Global analysis of patterns of gene expression during Drosophilaembryogenesis (2007)
Tomancak, Pavel, Berman, Benjamin P, Beaton, Amy, Weiszmann, Richard, Kwan, Elaine, Hartenstein, Volker, ...
Abstract Background Cell and tissue specific gene expression is a defining feature of embryonic development in multi-cellular organisms. However, the range of gene expression patterns, the extent of...
Global analyses of mRNA translational control during early Drosophilaembryogenesis (2007)
Qin, Xiaoli, Ahn, Soyeon, Speed, Terence P, Rubin, Gerald M
Abstract Background In many animals, the first few hours of life proceed with little or no transcription, and developmental regulation at these early stages is dependent on maternal cytoplasm rather...
Large-Scale Trends in the Evolution of Gene Structures within 11 Animal Genomes (2006)
Mark Yandell, Chris J. Mungall, Chris Smith, Simon Prochnik, Joshua Kaminker, George Hartzell, ...
We have used the annotations of six animal genomes (Homo sapiens, Mus musculus, Ciona intestinalis, Drosophila melanogaster, Anopheles gambiae, and Caenorhabditis elegans) together with the sequences...
Berman, Benjamin P, Pfeiffer, Barret D, Laverty, Todd R, Salzberg, Steven L, Rubin, Gerald M, Eisen, Michael B, ...
Abstract Background The identification of sequences that control transcription in metazoans is a major goal of genome analysis. In a previous study, we demonstrated that searching for clusters of...
Berman, Benjamin P., Pfeiffer, Barret D., Laverty, Todd R., Salzberg, Steven L., Rubin, Gerald M., Eisen, Michael B., ...
Barret D Pfeiffer, Roger A, Hoskins* Andreas Gnirke, Chris J Mungall, Adrienne M Wang, ...
Background: It is widely accepted that comparative sequence data can aid the functional annotation of genome sequences; however, the most informative species and features of genome evolution for...
Computational identification of DrosophilamicroRNA genes (2003)
Lai, Eric C, Tomancak, Pavel, Williams, Robert W, Rubin, Gerald M
Abstract Background MicroRNAs (miRNAs) are a large family of 21-22 nucleotide non-coding RNAs with presumed post-transcriptional regulatory activity. Most miRNAs were identified by direct cloning of...
Annotation of the Drosophila melanogaster euchromatic genome: a systematic review (2002)
Misra, Sima, Crosby, Madeline A, Mungall, Christopher J, Matthews, Beverley B, Campbell, Kathryn S, Hradecky, Pavel, ...
Abstract Background The recent completion of the Drosophila melanogaster genomic sequence to high quality and the availability of a greatly expanded set of Drosophila cDNA sequences, aligning to 78%...
Heterochromatic sequences in a Drosophila whole-genome shotgun assembly (2002)
Hoskins, Roger A, Smith, Christopher D, Carlson, Joseph W, Carvalho, A Bernardo, Halpern, Aaron, Kaminker, Joshua S, ...
Abstract Background Most eukaryotic genomes include a substantial repeat-rich fraction termed heterochromatin, which is concentrated in centric and telomeric regions. The repetitive nature of...
Bergman, Casey M, Pfeiffer, Barret D, Rincón-Limas, Diego E, Hoskins, Roger A, Gnirke, Andreas, Mungall, Chris J, ...
Abstract Background It is widely accepted that comparative sequence data can aid the functional annotation of genome sequences; however, the most informative species and features of genome evolution...
Celniker, Susan E, Wheeler, David A, Kronmiller, Brent, Carlson, Joseph W, Halpern, Aaron, Patel, Sandeep, ...
Abstract Background The Drosophila melanogaster genome was the first metazoan genome to have been sequenced by the whole-genome shotgun (WGS) method. Two issues relating to this achievement were...
A Drosophilafull-length cDNA resource (2002)
Stapleton, Mark, Carlson, Joe, Brokstein, Peter, Yu, Charles, Champe, Mark, George, Reed, ...
Abstract Background A collection of sequenced full-length cDNAs is an important resource both for functional genomics studies and for the determination of the intron-exon structure of genes....
The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective (2002)
Kaminker, Joshua S, Bergman, Casey M, Kronmiller, Brent, Carlson, Joseph, Svirskas, Robert, Patel, Sandeep, ...
Abstract Background Transposable elements are found in the genomes of nearly all eukaryotes. The recent completion of the Release 3 euchromatic genomic sequence of Drosophila melanogaster by the...
Systematic determination of patterns of gene expression during Drosophilaembryogenesis (2002)
Tomancak, Pavel, Beaton, Amy, Weiszmann, Richard, Kwan, Elaine, Shu, ShengQiang, Lewis, Suzanna E, ...
Abstract Background Cell-fate specification and tissue differentiation during development are largely achieved by the regulation of gene transcription. Results As a first step to creating a...
Computational analysis of core promoters in the Drosophilagenome (2002)
Ohler, Uwe, Liao, Guo-chun, Niemann, Heinrich, Rubin, Gerald M
Abstract Background The core promoter, a region of about 100 base-pairs flanking the transcription start site (TSS), serves as the recognition site for the basal transcription apparatus. Drosophila...
Evidence for large domains of similarly expressed genes in the Drosophila genome (2002)
Spellman, Paul T, Rubin, Gerald M
Abstract Background Transcriptional regulation in eukaryotes generally operates at the level of individual genes. Regulation of sets of adjacent genes by mechanisms operating at the level of...
Expression of baculovirus P35 prevents cell death in Drosophila (1994)
Hay, Bruce A., Wolff, Tanya, Rubin, Gerald M.
The baculovirus P35 protein functions to prevent apoptotic death of infected cells. We have expressed P35 in the developing embryo and eye of the fly Drosophila melanogaster. P35 eliminates most, if...
Insertion site preferences of the P transposable element in Drosophila melanogaster
Liao, Guo-chun, Rehm, E. Jay, Rubin, Gerald M.
We determined the genomic sequence at the site of insertion in 2,266 unselected P element insertion events. Estimating physical properties of the genomic DNA at these insertion sites—such as base...
The ryanodine receptor is essential for larval development in Drosophila melanogaster
Sullivan, Kathleen M. C., Scott, Kristin, Zuker, Charles S., Rubin, Gerald M.
We have investigated the role of the ryanodine receptor in Drosophila development by using pharmacological and genetic approaches. We identified a P element insertion in the Drosophila ryanodine...
Kopczynski, Casey C., Noordermeer, Jasprina N., Serano, Thomas L., Chen, Wei-Yu, Pendleton, John D., Lewis, Suzanna, ...
Secreted and transmembrane proteins play an essential role in intercellular communication during the development of multicellular organisms. Because only a small number of these genes have been...
Functional analysis of CNK in RAS signaling
Therrien, Marc, Wong, Allan M., Kwan, Elaine, Rubin, Gerald M.
Connector enhancer of KSR (CNK) is a multidomain protein required for RAS signaling. Its C-terminal portion (CNKC-term) directly binds to RAF. Herein, we show that the N-terminal portion of CNK...
KSR stimulates Raf-1 activity in a kinase-independent manner
Michaud, Neil R., Therrien, Marc, Cacace, Angela, Edsall, Lisa C., Spiegel, Sarah, Rubin, Gerald M., ...
Kinase suppressor of Ras (KSR) is an evolutionarily conserved component of Ras-dependent signaling pathways. Here, we find that murine KSR (mKSR1) translocates from the cytoplasm to the plasma...
P element insertion-dependent gene activation in the Drosophila eye
Hay, Bruce A., Maile, Randy, Rubin, Gerald M.
Insights into the function of a gene can be gained in multiple ways, including loss-of-function phenotype, sequence similarity, expression pattern, and by the consequences of its misexpression....
Targeted expression of teashirt induces ectopic eyes in Drosophila
teashirt was initially identified as a gene required for the specification of the trunk segments in Drosophila embryogenesis and encodes a transcription factor with zinc finger motifs. We report here...
Lai, Eric C., Rubin, Gerald M.
neuralized (neur) is a neurogenic mutant of Drosophila in which many signaling events mediated by the Notch (N) receptor are disrupted. Here, we analyze the role of neur during eye development. Neur...
Genome-wide analysis of the Drosophila immune response by using oligonucleotide microarrays
De Gregorio, Ennio, Spellman, Paul T., Rubin, Gerald M., Lemaitre, Bruno
To identify new Drosophila genes involved in the immune response, we monitored the gene expression profile of adult flies in response to microbial infection by using high-density oligonucleotide...
Cacace, Angela M., Michaud, Neil R., Therrien, Marc, Mathes, Karen, Copeland, Terry, Rubin, Gerald M., ...
Genetic and biochemical studies have identified kinase suppressor of Ras (KSR) to be a conserved component of Ras-dependent signaling pathways. To better understand the role of KSR in signal...
Berman, Benjamin P., Nibu, Yutaka, Pfeiffer, Barret D., Tomancak, Pavel, Celniker, Susan E., Levine, Michael, ...
A major challenge in interpreting genome sequences is understanding how the genome encodes the information that specifies when and where a gene will be expressed. The first step in this process is...
ARGONAUTE1 is required for efficient RNA interference in Drosophila embryos
Williams, Robert W., Rubin, Gerald M.
Double-stranded RNA (dsRNA) triggers homology-dependent posttranscriptional gene interference (RNAi) in a diverse range of eukaryotic organisms, in a process mechanistically related to viral and...
The Toll and Imd pathways are the major regulators of the immune response in Drosophila
De Gregorio, Ennio, Spellman, Paul T., Tzou, Phoebe, Rubin, Gerald M., Lemaitre, Bruno
Microarray studies have shown recently that microbial infection leads to extensive changes in the Drosophila gene expression programme. However, little is known about the control of most of the fly...
Celniker, Susan E, Wheeler, David A, Kronmiller, Brent, Carlson, Joseph W, Halpern, Aaron, Patel, Sandeep, ...
The Drosophila melanogaster genome was the first metazoan genome to be sequenced by whole-genome shotgun. Now, the sequence has been finished in a process designed to close gaps, improve sequence...
A Drosophila full-length cDNA resource
Stapleton, Mark, Carlson, Joe, Brokstein, Peter, Yu, Charles, Champe, Mark, George, Reed, ...
High-quality full-insert sequence for 8,921 putative full-length cDNA clones in the Drosophila Gene Collection has been generated and compared to the annotated Release 3 genomic sequence. More than...
Annotation of the Drosophila melanogaster euchromatic genome: a systematic review
Misra, Sima, Crosby, Madeline A, Mungall, Christopher J, Matthews, Beverley B, Campbell, Kathryn S, Hradecky, Pavel, ...
The recent completion of the Drosophila melanogaster genomic sequence to high quality, and the availability of a greatly expanded set of Drosophila cDNA sequences, afforded FlyBase the opportunity to...
The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective
Kaminker, Joshua S, Bergman, Casey M, Kronmiller, Brent, Carlson, Joseph, Svirskas, Robert, Patel, Sandeep, ...
Using Release 3 of the euchromatic genomic sequence of Drosophila melanogaster, 85 known and eight novel families of transposable element have been identified, varying in copy number from one to 146....
Heterochromatic sequences in a Drosophila whole-genome shotgun assembly
Hoskins, Roger A, Smith, Christopher D, Carlson, Joseph W, Carvalho, A Bernardo, Halpern, Aaron, Kaminker, Joshua S, ...
Annotation of an improved whole-genome shotgun assembly of the Drosophila melanogaster genome predicted 297 protein-coding genes and six non-protein-coding genes, including known heterochromatic...
Bergman, Casey M, Pfeiffer, Barret D, Rincón-Limas, Diego E, Hoskins, Roger A, Gnirke, Andreas, Mungall, Chris J, ...
Analysis of conservation in eight genomic regions (apterous, even-skipped, fushi tarazu, twist, and Rhodopsins 1, 2, 3 and 4) from four Drosophila species (D. erecta, D. pseudoobscura, D. willistoni,...
Computational analysis of core promoters in the Drosophila genome
Ohler, Uwe, Liao, Guo-chun, Niemann, Heinrich, Rubin, Gerald M
Candidate transcription start sites have been identified for about 2,000 Drosophila genes by aligning 5' expressed sequence tags (ESTs) from cap-trapped cDNA libraries to the genome. Examination of...
Systematic determination of patterns of gene expression during Drosophila embryogenesis
Tomancak, Pavel, Beaton, Amy, Weiszmann, Richard, Kwan, Elaine, Shu, ShengQiang, Lewis, Suzanna E, ...
As a first step to creating a comprehensive atlas of gene-expression patterns during Drosophila embryogenesis, 2,179 genes have been examinded by in situ hybridization to fixed Drosophila embryos. Of...
Targeted mutagenesis by homologous recombination in D. melanogaster
Rong, Yikang S., Titen, Simon W., Xie, Heng B., Golic, Mary M., Bastiani, Michael, Bandyopadhyay, Pradip, ...
We used a recently developed method to produce mutant alleles of five endogenous Drosophila genes, including the homolog of the p53 tumor suppressor. Transgenic expression of the FLP site-specific...
Stapleton, Mark, Liao, Guochun, Brokstein, Peter, Hong, Ling, Carninci, Piero, Shiraki, Toshiyuki, ...
Collections of full-length nonredundant cDNA clones are critical reagents for functional genomics. The first step toward these resources is the generation and single-pass sequencing of cDNA libraries...
Computational identification of Drosophila microRNA genes
Lai, Eric C, Tomancak, Pavel, Williams, Robert W, Rubin, Gerald M
An informatic procedure has been used to analyze the euchromatic sequences of Drosophila melanogaster and D. pseudoobscura for conserved sequences that adopt an extended stem-loop structure and...
Serano, Julia, Rubin, Gerald M.
The vertebrate synaptotagmin-like protein granuphilin binds to the vesicle-trafficking proteins Rab27a and Munc18 and can modulate exocytosis of insulin-containing secretory granules in pancreatic...
BioViews: Java-Based Tools for Genomic Data Visualization
Helt, Gregg A., Lewis, Suzanna, Loraine, Ann E., Rubin, Gerald M.
Visualization tools for bioinformatics ideally should provide universal access to the most current data in an interactive and intuitive graphical user interface. Since the introduction of Java, a...
A Computer Program for Aligning a cDNA Sequence with a Genomic DNA Sequence
Florea, Liliana, Hartzell, George, Zhang, Zheng, Rubin, Gerald M., Miller, Webb
We address the problem of efficiently aligning a transcribed and spliced DNA sequence with a genomic sequence containing that gene, allowing for introns in the genomic sequence and a relatively small...
Treisman, Jessica E., Luk, Alvin, Rubin, Gerald M., Heberlein, Ulrike
In Drosophila, pattern formation at multiple stages of embryonic and imaginal development depends on the same intercellular signaling pathways. We have identified a novel gene, eyelid (eld), which is...
mus304 encodes a novel DNA damage checkpoint protein required during Drosophila development
Brodsky, Michael H., Sekelsky, Jeff J., Tsang, Garson, Hawley, R. Scott, Rubin, Gerald M.
Checkpoints block cell cycle progression in eukaryotic cells exposed to DNA damaging agents. We show that several Drosophila homologs of checkpoint genes, mei-41, grapes, and 14-3-3ε, regulate a DNA...
Brodsky, Michael H., Weinert, Brian T., Tsang, Garson, Rong, Yikang S., McGinnis, Nadine M., Golic, Kent G., ...
We have used genetic and microarray analysis to determine how ionizing radiation (IR) induces p53-dependent transcription and apoptosis in Drosophila melanogaster. IR induces MNK/Chk2-dependent...
Transcription of the white locus in Drosophila melanogaster
O'Hare, Kevin, Levis, Robert, Rubin, Gerald M.
Genetic studies of the white locus have shown that it has a distal region where structural mutations occur and a proximal region where regulatory mutations occur. To better understand the molecular...
Berman, Benjamin P, Pfeiffer, Barret D, Laverty, Todd R, Salzberg, Steven L, Rubin, Gerald M, Eisen, Michael B, ...
27 predicted gene-regulatory regions in the Drosophila melanogaster genome were analyzed in vivo, confirming 15 active enhancer regions. A comparison with Drosophila pseudoobscura sequences revealed...
Yandell, Mark, Bailey, Adina M., Misra, Sima, Shu, ShengQiang, Wiel, Colin, Evans-Holm, Martha, ...
Five years after the completion of the sequence of the Drosophila melanogaster genome, the number of protein-coding genes it contains remains a matter of debate; the number of computational gene...
Lai, Eric C., Tam, Bergin, Rubin, Gerald M.
Although hundreds of distinct animal microRNAs (miRNAs) are known, the specific biological functions of only a handful are understood at present. Here, we demonstrate that three different families of...
Complementary miRNA pairs suggest a regulatory role for miRNA:miRNA duplexes
LAI, ERIC C., WIEL, COLIN, RUBIN, GERALD M.
microRNAs (miRNAs) are 21–22-nucleotide noncoding RNAs that are widely believed to regulate complementary mRNA targets. However, due to the modest amount of pairing involved, only a few out of the...
Large-Scale Trends in the Evolution of Gene Structures within 11 Animal Genomes
Yandell, Mark, Mungall, Chris J, Smith, Chris, Prochnik, Simon, Kaminker, Joshua, Hartzell, George, ...
We have used the annotations of six animal genomes (Homo sapiens, Mus musculus, Ciona intestinalis, Drosophila melanogaster, Anopheles gambiae, and Caenorhabditis elegans) together with the sequences...
Drosophila microRNAs exhibit diverse spatial expression patterns during embryonic development
Aboobaker, A. Aziz, Tomancak, Pavel, Patel, Nipam, Rubin, Gerald M., Lai, Eric C.
MicroRNAs (miRNAs) are an extensive class of regulatory RNA whose specific functions in animals are generally unknown. Although computational methods have identified many potential targets of miRNAs,...
Analysis of the Promoter of the ninaE Opsin Gene in Drosophila melanogaster
Mismer, Drzislav, Rubin, Gerald M.
We have analyzed the cis-acting regulatory sequences of the ninaE gene. This gene encodes the major Drosophila melanogaster opsin, the protein component of the primary chromophore of photoreceptor...
Sullivan, Kathleen M C, Rubin, Gerald M
Calcineurin is a Ca(2+)-calmodulin-activated, Ser-Thr protein phosphatase that is essential for the translation of Ca(2+) signals into changes in cell function and development. We carried out a...
Bellen, Hugo J, Levis, Robert W, Liao, Guochun, He, Yuchun, Carlson, Joseph W, Tsang, Garson, ...
The Berkeley Drosophila Genome Project (BDGP) strives to disrupt each Drosophila gene by the insertion of a single transposable element. As part of this effort, transposons in >30,000 fly strains...
Insertion site preferences of the P transposable element in Drosophila melanogaster
Liao, Guo-chun, Rehm, E. Jay, Rubin, Gerald M.
We determined the genomic sequence at the site of insertion in 2,266 unselected P element insertion events. Estimating physical properties of the genomic DNA at these insertion sites—such as base...
The ryanodine receptor is essential for larval development in Drosophila melanogaster
Sullivan, Kathleen M. C., Scott, Kristin, Zuker, Charles S., Rubin, Gerald M.
We have investigated the role of the ryanodine receptor in Drosophila development by using pharmacological and genetic approaches. We identified a P element insertion in the Drosophila ryanodine...
Kopczynski, Casey C., Noordermeer, Jasprina N., Serano, Thomas L., Chen, Wei-Yu, Pendleton, John D., Lewis, Suzanna, ...
Secreted and transmembrane proteins play an essential role in intercellular communication during the development of multicellular organisms. Because only a small number of these genes have been...
Functional analysis of CNK in RAS signaling
Therrien, Marc, Wong, Allan M., Kwan, Elaine, Rubin, Gerald M.
Connector enhancer of KSR (CNK) is a multidomain protein required for RAS signaling. Its C-terminal portion (CNKC-term) directly binds to RAF. Herein, we show that the N-terminal portion of CNK...
KSR stimulates Raf-1 activity in a kinase-independent manner
Michaud, Neil R., Therrien, Marc, Cacace, Angela, Edsall, Lisa C., Spiegel, Sarah, Rubin, Gerald M., ...
Kinase suppressor of Ras (KSR) is an evolutionarily conserved component of Ras-dependent signaling pathways. Here, we find that murine KSR (mKSR1) translocates from the cytoplasm to the plasma...
P element insertion-dependent gene activation in the Drosophila eye
Hay, Bruce A., Maile, Randy, Rubin, Gerald M.
Insights into the function of a gene can be gained in multiple ways, including loss-of-function phenotype, sequence similarity, expression pattern, and by the consequences of its misexpression....