Response to comment on "Human-specific gain of function in a developmental enhancer" (2009)
Prabhakar, Shyam, Visel, Axel, Akiyama, Jennifer A., Shoukry, Malak, Lewis, Keith D., Holt, Amy, ...
Duret and Galtier argue that human-specific sequence divergence and gain of function in the HACNS1 enhancer result from deleterious biased gene conversion (BGC) with no contribution from positive...
Response to comment on "Human-specific gain of function in a developmental enhancer" (2009)
Prabhakar, Shyam, Visel, Axel, Akiyama, Jennifer A., Shoukry, Malak, Lewis, Keith D., Holt, Amy, ...
Duret and Galtier argue that human-specific sequence divergence and gain of function in the HACNS1 enhancer result from deleterious biased gene conversion (BGC) with no contribution from positive...
Human-specific gain of function in a developmental enhancer (2008)
Prabhakar, Shyam, Visel, Axel, Akiyama, Jennifer A., Shoukry, Malak, Lewis, Keith D., Holt, Amy, ...
Changes in gene regulation are thought to have contributed to the evolution of human development. However, in vivo evidence for uniquely human developmental regulatory function has remained elusive....
Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons (2007)
Wang, Qian-fei, Prabhakar, Shyam, Chanan, Sumita, Cheng, Jan-Fang, Rubin, Edward M, Boffelli, Dario
Abstract Background Genomic comparisons between human and distant, non-primate mammals are commonly used to identify cis -regulatory elements based on constrained sequence evolution. However, these...
Primate-specific evolution of an LDLR enhancer (2006)
Wang, Qian-fei, Prabhakar, Shyam, Wang, Qianben, Moses, Alan M, Chanan, Sumita, Brown, Myles, ...
Background Sequence changes in regulatory regions have often been invoked to explain phenotypic divergence among species, but molecular examples of this have been difficult to obtain. Results In this...
Primate-Specific Evolution of an LDLR Enhancer (2006)
Wang, Qian-fei, Prabhakar, Shyam, Wang, Qianben, Moses, Alan M., Chanan, Sumita, Brown, Myles, ...
Sequence changes in regulatory regions have often been invoked to explain phenotypic divergence among species, but molecular examples of this have been difficult to obtain. In this study, we...
Detection of Weakly Conserved Ancestral Mammalian Regulatory Sequences by Primate Comparisons (2006)
Wang, Qian-fei, Prabhakar, Shyam, Chanan, Sumita, Cheng, Jan-Fang, Rubin, Edward M., Boffelli, Dario
Genomic comparisons between human and distant, non-primate mammals are commonly used to identify cis-regulatory elements based on constrained sequence evolution. However, these methods fail to detect...
In Vivo Enhancer Analysis Chromosome 16 Conserved Noncoding Sequences (2006)
Pennacchio, Len A., Ahituv, Nadav, Moses, Alan M., Nobrega, Marcelo, Prabhakar, Shyam, Shoukry, Malak, ...
The identification of enhancers with predicted specificities in vertebrate genomes remains a significant challenge that is hampered by a lack of experimentally validated training sets. In this study,...
Accelerated Evolution of Conserved Noncoding Sequences in Humans (2006)
Prabhakar, Shyam, Noonan, James, Pääbo, Svante, Rubin, Edward M.
Close sequence comparisons are sufficient to identify human cis-regulatory elements (2006)
Prabhakar, Shyam, Poulin, Francis, Shoukry, Malak, Afzal, Veena, Rubin, Edward M., Couronne, Olivier, ...
Cross-species DNA sequence comparison is the primary method used to identify functional noncoding elements in human and other large genomes. However, little is known about the relative merits of...
Close sequence comparisons are sufficient to identify human cis-regulatory elements (2006)
Prabhakar, Shyam, Poulin, Francis, Shoukry, Malak, Afzal, Veena, Rubin, Edward M., Couronne, Olivier, ...
Cross-species DNA sequence comparison is the primary method used to identify functional noncoding elements in human and other large genomes. However, little is known about the relative merits of...
Close Sequence Comparisons are Sufficient to Identify Human cis-Regulatory Elements (2005)
Prabhakar, Shyam, Poulin, Francis, Shoukry, Malak, Afzal, Veena, Rubin, Edward M., Couronne, Olivier, ...
Cross-species DNA sequence comparison is the primary method used to identify functional noncoding elements in human and other large genomes. However, little is known about the relative merits of...
Primate-specific evolution of an LDLR enhancer (2005)
Wang, Qian-Fei, Prabhakar, Shyam, Wang, Qianben, Moses, Alan M., Chanan, Sumita, Brown, Myles, ...
Ahituv, Nadav, Prabhakar, Shyam, Poulin, Francis, Rubin, Edward M., Couronne, Olivier
Our inability to associate distant regulatory elements with the genes that they regulate has largely precluded their examination for sequence alterations contributing to human disease. One major...
Ahituv, Nadav, Prabhakar, Shyam, Poulin, Francis, Rubin, Edward M., Couronne, Olivier
Our inability to associate distant regulatory elements with the genes they regulate has largely precluded their examination for sequence alterations contributing to human disease. One major obstacle...
The sequence and analysis of duplication rich human chromosome 16 (2004)
Martin, Joel, Han, Cliff, Gordon, Laurie A., Terry, Astrid, Prabhakar, Shyam, She, Xinwei, ...
We report here the 78,884,754 base pairs of finished human chromosome 16 sequence, representing over 99.9 percent of its euchromatin. Manual annotation revealed 880 protein coding genes confirmed by...
The complete sequence of human chromosome 5 (2004)
Schmutz, Jeremy, Martin, Joel, Terry, Astrid, Couronne, Olivier, Grimwood, Jane, Lowry, State, ...
Chromosome 5 is one of the largest human chromosomes yet has one of the lowest gene densities. This is partially explained by numerous gene-poor regions that display a remarkable degree of noncoding...
New diagnostics and cures for coupled-bunch instabilities / (2000)
Submitted to the Department of Applied Physics .
Zambon, Alexander C., Zhang, Lingzhi, Minovitsky, Simon, Kanter, Joan R., Prabhakar, Shyam, Salomonis, Nathan, ...
Although a substantial number of hormones and drugs increase cellular cAMP levels, the global impact of cAMP and its major effector mechanism, protein kinase A (PKA), on gene expression is not known....
Hughes, Jim R., Cheng, Jan-Fang, Ventress, Nicki, Prabhakar, Shyam, Clark, Kevin, Anguita, Eduardo, ...
An important step toward improving the annotation of the human genome is to identify cis-acting regulatory elements from primary DNA sequence. One approach is to compare sequences from multiple,...
Zambon, Alexander C., Zhang, Lingzhi, Minovitsky, Simon, Kanter, Joan R., Prabhakar, Shyam, Salomonis, Nathan, ...
Although a substantial number of hormones and drugs increase cellular cAMP levels, the global impact of cAMP and its major effector mechanism, protein kinase A (PKA), on gene expression is not known....
Hughes, Jim R., Cheng, Jan-Fang, Ventress, Nicki, Prabhakar, Shyam, Clark, Kevin, Anguita, Eduardo, ...
An important step toward improving the annotation of the human genome is to identify cis-acting regulatory elements from primary DNA sequence. One approach is to compare sequences from multiple,...
Close sequence comparisons are sufficient to identify human cis-regulatory elements
Prabhakar, Shyam, Poulin, Francis, Shoukry, Malak, Afzal, Veena, Rubin, Edward M., Couronne, Olivier, ...
Cross-species DNA sequence comparison is the primary method used to identify functional noncoding elements in human and other large genomes. However, little is known about the relative merits of...
Primate-specific evolution of an LDLR enhancer
Wang, Qian-fei, Prabhakar, Shyam, Wang, Qianben, Moses, Alan M, Chanan, Sumita, Brown, Myles, ...
Analysis of primate-specific evolution of the LDL receptor enhancer demonstrates a molecular mechanism by which ancestral mammalian regulatory elements can evolve to perform new functions.
Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons
Wang, Qian-fei, Prabhakar, Shyam, Chanan, Sumita, Cheng, Jan-Fang, Rubin, Edward M, Boffelli, Dario
Intra-primate genome comparisons identify functional modules that are undetected by comparisons with non-mammalian genomes.
Runx1-mediated hematopoietic stem-cell emergence is controlled by a Gata/Ets/SCL-regulated enhancer
Nottingham, Wade T., Jarratt, Andrew, Burgess, Matthew, Speck, Caroline L., Cheng, Jan-Fang, Prabhakar, Shyam, ...
The transcription factor Runx1/AML1 is an important regulator of hematopoiesis and is critically required for the generation of the first definitive hematopoietic stem cells (HSCs) in the major...