Browsing by Author "Carey, Lucas, 1980-"

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  • Jiang, Zhisheng; Generoso, Serena Francesca, 1988-; Badia, Marta; Payer, Bernhard; Carey, Lucas, 1980- (Public Library of Science (PLoS), 2021)
    Isogenic cells cultured together show heterogeneity in their proliferation rate. To determine the differences between fast and slow-proliferating cells, we developed a method to sort cells by proliferation rate, and performed ...
  • Pokusaeva, Victoria O.; Usmanova, Dinara R.; Putintseva, Ekaterina V.; Espinar, Lorena; Sarkisyan, Karen S.; Mishin, Alexander S.; Bogatyreva, Natalya S.; Ivankov, Dmitry N.; Akopyan, Arseniy V.; Avvakumov, Sergey Ya; Povolotskaya, Inna, 1986-; Filion, Guillaume; Carey, Lucas, 1980-; Kondrashov, Fyodor A., 1979- (Public Library of Science (PLoS), 2019)
    Characterizing the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted to create functional organisms. Here we determined the ...
  • Ivanova, Tsvetomira Georgieva, 1978-; Maier, Michael, 1983-; Missarova, Alsu, 1990-; Ziegler-Birling, Céline; Dam, Monica; Gomar-Alba, Mercè; Carey, Lucas, 1980-; Mendoza, Manuel (Mendoza Palomares) (Nature Research, 2020)
    To faithfully transmit genetic information, cells must replicate their entire genome before division. This is thought to be ensured by the temporal separation of replication and chromosome segregation. Here we show that ...
  • Opulente, Dana A.; Morales, Christopher M.; Carey, Lucas, 1980-; Rest, Joshua S. (Public Library of Science (PLoS), 2013)
    Phenotypic traits may be gained and lost together because of pleiotropy, the involvement of common genes and networks, or because of simultaneous selection for multiple traits across environments (multiple-trait coevolution). ...
  • Schmiedel, Jörn M.; Carey, Lucas, 1980-; Lehner, Ben, 1978- (Nature Research, 2019)
    The effects of cell-to-cell variation (noise) in gene expression have proven difficult to quantify because of the mechanistic coupling of noise to mean expression. To independently quantify the effects of changes in mean ...
  • Blevins, William Robert, 1987-; Tavella, Teresa; Moro, Simone G.; Blasco Moreno, Bernat, 1986-; Closa-Mosquera, Adrià; Díez Antón, Juana, 1962-; Carey, Lucas, 1980-; Albà Soler, Mar (Nature Research, 2019)
    Cells responds to diverse stimuli by changing the levels of specific effector proteins. These changes are usually examined using high throughput RNA sequencing data (RNA-Seq); transcriptional regulation is generally assumed ...
  • Di Stefano, Marco; Di Giovanni, Francesca, 1985-; Pozharskaia, Vasilia; Gomar-Alba, Mercè; Baù, Davide; Carey, Lucas, 1980-; Marti-Renom, Marc A.; Mendoza, Manuel (Mendoza Palomares) (Genetics Society of America, 2020)
    The three-dimensional (3D) organization of chromosomes can influence transcription. However, the frequency and magnitude of these effects remain debated. To determine how changes in chromosome positioning affect transcription ...
  • van Dijk, David; Sharon, Elion; Lotan Pompan, Maya; Weinberger, Adina; Segal, Eran; Carey, Lucas, 1980- (Cold Spring Harbor Laboratory Press (CSHL Press), 2017)
    Transcription factors (TFs) are key mediators that propagate extracellular and intracellular signals through to changes in gene expression profiles. However, the rules by which promoters decode the amount of active TF into ...
  • Carey, Lucas, 1980-; Shalem, Ophir; Zeevi, Danny; Sharon, Elion; Keren, Leeat; Weinberger, Adina; Dahan, Orna; Pilpel, Yitzhak; Segal, Eran (Public Library of Science (PLoS), 2013)
    A full understanding of gene regulation requires an understanding of the contributions that the various regulatory regions have on gene expression. Although it is well established that sequences downstream of the main ...
  • Rest, Joshua S.; Morales, Christopher M.; Waldron, John B.; Opulente, Dana A.; Fisher, Julius; Moon, Seungjae; Bullaughey, Kevin; Carey, Lucas, 1980-; Dedousis, Demitri (University of Chicago Press, 2013)
    Levels of gene expression show considerable variation in eukaryotes, but no fine-scale maps have been made of the fitness consequences of such variation in controlled genetic backgrounds and environments. To address this, ...
  • Schikora Tamarit, Miquel Àngel; López-Grado i Salinas, Guillem; González Navasa, Carolina; Calderón, Irene; Marcos Fa, Xavi; Sas, Miquel; Carey, Lucas, 1980- (Elsevier, 2018)
    Organisms regulate gene expression through changes in the activity of transcription factors (TFs). In yeast, the response of genes to changes in TF activity is generally assumed to be encoded in the promoter. To directly ...
  • Espinar, Lorena; Schikora Tamarit, Miquel Àngel; Domingo Espinós, Júlia, 1991-; Carey, Lucas, 1980- (Cold Spring Harbor Laboratory Press (CSHL Press), 2018)
    Information that regulates gene expression is encoded throughout each gene but if different regulatory regions can be understood in isolation, or if they interact, is unknown. Here we measure mRNA levels for 10,000 open ...
  • Carey, Lucas, 1980-; Dijk, David van; Sloot, Peter MA; Kaandorp, Jaap A.; Segal, Eran (Public Library of Science (PLoS), 2013)
    The ability of cells to accurately control gene expression levels in response to extracellular cues is limited by the inherently stochastic nature of transcriptional regulation. A change in transcription factor (TF) activity ...
  • Gabaldà Sagarra, Marçal,1988-; Carey, Lucas, 1980-; García Ojalvo, Jordi (American Institute of Physics (AIP), 2018)
    Cellular information processing is generally attributed to the complex networks of genes and proteins that regulate cell behavior. It is still unclear, however, what are the main features of those networks that allow a ...
  • Duan, Chaorui; Huan, Qing; Chen, Xiaoshu; Wu, Shaohuan; Carey, Lucas, 1980-; He, Xionglei; Qian, Wenfeng (BioMed Central, 2018)
    Background: Mutation rates vary across the genome. Many trans factors that influence mutation rates have been identified, as have specific sequence motifs at the 1–7-bp scale, but cis elements remain poorly characterized. ...
  • Carey, Lucas, 1980- (eLife, 2015)
    Errors during transcription may play an important role in determining cellular phenotypes: the RNA polymerase error rate is >4 orders of magnitude higher than that of DNA polymerase and errors are amplified >1000-fold due ...
  • Dhar, Riddhiman; Missarova, Alsu, 1990-; Lehner, Ben, 1978-; Carey, Lucas, 1980- (eLife, 2019)
    Mutations frequently have outcomes that differ across individuals, even when these individuals are genetically identical and share a common environment. Moreover, individual microbial and mammalian cells can vary substantially ...
  • Dijk, David van; Dhar, Riddhiman; Missarova, Alsu, 1990-; Espinar, Lorena; Blevins, William Robert, 1987-; Lehner, Ben, 1978-; Carey, Lucas, 1980- (Nature Publishing Group, 2015)
    Isogenic cells show a large degree of variability in growth rate, even when cultured in the same environment. Such cell-to-cell variability in growth can alter sensitivity to antibiotics, chemotherapy and environmental ...
  • Chen, Ying; Li, Ke; Chu, Xiao; Carey, Lucas, 1980-; Qian, Wenfeng (Cold Spring Harbor Laboratory Press (CSHL Press), 2019)
    DNA replication perturbs the dosage balance among genes; at mid-S phase, early-replicating genes have doubled their copies while late-replicating ones have not. Dosage imbalance among genes, especially within members of a ...
  • Blevins, William Robert, 1987-; Carey, Lucas, 1980-; Albà Soler, Mar (BioMed Central, 2019)
    Objective: The objective of this experiment was to identify transcripts in baker’s yeast (Saccharomyces cerevisiae) that could have originated from previously non-coding genomic regions, or de novo. We generated this data ...

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