Search Results - "Finkelstein, J"

Human cohesin compacts DNA by loop extrusion by Kim, Yoori, Shi, Zhubing, Zhang, Hongshan, Finkelstein, Ilya J, Yu, Hongtao

“…Cohesin is a chromosome-bound, multisubunit adenosine triphosphatase complex. After loading onto chromosomes, it generates loops to regulate chromosome…”
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Kinetic Basis for DNA Target Specificity of CRISPR-Cas12a by Strohkendl, Isabel, Saifuddin, Fatema A., Rybarski, James R., Finkelstein, Ilya J., Russell, Rick

“…Class 2 CRISPR-Cas nucleases are programmable genome editing tools with promising applications in human health and disease. However, DNA cleavage at off-target…”
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Structure-based design of prefusion-stabilized SARS-CoV-2 spikes by Hsieh, Ching-Lin, Goldsmith, Jory A, Schaub, Jeffrey M, DiVenere, Andrea M, Kuo, Hung-Che, Javanmardi, Kamyab, Le, Kevin C, Wrapp, Daniel, Lee, Alison G, Liu, Yutong, Chou, Chia-Wei, Byrne, Patrick O, Hjorth, Christy K, Johnson, Nicole V, Ludes-Meyers, John, Nguyen, Annalee W, Park, Juyeon, Wang, Nianshuang, Amengor, Dzifa, Lavinder, Jason J, Ippolito, Gregory C, Maynard, Jennifer A, Finkelstein, Ilya J, McLellan, Jason S

“…The coronavirus disease 2019 (COVID-19) pandemic has led to accelerated efforts to develop therapeutics and vaccines. A key target of these efforts is the…”
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Polymerase theta-helicase promotes end joining by stripping single-stranded DNA-binding proteins and bridging DNA ends by Schaub, Jeffrey M, Soniat, Michael M, Finkelstein, Ilya J

“…Abstract Homologous recombination-deficient cancers rely on DNA polymerase Theta (Polθ)-Mediated End Joining (TMEJ), an alternative double-strand break repair…”
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Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes by Voss, William N, Hou, Yixuan J, Johnson, Nicole V, Delidakis, George, Kim, Jin Eyun, Javanmardi, Kamyab, Horton, Andrew P, Bartzoka, Foteini, Paresi, Chelsea J, Tanno, Yuri, Chou, Chia-Wei, Abbasi, Shawn A, Pickens, Whitney, George, Katia, Boutz, Daniel R, Towers, Dalton M, McDaniel, Jonathan R, Billick, Daniel, Goike, Jule, Rowe, Lori, Batra, Dhwani, Pohl, Jan, Lee, Justin, Gangappa, Shivaprakash, Sambhara, Suryaprakash, Gadush, Michelle, Wang, Nianshuang, Person, Maria D, Iverson, Brent L, Gollihar, Jimmy D, Dye, John, Herbert, Andrew, Finkelstein, Ilya J, Baric, Ralph S, McLellan, Jason S, Georgiou, George, Lavinder, Jason J, Ippolito, Gregory C

“…The molecular composition and binding epitopes of the immunoglobulin G (IgG) antibodies that circulate in blood plasma following SARS-CoV-2 infection are…”
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Distinct horizontal transfer mechanisms for type I and type V CRISPR-associated transposons by Hu, Kuang, Chou, Chia-Wei, Wilke, Claus O., Finkelstein, Ilya J.

“…CASTs use both CRISPR-associated proteins and Tn7-family transposons for RNA-guided vertical and horizontal transmission. CASTs encode minimal CRISPR arrays…”
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Indel-correcting DNA barcodes for high-throughput sequencing by Hawkins, John A., Jones, Stephen K., Finkelstein, Ilya J., Press, William H.

“…Many large-scale, high-throughput experiments use DNA barcodes, short DNA sequences prepended to DNA libraries, for identification of individuals in pooled…”
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Poly(ADP-ribose) polymerase-1 antagonizes DNA resection at double-strand breaks by Caron, Marie-Christine, Sharma, Ajit K., O’Sullivan, Julia, Myler, Logan R., Ferreira, Maria Tedim, Rodrigue, Amélie, Coulombe, Yan, Ethier, Chantal, Gagné, Jean-Philippe, Langelier, Marie-France, Pascal, John M., Finkelstein, Ilya J., Hendzel, Michael J., Poirier, Guy G., Masson, Jean-Yves

“…PARP-1 is rapidly recruited and activated by DNA double-strand breaks (DSBs). Upon activation, PARP-1 synthesizes a structurally complex polymer composed of…”
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Comparison of modern Langevin integrators for simulations of coarse-grained polymer melts by Finkelstein, J., Fiorin, G., Seibold, B.

“…For a wide range of phenomena, current computational ability does not always allow for atomistic simulations of high-dimensional molecular systems to reach…”
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Massively parallel profiling of RNA-targeting CRISPR-Cas13d by Kuo, Hung-Che, Prupes, Joshua, Chou, Chia-Wei, Finkelstein, Ilya J.

“…CRISPR-Cas13d cleaves RNA and is used in vivo and for diagnostics. However, a systematic understanding of its RNA binding and cleavage specificity is lacking…”
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High-fidelity intravoxel incoherent motion parameter mapping using locally low-rank and subspace modeling by Finkelstein, Alan J., Liao, Congyu, Cao, Xiaozhi, Mani, Merry, Schifitto, Giovanni, Zhong, Jianhui

“…•Incorporation of advanced reconstruction techniques, including correction of motion-induced phase errors, locally low-rank constraint, and subspace modeling,…”
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Assembly and Translocation of a CRISPR-Cas Primed Acquisition Complex by Dillard, Kaylee E., Brown, Maxwell W., Johnson, Nicole V., Xiao, Yibei, Dolan, Adam, Hernandez, Erik, Dahlhauser, Samuel D., Kim, Yoori, Myler, Logan R., Anslyn, Eric V., Ke, Ailong, Finkelstein, Ilya J.

“…CRISPR-Cas systems confer an adaptive immunity against viruses. Following viral injection, Cas1-Cas2 integrates segments of the viral genome (spacers) into the…”
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Vitamin B12 status in pregnant women and their infants in South India by Finkelstein, J L, Kurpad, A V, Thomas, T, Srinivasan, K, Duggan, C

“…Background/Objectives: Vitamin B 12 deficiency during pregnancy has been associated with increased risk of adverse perinatal outcomes. However, few studies…”
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Intrinsically disordered regions regulate both catalytic and non-catalytic activities of the MutLα mismatch repair complex by Kim, Yoori, Furman, Christopher M, Manhart, Carol M, Alani, Eric, Finkelstein, Ilya J

“…Abstract Intrinsically disordered regions (IDRs) are present in at least 30% of the eukaryotic proteome and are enriched in chromatin-associated proteins…”
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Asgard archaea defense systems and their roles in the origin of eukaryotic immunity by Leão, Pedro, Little, Mary E., Appler, Kathryn E., Sahaya, Daphne, Aguilar-Pine, Emily, Currie, Kathryn, Finkelstein, Ilya J., De Anda, Valerie, Baker, Brett J.

“…Dozens of new antiviral systems have been recently characterized in bacteria. Some of these systems are present in eukaryotes and appear to have originated in…”
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Massively Parallel Biophysical Analysis of CRISPR-Cas Complexes on Next Generation Sequencing Chips by Jung, Cheulhee, Hawkins, John A., Jones, Stephen K., Xiao, Yibei, Rybarski, James R., Dillard, Kaylee E., Hussmann, Jeffrey, Saifuddin, Fatema A., Savran, Cagri A., Ellington, Andrew D., Ke, Ailong, Press, William H., Finkelstein, Ilya J.

“…CRISPR-Cas nucleoproteins target foreign DNA via base pairing with a crRNA. However, a quantitative description of protein binding and nuclease activation at…”
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The promoter-search mechanism of Escherichia coli RNA polymerase is dominated by three-dimensional diffusion by Wang, Feng, Redding, Sy, Finkelstein, Ilya J, Gorman, Jason, Reichman, David R, Greene, Eric C

“…The transcription machinery must locate specific promoter sequences among a vast excess of nonspecific DNA. Real-time single-molecule experiments with E. coli…”
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Vitamin B 12 status in pregnant women and their infants in South India by Finkelstein, J L, Kurpad, A V, Thomas, T, Srinivasan, K, Duggan, C

“…Vitamin B deficiency during pregnancy has been associated with increased risk of adverse perinatal outcomes. However, few studies have investigated the burden…”
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Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9 by Hibshman, Grace N., Bravo, Jack P. K., Hooper, Matthew M., Dangerfield, Tyler L., Zhang, Hongshan, Finkelstein, Ilya J., Johnson, Kenneth A., Taylor, David W.

“…CRISPR-Cas9 is a powerful tool for genome editing, but the strict requirement for an NGG protospacer-adjacent motif (PAM) sequence immediately next to the DNA…”
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Single-Molecule Imaging of FtsK Translocation Reveals Mechanistic Features of Protein-Protein Collisions on DNA by Lee, Ja Yil, Finkelstein, Ilya J., Arciszewska, Lidia K., Sherratt, David J., Greene, Eric C.

“…In physiological settings, DNA translocases will encounter DNA-bound proteins, which must be dislodged or bypassed to allow continued translocation. FtsK is a…”
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