Dharia, Neekesh V, Sidhu, Amar, Cassera, María, Westenberger, Scott J, Bopp, Selina ER, Eastman, Rich T, ...
Abstract Background The identification of genetic changes that confer drug resistance or other phenotypic changes in pathogens can help optimize treatment strategies, support the development of new...
Le Roch, Karine G, Johnson, Jeffrey R, Ahiboh, Hugues, Chung, Duk-Won D, Prudhomme, Jacques, Plouffe, David, ...
Abstract Background In recent years, a major increase in the occurrence of drug resistant falciparum malaria has been reported. Choline analogs, such as the bisthiazolium T4, represent a novel class...
In silicodiscovery of transcription regulatory elements in Plasmodium falciparum (2008)
Young, Jason A, Johnson, Jeffery R, Benner, Chris, Yan, S Frank, Chen, Kaisheng, Le Roch, Karine G, ...
Abstract Background With the sequence of the Plasmodium falciparum genome and several global mRNA and protein life cycle expression profiling projects now completed, elucidating the underlying...
Correction: A Systematic Map of Genetic Variation in Plasmodium falciparum (2006)
Claire Kidgell, Sarah K. Volkman, Johanna Daily, Justin O. Borevitz, David Plouffe, Yingyao Zhou, ...
A Systematic Map of Genetic Variation in Plasmodium falciparum (2006)
Claire Kidgell, Sarah K. Volkman, Johanna Daily, Justin O. Borevitz, David Plouffe, Yingyao Zhou, ...
Discovering novel genes involved in immune evasion and drug resistance in the human malaria parasite, Plasmodium falciparum, is of critical importance to global health. Such knowledge may assist in...
Sam-Yellowe, Tobili Y., Florens, Laurence, Johnson, Jeffrey R., Wang, Tongmin, Drazba, Judith A., Le Roch, Karine G., ...
Upon invasion of the erythrocyte cell, the malaria parasite remodels its environment; in particular, it establishes a complex membrane network, which connects the parasitophorous vacuole to the host...
In vivotranscriptional profiling of Plasmodium falciparum (2004)
Daily, Johanna P, Le Roch, Karine G, Sarr, Ousmane, Fang, Xuemin, Zhou, Yingyao, Ndir, Omar, ...
Abstract Background Both host and pathogen factors contribute to disease outcome in Plasmodium falciparum infection. The feasibility of studying the P. falciparum in vivo transcriptome to understand...
Running Title: Ontology-based Pattern Identification (2004)
Yingyao Zhou, Jason A. Young, Andrey Santrosyan, Kaisheng Chen, Frank S. Yan, Elizabeth A. Winzeler
Malaria Journal 2004, 3:30 doi:10.1186/1475-2875-3-30 (2004)
Malaria Journal Doi, Johanna P Daily, Karine G Leroch, Yingyao Zhou, Elizabeth A Winzeler, Dyann F Wirth, ...
Background Both host and pathogen factors contribute to disease outcome in Plasmodium falciparum infection. The feasibility of studying the P. falciparum in vivo transcriptome to understand parasite...
Sam-Yellowe, Tobili Y., Florens, Laurence, Johnson, Jeffrey R., Wang, Tongmin, Drazba, Judith A., Le Roch, Karine G., ...
Upon invasion of the erythrocyte cell, the malaria parasite remodels its environment; in particular, it establishes a complex membrane network, which connects the parasitophorous vacuole to the host...
In silico gene function prediction using ontology-based pattern identification (2004)
Zhou, Yingyao, Young, Jason A., Santrosyan, Andrey, Chen, Kaisheng, Yan, Frank S., Winzeler, Elizabeth A.
Motivation: With the emergence of genome-wide expression profiling data sets, the guilt by association (GBA) principle has been a cornerstone for deriving gene functional interpretations in silico....
Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle (2004)
Le Roch, Karine G., Johnson, Jeffrey R., Florens, Laurence, Zhou, Yingyao, Santrosyan, Andrey, Grainger, Munira, ...
To investigate the role of post-transcriptional controls in the regulation of protein expression for the malaria parasite, Plasmodium falciparum, we have compared mRNA transcript and protein...
Sam-Yellowe, Tobili Y., Florens, Laurence, Johnson, Jeffrey R., Wang, Tongmin, Drazba, Judith A., Le Roch, Karine G., ...
Upon invasion of the erythrocyte cell, the malaria parasite remodels its environment; in particular, it establishes a complex membrane network, which connects the parasitophorous vacuole to the host...
Coordinated functions of WSS1, PSY2 and TOF1 in the DNA damage response (2004)
O'Neill, Bryan M., Hanway, Denise, Winzeler, Elizabeth A., Romesberg, Floyd E.
The stabilization and processing of stalled replication forks is required to maintain genome integrity in all organisms. In an effort to identify novel proteins that might be involved in stabilizing...
In silico gene function prediction using ontology-based pattern identification (2004)
Zhou, Yingyao, Young, Jason A., Santrosyan, Andrey, Chen, Kaisheng, Yan, Frank S., Winzeler, Elizabeth A.
Motivation: With the emergence of genome-wide expression profiling data sets, the guilt by association (GBA) principle has been a cornerstone for deriving gene functional interpretations in silico....
Parallel Identification of New Genes in Saccharomyces cerevisiae (2002)
Oshiro, Guy, Wodicka, Lisa M., Washburn, Michael P., Yates, John R., Lockhart, David J., Winzeler, Elizabeth A.
The effects of pH on the torsional flexibility of DNA bound to a nucleosome core particle / (1990)
Typescript (photocopy).
Previously uncharacterized genes in the UV- and MMS-induced DNA damage response in yeast
Hanway, Denise, Chin, Jodie K., Xia, Gang, Oshiro, Guy, Winzeler, Elizabeth A., Romesberg, Floyd E.
A competitive growth assay has been used to identify yeast genes involved in the repair of UV- or MMS-induced DNA damage. A collection of 2,827 yeast strains was analyzed in which each strain has a...
The Ume6 regulon coordinates metabolic and meiotic gene expression in yeast
Williams, Roy M., Primig, Michael, Washburn, Brian K., Winzeler, Elizabeth A., Bellis, Michel, Sarrauste De Menthière, Cyril, ...
The Ume6 transcription factor in yeast is known to both repress and activate expression of diverse genes during growth and meiotic development. To obtain a more complete profile of the functions...
Parallel Identification of New Genes in Saccharomyces cerevisiae
Oshiro, Guy, Wodicka, Lisa M., Washburn, Michael P., Yates, John R., Lockhart, David J., Winzeler, Elizabeth A.
Short open reading frames (ORFs) occur frequently in primary genome sequence. Distinguishing bona fide small genes from the tens of thousands of short ORFs is one of the most challenging aspects of...
Sam-Yellowe, Tobili Y., Florens, Laurence, Johnson, Jeffrey R., Wang, Tongmin, Drazba, Judith A., Le Roch, Karine G., ...
Upon invasion of the erythrocyte cell, the malaria parasite remodels its environment; in particular, it establishes a complex membrane network, which connects the parasitophorous vacuole to the host...
In vivo transcriptional profiling of Plasmodium falciparum
Daily, Johanna P, Le Roch, Karine G, Sarr, Ousmane, Fang, Xuemin, Zhou, Yingyao, Ndir, Omar, ...
Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle
Le Roch, Karine G., Johnson, Jeffrey R., Florens, Laurence, Zhou, Yingyao, Santrosyan, Andrey, Grainger, Munira, ...
To investigate the role of post-transcriptional controls in the regulation of protein expression for the malaria parasite, Plasmodium falciparum, we have compared mRNA transcript and protein...
Coordinated functions of WSS1, PSY2 and TOF1 in the DNA damage response
O'Neill, Bryan M., Hanway, Denise, Winzeler, Elizabeth A., Romesberg, Floyd E.
The stabilization and processing of stalled replication forks is required to maintain genome integrity in all organisms. In an effort to identify novel proteins that might be involved in stabilizing...
A Systematic Map of Genetic Variation in Plasmodium falciparum
Kidgell, Claire, Volkman, Sarah K, Daily, Johanna, Borevitz, Justin O, Plouffe, David, Zhou, Yingyao, ...
Discovering novel genes involved in immune evasion and drug resistance in the human malaria parasite, Plasmodium falciparum, is of critical importance to global health. Such knowledge may assist in...
Genetic diversity in yeast assessed with whole-genome oligonucleotide arrays.
Winzeler, Elizabeth A, Castillo-Davis, Cristian I, Oshiro, Guy, Liang, David, Richards, Daniel R, Zhou, Yingyao, ...
The availability of a complete genome sequence allows the detailed study of intraspecies variability. Here we use high-density oligonucleotide arrays to discover 11,115 single-feature polymorphisms...
Correction: A Systematic Map of Genetic Variation in Plasmodium falciparum
Kidgell, Claire, Volkman, Sarah K, Daily, Johanna, Borevitz, Justin O, Plouffe, David, Zhou, Yingyao, ...
Previously uncharacterized genes in the UV- and MMS-induced DNA damage response in yeast
Hanway, Denise, Chin, Jodie K., Xia, Gang, Oshiro, Guy, Winzeler, Elizabeth A., Romesberg, Floyd E.
A competitive growth assay has been used to identify yeast genes involved in the repair of UV- or MMS-induced DNA damage. A collection of 2,827 yeast strains was analyzed in which each strain has a...
The Ume6 regulon coordinates metabolic and meiotic gene expression in yeast
Williams, Roy M., Primig, Michael, Washburn, Brian K., Winzeler, Elizabeth A., Bellis, Michel, Sarrauste De Menthière, Cyril, ...
The Ume6 transcription factor in yeast is known to both repress and activate expression of diverse genes during growth and meiotic development. To obtain a more complete profile of the functions...
Parallel Identification of New Genes in Saccharomyces cerevisiae
Oshiro, Guy, Wodicka, Lisa M., Washburn, Michael P., Yates, John R., Lockhart, David J., Winzeler, Elizabeth A.
Short open reading frames (ORFs) occur frequently in primary genome sequence. Distinguishing bona fide small genes from the tens of thousands of short ORFs is one of the most challenging aspects of...
Sam-Yellowe, Tobili Y., Florens, Laurence, Johnson, Jeffrey R., Wang, Tongmin, Drazba, Judith A., Le Roch, Karine G., ...
Upon invasion of the erythrocyte cell, the malaria parasite remodels its environment; in particular, it establishes a complex membrane network, which connects the parasitophorous vacuole to the host...
In vivo transcriptional profiling of Plasmodium falciparum
Daily, Johanna P, Le Roch, Karine G, Sarr, Ousmane, Fang, Xuemin, Zhou, Yingyao, Ndir, Omar, ...
Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle
Le Roch, Karine G., Johnson, Jeffrey R., Florens, Laurence, Zhou, Yingyao, Santrosyan, Andrey, Grainger, Munira, ...
To investigate the role of post-transcriptional controls in the regulation of protein expression for the malaria parasite, Plasmodium falciparum, we have compared mRNA transcript and protein...
Coordinated functions of WSS1, PSY2 and TOF1 in the DNA damage response
O'Neill, Bryan M., Hanway, Denise, Winzeler, Elizabeth A., Romesberg, Floyd E.
The stabilization and processing of stalled replication forks is required to maintain genome integrity in all organisms. In an effort to identify novel proteins that might be involved in stabilizing...
Genetic diversity in yeast assessed with whole-genome oligonucleotide arrays.
Winzeler, Elizabeth A, Castillo-Davis, Cristian I, Oshiro, Guy, Liang, David, Richards, Daniel R, Zhou, Yingyao, ...
The availability of a complete genome sequence allows the detailed study of intraspecies variability. Here we use high-density oligonucleotide arrays to discover 11,115 single-feature polymorphisms...
A Systematic Map of Genetic Variation in Plasmodium falciparum
Kidgell, Claire, Volkman, Sarah K, Daily, Johanna, Borevitz, Justin O, Plouffe, David, Zhou, Yingyao, ...
Discovering novel genes involved in immune evasion and drug resistance in the human malaria parasite, Plasmodium falciparum, is of critical importance to global health. Such knowledge may assist in...
Correction: A Systematic Map of Genetic Variation in Plasmodium falciparum
Kidgell, Claire, Volkman, Sarah K, Daily, Johanna, Borevitz, Justin O, Plouffe, David, Zhou, Yingyao, ...
Evidence-Based Annotation of the Malaria Parasite's Genome Using Comparative Expression Profiling
Zhou, Yingyao, Ramachandran, Vandana, Kumar, Kota Arun, Westenberger, Scott, Refour, Phillippe, Zhou, Bin, ...
A fundamental problem in systems biology and whole genome sequence analysis is how to infer functions for the many uncharacterized proteins that are identified, whether they are conserved across...
In silico discovery of transcription regulatory elements in Plasmodium falciparum
Young, Jason A, Johnson, Jeffery R, Benner, Chris, Yan, S Frank, Chen, Kaisheng, Le Roch, Karine G, ...
Le Roch, Karine G, Johnson, Jeffrey R, Ahiboh, Hugues, Chung, Duk-Won D, Prudhomme, Jacques, Plouffe, David, ...
Plouffe, David, Brinker, Achim, McNamara, Case, Henson, Kerstin, Kato, Nobutaka, Kuhen, Kelli, ...
The growing resistance to current first-line antimalarial drugs represents a major health challenge. To facilitate the discovery of new antimalarials, we have implemented an efficient and robust...
Dharia, Neekesh V, Sidhu, Amar Bir Singh, Cassera, María Belén, Westenberger, Scott J, Bopp, Selina ER, Eastman, Rich T, ...
Using tiling microarrays, a mechanism by which Plasmodium falciparum parasites acquire resistance to the antimalarial fosmidomycin has been elucidated