Vanessa Cheung, Gordon Chua, Nizar N. Batada, Christian R. Landry, Stephen W. Michnick, Timothy R. Hughes, ...
Previous studies in Saccharomyces cerevisiae have demonstrated that cryptic promoters within coding regions activate transcription in particular mutants. We have performed a comprehensive analysis of...
Peña-Castillo, Lourdes, Tasan, Murat, Myers, Chad L, Lee, Hyunju, Joshi, Trupti, Zhang, Chao, ...
Abstract Background: Several years after sequencing the human genome and the mouse genome, much remains to be discovered about the functions of most human and mouse genes. Computational prediction of...
A race through the maze of genomic evidence (2008)
Hughes, Timothy R, Roth, Frederick P
No abstract available.
Lovegrove, Fiona E., Gharib, Sina A., Patel, Samir N., Ruzinski, John T., Hughes, Timothy R., ...
Although acute lung injury (ALI) is a common complication of severe malaria, little is known about the underlying molecular basis of lung dysfunction. Animal models have provided powerful insights...
Functional coordination of alternative splicing in the mammalian central nervous system (2007)
Fagnani, Matthew, Barash, Yoseph, Ip, Joanna Y, Misquitta, Christine, Pan, Qun, Saltzman, Arneet L, ...
Abstract Background Alternative splicing (AS) functions to expand proteomic complexity and plays numerous important roles in gene regulation. However, the extent to which AS coordinates functions in...
Babak, Tomas, Blencowe, Benjamin J, Hughes, Timothy R
Abstract Background Accurate identification of novel, functional noncoding (nc) RNA features in genome sequence has proven more difficult than for exons. Current algorithms identify and score...
Lecuyer, Eric, Yoshida, Hideki, Parthasarathy, Neela, Alm, Christina, Babak, Tomas, Cerovina, Tanja, ...
Although subcellular mRNA trafficking has been demonstrated as a mechanism to control protein distribution, it is generally believed that most protein localization occurs subsequent to translation....
Lovegrove, Fiona E, Peña-Castillo, Lourdes, Mohammad, Naveed, Liles, W Conrad, Hughes, Timothy R, Kain, Kevin C
Abstract Background The development and outcome of cerebral malaria (CM) reflects a complex interplay between parasite-expressed virulence factors and host response to infection. The murine CM model,...
Krogan, Nevan J, Hughes, Timothy R
A report on the 2006 Keystone Conference on Signaling Networks, Vancouver, Canada, 30 January-4 February 2006.
Babak, Tomas, Blencowe, Benjamin J, Hughes, Timothy R
Abstract Background Systematic identification and functional characterization of novel types of noncoding (nc)RNA in genomes is more difficult than it is for protein coding mRNAs, since ncRNAs...
The functional landscape of mouse gene expression (2004)
Zhang, Wen, Morris, Quaid D, Chang, Richard, Shai, Ofer, Bakowski, Malina A, Mitsakakis, Nicholas, ...
Abstract Background Large-scale quantitative analysis of transcriptional co-expression has been used to dissect regulatory networks and to predict the functions of new genes discovered by genome...
FunSpec: a web-based cluster interpreter for yeast (2003)
Bmc Bioinformatics, Mark D Robinson, Jrg Grigull, Naveed Mohammad, Timothy R Hughes
Background: For effective exposition of biological information, especially with regard to analysis of large-scale data types, researchers need immediate access to multiple categorical knowledge bases...
FunSpec: a web-based cluster interpreter for yeast (2002)
Robinson, Mark D, Grigull, Jörg, Mohammad, Naveed, Hughes, Timothy R
Abstract Background For effective exposition of biological information, especially with regard to analysis of large-scale data types, researchers need immediate access to multiple categorical...
Thesis (Ph. D.)--Baylor College of Medicine. Cell and Molecular Biology Program, 1998.
"Presented to the faculty of the Department of Psychology ... in partial fulfillment of the requirements for the degree Master of Arts in Psychology."
Hughes, Timothy R., Weilbaecher, Rodney G., Walterscheid, Monika, Lundblad, Victoria
The CDC13 gene of Saccharomyces cerevisiae is required both to protect telomeric DNA and to ensure proper function of yeast telomerase in vivo. We have previously demonstrated that Cdc13p has a high...
Three Ever Shorter Telomere (EST) genes are dispensable for in vitro yeast telomerase activity
Lingner, Joachim, Cech, Thomas R., Hughes, Timothy R., Lundblad, Victoria
Telomerase is a specialized reverse transcriptase consisting of both RNA and protein components. Previous characterization of yeast telomerase function in vivo identified four EST (for ever shorter...
Kockar, Feray Tura, Foka, Pelagia, Hughes, Timothy R., Kousteni, Stavroula, Ramji, Dipak P.
Transcription factors belonging to the CCAAT-enhancer binding protein (C/EBP) family have been implicated in the regulation of gene expression during differentiation, development and disease....
FunSpec: a web-based cluster interpreter for yeast
Robinson, Mark D, Grigull, Jörg, Mohammad, Naveed, Hughes, Timothy R
Nelson, Bryce, Kurischko, Cornelia, Horecka, Joe, Mody, Manali, Nair, Pradeep, Pratt, Lana, ...
In Saccharomyces cerevisiae, polarized morphogenesis is critical for bud site selection, bud development, and cell separation. The latter is mediated by Ace2p transcription factor, which controls the...
ESF1 is required for 18S rRNA synthesis in Saccharomyces cerevisiae
Peng, Wen-Tao, Krogan, Nevan J., Richards, Dawn P., Greenblatt, Jack F., Hughes, Timothy R.
We report that Esf1p (Ydr365cp), an essential, evolutionarily conserved nucleolar protein, is required for the biogenesis of 18S rRNA in Saccharomyces cerevisiae. Depletion of Esf1p resulted in...
Grigull, Jörg, Mnaimneh, Sanie, Pootoolal, Jeffrey, Robinson, Mark D., Hughes, Timothy R.
Using DNA microarrays, we compared global transcript stability profiles following chemical inhibition of transcription to rpb1-1 (a temperature-sensitive allele of yeast RNA polymerase II). Among the...
Jeronimo, Célia, Langelier, Marie-France, Zeghouf, Mahel, Cojocaru, Marilena, Bergeron, Dominique, Baali, Dania, ...
We have programmed human cells to express physiological levels of recombinant RNA polymerase II (RNAPII) subunits carrying tandem affinity purification (TAP) tags. Double-affinity chromatography...
Krogan, Nevan J., Baetz, Kristin, Keogh, Michael-Christopher, Datta, Nira, Sawa, Chika, Kwok, Trevor C. Y., ...
NuA4, the only essential histone acetyltransferase complex in Saccharomyces cerevisiae, acetylates the N-terminal tails of histones H4 and H2A. Affinity purification of NuA4 revealed the presence of...
Ingvarsdottir, Kristin, Krogan, Nevan J., Emre, N. C. Tolga, Wyce, Anastasia, Thompson, Natalie J., Emili, Andrew, ...
The SAGA complex is a multisubunit protein complex involved in transcriptional regulation in Saccharomyces cerevisiae. SAGA combines proteins involved in interactions with DNA-bound activators and...
Detection and discovery of RNA modifications using microarrays
Hiley, Shawna L., Jackman, Jane, Babak, Tomas, Trochesset, Miles, Morris, Quaid D., Phizicky, Eric, ...
Using a microarray that tiles all known yeast non-coding RNAs, we compared RNA from wild-type cells with RNA from mutants encoding known and putative RNA modifying enzymes. We show that at least five...
The functional landscape of mouse gene expression
Zhang, Wen, Morris, Quaid D, Chang, Richard, Shai, Ofer, Bakowski, Malina A, Mitsakakis, Nicholas, ...
Hiley, Shawna L., Babak, Tomas, Hughes, Timothy R.
We used a microarray containing probes that tile all known yeast noncoding RNAs (ncRNAs) to investigate RNA biogenesis on a global scale. The microarray verified a general loss of Box C/D snoRNAs in...
Esf2p, a U3-Associated Factor Required for Small-Subunit Processome Assembly and Compaction
Hoang, Tran, Peng, Wen-Tao, Vanrobays, Emmanuel, Krogan, Nevan, Hiley, Shawna, Beyer, Ann L., ...
Esf2p is the Saccharomyces cerevisiae homolog of mouse ABT1, a protein previously identified as a putative partner of the TATA-element binding protein. However, large-scale studies have indicated...
The Splicing Factor Prp43p, a DEAH Box ATPase, Functions in Ribosome Biogenesis
Leeds, Nina B., Small, Eliza C., Hiley, Shawna L., Hughes, Timothy R., Staley, Jonathan P.
Biogenesis of the small and large ribosomal subunits requires modification, processing, and folding of pre-rRNA to yield mature rRNA. Here, we report that efficient biogenesis of both small- and...
Probing microRNAs with microarrays: Tissue specificity and functional inference
BABAK, TOMAS, ZHANG, WEN, MORRIS, QUAID, BLENCOWE, BENJAMIN J., HUGHES, TIMOTHY R.
MicroRNAs (miRNAs) are short, stable, noncoding RNAs involved in post-transcriptional gene silencing via hybridization to mRNA. Few have been thoroughly characterized in any species. Here, we...
Probing microRNAs with microarrays: Tissue specificity and functional inference
BABAK, TOMAS, ZHANG, WEN, MORRIS, QUAID, BLENCOWE, BENJAMIN J., HUGHES, TIMOTHY R.
HENRAS, ANTHONY K., SAM, MUI, HILEY, SHAWNA L., WU, HAIHONG, HUGHES, TIMOTHY R., FEIGON, JULI, ...
Members of the RNase III family of double-stranded RNA (dsRNA) endonucleases are important enzymes of RNA metabolism in eukaryotic cells. Rnt1p is the only known member of the RNase III family of...
Cdc13 both positively and negatively regulates telomere replication
Chandra, Abha, Hughes, Timothy R., Nugent, Constance I., Lundblad, Victoria
Cdc13 is a single-strand telomeric DNA-binding protein that positively regulates yeast telomere replication by recruiting telomerase to chromosome termini through a site on Cdc13 that is eliminated...
Krogan, Nevan J, Hughes, Timothy R
A report on the 2006 Keystone Conference on Signaling Networks, Vancouver, Canada, 30 January-4 February 2006.
Zfp206 regulates ES cell gene expression and differentiation
Zhang, Wen, Walker, Emily, Tamplin, Owen J., Rossant, Janet, Stanford, William L., Hughes, Timothy R.
Understanding transcriptional regulation in early developmental stages is fundamental to understanding mammalian development and embryonic stem (ES) cell properties. Expression surveys suggest that...
Lovegrove, Fiona E, Peña-Castillo, Lourdes, Mohammad, Naveed, Liles, W Conrad, Hughes, Timothy R, Kain, Kevin C
Hughes, Timothy R., Weilbaecher, Rodney G., Walterscheid, Monika, Lundblad, Victoria
The CDC13 gene of Saccharomyces cerevisiae is required both to protect telomeric DNA and to ensure proper function of yeast telomerase in vivo. We have previously demonstrated that Cdc13p has a high...
Three Ever Shorter Telomere (EST) genes are dispensable for in vitro yeast telomerase activity
Lingner, Joachim, Cech, Thomas R., Hughes, Timothy R., Lundblad, Victoria
Telomerase is a specialized reverse transcriptase consisting of both RNA and protein components. Previous characterization of yeast telomerase function in vivo identified four EST (for ever shorter...
Kockar, Feray Tura, Foka, Pelagia, Hughes, Timothy R., Kousteni, Stavroula, Ramji, Dipak P.
Transcription factors belonging to the CCAAT-enhancer binding protein (C/EBP) family have been implicated in the regulation of gene expression during differentiation, development and disease....
FunSpec: a web-based cluster interpreter for yeast
Robinson, Mark D, Grigull, Jörg, Mohammad, Naveed, Hughes, Timothy R
Nelson, Bryce, Kurischko, Cornelia, Horecka, Joe, Mody, Manali, Nair, Pradeep, Pratt, Lana, ...
In Saccharomyces cerevisiae, polarized morphogenesis is critical for bud site selection, bud development, and cell separation. The latter is mediated by Ace2p transcription factor, which controls the...
Cdc13 both positively and negatively regulates telomere replication
Chandra, Abha, Hughes, Timothy R., Nugent, Constance I., Lundblad, Victoria
Cdc13 is a single-strand telomeric DNA-binding protein that positively regulates yeast telomere replication by recruiting telomerase to chromosome termini through a site on Cdc13 that is eliminated...
ESF1 is required for 18S rRNA synthesis in Saccharomyces cerevisiae
Peng, Wen-Tao, Krogan, Nevan J., Richards, Dawn P., Greenblatt, Jack F., Hughes, Timothy R.
We report that Esf1p (Ydr365cp), an essential, evolutionarily conserved nucleolar protein, is required for the biogenesis of 18S rRNA in Saccharomyces cerevisiae. Depletion of Esf1p resulted in...
Grigull, Jörg, Mnaimneh, Sanie, Pootoolal, Jeffrey, Robinson, Mark D., Hughes, Timothy R.
Using DNA microarrays, we compared global transcript stability profiles following chemical inhibition of transcription to rpb1-1 (a temperature-sensitive allele of yeast RNA polymerase II). Among the...
Jeronimo, Célia, Langelier, Marie-France, Zeghouf, Mahel, Cojocaru, Marilena, Bergeron, Dominique, Baali, Dania, ...
We have programmed human cells to express physiological levels of recombinant RNA polymerase II (RNAPII) subunits carrying tandem affinity purification (TAP) tags. Double-affinity chromatography...
Krogan, Nevan J., Baetz, Kristin, Keogh, Michael-Christopher, Datta, Nira, Sawa, Chika, Kwok, Trevor C. Y., ...
NuA4, the only essential histone acetyltransferase complex in Saccharomyces cerevisiae, acetylates the N-terminal tails of histones H4 and H2A. Affinity purification of NuA4 revealed the presence of...
Ingvarsdottir, Kristin, Krogan, Nevan J., Emre, N. C. Tolga, Wyce, Anastasia, Thompson, Natalie J., Emili, Andrew, ...
The SAGA complex is a multisubunit protein complex involved in transcriptional regulation in Saccharomyces cerevisiae. SAGA combines proteins involved in interactions with DNA-bound activators and...
Detection and discovery of RNA modifications using microarrays
Hiley, Shawna L., Jackman, Jane, Babak, Tomas, Trochesset, Miles, Morris, Quaid D., Phizicky, Eric, ...
Using a microarray that tiles all known yeast non-coding RNAs, we compared RNA from wild-type cells with RNA from mutants encoding known and putative RNA modifying enzymes. We show that at least five...
The functional landscape of mouse gene expression
Zhang, Wen, Morris, Quaid D, Chang, Richard, Shai, Ofer, Bakowski, Malina A, Mitsakakis, Nicholas, ...
Hiley, Shawna L., Babak, Tomas, Hughes, Timothy R.
We used a microarray containing probes that tile all known yeast noncoding RNAs (ncRNAs) to investigate RNA biogenesis on a global scale. The microarray verified a general loss of Box C/D snoRNAs in...
Esf2p, a U3-Associated Factor Required for Small-Subunit Processome Assembly and Compaction
Hoang, Tran, Peng, Wen-Tao, Vanrobays, Emmanuel, Krogan, Nevan, Hiley, Shawna, Beyer, Ann L., ...
Esf2p is the Saccharomyces cerevisiae homolog of mouse ABT1, a protein previously identified as a putative partner of the TATA-element binding protein. However, large-scale studies have indicated...
The Splicing Factor Prp43p, a DEAH Box ATPase, Functions in Ribosome Biogenesis
Leeds, Nina B., Small, Eliza C., Hiley, Shawna L., Hughes, Timothy R., Staley, Jonathan P.
Biogenesis of the small and large ribosomal subunits requires modification, processing, and folding of pre-rRNA to yield mature rRNA. Here, we report that efficient biogenesis of both small- and...
Probing microRNAs with microarrays: Tissue specificity and functional inference
BABAK, TOMAS, ZHANG, WEN, MORRIS, QUAID, BLENCOWE, BENJAMIN J., HUGHES, TIMOTHY R.
MicroRNAs (miRNAs) are short, stable, noncoding RNAs involved in post-transcriptional gene silencing via hybridization to mRNA. Few have been thoroughly characterized in any species. Here, we...
Probing microRNAs with microarrays: Tissue specificity and functional inference
BABAK, TOMAS, ZHANG, WEN, MORRIS, QUAID, BLENCOWE, BENJAMIN J., HUGHES, TIMOTHY R.
HENRAS, ANTHONY K., SAM, MUI, HILEY, SHAWNA L., WU, HAIHONG, HUGHES, TIMOTHY R., FEIGON, JULI, ...
Members of the RNase III family of double-stranded RNA (dsRNA) endonucleases are important enzymes of RNA metabolism in eukaryotic cells. Rnt1p is the only known member of the RNase III family of...
Krogan, Nevan J, Hughes, Timothy R
A report on the 2006 Keystone Conference on Signaling Networks, Vancouver, Canada, 30 January-4 February 2006.
Zfp206 regulates ES cell gene expression and differentiation
Zhang, Wen, Walker, Emily, Tamplin, Owen J., Rossant, Janet, Stanford, William L., Hughes, Timothy R.
Understanding transcriptional regulation in early developmental stages is fundamental to understanding mammalian development and embryonic stem (ES) cell properties. Expression surveys suggest that...
Lovegrove, Fiona E, Peña-Castillo, Lourdes, Mohammad, Naveed, Liles, W Conrad, Hughes, Timothy R, Kain, Kevin C
A Survey of Essential Gene Function in the Yeast Cell Division Cycle
Yu, Lisa, Castillo, Lourdes Peña, Mnaimneh, Sanie, Hughes, Timothy R., Brown, Grant W.
Mutations impacting specific stages of cell growth and division have provided a foundation for dissecting mechanisms that underlie cell cycle progression. We have undertaken an objective examination...
Identifying transcription factor functions and targets by phenotypic activation
Chua, Gordon, Morris, Quaid D., Sopko, Richelle, Robinson, Mark D., Ryan, Owen, Chan, Esther T., ...
Mapping transcriptional regulatory networks is difficult because many transcription factors (TFs) are activated only under specific conditions. We describe a generic strategy for identifying genes...
Why Are There Still Over 1000 Uncharacterized Yeast Genes?
Peña-Castillo, Lourdes, Hughes, Timothy R.
The yeast genetics community has embraced genomic biology, and there is a general understanding that obtaining a full encyclopedia of functions of the ∼6000 genes is a worthwhile goal. The yeast...
Lovegrove, Fiona E., Gharib, Sina A., Peña-Castillo, Lourdes, Patel, Samir N., Ruzinski, John T., Hughes, Timothy R., ...
Although acute lung injury (ALI) is a common complication of severe malaria, little is known about the underlying molecular basis of lung dysfunction. Animal models have provided powerful insights...