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1. Additional file 2: of New var reconstruction algorithm exposes high var sequence diversity in a single geographic location in Mali

Author

Dara, Antoine, DrĂĄbek, Elliott, Travassos, Mark, Moser, Kara, Delcher, Arthur, Su, Qi, Hostelley, Timothy, Drissa Coulibaly, Modibo Daou, Ahmadou Dembele, Diarra, Issa, Abdoulaye Kone, Bourema Kouriba, Laurens, Matthew, Amadou Niangaly, Traore, Karim, Tolo, Youssouf, Fraser, Claire, Mahamadou Thera, Abdoulaye Djimde, Ogobara Doumbo, Plowe, Christopher, and Silva, Joana

Subjects
parasitic diseases, food and beverages
Abstract

Contig pile-ups of the genome of 12 P. falciparum isolates from Mali aligned against the reference 3D7 genome. The genome assembly of each of the 12 isolates, represented by its constituent contigs (blue lines in between blue circles) is aligned against each of the 14 nuclear chromosomes of the reference P. falciparum 3D7 strain (black). The location of var gene sequences is shown (red) in both the 3D7 genome and the contigs aligned to it. (PDF 1608 kb)

Published
2017
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2. Additional file 3: of New var reconstruction algorithm exposes high var sequence diversity in a single geographic location in Mali

Author

Dara, Antoine, DrĂĄbek, Elliott, Travassos, Mark, Moser, Kara, Delcher, Arthur, Su, Qi, Hostelley, Timothy, Drissa Coulibaly, Modibo Daou, Ahmadou Dembele, Diarra, Issa, Abdoulaye Kone, Bourema Kouriba, Laurens, Matthew, Amadou Niangaly, Traore, Karim, Tolo, Youssouf, Fraser, Claire, Mahamadou Thera, Abdoulaye Djimde, Ogobara Doumbo, Plowe, Christopher, and Silva, Joana

Abstract

A file containing Supplementary Figures S1â S5. Figure S1: Domain organization of PfEMP1 in each of 12 Malian isolates. Figure S2: Maximum likelihood phylogeny of DBLÎą domain sequences. Figure S3: Maximum likelihood phylogeny of CIDRÎą domain sequences. Figure S4: Detection and visualization of recombination events within and between var2csa sequences. Figure S5: Phylogenetic tree of reconstructed var2csa exon 1 sequences. (DOCX 3594 kb)

Published
2017
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3. Additional file 1: of New var reconstruction algorithm exposes high var sequence diversity in a single geographic location in Mali

Author

Dara, Antoine, DrĂĄbek, Elliott, Travassos, Mark, Moser, Kara, Delcher, Arthur, Su, Qi, Hostelley, Timothy, Drissa Coulibaly, Modibo Daou, Ahmadou Dembele, Diarra, Issa, Abdoulaye Kone, Bourema Kouriba, Laurens, Matthew, Amadou Niangaly, Traore, Karim, Tolo, Youssouf, Fraser, Claire, Mahamadou Thera, Abdoulaye Djimde, Ogobara Doumbo, Plowe, Christopher, and Silva, Joana

Abstract

A file containing Supplementary Tables S1â S7. Table S1: Samples and respective metadata. Table S2: Genomic DNA: Illumina and PacBio Sequencing Statistics. Table S3: Assembly characteristics for 12 Malian samples generated by Sprai and Celera assemblers. Table S4: Exon 1 var sequences recovered with ETHA compared to raw var-like sequences extracted directly from assemblies. Table S5: Percent of extracted sequence absent from the ETHA output. Table S6: Comparison of PfEMP1 constitutive domains reconstructed from 12 samples to the reference 3D7. Table S7: Average percent (%) amino acid identity within PfEMP1 constitutive domains. (DOCX 64 kb)

Published
2017
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4. MOESM2 of Phase 1 randomized controlled trial to evaluate the safety and immunogenicity of recombinant Pichia pastoris-expressed Plasmodium falciparum apical membrane antigen 1 (PfAMA1-FVO [25-545]) in healthy Malian adults in Bandiagara

Author

Mahamadou Thera, Drissa Coulibaly, Abdoulaye Kone, Guindo, Ando, Traore, Karim, Abdourhamane Sall, Diarra, Issa, Modibo Daou, Idrissa Traore, Tolo, Youssouf, Sissoko, Mady, Amadou Niangaly, Arama, Charles, Mounirou Baby, Bourema Kouriba, Mahamadou Sissoko, Issaka Sagara, Ousmane Toure, Amagana Dolo, Dapa Diallo, Remarque, Edmond, Chilengi, Roma, Ramadhani Noor, Sesay, Sanie, Thomas, Alan, Kocken, Clemens, Faber, Bart, Egeruan Imoukhuede, Leroy, Odile, and Ogobara Doumbo

Abstract

Additional file 2. Solicited adverse event intensity scale.

Published
2016
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5. MOESM5 of Expression of complement and toll-like receptor pathway genes is associated with malaria severity in Mali: a pilot case control study

Author

Sobota, Rafal, Dara, Antoine, Manning, Jessica, Amadou Niangaly, Bailey, Jason, Abdoulaye Kone, Mahamadou Thera, Abdoulaye DjimdĂŠ, Vernet, Guy, Leissner, Philippe, Williams, Scott, Plowe, Christopher, and Ogobara Doumbo

Subjects
fungi, natural sciences, macromolecular substances, 3. Good health
Abstract

Additional file 5: Table S4. Top differentially expressed KEGG pathways between severe cases and uncomplicated controls during convalescence.

6. MOESM6 of Expression of complement and toll-like receptor pathway genes is associated with malaria severity in Mali: a pilot case control study

Author

Sobota, Rafal, Dara, Antoine, Manning, Jessica, Amadou Niangaly, Bailey, Jason, Abdoulaye Kone, Mahamadou Thera, Abdoulaye DjimdĂŠ, Vernet, Guy, Leissner, Philippe, Williams, Scott, Plowe, Christopher, and Ogobara Doumbo

Subjects
fungi, natural sciences, macromolecular substances, 3. Good health
Abstract

Additional file 6: Table S5. Top differentially expressed KEGG pathways between severe cases and uncomplicated controls during late convalescence.

7. MOESM5 of Expression of complement and toll-like receptor pathway genes is associated with malaria severity in Mali: a pilot case control study

Author

Sobota, Rafal, Dara, Antoine, Manning, Jessica, Amadou Niangaly, Bailey, Jason, Abdoulaye Kone, Mahamadou Thera, Abdoulaye DjimdĂŠ, Vernet, Guy, Leissner, Philippe, Williams, Scott, Plowe, Christopher, and Ogobara Doumbo

Subjects
fungi, natural sciences, macromolecular substances, 3. Good health
Abstract

Additional file 5: Table S4. Top differentially expressed KEGG pathways between severe cases and uncomplicated controls during convalescence.

8. MOESM3 of Expression of complement and toll-like receptor pathway genes is associated with malaria severity in Mali: a pilot case control study

Author

Sobota, Rafal, Dara, Antoine, Manning, Jessica, Amadou Niangaly, Bailey, Jason, Abdoulaye Kone, Mahamadou Thera, Abdoulaye DjimdĂŠ, Vernet, Guy, Leissner, Philippe, Williams, Scott, Plowe, Christopher, and Ogobara Doumbo

Subjects
3. Good health
Abstract

Additional file 3: Table S2. Clinical characteristics of enrolled patients for the Dry Season time point.

9. MOESM1 of Expression of complement and toll-like receptor pathway genes is associated with malaria severity in Mali: a pilot case control study

Author

Sobota, Rafal, Dara, Antoine, Manning, Jessica, Amadou Niangaly, Bailey, Jason, Abdoulaye Kone, Mahamadou Thera, Abdoulaye DjimdĂŠ, Vernet, Guy, Leissner, Philippe, Williams, Scott, Plowe, Christopher, and Ogobara Doumbo

Subjects
3. Good health
Abstract

Additional file 1: Figure S1. Power as a function of sample size for an Affymetrix Human Genome U133 Plus 2.0 GeneChip with alpha 0.05, FDR 0.05, and a standard deviation of 0.6 under the assumption that 90% of the genes on the chip remain undifferentiated in their expression.

10. MOESM2 of Expression of complement and toll-like receptor pathway genes is associated with malaria severity in Mali: a pilot case control study

Author

Sobota, Rafal, Dara, Antoine, Manning, Jessica, Amadou Niangaly, Bailey, Jason, Abdoulaye Kone, Mahamadou Thera, Abdoulaye DjimdĂŠ, Vernet, Guy, Leissner, Philippe, Williams, Scott, Plowe, Christopher, and Ogobara Doumbo

Subjects
3. Good health
Abstract

Additional file 2: Table S1. Clinical characteristics of enrolled patients for the acute illness and convalescence time points.

11. MOESM2 of Expression of complement and toll-like receptor pathway genes is associated with malaria severity in Mali: a pilot case control study

Author

Sobota, Rafal, Dara, Antoine, Manning, Jessica, Amadou Niangaly, Bailey, Jason, Abdoulaye Kone, Mahamadou Thera, Abdoulaye DjimdĂŠ, Vernet, Guy, Leissner, Philippe, Williams, Scott, Plowe, Christopher, and Ogobara Doumbo

Subjects
3. Good health
Abstract

Additional file 2: Table S1. Clinical characteristics of enrolled patients for the acute illness and convalescence time points.

12. MOESM6 of Expression of complement and toll-like receptor pathway genes is associated with malaria severity in Mali: a pilot case control study

Author

Sobota, Rafal, Dara, Antoine, Manning, Jessica, Amadou Niangaly, Bailey, Jason, Abdoulaye Kone, Mahamadou Thera, Abdoulaye DjimdĂŠ, Vernet, Guy, Leissner, Philippe, Williams, Scott, Plowe, Christopher, and Ogobara Doumbo

Subjects
fungi, natural sciences, macromolecular substances, 3. Good health
Abstract

Additional file 6: Table S5. Top differentially expressed KEGG pathways between severe cases and uncomplicated controls during late convalescence.

13. MOESM3 of Expression of complement and toll-like receptor pathway genes is associated with malaria severity in Mali: a pilot case control study

Author

Sobota, Rafal, Dara, Antoine, Manning, Jessica, Amadou Niangaly, Bailey, Jason, Abdoulaye Kone, Mahamadou Thera, Abdoulaye DjimdĂŠ, Vernet, Guy, Leissner, Philippe, Williams, Scott, Plowe, Christopher, and Ogobara Doumbo

Subjects
3. Good health
Abstract

Additional file 3: Table S2. Clinical characteristics of enrolled patients for the Dry Season time point.

14. MOESM7 of Expression of complement and toll-like receptor pathway genes is associated with malaria severity in Mali: a pilot case control study

Author

Sobota, Rafal, Dara, Antoine, Manning, Jessica, Amadou Niangaly, Bailey, Jason, Abdoulaye Kone, Mahamadou Thera, Abdoulaye DjimdĂŠ, Vernet, Guy, Leissner, Philippe, Williams, Scott, Plowe, Christopher, and Ogobara Doumbo

Subjects
body regions, 3. Good health
Abstract

Additional file 7: Table S6. RT-PCR validation of GeneChip expression data with RT-PCR (probes for CYP1B1, IL18R1 and C1QB failed to consistently amplify, failing the inclusion criteria; therefore they were not included in the final validation analysis).

15. MOESM4 of Expression of complement and toll-like receptor pathway genes is associated with malaria severity in Mali: a pilot case control study

Author

Sobota, Rafal, Dara, Antoine, Manning, Jessica, Amadou Niangaly, Bailey, Jason, Abdoulaye Kone, Mahamadou Thera, Abdoulaye DjimdĂŠ, Vernet, Guy, Leissner, Philippe, Williams, Scott, Plowe, Christopher, and Ogobara Doumbo

Subjects
3. Good health
Abstract

Additional file 4: Table S3. All statistically significant probes for testing gene expression difference between severe cases and uncomplicated controls during acute illness (function designated by Ingenuity Pathway Analysis).

16. MOESM7 of Expression of complement and toll-like receptor pathway genes is associated with malaria severity in Mali: a pilot case control study

Author

Sobota, Rafal, Dara, Antoine, Manning, Jessica, Amadou Niangaly, Bailey, Jason, Abdoulaye Kone, Mahamadou Thera, Abdoulaye DjimdĂŠ, Vernet, Guy, Leissner, Philippe, Williams, Scott, Plowe, Christopher, and Ogobara Doumbo

Subjects
body regions, 3. Good health
Abstract

Additional file 7: Table S6. RT-PCR validation of GeneChip expression data with RT-PCR (probes for CYP1B1, IL18R1 and C1QB failed to consistently amplify, failing the inclusion criteria; therefore they were not included in the final validation analysis).

17. MOESM4 of Expression of complement and toll-like receptor pathway genes is associated with malaria severity in Mali: a pilot case control study

Author

Sobota, Rafal, Dara, Antoine, Manning, Jessica, Amadou Niangaly, Bailey, Jason, Abdoulaye Kone, Mahamadou Thera, Abdoulaye DjimdĂŠ, Vernet, Guy, Leissner, Philippe, Williams, Scott, Plowe, Christopher, and Ogobara Doumbo

Subjects
3. Good health
Abstract

Additional file 4: Table S3. All statistically significant probes for testing gene expression difference between severe cases and uncomplicated controls during acute illness (function designated by Ingenuity Pathway Analysis).

18. MOESM1 of Expression of complement and toll-like receptor pathway genes is associated with malaria severity in Mali: a pilot case control study

Author

Sobota, Rafal, Dara, Antoine, Manning, Jessica, Amadou Niangaly, Bailey, Jason, Abdoulaye Kone, Mahamadou Thera, Abdoulaye DjimdĂŠ, Vernet, Guy, Leissner, Philippe, Williams, Scott, Plowe, Christopher, and Ogobara Doumbo

Subjects
3. Good health
Abstract

Additional file 1: Figure S1. Power as a function of sample size for an Affymetrix Human Genome U133 Plus 2.0 GeneChip with alpha 0.05, FDR 0.05, and a standard deviation of 0.6 under the assumption that 90% of the genes on the chip remain undifferentiated in their expression.

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