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...
Rines, Daniel R, Gomez-Ferreria, Maria, Zhou, Yingyao, DeJesus, Paul, Grob, Seanna, Batalov, Serge, ...
Abstract Background The mitotic spindle is a complex mechanical apparatus required for accurate segregation of sister chromosomes during mitosis. We designed a genetic screen using automated...
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...
Efficient Stochastic Global Optimization For Protein Structure Prediction (2007)
Yingyao Zhou And, Yingyao Zhou, Ruben Abagyan
INTRODUCTION: Why not MD or MC? Biological macromolecules, large chain molecules with hundreds of torsion angles, adopt compact, uniquely folded and rigid conformations that correspond to their...
© 2002 Zhou and Abagyan; licensee BioMed Central Ltd. Verbatim copying and redistribution of this article are permitted in any medium for any purpose, provided this notice is preserved along with...
Bmc Bioinformatics, Yingyao Zhou, Yingyao Zhou, Ruben Abagyan, Ruben Abagyan
This 'Manuscript PDF ' corresponds to the article as it appeared upon acceptance. The fully-formatted PDF version will become available within a few days, from the URL listed below....
Study of gene function based on spatial co-expression in a high-resolution mouse brain atlas (2007)
Liu, Zheng, Yan, S Frank, Walker, John R, Zwingman, Theresa A, Jiang, Tao, Li, Jing, ...
Abstract Background The Allen Brain Atlas (ABA) project systematically profiles three-dimensional high-resolution gene expression in postnatal mouse brains for thousands of genes. By unveiling gene...
Study of gene function based on spatial co-expression in a high-resolution mouse brain atlas. (2007)
Liu, Zheng, Yan, S Frank, Walker, John R, Zwingman, Theresa A, Jiang, Tao, Li, Jing, ...
BACKGROUND: The Allen Brain Atlas (ABA) project systematically profiles three-dimensional high-resolution gene expression in postnatal mouse brains for thousands of genes. By unveiling gene behaviors...
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...
Haplotype-based quantitative trait mapping using a clustering algorithm (2006)
Li, Jing, Zhou, Yingyao, Elston, Robert C
Abstract Background With the availability of large-scale, high-density single-nucleotide polymorphism (SNP) markers, substantial effort has been made in identifying disease-causing genes using...
Global Analysis of Transcript and Protein Levels Across the Plasmodium falciparum Life Cycle (2006)
LeRoch, Karine G., Johnson, Jeffrey R., Florens, Laurence, Zhou, Yingyao, Santrosyan, Audrey, 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...
Haplotype-based quantitative trait mapping using a clustering algorithm. (2006)
Li, Jing, Zhou, Yingyao, Elston, Robert C
BACKGROUND: With the availability of large-scale, high-density single-nucleotide polymorphism (SNP) markers, substantial effort has been made in identifying disease-causing genes using linkage...
BMC Bioinformatics Methodology article (2006)
Haplotype-based quantitative trait mapping using a clustering algorithm
In silico gene function prediction using ontology-based pattern identification (2005)
Zhou, Yingyao, Young, Jason A., Santrosyan, Andrey, Chen, Kaisheng, Yan, S. Frank, 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....
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...
Barrera, Leah, Benner, Chris, Tao, Yong-Chuan, Winzeler, Elizabeth, Zhou, Yingyao
Abstract Background To identify differentially expressed genes across experimental conditions in oligonucleotide microarray experiments, existing statistical methods commonly use a summary of...
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...
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....
Abstract Background High-density oligonucleotide arrays have become a valuable tool for high-throughput gene expression profiling. Increasing the array information density and improving the analysis...
Genetic Linkage Mapping of Zebrafish Genes and ESTs (2000)
Kelly, Peter D., Chu, Felicia, Woods, Ian G., Ngo-Hazelett, Phuong, Cardozo, Timothy, Huang, Hui, ...
How and why phosphotyrosine-containing peptides bind to the SH2 and PTB domains. Fold. Des (1998)
Background: Specific recognition of phosphotyrosine-containing protein segments by Src homology 2 (SH2) and phosphotyrosine-binding (PTB) domains plays an important role in intracellular signal...
Genetic Linkage Mapping of Zebrafish Genes and ESTs
Kelly, Peter D., Chu, Felicia, Woods, Ian G., Ngo-Hazelett, Phuong, Cardozo, Timothy, Huang, Hui, ...
Genetic screens in zebrafish (Danio rerio) have isolated mutations in hundreds of genes essential for vertebrate development, physiology, and behavior. We have constructed a genetic linkage map that...
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...
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...
An efficient rapid system for profiling the cellular activities of molecular libraries
Melnick, Jonathan S., Janes, Jeff, Kim, Sungjoon, Chang, Jim Y., Sipes, Daniel G., Gunderson, Drew, ...
Rapid quantitative methods for characterizing small molecules, peptides, proteins, or RNAs in a broad array of cellular assays would allow one to discover new biological activities associated with...
Collins, Cynthia S., Hong, Jiyong, Sapinoso, Lisa, Zhou, Yingyao, Liu, Zheng, Micklash, Kenneth, ...
Cell motility is a complex biological process, involved in development, inflammation, homeostasis, and pathological processes such as the invasion and metastatic spread of cancer. Here, we describe a...
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, ...
Genetic Linkage Mapping of Zebrafish Genes and ESTs
Kelly, Peter D., Chu, Felicia, Woods, Ian G., Ngo-Hazelett, Phuong, Cardozo, Timothy, Huang, Hui, ...
Genetic screens in zebrafish (Danio rerio) have isolated mutations in hundreds of genes essential for vertebrate development, physiology, and behavior. We have constructed a genetic linkage map that...
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...
Collins, Cynthia S., Hong, Jiyong, Sapinoso, Lisa, Zhou, Yingyao, Liu, Zheng, Micklash, Kenneth, ...
Cell motility is a complex biological process, involved in development, inflammation, homeostasis, and pathological processes such as the invasion and metastatic spread of cancer. Here, we describe a...
An efficient rapid system for profiling the cellular activities of molecular libraries
Melnick, Jonathan S., Janes, Jeff, Kim, Sungjoon, Chang, Jim Y., Sipes, Daniel G., Gunderson, Drew, ...
Rapid quantitative methods for characterizing small molecules, peptides, proteins, or RNAs in a broad array of cellular assays would allow one to discover new biological activities associated with...
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, ...
Study of gene function based on spatial co-expression in a high-resolution mouse brain atlas
Liu, Zheng, Yan, S Frank, Walker, John R, Zwingman, Theresa A, Jiang, Tao, Li, Jing, ...
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, ...
A role for IκB kinase 2 in bipolar spindle assembly
Irelan, Jeffrey T., Murphy, Thomas J., DeJesus, Paul D., Teo, Hsiangling, Xu, DingYue, Gomez-Ferreria, Maria A., ...
IκB kinase 2 (IKK2 or IKKβ) is a component of the IKK complex that coordinates the cellular response to a diverse set of extracellular stimuli, including cytokines, microbial infection, and stress....
Rines, Daniel R, Gomez-Ferreria, Maria Ana, Zhou, Yingyao, DeJesus, Paul, Grob, Seanna, Batalov, Serge, ...
A loss-of-function screen for siRNAs that arrest human cells in metaphase reveals genes involved in mitotic spindle integrity.
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