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Siddharth S. Dey, Ph.D. - Publications

Affiliations: 
Chemical Engineering University of California, Berkeley, Berkeley, CA, United States 
Area:
viral gene delivery, stem cells
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18 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Batjargal T, Zappa F, Grant RJ, Piscopio RA, Chialastri A, Dey SS, Acosta-Alvear D, Wilson MZ. Optogenetic control of the integrated stress response reveals proportional encoding and the stress memory landscape. Cell Systems. 14: 551-562.e5. PMID 37473728 DOI: 10.1016/j.cels.2023.06.001  0.649
2023 Chialastri A, Sarkar S, Schauer EE, Lamba S, Dey SS. Combinatorial quantification of 5mC and 5hmC at individual CpG dyads and the transcriptome in single cells reveals modulators of DNA methylation maintenance fidelity. Biorxiv : the Preprint Server For Biology. PMID 37205524 DOI: 10.1101/2023.05.06.539708  0.729
2021 Chialastri A, Wangsanuwat C, Dey SS. Integrated single-cell sequencing of 5-hydroxymethylcytosine and genomic DNA using scH&G-seq. Star Protocols. 2: 101016. PMID 34950891 DOI: 10.1016/j.xpro.2021.101016  0.743
2021 Wangsanuwat C, Chialastri A, Aldeguer JF, Rivron NC, Dey SS. A probabilistic framework for cellular lineage reconstruction using integrated single-cell 5-hydroxymethylcytosine and genomic DNA sequencing. Cell Reports Methods. 1. PMID 34590075 DOI: 10.1016/j.crmeth.2021.100060  0.738
2021 Sen M, Mooijman D, Chialastri A, Boisset JC, Popovic M, Heindryckx B, Chuva de Sousa Lopes SM, Dey SS, van Oudenaarden A. Strand-specific single-cell methylomics reveals distinct modes of DNA demethylation dynamics during early mammalian development. Nature Communications. 12: 1286. PMID 33627650 DOI: 10.1038/s41467-021-21532-6  0.764
2020 Markodimitraki CM, Rang FJ, Rooijers K, de Vries SS, Chialastri A, de Luca KL, Lochs SJA, Mooijman D, Dey SS, Kind J. Simultaneous quantification of protein-DNA interactions and transcriptomes in single cells with scDam&T-seq. Nature Protocols. PMID 32350457 DOI: 10.1038/S41596-020-0314-8  0.743
2020 Gell JJ, Liu W, Sosa E, Chialastri A, Hancock G, Tao Y, Wamaitha SE, Bower G, Dey SS, Clark AT. An Extended Culture System that Supports Human Primordial Germ Cell-like Cell Survival and Initiation of DNA Methylation Erasure. Stem Cell Reports. PMID 32059791 DOI: 10.1016/J.Stemcr.2020.01.009  0.738
2019 Jang J, Han D, Golkaram M, Audouard M, Liu G, Bridges D, Hellander S, Chialastri A, Dey SS, Petzold LR, Kosik KS. Control over single-cell distribution of G1 lengths by WNT governs pluripotency. Plos Biology. 17: e3000453. PMID 31557150 DOI: 10.1371/Journal.Pbio.3000453  0.7
2019 Rooijers K, Markodimitraki CM, Rang FJ, de Vries SS, Chialastri A, de Luca KL, Mooijman D, Dey SS, Kind J. Simultaneous quantification of protein-DNA contacts and transcriptomes in single cells. Nature Biotechnology. PMID 31209373 DOI: 10.1038/S41587-019-0150-Y  0.761
2016 Mooijman D, Dey SS, Boisset JC, Crosetto N, van Oudenaarden A. Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction. Nature Biotechnology. PMID 27347753 DOI: 10.1038/Nbt.3598  0.683
2015 Kind J, Pagie L, de Vries SS, Nahidiazar L, Dey SS, Bienko M, Zhan Y, Lajoie B, de Graaf CA, Amendola M, Fudenberg G, Imakaev M, Mirny LA, Jalink K, Dekker J, et al. Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells. Cell. 163: 134-47. PMID 26365489 DOI: 10.1016/J.Cell.2015.08.040  0.619
2015 Dey SS, Foley JE, Limsirichai P, Schaffer DV, Arkin AP. Orthogonal control of expression mean and variance by epigenetic features at different genomic loci. Molecular Systems Biology. 11: 806. PMID 25943345 DOI: 10.15252/Msb.20145704  0.649
2015 Dey SS, Kester L, Spanjaard B, Bienko M, van Oudenaarden A. Integrated genome and transcriptome sequencing of the same cell. Nature Biotechnology. 33: 285-9. PMID 25599178 DOI: 10.1038/Nbt.3129  0.677
2012 Miller-Jensen K, Dey SS, Pham N, Foley JE, Arkin AP, Schaffer DV. Chromatin accessibility at the HIV LTR promoter sets a threshold for NF-κB mediated viral gene expression. Integrative Biology : Quantitative Biosciences From Nano to Macro. 4: 661-71. PMID 22555315 DOI: 10.1039/C2Ib20009K  0.65
2012 Dey SS, Xue Y, Joachimiak MP, Friedland GD, Burnett JC, Zhou Q, Arkin AP, Schaffer DV. Mutual information analysis reveals coevolving residues in Tat that compensate for two distinct functions in HIV-1 gene expression. The Journal of Biological Chemistry. 287: 7945-55. PMID 22253435 DOI: 10.1074/Jbc.M111.302653  0.608
2011 Miller-Jensen K, Dey SS, Schaffer DV, Arkin AP. Varying virulence: epigenetic control of expression noise and disease processes. Trends in Biotechnology. 29: 517-25. PMID 21700350 DOI: 10.1016/J.Tibtech.2011.05.004  0.532
2005 Mehta G, Sen S, Dey S. (1S*,2S*,4S*,5S*)-Cyclohexane-1,2,4,5-tetrol monohydrate. Acta Crystallographica. Section C, Crystal Structure Communications. 61: o358-60. PMID 15930683 DOI: 10.1107/S0108270105011066  0.366
2005 Mehta G, Sen S, Dey S. (1R*,2S*,4S*,5S*)-Cyclohexane-1,2,4,5-tetrol Acta Crystallographica Section E Structure Reports Online. 61: o920-o922. DOI: 10.1107/S1600536805006653  0.363
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