages in the Per...

Additional file 1: of Genome-wide identification and characterization of transfer RNA-derived small RNAs in Plasmodium falciparum

Zhensheng Wang (548619)
Chunyan Wei (548617)
Xiao Hao (6211553)
Weiwei Deng (2550691)
Lianhui Zhang (548620)
Zenglei Wang (160548)
Heng Wang (76752)

January 2019

Table S1. Sequences of specific stem-loop reverse transcription primers. Table S2. Sequences of PCR ...

Additional file 1: of Genetic diversity of Plasmodium falciparum isolates from Baka Pygmies and their Bantu neighbours in the north of Gabon

Bertrand Mvé-Ondo (3512009)
Dieudonné Nkoghe (184002)
Céline Arnathau (264001)
Virginie Rougeron (191120)
Ulrich Bisvigou (184038)
Lauriane Mouele (3512012)
Larson Boundenga (749176)
Patrick Durand (72585)
Eric Elguero (271203)
Simone Lemmers (3512000)
Lucrèce Délicat-Loembet (3512003)
Nancy Diamella-Moukodoum (3512006)
Christophe Paupy (184029)
François Renaud (63587)
Franck Prugnolle (21227)
Benjamin Ollomo (201531)

October 2015

Sequences of primers used for genotyping P. falciparum genes. This table shows the primers sequences...

Additional file 9: of In-depth comparative analysis of malaria parasite genomes reveals protein-coding genes linked to human disease in Plasmodium falciparum genome

Xuewu Liu (457532)
Yuanyuan Wang (20181)
Jiao Liang (5162900)
Luojun Wang (5162903)
Na Qin (774536)
Ya Zhao (807581)
Gang Zhao (161405)

May 2018

Table S5. Candidate genes related to virulence of the P. falciparum parasite. (XLSX 31Â kb

Additional file 1: of Prevalence of K13-propeller gene polymorphisms among Plasmodium falciparum parasites isolated from adult symptomatic patients in northern Uganda

Moses Ocan (540836)
Freddie Bwanga (221684)
Alfred Okeng (133434)
Fred Katabazi (3421877)
Edgar Kigozi (724127)
Samuel Kyobe (133439)
Jasper Ogwal-Okeng (518357)
Celestino Obua (375449)

August 2016

Nucleotide sequences of Plasmodium falciparum DNA samples with mutations. This file contains the nuc...

Additional file 2: Figure S1. of Genome content analysis yields new insights into the relationship between the human malaria parasite Plasmodium falciparum and its anopheline vectors

Sara Oppenheim (3799420)
Jeffrey Rosenfeld (403548)
Rob DeSalle (175611)

February 2017

Flowchart of methods used to identify and annotate gain/loss protein families. (PDF 38Â kb

Additional file 11: of In-depth comparative analysis of malaria parasite genomes reveals protein-coding genes linked to human disease in Plasmodium falciparum genome

Xuewu Liu (457532)
Yuanyuan Wang (20181)
Jiao Liang (5162900)
Luojun Wang (5162903)
Na Qin (774536)
Ya Zhao (807581)
Gang Zhao (161405)

May 2018

Table S6. Identified P. falciparum genes that possibly contribute to cerebral malaria. (XLSX 12Â kb

Additional file 2: of Rapid multiplex gene expression assays for monitoring metabolic resistance in the major malaria vector Anopheles gambiae

Konstantinos Mavridis (6178208)
Nadja Wipf (6178211)
Sandrine Medves (819337)
Ignacio Erquiaga (6178214)
Pie Müller (68677)
John Vontas (154766)

January 2019

Figure S1. Primer and probe design strategy using Detox (A), consisting of RPS7 (normaliser), CYP6P3...