Korbel, Jan O, Abyzov, Alexej, Mu, Xinmeng, Carriero, Nicholas, Cayting, Philip, Zhang, Zhengdong, ...
Abstract Personal-genomics endeavors, such as the 1000 Genomes project, are generating maps of genomic structural variants by analyzing ends of massively sequenced genome fragments. To process these...
Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing (2009)
Lefrançois, Philippe, Euskirchen, Ghia M, Auerbach, Raymond K, Rozowsky, Joel, Gibson, Theodore, Yellman, Christopher M, ...
Abstract Background Short-read high-throughput DNA sequencing technologies provide new tools to answer biological questions. However, high cost and low throughput limit their widespread use,...
Dynamic and complex transcription factor binding during an inducible response in yeast (2009)
Ni, Li, Bruce, Can, Hart, Christopher, Leigh-Bell, Justine, Gelperin, Daniel, Umansky, Lara, ...
Complex biological processes are often regulated, at least in part, by the binding of transcription factors to their targets. Recently, considerable effort has been made to analyze the binding of...
Theodorou, Elias, Dalembert, George, Heffelfinger, Christopher, White, Eric, Weissman, Sherman, Corcoran, Lynn, ...
Neuronal differentiation is a complex process that involves a plethora of regulatory steps. To identify transcription factors that influence neuronal differentiation we developed a high throughput...
MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays (2009)
Popescu, Sorina C., Popescu, George V., Bachan, Shawn, Zhang, Zimei, Gerstein, Mark, Snyder, Michael, ...
Signaling through mitogen-activated protein kinases (MPKs) cascades is a complex and fundamental process in eukaryotes, requiring MPK-activating kinases (MKKs) and MKK-activating kinases (MKKKs)....
MSB: A mean-shift-based approach for the analysis of structural variation in the genome (2009)
Wang, Lu-yong, Abyzov, Alexej, Korbel, Jan O., Snyder, Michael, Gerstein, Mark
Genome structural variation includes segmental duplications, deletions, and other rearrangements, and array-based comparative genomic hybridization (array-CGH) is a popular technology for determining...
Seringhaus, Michael, Rozowsky, Joel, Royce, Thomas, Nagalakshmi, Ugrappa, Jee, Justin, Snyder, Michael, ...
Abstract Background Mismatched oligonucleotides are widely used on microarrays to differentiate specific from nonspecific hybridization. While many experiments rely on such oligos, the hybridization...
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Jiang Du, Joel S. Rozowsky, Jan O. Korbel, Zhengdong D. Zhang, Thomas E. Royce, ...
doi:10.1093/bioinformatics/btl515 A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating...
Jiang Du, Joel S. Rozowsky, Jan O. Korbel, Zhengdong D. Zhang, Thomas E. Royce, Martin H. Schultz, ...
Motivation: Large-scale tiling array experiments are becoming increasingly common in genomics. In particular, the ENCODE project requires the consistent segmentation of many different tiling array...
Photonic Dipole Contours of Ferrofluid Hele-Shaw Cell (2008)
Snyder, Michael, Frederick, Jonathan
This investigation describes and demonstrates a novel technique for the visualization of magnetic fields. Two ferrofluid Hele-Shaw cells have been constructed to facilitate the imaging of magnetic...
Studies in American Indian Literatures - Volume 20, Number 1, Spring 2008
RNA polymerase II stalling: loading at the start prepares genes for a sprint (2008)
Abstract Stalling of RNA polymerase II near the promoter has recently been found to be much more common than previously thought. Genome-wide surveys of the phenomenon suggest that it is likely to be...
DRAFT 2 Functions of the Arabidopsis microRNA and siRNA Systems (2008)
Michael Snyder, Heng Zhu, Christine Horak, Anuj Kumar, Ghia Euskirchen, Rebecca Goetsch, ...
The genomes of a wide variety of organisms have now been sequenced; a major challenge ahead is to identify genes and their encoded projects and to understand their function and regulation. For the...
The FASEB Journal express article 10.1096/fj.04-2098fje. Published online June 6, 2005. (2008)
Jaebum Park, Moon Hi Han, Michael Snyder, Eui Yul Choi
Calixarene derivative as a tool for highly sensitive detection and oriented immobilization of proteins in a microarray format through noncovalent molecular interaction
Wu, Jia, Du, Jiang, Rozowsky, Joel, Zhang, Zhengdong, Urban, Alexander E, Euskirchen, Ghia, ...
Abstract Background Recent studies of the mammalian transcriptome have revealed a large number of additional transcribed regions and extraordinary complexity in transcript diversity. However, there...
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. (2008)
Johnson, David S., Li, Wei, Gordon, D. Benjamin, Bhattacharjee, Arindam, Curry, Bo, Ghosh, Jayati, ...
The most widely used method for detecting genome-wide protein-DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first...
Gong, Wei, He, Kun, Covington, Mike, Dinesh-Kumar, S. P., Snyder, Michael, Harmer, Stacey L., ...
We used our collection of Arabidopsis transcription factor (TF) ORFeome clones to construct protein microarrays containing as many as 802 TF proteins. These protein microarrays were used for both...
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets (2008)
Johnson, David S., Li, Wei, Gordon, D. Benjamin, Bhattacharjee, Arindam, Curry, Bo, Ghosh, Jayati, ...
The most widely used method for detecting genome-wide protein–DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first...
Lian, Zheng, Karpikov, Alexander, Lian, Jin, Mahajan, Milind C., Hartman, Stephen, Gerstein, Mark, ...
Genomic analyses have been applied extensively to analyze the process of transcription initiation in mammalian cells, but less to transcript 3′ end formation and transcription termination. We used...
Kim, Philip M., Lam, Hugo Y.K., Urban, Alexander E., Korbel, Jan O., Affourtit, Jason, Grubert, Fabian, ...
Segmental duplications (SDs) are operationally defined as >1 kb stretches of duplicated DNA with high sequence identity. They arise from copy number variants (CNVs) fixed in the population. To...
Robertson, A. Gordon, Bilenky, Mikhail, Tam, Angela, Zhao, Yongjun, Zeng, Thomas, Thiessen, Nina, ...
We characterized the relationship of H3K4me1 and H3K4me3 at distal and proximal regulatory elements by comparing ChIP-seq profiles for these histone modifications and for two functionally different...
Chang, Wakam, Zaarour, Rania F., Reck-Peterson, Samara, Rinn, John, Singer, Robert H., Snyder, Michael, ...
Myo2p is an essential class V myosin in budding yeast with several identified functions in organelle trafficking and spindle orientation. The present study demonstrates that Myo2p is a component of a...
Human Factors Design Guide (2007)
Faa Technical Center, Dan Wagner Act, Joseph A. Birt, Michael Snyder, James P. Duncanson
The Human Factors Design Guide (HFDG) provides reference information to assist in the selection, analysis, design, development, and evaluation of new and modified Federal Aviation Administration...
Paul Bertone, Bhaskar Dasgupta, Mark Gerstein, Ming-yang Kao, Michael Snyder
A preliminary version of this paper appeared in the 2 nd Workshop on Algorithms in Bioinformatics,
Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search (2007)
Piotr Berman, Paul Bertone, Bhaskar Dasgupta, Mark Gerstein, Ming-yang Kao, Michael Snyder
In this paper we consider several variations of the following basic tiling problem: given a sequence of real numbers with two size bound parameters, we want to find a set of tiles such that they...
What is a gene, post-ENCODE? History and updated definition (2007)
Gerstein, Mark B., Bruce, Can, Rozowsky, Joel S., Zheng, Deyou, Du, Jiang, Korbel, Jan O., ...
While sequencing of the human genome surprised us with how many protein-coding genes there are, it did not fundamentally change our perspective on what a gene is. In contrast, the complex patterns of...
Trinklein, Nathan D., Karaöz, Ulas, Wu, Jiaqian, Halees, Anason, Force Aldred, Shelley, Collins, Patrick J., ...
The regulation of transcriptional initiation in the human genome is a critical component of global gene regulation, but a complete catalog of human promoters currently does not exist. In order to...
Rozowsky, Joel S., Newburger, Daniel, Sayward, Fred, Wu, Jiaqian, Jordan, Greg, Korbel, Jan O., ...
For the ∼1% of the human genome in the ENCODE regions, only about half of the transcriptionally active regions (TARs) identified with tiling microarrays correspond to annotated exons. Here we...
Zhang, Zhengdong D., Paccanaro, Alberto, Fu, Yutao, Weissman, Sherman, Weng, Zhiping, Chang, Joseph, ...
The comprehensive inventory of functional elements in 44 human genomic regions carried out by the ENCODE Project Consortium enables for the first time a global analysis of the genomic distribution of...
Zheng, Deyou, Frankish, Adam, Baertsch, Robert, Kapranov, Philipp, Reymond, Alexandre, Choo, Siew Woh, ...
Arising from either retrotransposition or genomic duplication of functional genes, pseudogenes are “genomic fossils” valuable for exploring the dynamics and evolution of genes and genomes....
Structured RNAs in the ENCODE selected regions of the human genome (2007)
Washietl, Stefan, Pedersen, Jakob S., Korbel, Jan O., Stocsits, Claudia, Gruber, Andreas R., Hackermüller, Jörg, ...
Functional RNA structures play an important role both in the context of noncoding RNA transcripts as well as regulatory elements in mRNAs. Here we present a computational study to detect functional...
Emanuelsson, Olof, Nagalakshmi, Ugrappa, Zheng, Deyou, Rozowsky, Joel S., Urban, Alexander E., Du, Jiang, ...
Genomic tiling microarrays have become a popular tool for interrogating the transcriptional activity of large regions of the genome in an unbiased fashion. There are several key parameters associated...
Euskirchen, Ghia M., Rozowsky, Joel S., Wei, Chia-Lin, Lee, Wah Heng, Zhang, Zhengdong D., Hartman, Stephen, ...
Recent progress in mapping transcription factor (TF) binding regions can largely be credited to chromatin immunoprecipitation (ChIP) technologies. We compared strategies for mapping TF binding...
Bhinge, Akshay A., Kim, Jonghwan, Euskirchen, Ghia M., Snyder, Michael, Iyer, Vishwanath R.
Identifying the genome-wide binding sites of transcription factors is important in deciphering transcriptional regulatory networks. ChIP-chip (Chromatin immunoprecipitation combined with microarrays)...
Tilescope: online analysis pipeline for high-density tiling microarray data (2007)
Zhang, Zhengdong D, Rozowsky, Joel, Lam, Hugo YK, Du, Jiang, Snyder, Michael, Gerstein, Mark
Abstract We developed Tilescope, a fully integrated data processing pipeline for analyzing high-density tiling-array data http://tilescope.gersteinlab.org . In a completely automated fashion,...
Getting connected: analysis and principles of biological networks (2007)
Zhu, Xiaowei, Gerstein, Mark, Snyder, Michael
The execution of complex biological processes requires the precise interaction and regulation of thousands of molecules. Systematic approaches to study large numbers of proteins, metabolites, and...
Tilescope: online analysis pipeline for high-density tiling microarray data (2007)
Zhengdong D. Zhang, Joel Rozowsky, Jiang Du, Michael Snyder, Mark Gerstein
Running title: microarray data analysis pipeline Key words: high-density tiling microarray, high-density oligonucleotide microarray, microarray data analysis For test data sets, sample result web...
Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome (2007)
Korbel, Jan O., Urban, Alexander Eckehart, Affourtit, Jason P., Godwin, Brian, Grubert, Fabian, Simons, Jan Fredrik, ...
Structured RNAs in the ENCODE Selected Regions of the Human Genome (2007)
Washietl, Stefan, Pedersen, Jakob S., Korbel, Jan O., Fried, Claudia, Gruber, Andreas R., Hackermüller, Jörg, ...
Smith, Michael G., Gianoulis, Tara A., Pukatzki, Stefan, Mekalanos, John J., Ornston, L. Nicholas, Gerstein, Mark, ...
Acinetobacter baumannii has emerged as an important and problematic human pathogen as it is the causative agent of several types of infections including pneumonia, meningitis, septicemia, and urinary...
Yu, Haiyuan, Nguyen, Katherine, Royce, Tom, Qian, Jiang, Nelson, Kenneth, Snyder, Michael, ...
Microarray technology is currently one of the most widely-used technologies in biology. Many studies focus on inferring the function of an unknown gene from its co-expressed genes. Here, we are able...
ProCAT: a data analysis approach for protein microarrays (2006)
Zhu, Xiaowei, Gerstein, Mark, Snyder, Michael
Abstract Protein microarrays provide a versatile method for the analysis of many protein biochemical activities. Existing DNA microarray analytical methods do not translate to protein microarrays due...
Wang, Lu-yong, Snyder, Michael, Gerstein, Mark
Abstract Comprehensive mapping of transcription factor binding sites is essential in postgenomic biology. For this, we propose a mining approach combining noisy data from ChIP (chromatin...
Design optimization methods for genomic DNA tiling arrays (2006)
Paul Bertone, Valery Trifonov, Joel S. Rozowsky, Falk Schubert, Olof Emanuelsson, John Karro, ...
A recent development in microarray construction entails the unbiased coverage, or tiling, of non-repetitive genomic DNA for the experimental identification of unannotated transcribed sequences and...
Predicting essential genes in fungal genomes (2006)
Seringhaus, Michael, Paccanaro, Alberto, Borneman, Anthony, Snyder, Michael, Gerstein, Mark
Essential genes are required for an organism's viability, and the ability to identify these genes in pathogens is crucial to directed drug development. Predicting essential genes through...
Yu, Haiyuan, Nguyen, Katherine, Royce, Tom, Qian, Jiang, Nelson, Kenneth, Snyder, Michael, ...
Microarray technology is currently one of the most widely-used technologies in biology. Many studies focus on inferring the function of an unknown gene from its co-expressed genes. Here, we are able...
Target hub proteins serve as master regulators of development in yeast (2006)
Borneman, Anthony R., Leigh-Bell, Justine A., Yu, Haiyuan, Bertone, Paul, Gerstein, Mark, Snyder, Michael
To understand the organization of the transcriptional networks that govern cell differentiation, we have investigated the transcriptional circuitry controlling pseudohyphal development in...
Emanuelsson, Olof, Nagalakshmi, Ugrappa, Zheng, Deyou, Rozowsky, Joel S., Urban, Alexander E., Du, Jiang, ...
Genomic tiling microarrays have become a popular tool for interrogating the transcriptional activity of large regions of the genome in an unbiased fashion. There are several key parameters associated...
Predicting essential genes in fungal genomes (2006)
Seringhaus, Michael, Paccanaro, Alberto, Borneman, Anthony, Snyder, Michael, Gerstein, Mark
Essential genes are required for an organism’s viability, and the ability to identify these genes in pathogens is crucial to directed drug development. Predicting essential genes through...
Target hub proteins serve as master regulators of development in yeast (2006)
Borneman, Anthony R., Leigh-Bell, Justine A., Yu, Haiyuan, Bertone, Paul, Gerstein, Mark, Snyder, Michael
To understand the organization of the transcriptional networks that govern cell differentiation, we have investigated the transcriptional circuitry controlling pseudohyphal development in...
Yu, Haiyuan, Nguyen, Katherine, Royce, Tom, Qian, Jiang, Nelson, Kenneth, Snyder, Michael, ...
Microarray technology is currently one of the most widely-used technologies in biology. Many studies focus on inferring the function of an unknown gene from its co-expressed genes. Here, we are able...
Mah, Angie S., Elia, Andrew E. H., Devgan, Geeta, Ptacek, Jason, Schutkowski, Mike, Snyder, Michael, ...
Background: The mitotic exit network (MEN) is a group of proteins that form a signaling cascade that is essential for cells to exit mitosis in Saccharomyces cerevisiae. The MEN has also been...
Mah, Angie S, Elia, Andrew EH, Devgan, Geeta, Ptacek, Jason, Schutkowski, Mike, Snyder, Michael, ...
Abstract Background The mitotic exit network (MEN) is a group of proteins that form a signaling cascade that is essential for cells to exit mitosis in Saccharomyces cerevisiae . The MEN has also been...
Hartman, Stephen E., Bertone, Paul, Nath, Anjali K., Royce, Thomas E., Gerstein, Mark, Weissman, Sherman, ...
The STAT (signal transducer and activator of transcription) proteins play a crucial role in the regulation of gene expression, but their targets and the manner in which they select them remain...
Hartman, Stephen E., Bertone, Paul, Nath, Anjali K., Royce, Thomas E., Gerstein, Mark, Weissman, Sherman, ...
The STAT (signal transducer and activator of transcription) proteins play a crucial role in the regulation of gene expression, but their targets and the manner in which they select them remain...
Biochemical and genetic analysis of the yeast proteome with a movable ORF collection (2005)
Gelperin, Daniel M., White, Michael A., Wilkinson, Martha L., Kon, Yoshiko, Kung, Li A., Wise, Kevin J., ...
Functional analysis of the proteome is an essential part of genomic research. To facilitate different proteomic approaches, a MORF (moveable ORF) library of 5854 yeast expression plasmids was...
Design optimization methods for genomic DNA tiling arrays (2005)
Bertone, Paul, Trifonov, Valery, Rozowsky, Joel S., Schubert, Falk, Emanuelsson, Olof, Karro, John, ...
A recent development in microarray research entails the unbiased coverage, or tiling, of genomic DNA for the large-scale identification of transcribed sequences and regulatory elements. A central...
Hartman, Stephen E., Bertone, Paul, Nath, Anjali K., Royce, Thomas E., Gerstein, Mark, Weissman, Sherman, ...
The STAT (signal transducer and activator of transcription) proteins play a crucial role in the regulation of gene expression, but their targets and the manner in which they select them remain...
Large-Scale Mutagenesis of the Yeast Genome Using a Tn7-Derived Multipurpose Transposon (2004)
Kumar, Anuj, Seringhaus, Michael, Biery, Matthew C., Sarnovsky, Robert J., Umansky, Lara, Piccirillo, Stacy, ...
We present here an unbiased and extremely versatile insertional library of yeast genomic DNA generated by in vitro mutagenesis with a multipurpose element derived from the bacterial transposon Tn7....
Protein analysis on a proteomic scale (2003)
Phizicky, Eric, Bastiaens, Philippe I. H., Zhu, Heng, Snyder, Michael, Fields, Stanley
Memories of Travel Page 1 of 46 Memories of Travel: Dead Reckoning Within the Cognitive Map (2003)
Edward H. Cornell, C. Donald Heth, Michael Snyder
When Herman Melville reveals the dark obsessions of Captain Ahab’s soul, he does so by having Ahab destroy the ship’s quadrant and revert to a more elemental form of navigation: “…Curse thee,...
ExpressYourself: a modular platform for processing and visualizing microarray data (2003)
Luscombe, Nicholas M., Royce, Thomas E., Bertone, Paul, Echols, Nathaniel, Horak, Christine E., Chang, Joseph T., ...
DNA microarrays are widely used in biological research; by analyzing differential hybridization on a single microarray slide, one can detect changes in mRNA expression levels, increases in DNA copy...
The transcriptional activity of human Chromosome 22 (2003)
Rinn, John L., Euskirchen, Ghia, Bertone, Paul, Martone, Rebecca, Luscombe, Nicholas M., Hartman, Stephen, ...
Negative regulation of calcineurin signaling by Hrr25p, a yeast homolog of casein kinase I (2003)
Kafadar, Kimberly A., Zhu, Heng, Snyder, Michael, Cyert, Martha S.
Calcineurin is a Ca2+/calmodulin-regulated protein phosphatase required for Saccharomyces cerevisiae to respond to a variety of environmental stresses. Calcineurin promotes cell survival during...
Concept Definition Study for In-Space (2002)
Structural Characterization Of, Thomas W. Jones, Regina Spellman, Willis Scott, Eric M. Mockensturm, ...
A Concept Definition Study (CDS) was conducted to develop a proposed "Lightweight High-Voltage Stretched-Lens Concentrator Solar Array Experiment" under NASA's New Millennium Program...
Fast optimal genome tiling with applications to microarray design and homology search (2002)
Piotr Berman, Paul Bertone, Bhaskar Dasgupta, Mark Gerstein, Ming-yang Kao, Michael Snyder
In this paper we consider several variations of the following basic tiling problem: given a sequence of real numbers with two size bound parameters, we want to find a set of tiles of maximum total...
Fast optimal genome tiling with applications to microarray design and homology search (2002)
Piotr Berman, Paul Bertone, Bhaskar Dasgupta, Mark Gerstein, Ming-yang Kao, Michael Snyder, ...
Abstract. In this paper we consider several variations of the following basic tiling problem: given a sequence of real numbers with two size bound parameters, we want to nd a set of tiles such that...
The TRIPLES database: a community resource for yeast molecular biology (2002)
Kumar, Anuj, Cheung, Kei-Hoi, Tosches, Nick, Masiar, Peter, Liu, Yang, Miller, Perry, ...
TRIPLES is a web-accessible database of TRansposon-Insertion Phenotypes, Localization and Expression in Saccharomyces cerevisiae—a relational database housing nearly half a million data points...
Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae (2002)
Horak, Christine E., Luscombe, Nicholas M., Qian, Jiang, Bertone, Paul, Piccirrillo, Stacy, Gerstein, Mark, ...
A question of size: the eukaryotic proteome and the problems in defining it (2002)
Harrison, Paul M., Kumar, Anuj, Lang, Ning, Snyder, Michael, Gerstein, Mark
We discuss the problems in defining the extent of the proteomes for completely sequenced eukaryotic organisms (i.e. the total number of protein-coding sequences), focusing on yeast, worm, fly and...
TRIPLES: a database of gene function in Saccharomyces cerevisiae (2000)
Kumar, Anuj, Cheung, Kei-Hoi, Ross-Macdonald, Petra, Coelho, Paulo S. R., Miller, Perry, Snyder, Michael
Using a novel multipurpose mini-transposon, we have generated a collection of defined mutant alleles for the analysis of disruption phenotypes, protein localization, and gene expression in...
Printout.
Symbol Development Guidelines for Airway Facilities. (1997)
Wagner, Dan, Snyder, Michael, Dutra, Lisa, Dolan, Nancy
This document presents a general methodology for developing Airway Facilities (AF) symbols and provides guidelines for the coding of visual symbols and auditory signals. Coding refers to the...
Development of fetal putative blue retinal ganglion cells of RHESUS MACAQUE / (1997)
Includes abstract.
Sbe2p and Sbe22p, Two Homologous Golgi Proteins Involved in Yeast Cell Wall Formation
Santos, Beatriz, Snyder, Michael
The cell wall of fungal cells is important for cell integrity and cell morphogenesis and protects against harmful environmental conditions. The yeast cell wall is a complex structure consisting...
Barrett, Jennifer G., Manning, Brendan D., Snyder, Michael
Proteins that physically associate with members of the kinesin superfamily are critical for the functional diversity observed for these microtubule motor proteins. However, quaternary structures of...
Ross-Macdonald, Petra, Sheehan, Amy, Roeder, G. Shirleen, Snyder, Michael
Analysis of the function of a particular gene product typically involves determining the expression profile of the gene, the subcellular location of the protein, and the phenotype of a null strain...
Manning, Brendan D., Padmanabha, Ramesh, Snyder, Michael
Rom2p is a GDP/GTP exchange factor for Rho1p and Rho2p GTPases; Rho proteins have been implicated in control of actin cytoskeletal rearrangements. ROM2 and RHO2 were identified in a screen for...
A Genomic Study of the Bipolar Bud Site Selection Pattern in Saccharomyces cerevisiae
A genome-wide screen of 4168 homozygous diploid yeast deletion strains has been performed to identify nonessential genes that participate in the bipolar budding pattern. By examining bud scar...
Polarized Growth Controls Cell Shape and Bipolar Bud Site Selection in Saccharomyces cerevisiae
Sheu, Yi-Jun, Barral, Yves, Snyder, Michael
We examined the relationship between polarized growth and division site selection, two fundamental processes important for proper development of eukaryotes. Diploid Saccharomyces cerevisiae cells...
Bidlingmaier, Scott, Weiss, Eric L., Seidel, Chris, Drubin, David G., Snyder, Michael
During the early stages of budding, cell wall remodeling and polarized secretion are concentrated at the bud tip (apical growth). The CBK1 gene, encoding a putative serine/threonine protein kinase,...
The TRIPLES database: a community resource for yeast molecular biology
Kumar, Anuj, Cheung, Kei-Hoi, Tosches, Nick, Masiar, Peter, Liu, Yang, Miller, Perry, ...
TRIPLES is a web-accessible database of TRansposon-Insertion Phenotypes, Localization and Expression in Saccharomyces cerevisiae—a relational database housing nearly half a million data points...
A question of size: the eukaryotic proteome and the problems in defining it
Harrison, Paul M., Kumar, Anuj, Lang, Ning, Snyder, Michael, Gerstein, Mark
We discuss the problems in defining the extent of the proteomes for completely sequenced eukaryotic organisms (i.e. the total number of protein-coding sequences), focusing on yeast, worm, fly and...
TRIPLES: a database of gene function in Saccharomyces cerevisiae
Kumar, Anuj, Cheung, Kei-Hoi, Ross-Macdonald, Petra, Coelho, Paulo S. R., Miller, Perry, Snyder, Michael
Using a novel multipurpose mini-transposon, we have generated a collection of defined mutant alleles for the analysis of disruption phenotypes, protein localization, and gene expression in...
Sheu, Yi-Jun, Santos, Beatriz, Fortin, Nathalie, Costigan, Christine, Snyder, Michael
The yeast protein Spa2p localizes to growth sites and is important for polarized morphogenesis during budding, mating, and pseudohyphal growth. To better understand the role of Spa2p in polarized...
GATA-1 binding sites mapped in the β-globin locus by using mammalian chIp-chip analysis
Horak, Christine E., Mahajan, Milind C., Luscombe, Nicholas M., Gerstein, Mark, Weissman, Sherman M., Snyder, Michael
The expression of the β-like globin genes is intricately regulated by a series of both general and tissue-restricted transcription factors. The hemapoietic lineage-specific transcription factor...
Casamayor, Antonio, Snyder, Michael
The septins are a family of cytoskeletal proteins present in animal and fungal cells. They were first identified for their essential role in cytokinesis, but more recently, they have been found to...
ExpressYourself: a modular platform for processing and visualizing microarray data
Luscombe, Nicholas M., Royce, Thomas E., Bertone, Paul, Echols, Nathaniel, Horak, Christine E., Chang, Joseph T., ...
DNA microarrays are widely used in biological research; by analyzing differential hybridization on a single microarray slide, one can detect changes in mRNA expression levels, increases in DNA copy...
Santos, Beatriz, Snyder, Michael
In budding yeast, chs5 mutants are defective in chitin synthesis and cell fusion during mating. Chs5p is a late-Golgi protein required for the polarized transport of the chitin synthase Chs3p to the...
A novel mitochondrial protein, Tar1p, is encoded on the antisense strand of the nuclear 25S rDNA
Coelho, Paulo S.R., Bryan, Anthony C., Kumar, Anuj, Shadel, Gerald S., Snyder, Michael
In eukaryotes, it is widely assumed that genes coding for proteins and structural RNAs do not overlap. Using a transposon-tagging strategy to globally analyze the Saccharomyces cerevisiae genome for...
Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae
Horak, Christine E., Luscombe, Nicholas M., Qian, Jiang, Bertone, Paul, Piccirrillo, Stacy, Gerstein, Mark, ...
In the yeast Saccharomyces cerevisiae, SBF (Swi4–Swi6 cell cycle box binding factor) and MBF (MluI binding factor) are the major transcription factors regulating the START of the cell cycle, a time...
The transcriptional activity of human Chromosome 22
Rinn, John L., Euskirchen, Ghia, Bertone, Paul, Martone, Rebecca, Luscombe, Nicholas M., Hartman, Stephen, ...
A DNA microarray representing nearly all of the unique sequences of human Chromosome 22 was constructed and used to measure global-transcriptional activity in placental poly(A)+ RNA. We found that...
Distribution of NF-κB-binding sites across human chromosome 22
Martone, Rebecca, Euskirchen, Ghia, Bertone, Paul, Hartman, Stephen, Royce, Thomas E., Luscombe, Nicholas M., ...
We have mapped the chromosomal binding site distribution of a transcription factor in human cells. The NF-κB family of transcription factors plays an essential role in regulating the induction of...
Negative regulation of calcineurin signaling by Hrr25p, a yeast homolog of casein kinase I
Kafadar, Kimberly A., Zhu, Heng, Snyder, Michael, Cyert, Martha S.
Calcineurin is a Ca2+/calmodulin-regulated protein phosphatase required for Saccharomyces cerevisiae to respond to a variety of environmental stresses. Calcineurin promotes cell survival during...
Barral, Yves, Parra, Macarena, Bidlingmaier, Scott, Snyder, Michael
The mechanisms that couple cell cycle progression with the organization of the peripheral cytoskeleton are poorly understood. In Saccharomyces cerevisiae, the Swe1 protein has been shown previously...
Microbial Synergy via an Ethanol-Triggered Pathway
Smith, Michael G., Des Etages, Shelley G., Snyder, Michael
We have discovered a microbial interaction between yeast, bacteria, and nematodes. Upon coculturing, Saccharomyces cerevisiae stimulated the growth of several species of Acinetobacter, including, A....
CREB Binds to Multiple Loci on Human Chromosome 22
Euskirchen, Ghia, Royce, Thomas E., Bertone, Paul, Martone, Rebecca, Rinn, John L., Nelson, F. Kenneth, ...
The cyclic AMP-responsive element-binding protein (CREB) is an important transcription factor that can be activated by hormonal stimulation and regulates neuronal function and development. An...
Large-Scale Mutagenesis of the Yeast Genome Using a Tn7-Derived Multipurpose Transposon
Kumar, Anuj, Seringhaus, Michael, Biery, Matthew C., Sarnovsky, Robert J., Umansky, Lara, Piccirillo, Stacy, ...
We present here an unbiased and extremely versatile insertional library of yeast genomic DNA generated by in vitro mutagenesis with a multipurpose element derived from the bacterial transposon Tn7....
Huang, Jing, Zhu, Heng, Haggarty, Stephen J., Spring, David R., Hwang, Heejun, Jin, Fulai, ...
The TOR (target of rapamycin) proteins play important roles in nutrient signaling in eukaryotic cells. Rapamycin treatment induces a state reminiscent of the nutrient starvation response, often...
White, Eric J., Emanuelsson, Olof, Scalzo, David, Royce, Thomas, Kosak, Steven, Oakeley, Edward J., ...
Duplication of the genome during the S phase of the cell cycle does not occur simultaneously; rather, different sequences are replicated at different times. The replication timing of specific...
Mah, Angie S, Elia, Andrew EH, Devgan, Geeta, Ptacek, Jason, Schutkowski, Mike, Snyder, Michael, ...
Subcellular localization of the yeast proteome
Kumar, Anuj, Agarwal, Seema, Heyman, John A., Matson, Sandra, Heidtman, Matthew, Piccirillo, Stacy, ...
Protein localization data are a valuable information resource helpful in elucidating eukaryotic protein function. Here, we report the first proteome-scale analysis of protein localization within any...
Seringhaus, Michael, Kumar, Anuj, Hartigan, John, Snyder, Michael, Gerstein, Mark
Transposons are widely employed as tools for gene disruption. Ideally, they should display unbiased insertion behavior, and incorporate readily into any genomic DNA to which they are exposed....
Biochemical and genetic analysis of the yeast proteome with a movable ORF collection
Gelperin, Daniel M., White, Michael A., Wilkinson, Martha L., Kon, Yoshiko, Kung, Li A., Wise, Kevin J., ...
Functional analysis of the proteome is an essential part of genomic research. To facilitate different proteomic approaches, a MORF (moveable ORF) library of 5854 yeast expression plasmids was...
Global changes in STAT target selection and transcription regulation upon interferon treatments
Hartman, Stephen E., Bertone, Paul, Nath, Anjali K., Royce, Thomas E., Gerstein, Mark, Weissman, Sherman, ...
The STAT (signal transducer and activator of transcription) proteins play a crucial role in the regulation of gene expression, but their targets and the manner in which they select them remain...
Design optimization methods for genomic DNA tiling arrays
Bertone, Paul, Trifonov, Valery, Rozowsky, Joel S., Schubert, Falk, Emanuelsson, Olof, Karro, John, ...
A recent development in microarray research entails the unbiased coverage, or tiling, of genomic DNA for the large-scale identification of transcribed sequences and regulatory elements. A central...
Target hub proteins serve as master regulators of development in yeast
Borneman, Anthony R., Leigh-Bell, Justine A., Yu, Haiyuan, Bertone, Paul, Gerstein, Mark, Snyder, Michael
To understand the organization of the transcriptional networks that govern cell differentiation, we have investigated the transcriptional circuitry controlling pseudohyphal development in...
Severe acute respiratory syndrome diagnostics using a coronavirus protein microarray
Zhu, Heng, Hu, Shaohui, Jona, Ghil, Zhu, Xiaowei, Kreiswirth, Nate, Willey, Barbara M., ...
To monitor severe acute respiratory syndrome (SARS) infection, a coronavirus protein microarray that harbors proteins from SARS coronavirus (SARS-CoV) and five additional coronaviruses was...
Urban, Alexander Eckehart, Korbel, Jan O., Selzer, Rebecca, Richmond, Todd, Hacker, April, Popescu, George V., ...
Deletions and amplifications of the human genomic sequence (copy number polymorphisms) are the cause of numerous diseases and a potential cause of phenotypic variation in the normal population....
Defined culture conditions of human embryonic stem cells
Lu, Jean, Hou, Runhua, Booth, Carmen Jane, Yang, Shih-Hung, Snyder, Michael
Human embryonic stem cells (hESCs) are pluripotent cells that have the potential to differentiate into any tissue in the human body; therefore, they are a valuable resource for regenerative medicine,...
Sbe2p and Sbe22p, Two Homologous Golgi Proteins Involved in Yeast Cell Wall Formation
Santos, Beatriz, Snyder, Michael
The cell wall of fungal cells is important for cell integrity and cell morphogenesis and protects against harmful environmental conditions. The yeast cell wall is a complex structure consisting...
Barrett, Jennifer G., Manning, Brendan D., Snyder, Michael
Proteins that physically associate with members of the kinesin superfamily are critical for the functional diversity observed for these microtubule motor proteins. However, quaternary structures of...
Ross-Macdonald, Petra, Sheehan, Amy, Roeder, G. Shirleen, Snyder, Michael
Analysis of the function of a particular gene product typically involves determining the expression profile of the gene, the subcellular location of the protein, and the phenotype of a null strain...
Manning, Brendan D., Padmanabha, Ramesh, Snyder, Michael
Rom2p is a GDP/GTP exchange factor for Rho1p and Rho2p GTPases; Rho proteins have been implicated in control of actin cytoskeletal rearrangements. ROM2 and RHO2 were identified in a screen for...
A Genomic Study of the Bipolar Bud Site Selection Pattern in Saccharomyces cerevisiae
A genome-wide screen of 4168 homozygous diploid yeast deletion strains has been performed to identify nonessential genes that participate in the bipolar budding pattern. By examining bud scar...
Polarized Growth Controls Cell Shape and Bipolar Bud Site Selection in Saccharomyces cerevisiae
Sheu, Yi-Jun, Barral, Yves, Snyder, Michael
We examined the relationship between polarized growth and division site selection, two fundamental processes important for proper development of eukaryotes. Diploid Saccharomyces cerevisiae cells...
Bidlingmaier, Scott, Weiss, Eric L., Seidel, Chris, Drubin, David G., Snyder, Michael
During the early stages of budding, cell wall remodeling and polarized secretion are concentrated at the bud tip (apical growth). The CBK1 gene, encoding a putative serine/threonine protein kinase,...
The TRIPLES database: a community resource for yeast molecular biology
Kumar, Anuj, Cheung, Kei-Hoi, Tosches, Nick, Masiar, Peter, Liu, Yang, Miller, Perry, ...
TRIPLES is a web-accessible database of TRansposon-Insertion Phenotypes, Localization and Expression in Saccharomyces cerevisiae—a relational database housing nearly half a million data points...
A question of size: the eukaryotic proteome and the problems in defining it
Harrison, Paul M., Kumar, Anuj, Lang, Ning, Snyder, Michael, Gerstein, Mark
We discuss the problems in defining the extent of the proteomes for completely sequenced eukaryotic organisms (i.e. the total number of protein-coding sequences), focusing on yeast, worm, fly and...
TRIPLES: a database of gene function in Saccharomyces cerevisiae
Kumar, Anuj, Cheung, Kei-Hoi, Ross-Macdonald, Petra, Coelho, Paulo S. R., Miller, Perry, Snyder, Michael
Using a novel multipurpose mini-transposon, we have generated a collection of defined mutant alleles for the analysis of disruption phenotypes, protein localization, and gene expression in...
Sheu, Yi-Jun, Santos, Beatriz, Fortin, Nathalie, Costigan, Christine, Snyder, Michael
The yeast protein Spa2p localizes to growth sites and is important for polarized morphogenesis during budding, mating, and pseudohyphal growth. To better understand the role of Spa2p in polarized...
GATA-1 binding sites mapped in the β-globin locus by using mammalian chIp-chip analysis
Horak, Christine E., Mahajan, Milind C., Luscombe, Nicholas M., Gerstein, Mark, Weissman, Sherman M., Snyder, Michael
The expression of the β-like globin genes is intricately regulated by a series of both general and tissue-restricted transcription factors. The hemapoietic lineage-specific transcription factor...
Casamayor, Antonio, Snyder, Michael
The septins are a family of cytoskeletal proteins present in animal and fungal cells. They were first identified for their essential role in cytokinesis, but more recently, they have been found to...
Subcellular localization of the yeast proteome
Kumar, Anuj, Agarwal, Seema, Heyman, John A., Matson, Sandra, Heidtman, Matthew, Piccirillo, Stacy, ...
Protein localization data are a valuable information resource helpful in elucidating eukaryotic protein function. Here, we report the first proteome-scale analysis of protein localization within any...
ExpressYourself: a modular platform for processing and visualizing microarray data
Luscombe, Nicholas M., Royce, Thomas E., Bertone, Paul, Echols, Nathaniel, Horak, Christine E., Chang, Joseph T., ...
DNA microarrays are widely used in biological research; by analyzing differential hybridization on a single microarray slide, one can detect changes in mRNA expression levels, increases in DNA copy...
Santos, Beatriz, Snyder, Michael
In budding yeast, chs5 mutants are defective in chitin synthesis and cell fusion during mating. Chs5p is a late-Golgi protein required for the polarized transport of the chitin synthase Chs3p to the...
A novel mitochondrial protein, Tar1p, is encoded on the antisense strand of the nuclear 25S rDNA
Coelho, Paulo S.R., Bryan, Anthony C., Kumar, Anuj, Shadel, Gerald S., Snyder, Michael
In eukaryotes, it is widely assumed that genes coding for proteins and structural RNAs do not overlap. Using a transposon-tagging strategy to globally analyze the Saccharomyces cerevisiae genome for...
Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae
Horak, Christine E., Luscombe, Nicholas M., Qian, Jiang, Bertone, Paul, Piccirrillo, Stacy, Gerstein, Mark, ...
In the yeast Saccharomyces cerevisiae, SBF (Swi4–Swi6 cell cycle box binding factor) and MBF (MluI binding factor) are the major transcription factors regulating the START of the cell cycle, a time...
The transcriptional activity of human Chromosome 22
Rinn, John L., Euskirchen, Ghia, Bertone, Paul, Martone, Rebecca, Luscombe, Nicholas M., Hartman, Stephen, ...
A DNA microarray representing nearly all of the unique sequences of human Chromosome 22 was constructed and used to measure global-transcriptional activity in placental poly(A)+ RNA. We found that...
Distribution of NF-κB-binding sites across human chromosome 22
Martone, Rebecca, Euskirchen, Ghia, Bertone, Paul, Hartman, Stephen, Royce, Thomas E., Luscombe, Nicholas M., ...
We have mapped the chromosomal binding site distribution of a transcription factor in human cells. The NF-κB family of transcription factors plays an essential role in regulating the induction of...
Negative regulation of calcineurin signaling by Hrr25p, a yeast homolog of casein kinase I
Kafadar, Kimberly A., Zhu, Heng, Snyder, Michael, Cyert, Martha S.
Calcineurin is a Ca2+/calmodulin-regulated protein phosphatase required for Saccharomyces cerevisiae to respond to a variety of environmental stresses. Calcineurin promotes cell survival during...
Barral, Yves, Parra, Macarena, Bidlingmaier, Scott, Snyder, Michael
The mechanisms that couple cell cycle progression with the organization of the peripheral cytoskeleton are poorly understood. In Saccharomyces cerevisiae, the Swe1 protein has been shown previously...
Microbial Synergy via an Ethanol-Triggered Pathway
Smith, Michael G., Des Etages, Shelley G., Snyder, Michael
We have discovered a microbial interaction between yeast, bacteria, and nematodes. Upon coculturing, Saccharomyces cerevisiae stimulated the growth of several species of Acinetobacter, including, A....
CREB Binds to Multiple Loci on Human Chromosome 22
Euskirchen, Ghia, Royce, Thomas E., Bertone, Paul, Martone, Rebecca, Rinn, John L., Nelson, F. Kenneth, ...
The cyclic AMP-responsive element-binding protein (CREB) is an important transcription factor that can be activated by hormonal stimulation and regulates neuronal function and development. An...
Large-Scale Mutagenesis of the Yeast Genome Using a Tn7-Derived Multipurpose Transposon
Kumar, Anuj, Seringhaus, Michael, Biery, Matthew C., Sarnovsky, Robert J., Umansky, Lara, Piccirillo, Stacy, ...
We present here an unbiased and extremely versatile insertional library of yeast genomic DNA generated by in vitro mutagenesis with a multipurpose element derived from the bacterial transposon Tn7....
Huang, Jing, Zhu, Heng, Haggarty, Stephen J., Spring, David R., Hwang, Heejun, Jin, Fulai, ...
The TOR (target of rapamycin) proteins play important roles in nutrient signaling in eukaryotic cells. Rapamycin treatment induces a state reminiscent of the nutrient starvation response, often...
White, Eric J., Emanuelsson, Olof, Scalzo, David, Royce, Thomas, Kosak, Steven, Oakeley, Edward J., ...
Duplication of the genome during the S phase of the cell cycle does not occur simultaneously; rather, different sequences are replicated at different times. The replication timing of specific...
Mah, Angie S, Elia, Andrew EH, Devgan, Geeta, Ptacek, Jason, Schutkowski, Mike, Snyder, Michael, ...
Biochemical and genetic analysis of the yeast proteome with a movable ORF collection
Gelperin, Daniel M., White, Michael A., Wilkinson, Martha L., Kon, Yoshiko, Kung, Li A., Wise, Kevin J., ...
Functional analysis of the proteome is an essential part of genomic research. To facilitate different proteomic approaches, a MORF (moveable ORF) library of 5854 yeast expression plasmids was...
Global changes in STAT target selection and transcription regulation upon interferon treatments
Hartman, Stephen E., Bertone, Paul, Nath, Anjali K., Royce, Thomas E., Gerstein, Mark, Weissman, Sherman, ...
The STAT (signal transducer and activator of transcription) proteins play a crucial role in the regulation of gene expression, but their targets and the manner in which they select them remain...
Design optimization methods for genomic DNA tiling arrays
Bertone, Paul, Trifonov, Valery, Rozowsky, Joel S., Schubert, Falk, Emanuelsson, Olof, Karro, John, ...
A recent development in microarray research entails the unbiased coverage, or tiling, of genomic DNA for the large-scale identification of transcribed sequences and regulatory elements. A central...
Target hub proteins serve as master regulators of development in yeast
Borneman, Anthony R., Leigh-Bell, Justine A., Yu, Haiyuan, Bertone, Paul, Gerstein, Mark, Snyder, Michael
To understand the organization of the transcriptional networks that govern cell differentiation, we have investigated the transcriptional circuitry controlling pseudohyphal development in...
Severe acute respiratory syndrome diagnostics using a coronavirus protein microarray
Zhu, Heng, Hu, Shaohui, Jona, Ghil, Zhu, Xiaowei, Kreiswirth, Nate, Willey, Barbara M., ...
To monitor severe acute respiratory syndrome (SARS) infection, a coronavirus protein microarray that harbors proteins from SARS coronavirus (SARS-CoV) and five additional coronaviruses was...
Urban, Alexander Eckehart, Korbel, Jan O., Selzer, Rebecca, Richmond, Todd, Hacker, April, Popescu, George V., ...
Deletions and amplifications of the human genomic sequence (copy number polymorphisms) are the cause of numerous diseases and a potential cause of phenotypic variation in the normal population....
Seringhaus, Michael, Kumar, Anuj, Hartigan, John, Snyder, Michael, Gerstein, Mark
Transposons are widely employed as tools for gene disruption. Ideally, they should display unbiased insertion behavior, and incorporate readily into any genomic DNA to which they are exposed....
Defined culture conditions of human embryonic stem cells
Lu, Jean, Hou, Runhua, Booth, Carmen Jane, Yang, Shih-Hung, Snyder, Michael
Human embryonic stem cells (hESCs) are pluripotent cells that have the potential to differentiate into any tissue in the human body; therefore, they are a valuable resource for regenerative medicine,...
Linking DNA-binding proteins to their recognition sequences by using protein microarrays
Ho, Su-Wen, Jona, Ghil, Chen, Christina T. L., Johnston, Mark, Snyder, Michael
Analyses of whole-genome sequences and experimental data sets have revealed a large number of DNA sequence motifs that are conserved in many species and may be functional. However, methods of...
TOS9 Regulates White-Opaque Switching in Candida albicans▿ †
Srikantha, Thyagarajan, Borneman, Anthony R., Daniels, Karla J., Pujol, Claude, Wu, Wei, Seringhaus, Michael R., ...
In Candida albicans, the a1-α2 complex represses white-opaque switching, as well as mating. Based upon the assumption that the a1-α2 corepressor complex binds to the gene that regulates...
ProCAT: a data analysis approach for protein microarrays
Zhu, Xiaowei, Gerstein, Mark, Snyder, Michael
ProCAT, a powerful and flexible new approach for analyzing many types of protein microarrays, is described.
BoCaTFBS: a boosted cascade learner to refine the binding sites suggested by ChIP-chip experiments
Wang, Lu-yong, Snyder, Michael, Gerstein, Mark
BoCaTFBS, a new method that combines noisy data from ChIP-chip experiments with known binding-site patterns, is described and applied to the ENCODE project.
Predicting essential genes in fungal genomes
Seringhaus, Michael, Paccanaro, Alberto, Borneman, Anthony, Snyder, Michael, Gerstein, Mark
Essential genes are required for an organism's viability, and the ability to identify these genes in pathogens is crucial to directed drug development. Predicting essential genes through...
Yu, Haiyuan, Nguyen, Katherine, Royce, Tom, Qian, Jiang, Nelson, Kenneth, Snyder, Michael, ...
Microarray technology is currently one of the most widely-used technologies in biology. Many studies focus on inferring the function of an unknown gene from its co-expressed genes. Here, we are able...
Tilescope: online analysis pipeline for high-density tiling microarray data
Zhang, Zhengdong D, Rozowsky, Joel, Lam, Hugo YK, Du, Jiang, Snyder, Michael, Gerstein, Mark
Tilescope is a fully integrated and automated new data-processing pipeline for analyzing high-density tiling-array data.
Smith, Michael G., Gianoulis, Tara A., Pukatzki, Stefan, Mekalanos, John J., Ornston, L. Nicholas, Gerstein, Mark, ...
Acinetobacter baumannii has emerged as an important and problematic human pathogen as it is the causative agent of several types of infections including pneumonia, meningitis, septicemia, and urinary...
Popescu, Sorina C., Popescu, George V., Bachan, Shawn, Zhang, Zimei, Seay, Montrell, Gerstein, Mark, ...
Calmodulins (CaMs) are the most ubiquitous calcium sensors in eukaryotes. A number of CaM-binding proteins have been identified through classical methods, and many proteins have been predicted to...
Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome
Trinklein, Nathan D., Karaöz, Ulaş, Wu, Jiaqian, Halees, Anason, Force Aldred, Shelley, Collins, Patrick J., ...
The regulation of transcriptional initiation in the human genome is a critical component of global gene regulation, but a complete catalog of human promoters currently does not exist. In order to...
Rozowsky, Joel S., Newburger, Daniel, Sayward, Fred, Wu, Jiaqian, Jordan, Greg, Korbel, Jan O., ...
For the ∼1% of the human genome in the ENCODE regions, only about half of the transcriptionally active regions (TARs) identified with tiling microarrays correspond to annotated exons. Here we...
Zhang, Zhengdong D., Paccanaro, Alberto, Fu, Yutao, Weissman, Sherman, Weng, Zhiping, Chang, Joseph, ...
The comprehensive inventory of functional elements in 44 human genomic regions carried out by the ENCODE Project Consortium enables for the first time a global analysis of the genomic distribution of...
Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution
Zheng, Deyou, Frankish, Adam, Baertsch, Robert, Kapranov, Philipp, Reymond, Alexandre, Choo, Siew Woh, ...
Arising from either retrotransposition or genomic duplication of functional genes, pseudogenes are “genomic fossils” valuable for exploring the dynamics and evolution of genes and genomes....
Structured RNAs in the ENCODE selected regions of the human genome
Washietl, Stefan, Pedersen, Jakob S., Korbel, Jan O., Stocsits, Claudia, Gruber, Andreas R., Hackermüller, Jörg, ...
Functional RNA structures play an important role both in the context of noncoding RNA transcripts as well as regulatory elements in mRNAs. Here we present a computational study to detect functional...
Emanuelsson, Olof, Nagalakshmi, Ugrappa, Zheng, Deyou, Rozowsky, Joel S., Urban, Alexander E., Du, Jiang, ...
Genomic tiling microarrays have become a popular tool for interrogating the transcriptional activity of large regions of the genome in an unbiased fashion. There are several key parameters associated...
Euskirchen, Ghia M., Rozowsky, Joel S., Wei, Chia-Lin, Lee, Wah Heng, Zhang, Zhengdong D., Hartman, Stephen, ...
Recent progress in mapping transcription factor (TF) binding regions can largely be credited to chromatin immunoprecipitation (ChIP) technologies. We compared strategies for mapping TF binding...
Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE)
Bhinge, Akshay A., Kim, Jonghwan, Euskirchen, Ghia M., Snyder, Michael, Iyer, Vishwanath R.
Identifying the genome-wide binding sites of transcription factors is important in deciphering transcriptional regulatory networks. ChIP-chip (Chromatin immunoprecipitation combined with microarrays)...
Korbel, Jan O., Urban, Alexander Eckehart, Grubert, Fabian, Du, Jiang, Royce, Thomas E., Starr, Peter, ...
Copy-number variants (CNVs) are an abundant form of genetic variation in humans. However, approaches for determining exact CNV breakpoint sequences (physical deletion or duplication boundaries)...
Bidlingmaier, Scott, Snyder, Michael
The dynamic regulation of polarized cell growth allows cells to form structures of defined size and shape. We have studied the regulation of polarized growth using mating yeast as a model. Haploid...
Hudson, Michael E., Pozdnyakova, Irina, Haines, Kenneth, Mor, Gil, Snyder, Michael
Ovarian cancer is a leading cause of deaths, yet many aspects of the biology of the disease and a routine means of its detection are lacking. We have used protein microarrays and autoantibodies from...
Targeting of Chitin Synthase 3 to Polarized Growth Sites in Yeast Requires Chs5p and Myo2p
Santos, Beatriz, Snyder, Michael
Chitin is an essential structural component of the yeast cell wall whose deposition is regulated throughout the yeast life cycle. The temporal and spatial regulation of chitin synthesis was...
Pheromone-regulated Genes Required for Yeast Mating Differentiation
Erdman, Scott, Lin, Li, Malczynski, Michael, Snyder, Michael
Yeast cells mate by an inducible pathway that involves agglutination, mating projection formation, cell fusion, and nuclear fusion. To obtain insight into the mating differentiation of Saccharomyces...
A Nonerythroid Isoform of Protein 4.1R Interacts with the Nuclear Mitotic Apparatus (NuMA) Protein
Mattagajasingh, Subhendra N., Huang, Shu-Ching, Hartenstein, Julia S., Snyder, Michael, Marchesi, Vincent T., Benz, Edward J.
Red blood cell protein 4.1 (4.1R) is an 80- kD erythrocyte phosphoprotein that stabilizes the spectrin/actin cytoskeleton. In nonerythroid cells, multiple 4.1R isoforms arise from a single gene by...
Manning, Brendan D., Barrett, Jennifer G., Wallace, Julie A., Granok, Howard, Snyder, Michael
The mechanisms by which kinesin-related proteins interact with other proteins to carry out specific cellular processes is poorly understood. The kinesin-related protein, Kar3p, has been implicated in...
Wu, Jia Qian, Du, Jiang, Rozowsky, Joel, Zhang, Zhengdong, Urban, Alexander E, Euskirchen, Ghia, ...
RACE sequencing of ENCODE regions shows that much of the human genome is represented in poly(A)+ RNA.
RNA polymerase II stalling: loading at the start prepares genes for a sprint
Promoter-proximal polymerase II stalling prepares genes for prompt expression when signals are received.
Reed, Brian D., Charos, Alexandra E., Szekely, Anna M., Weissman, Sherman M., Snyder, Michael
The sterol regulatory element-binding protein (SREBP) family member SREBP1 is a critical transcriptional regulator of cholesterol and fatty acid metabolism and has been implicated in insulin...
Modeling ChIP Sequencing In Silico with Applications
Zhang, Zhengdong D., Rozowsky, Joel, Snyder, Michael, Chang, Joseph, Gerstein, Mark
ChIP sequencing (ChIP-seq) is a new method for genomewide mapping of protein binding sites on DNA. It has generated much excitement in functional genomics. To score data and determine adequate...
Chang, Wakam, Zaarour, Rania F., Reck-Peterson, Samara, Rinn, John, Singer, Robert H., Snyder, Michael, ...
Myo2p is an essential class V myosin in budding yeast with several identified functions in organelle trafficking and spindle orientation. The present study demonstrates that Myo2p is a component of a...
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
Johnson, David S., Li, Wei, Gordon, D. Benjamin, Bhattacharjee, Arindam, Curry, Bo, Ghosh, Jayati, ...
The most widely used method for detecting genome-wide protein–DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first...
Nath, Anjali K., Brown, Rachel M., Michaud, Michael, Sierra-Honigmann, M. Rocio, Snyder, Michael, Madri, Joseph A.
Blood circulation is dependent on heart valves to direct blood flow through the heart and great vessels. Valve development relies on epithelial to mesenchymal transition (EMT), a central feature of...
High-Resolution Copy-Number Variation Map Reflects Human Olfactory Receptor Diversity and Evolution
Hasin, Yehudit, Olender, Tsviya, Khen, Miriam, Gonzaga-Jauregui, Claudia, Kim, Philip M., Urban, Alexander Eckehart, ...
Olfactory receptors (ORs), which are involved in odorant recognition, form the largest mammalian protein superfamily. The genomic content of OR genes is considerably reduced in humans, as reflected...
YMD: a microarray database for large-scale gene expression analysis.
Cheung, Kei-Hoi, White, Kevin, Hager, Janet, Gerstein, Mark, Reinke, Valerie, Nelson, Kenneth, ...
The use of microarray technology to perform parallel analysis of the expression pattern of a large number of genes in a single experiment has created a new frontier of medical research. The vast...
Nath, Anjali K., Krauthammer, Michael, Li, Puyao, Davidov, Eugene, Butler, Lucas C., Copel, Joshua, ...
Lian, Zheng, Karpikov, Alexander, Lian, Jin, Mahajan, Milind C., Hartman, Stephen, Gerstein, Mark, ...
Genomic analyses have been applied extensively to analyze the process of transcription initiation in mammalian cells, but less to transcript 3′ end formation and transcription termination. We used...
Mismatch oligonucleotides in human and yeast: guidelines for probe design on tiling microarrays
Seringhaus, Michael, Rozowsky, Joel, Royce, Thomas, Nagalakshmi, Ugrappa, Jee, Justin, Snyder, Michael, ...
Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing
Lefrançois, Philippe, Euskirchen, Ghia M, Auerbach, Raymond K, Rozowsky, Joel, Gibson, Theodore, Yellman, Christopher M, ...
A procedure for highly specific, sensitive, and unbiased whole-genome amplification
Pan, Xinghua, Urban, Alexander Eckehart, Palejev, Dean, Schulz, Vincent, Grubert, Fabian, Hu, Yiping, ...
Highly specific amplification of complex DNA pools without bias or template-independent products (TIPs) remains a challenge. We have developed a method using phi29 DNA polymerase and trehalose and...
Korbel, Jan O, Abyzov, Alexej, Mu, Xinmeng Jasmine, Carriero, Nicholas, Cayting, Philip, Zhang, Zhengdong, ...
Paired-End Mapper (PEMer) enables mapping of genomic structural variants at considerably enhanced sensitivity, specificity and resolution over previous approaches.
Kim, Philip M., Lam, Hugo Y.K., Urban, Alexander E., Korbel, Jan O., Affourtit, Jason, Grubert, Fabian, ...
Segmental duplications (SDs) are operationally defined as >1 kb stretches of duplicated DNA with high sequence identity. They arise from copy number variants (CNVs) fixed in the population. To...
Robertson, A. Gordon, Bilenky, Mikhail, Tam, Angela, Zhao, Yongjun, Zeng, Thomas, Thiessen, Nina, ...
We characterized the relationship of H3K4me1 and H3K4me3 at distal and proximal regulatory elements by comparing ChIP-seq profiles for these histone modifications and for two functionally different...
Quantifying environmental adaptation of metabolic pathways in metagenomics
Gianoulis, Tara A., Raes, Jeroen, Patel, Prianka V., Bjornson, Robert, Korbel, Jan O., Letunic, Ivica, ...
Recently, approaches have been developed to sample the genetic content of heterogeneous environments (metagenomics). However, by what means these sequences link distinct environmental conditions with...
Popescu, Sorina C, Snyder, Michael, Dinesh-Kumar, SP
Protein microarray technology has emerged as a powerful new approach for the study of thousands of proteins simultaneously. Protein microarrays have been used for a wide variety of applications for...
MSB: A mean-shift-based approach for the analysis of structural variation in the genome
Wang, Lu-yong, Abyzov, Alexej, Korbel, Jan O., Snyder, Michael, Gerstein, Mark
Genome structural variation includes segmental duplications, deletions, and other rearrangements, and array-based comparative genomic hybridization (array-CGH) is a popular technology for determining...
MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays
Popescu, Sorina C., Popescu, George V., Bachan, Shawn, Zhang, Zimei, Gerstein, Mark, Snyder, Michael, ...
Signaling through mitogen-activated protein kinases (MPKs) cascades is a complex and fundamental process in eukaryotes, requiring MPK-activating kinases (MKKs) and MKK-activating kinases (MKKKs)....
Du, Jiang, Bjornson, Robert D., Zhang, Zhengdong D., Kong, Yong, Snyder, Michael, Gerstein, Mark B.
The goal of human genome re-sequencing is obtaining an accurate assembly of an individual's genome. Recently, there has been great excitement in the development of many technologies for this (e.g....
Korbel, Jan O., Tirosh-Wagner, Tal, Urban, Alexander Eckehart, Chen, Xiao-Ning, Kasowski, Maya, Dai, Li, ...
Down syndrome (DS), or trisomy 21, is a common disorder associated with several complex clinical phenotypes. Although several hypotheses have been put forward, it is unclear as to whether particular...
Impact of Chromatin Structures on DNA Processing for Genomic Analyses
Teytelman, Leonid, Özaydın, Bilge, Zill, Oliver, Lefrançois, Philippe, Snyder, Michael, Rine, Jasper, ...
Chromatin has an impact on recombination, repair, replication, and evolution of DNA. Here we report that chromatin structure also affects laboratory DNA manipulation in ways that distort the results...
Theodorou, Elias, Dalembert, George, Heffelfinger, Christopher, White, Eric, Weissman, Sherman, Corcoran, Lynn, ...
Neuronal differentiation is a complex process that involves a plethora of regulatory steps. To identify transcription factors that influence neuronal differentiation we developed a high throughput...
Kung, Li A, Tao, Sheng-Ce, Qian, Jiang, Smith, Michael G, Snyder, Michael, Zhu, Heng
To further understand the roles of protein glycosylation in eukaryotes, we globally identified glycan-containing proteins in yeast. A fluorescent lectin binding assay was developed and used to screen...