Search Results - "Fordyce, Polly"

On the dependent recognition of some long zinc finger proteins by Zuo, Zheng, Billings, Timothy, Walker, Michael, Petkov, Petko M, Fordyce, Polly M, Stormo, Gary D

“…Abstract The human genome contains about 800 C2H2 zinc finger proteins (ZFPs), and most of them are composed of long arrays of zinc fingers. Standard ZFP…”
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micrIO: an open-source autosampler and fraction collector for automated microfluidic input-output by Longwell, Scott A, Fordyce, Polly M

“…Microfluidic devices are an enabling technology for many labs, facilitating a wide range of applications spanning high-throughput encapsulation, molecular…”
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Tuning T cell receptor sensitivity through catch bond engineering by Zhao, Xiang, Kolawole, Elizabeth M, Chan, Waipan, Feng, Yinnian, Yang, Xinbo, Gee, Marvin H, Jude, Kevin M, Sibener, Leah V, Fordyce, Polly M, Germain, Ronald N, Evavold, Brian D, Garcia, K Christopher

“…Adoptive cell therapy using engineered T cell receptors (TCRs) is a promising approach for targeting cancer antigens, but tumor-reactive TCRs are often weakly…”
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A bead-based method for high-throughput mapping of the sequence- and force-dependence of T cell activation by Feng, Yinnian, Zhao, Xiang, White, Adam K., Garcia, K. Christopher, Fordyce, Polly M.

“…Adaptive immunity relies on T lymphocytes that use αβ T cell receptors (TCRs) to discriminate among peptides presented by major histocompatibility complex…”
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Comprehensive, high-resolution binding energy landscapes reveal context dependencies of transcription factor binding by Le, Daniel D., Shimko, Tyler C., Aditham, Arjun K., Keys, Allison M., Longwell, Scott A., Orenstein, Yaron, Fordyce, Polly M.

“…Transcription factors (TFs) are primary regulators of gene expression in cells, where they bind specific genomic target sites to control transcription…”
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Double Emulsion Picoreactors for High-Throughput Single-Cell Encapsulation and Phenotyping via FACS by Brower, Kara K, Khariton, Margarita, Suzuki, Peter H, Still, Chris, Kim, Gaeun, Calhoun, Suzanne G. K, Qi, Lei S, Wang, Bo, Fordyce, Polly M

“…In the past five years, droplet microfluidic techniques have unlocked new opportunities for the high-throughput genome-wide analysis of single cells,…”
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High-throughput chromatin accessibility profiling at single-cell resolution by Mezger, Anja, Klemm, Sandy, Mann, Ishminder, Brower, Kara, Mir, Alain, Bostick, Magnolia, Farmer, Andrew, Fordyce, Polly, Linnarsson, Sten, Greenleaf, William

“…Here we develop a high-throughput single-cell ATAC-seq (assay for transposition of accessible chromatin) method to measure physical access to DNA in whole…”
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Design automation of microfluidic single and double emulsion droplets with machine learning by Lashkaripour, Ali, McIntyre, David P., Calhoun, Suzanne G. K., Krauth, Karl, Densmore, Douglas M., Fordyce, Polly M.

“…Droplet microfluidics enables kHz screening of picoliter samples at a fraction of the cost of other high-throughput approaches. However, generating stable…”
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Double emulsion flow cytometry with high-throughput single droplet isolation and nucleic acid recovery by Brower, Kara K, Carswell-Crumpton, Catherine, Klemm, Sandy, Cruz, Bianca, Kim, Gaeun, Calhoun, Suzanne G K, Nichols, Lisa, Fordyce, Polly M

“…Droplet microfluidics has made large impacts in diverse areas such as enzyme evolution, chemical product screening, polymer engineering, and single-cell…”
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DeCoDe: degenerate codon design for complete protein-coding DNA libraries by Shimko, Tyler C, Fordyce, Polly M, Orenstein, Yaron

“…Abstract Motivation High-throughput protein screening is a critical technique for dissecting and designing protein function. Libraries for these assays can be…”
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Diversification of DNA binding specificities enabled SREBP transcription regulators to expand the repertoire of cellular functions that they govern in fungi by Del Olmo Toledo, Valentina, Puccinelli, Robert, Fordyce, Polly M, Pérez, J Christian

“…The Sterol Regulatory Element Binding Proteins (SREBPs) are basic-helix-loop-helix transcription regulators that control the expression of sterol biosynthesis…”
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Decoupling of catalysis and transition state analog binding from mutations throughout a phosphatase revealed by high-throughput enzymology by Markin, Craig J, Mokhtari, Daniel A, Du, Siyuan, Doukov, Tzanko, Sunden, Fanny, Cook, Jordan A, Fordyce, Polly M, Herschlag, Daniel

“…Using high-throughput microfluidic enzyme kinetics (HT-MEK), we measured over 9,000 inhibition curves detailing impacts of 1,004 single-site mutations…”
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An open-source software analysis package for Microspheres with Ratiometric Barcode Lanthanide Encoding (MRBLEs) by Harink, Björn, Nguyen, Huy, Thorn, Kurt, Fordyce, Polly

“…Multiplexed bioassays, in which multiple analytes of interest are probed in parallel within a single small volume, have greatly accelerated the pace of…”
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Structure of the transcriptional network controlling white‐opaque switching in Candida albicans by Hernday, Aaron D., Lohse, Matthew B., Fordyce, Polly M., Nobile, Clarissa J., DeRisi, Joseph L., Johnson, Alexander D.

“…Summary The human fungal pathogen Candida albicans can switch between two phenotypic cell types, termed ‘white’ and ‘opaque’. Both cell types are heritable for…”
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Alleviating Cell Lysate-Induced Inhibition to Enable RT-PCR from Single Cells in Picoliter-Volume Double Emulsion Droplets by Khariton, Margarita, McClune, Conor J., Brower, Kara K., Klemm, Sandy, Sattely, Elizabeth S., Fordyce, Polly M., Wang, Bo

“…Microfluidic droplet assays enable single-cell polymerase chain reaction (PCR) and sequencing analyses at unprecedented scales, with most methods encapsulating…”
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Phosphatase specificity principles uncovered by MRBLE:Dephos and global substrate identification by Hein, Jamin B, Nguyen, Hieu T, Garvanska, Dimitriya H, Nasa, Isha, Kruse, Thomas, Feng, Yinnian, Lopez Mendez, Blanca, Davey, Norman, Kettenbach, Arminja N, Fordyce, Polly M, Nilsson, Jakob

“…Phosphoprotein phosphatases (PPPs) regulate major signaling pathways, but the determinants of phosphatase specificity are poorly understood. This is because…”
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Microfluidic encapsulation of photosynthetic cyanobacteria in hydrogel microparticles augments oxygen delivery to rescue ischemic myocardium by Stapleton, Lyndsay Mariah, Farry, Justin Michael, Zhu, Yuanjia, Lucian, Haley Joan, Wang, Hanjay, Paulsen, Michael John, Totherow, Kailey Pearl, Roth, Gillie Agmon, Brower, Kara Kimberly, Fordyce, Polly Morrell, Appel, Eric Andrew, Woo, Yi-Ping Joseph

“…Cardiovascular disease, primarily caused by coronary artery disease, is the leading cause of death in the United States. While standard clinical interventions…”
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De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis by DeRisi, Joseph L, Quake, Stephen R, Fordyce, Polly M, Gerber, Doron, Tran, Danh, Zheng, Jiashun, Li, Hao

“…Gene expression is regulated in part by protein transcription factors that bind target regulatory DNA sequences. Predicting DNA binding sites and affinities…”
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Quantitative mapping of protein-peptide affinity landscapes using spectrally encoded beads by Nguyen, Huy Quoc, Roy, Jagoree, Harink, Björn, Damle, Nikhil P, Latorraca, Naomi R, Baxter, Brian C, Brower, Kara, Longwell, Scott A, Kortemme, Tanja, Thorn, Kurt S, Cyert, Martha S, Fordyce, Polly Morrell

“…Transient, regulated binding of globular protein domains to Short Linear Motifs (SLiMs) in disordered regions of other proteins drives cellular signaling…”
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Satb1 integrates DNA binding site geometry and torsional stress to differentially target nucleosome-dense regions by Ghosh, Rajarshi P., Shi, Quanming, Yang, Linfeng, Reddick, Michael P., Nikitina, Tatiana, Zhurkin, Victor B., Fordyce, Polly, Stasevich, Timothy J., Chang, Howard Y., Greenleaf, William J., Liphardt, Jan T.

“…The Satb1 genome organizer regulates multiple cellular and developmental processes. It is not yet clear how Satb1 selects different sets of targets throughout…”
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