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2. 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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3. 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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4. 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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7. IDENTIFYING RIFIN AND STEVOR EPITOPES ASSOCIATED WITH MALARIA EXPOSURE USING PEPTIDE AND PROTEIN MICROARRAYS

Author

Albert Zhou, Berry, Andrea A., Bailey, Jason A., Pike, Andrew, Dara, Antoine, Agrawal, Sonia, Ouattara, Amed, Coulibaly, Drissa, Tolo, Youssouf, Lyke, Kristen, Laurens, Matthew B., Adams, Matthew, Harrison, Shannon Takala, Pablo, Jozelyn, Jasinskas, Algis, Nakajima, Rie, Niangaly, Amadou, Kouriba, Bourema, Kone, Abdoulaye K., Rowe, J. Alexandra, Doumbo, Ogobara K., Thera, Mahamadou A., Nyunt, Myaing M., Patel, Jigar J., Tan, John C., Felgner, Phillip L., Plowe, Christopher V., and Travassos, Mark A.

9. MALIAN CHILDREN WITH SEVERE MALARIA SUBTYPES HAVE DISTINCT ANTIBODY GAPS TO VIRULENT PFEMP1S

Author

Travassos, Mark A., Han, Paul, Coulibaly, Drissa, Albert Zhou, Dara, Antoine, Shrestha, Biraj, Nakajima, Rie, Jain, Aarti, Taghavian, Omid, Jasinskas, Algis, Laurens, Matthew B., Niangaly, Amadou, Ouattara, Amed, Berry, Andrea A., Adams, Matthew, Takala-Harrison, Shannon, Kouriba, Bourema, Kone, Abdoulaye K., Rowe, J. Alexandra, Doumbo, Ogobara K., Lyke, Kirsten E., Felgner, Philip L., Plowe, Christopher V., and Thera, Mahamadou A.

10. Additional file 2. of Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential

Author

Moser, Kara, DráBek, Elliott, Dwivedi, Ankit, Stucke, Emily, Crabtree, Jonathan, Dara, Antoine, Zalak Shah, Adams, Matthew, Li, Tao, Rodrigues, Priscila, Koren, Sergey, Phillippy, Adam, Munro, James, Amed Ouattara, Sparklin, Benjamin, Hotopp, Julie Dunning, Lyke, Kirsten, Sadzewicz, Lisa, Tallon, Luke, Spring, Michele, Krisada Jongsakul, Chanthap Lon, Saunders, David, Ferreira, Marcelo, Myaing Nyunt, Laufer, Miriam, Travassos, Mark, Sauerwein, Robert, Takala-Harrison, Shannon, Fraser, Claire, B. Sim, Hoffman, Stephen, Plowe, Christopher, and Silva, Joana

Subjects
3. Good health
Abstract

Supplemental Text, Tables, and Figures. Word document containing supplemental information as cited in the main manuscript.

12. Additional file 2. of Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential

Author

Moser, Kara, DráBek, Elliott, Dwivedi, Ankit, Stucke, Emily, Crabtree, Jonathan, Dara, Antoine, Zalak Shah, Adams, Matthew, Li, Tao, Rodrigues, Priscila, Koren, Sergey, Phillippy, Adam, Munro, James, Amed Ouattara, Sparklin, Benjamin, Hotopp, Julie Dunning, Lyke, Kirsten, Sadzewicz, Lisa, Tallon, Luke, Spring, Michele, Krisada Jongsakul, Chanthap Lon, Saunders, David, Ferreira, Marcelo, Myaing Nyunt, Laufer, Miriam, Travassos, Mark, Sauerwein, Robert, Takala-Harrison, Shannon, Fraser, Claire, B. Sim, Hoffman, Stephen, Plowe, Christopher, and Silva, Joana

Subjects
3. Good health
Abstract

Supplemental Text, Tables, and Figures. Word document containing supplemental information as cited in the main manuscript.

13. MALIAN CHILDREN WITH SEVERE MALARIA EXHIBIT DISTINCT PFEMP1 ANTIBODY PROFILES THAT DIFFER BY BLOOD TYPE

Author

Albert Zhou, Han, Paul, Berry, Andrea A., Coulibaly, Drissa, Stucke, Emily M., Ouattara, Amed, Shrestha, Biraj, Laurens, Matthew B., Nakajima, Rie, Jain, Aarti, Taghavian, Omid, Obiero, Joshua M., Liang, Li, Jasinskas, Algis, Niangaly, Amadou, Kouriba, Bourema, Kone, Abdoulaye, Doumbo, Ogobara K., Rowe, J. Alexandra, Takala-Harrison, Shannon, Lyke, Kirsten E., Plowe, Christopher V., Felgner, Philip L., Thera, Mahamadou A., and Travassos, Mark A.

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