Search Results - "Fields, Alexander P"

Pervasive functional translation of noncanonical human open reading frames by Chen, Jin, Brunner, Andreas-David, Cogan, J Zachery, Nuñez, James K, Fields, Alexander P, Adamson, Britt, Itzhak, Daniel N, Li, Jason Y, Mann, Matthias, Leonetti, Manuel D, Weissman, Jonathan S

“…Ribosome profiling has revealed pervasive but largely uncharacterized translation outside of canonical coding sequences (CDSs). In this work, we exploit a…”
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A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation by Fields, Alexander P., Rodriguez, Edwin H., Jovanovic, Marko, Stern-Ginossar, Noam, Haas, Brian J., Mertins, Philipp, Raychowdhury, Raktima, Hacohen, Nir, Carr, Steven A., Ingolia, Nicholas T., Regev, Aviv, Weissman, Jonathan S.

“…A fundamental goal of genomics is to identify the complete set of expressed proteins. Automated annotation strategies rely on assumptions about protein-coding…”
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Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation by Horlbeck, Max A, Gilbert, Luke A, Villalta, Jacqueline E, Adamson, Britt, Pak, Ryan A, Chen, Yuwen, Fields, Alexander P, Park, Chong Yon, Corn, Jacob E, Kampmann, Martin, Weissman, Jonathan S

“…We recently found that nucleosomes directly block access of CRISPR/Cas9 to DNA (Horlbeck et al., 2016). Here, we build on this observation with a comprehensive…”
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Dynamic profiling of the protein life cycle in response to pathogens by Jovanovic, Marko, Rooney, Michael S., Mertins, Philipp, Przybylski, Dariusz, Chevrier, Nicolas, Satija, Rahul, Rodriguez, Edwin H., Fields, Alexander P., Schwartz, Schraga, Raychowdhury, Raktima, Mumbach, Maxwell R., Eisenhaure, Thomas, Rabani, Michal, Gennert, Dave, Lu, Diana, Delorey, Toni, Weissman, Jonathan S., Carr, Steven A., Hacohen, Nir, Regev, Aviv

“…How the immune system readies for battle Although gene expression is tightly controlled at both the RNA and protein levels, the quantitative contribution of…”
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Electrokinetic trapping at the one nanometer limit by Fields, Alexander P, Cohen, Adam E

“…Anti-Brownian electrokinetic traps have been used to trap and study the free-solution dynamics of large protein complexes and long chains of DNA. Small…”
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Translation Initiation Site Profiling Reveals Widespread Synthesis of Non-AUG-Initiated Protein Isoforms in Yeast by Eisenberg, Amy R, Higdon, Andrea L, Hollerer, Ina, Fields, Alexander P, Jungreis, Irwin, Diamond, Paige D, Kellis, Manolis, Jovanovic, Marko, Brar, Gloria A

“…Genomic analyses in budding yeast have helped define the foundational principles of eukaryotic gene expression. However, in the absence of empirical methods…”
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Ultrasensitive Measurements of Microbial Rhodopsin Photocycles Using Photochromic FRET by Bayraktar, Halil, Fields, Alexander P., Kralj, Joel M., Spudich, John L., Rothschild, Kenneth J., Cohen, Adam E.

“…Microbial rhodopsins are an important class of light‐activated transmembrane proteins whose function is typically studied on bulk samples. Herein, we apply…”
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Evaluation of cell-free DNA approaches for multi-cancer early detection by Jamshidi, Arash, Liu, Minetta C., Klein, Eric A., Venn, Oliver, Hubbell, Earl, Beausang, John F., Gross, Samuel, Melton, Collin, Fields, Alexander P., Liu, Qinwen, Zhang, Nan, Fung, Eric T., Kurtzman, Kathryn N., Amini, Hamed, Betts, Craig, Civello, Daniel, Freese, Peter, Calef, Robert, Davydov, Konstantin, Fayzullina, Saniya, Hou, Chenlu, Jiang, Roger, Jung, Byoungsok, Tang, Susan, Demas, Vasiliki, Newman, Joshua, Sakarya, Onur, Scott, Eric, Shenoy, Archana, Shojaee, Seyedmehdi, Steffen, Kristan K., Nicula, Virgil, Chien, Tom C., Bagaria, Siddhartha, Hunkapiller, Nathan, Desai, Mohini, Dong, Zhao, Richards, Donald A., Yeatman, Timothy J., Cohn, Allen L., Thiel, David D., Berry, Donald A., Tummala, Mohan K., McIntyre, Kristi, Sekeres, Mikkael A., Bryce, Alan, Aravanis, Alexander M., Seiden, Michael V., Swanton, Charles

“…In the Circulating Cell-free Genome Atlas (NCT02889978) substudy 1, we evaluate several approaches for a circulating cell-free DNA (cfDNA)-based multi-cancer…”
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Convex Lens-Induced Confinement for Imaging Single Molecules by Leslie, Sabrina R, Fields, Alexander P, Cohen, Adam E

“…Fluorescence imaging is used to study the dynamics of a wide variety of single molecules in solution or attached to a surface. Two key challenges in this…”
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Euler buckling and nonlinear kinking of double-stranded DNA by Fields, Alexander P, Meyer, Elisabeth A, Cohen, Adam E

“…The bending stiffness of double-stranded DNA (dsDNA) at high curvatures is fundamental to its biological activity, yet this regime has been difficult to probe…”
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Optimal tracking of a Brownian particle by Fields, Alexander P, Cohen, Adam E

“…Optical tracking of a fluorescent particle in solution faces fundamental constraints due to Brownian motion, diffraction, and photon shot noise. Background…”
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The Cat That Caught the Canary: What To Do with Single-Molecule Trapping by Cohen, Adam E, Fields, Alexander P

“…It has recently become possible to trap individual fluorescent biomolecules in aqueous solution by using real-time tracking and active feedback to suppress…”
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Anti-Brownian traps for studies on single molecules by Fields, Alexander P, Cohen, Adam E

“…Until recently, Brownian motion was seen as an immutable feature of small particles in room-temperature liquids. Molecules, viruses, organelles, and small…”
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In Honor of W.E. Moerner: Confining Molecules for Single-Molecule Spectroscopy by Cohen, Adam E., Fields, Alexander P., Hou, Jennifer H., Leslie, Sabrina R., Shon, Min Ju

“…Single‐molecule spectroscopy provides a wealth of information on the dynamics and interactions of complex biological molecules. Yet these measurements are…”
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Abstract 2114: HPV-driven cancers show distinct methylation signatures in cell-free DNA (cfDNA) by Calef, Robert, Venn, Oliver, Maher, M. Cyrus, Beausang, John F., Hubbell, Earl, Patel, Aman, Fields, Alexander P., Bredno, Joerg, Jamshidi, Arash, Aravanis, Alexander M.

“…Abstract Accurate tissue of origin (TOO) prediction is crucial for effective clinical follow-up in early cancer detection from blood. In the second substudy of…”
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Abstract 2308: Classifier performance of a cfDNA-based multi-cancer detection test on uncommon cancer types by Bredno, Joerg, Gross, Samuel, Fields, Alexander P., Kurtzman, Kathryn N., Shaknovich, Rita, Yecies, Jessica, Chen, Xiaoji, Schellenberger, Jan, Scott, Eric, Dong, Zhao, Fung, Eric T., Hartman, Anne-Renee, Hubbell, Earl, Jamshidi, Arash, Aravanis, Alexander M., Venn, Oliver

“…Abstract Introduction: We previously reported multi-cancer detection capabilities across 20 cancer types in the Circulating Cell-free Genome Atlas study (CCGA;…”
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Abstract 139: cfDNA methylation profiling distinguishes lineage-specific hematologic malignancies by Liu, Qinwen, Shaknovich, Rita, Chen, Xiaoji, Dong, Zhao, Maher, M. C., Gross, Samuel, Fields, Alexander P., Schellenberger, Jan, Kurtzman, Kathryn N., Fung, Eric T., Hartman, Anne-Renee, Hubbell, Earl, Jamshidi, Arash, Aravanis, Alexander M., Venn, Oliver

“…Abstract Introduction: Hematologic (heme) malignancies and their precursor conditions are highly prevalent. They are also diverse in biology, clinical…”
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Simultaneous multi-cancer detection and tissue of origin (TOO) localization using targeted bisulfite sequencing of plasma cell-free DNA (cfDNA) by Oxnard, Geoffrey R., Klein, Eric A., Seiden, Michael, Hubbell, Earl, Venn, Oliver, Jamshidi, Arash, Zhang, Nan, Beausang, John F., Gross, Samuel, Kurtzman, Kathryn N., Fung, Eric T., Yecies, Jessica, Shaknovich, Rita, Fields, Alexander P., Sekeres, Mikkael A., Richards, Donald A., Yu, Peter Paul, Aravanis, Alex, Hartman, Anne-Renee, Liu, Minetta C.

“…Abstract only 44 Background: A noninvasive cfDNA blood test detecting multiple cancers at earlier stages could decrease cancer mortality. In earlier discovery…”
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Tu1836 TUMOR AREA AND MICROSCOPIC EXTENT OF INVASION DETERMINE CIRCULATING TUMOR CELL-FREE DNA FRACTION IN PLASMA AND DETECTABILITY OF COLORECTAL CANCER by Bredno, Joerg, Lipson, Jafi, Venn, Oliver, Gross, Samuel, Fields, Alexander P., Beausang, John, Liu, Qinwen, Brooks, Jackie, Chen, Xiaoji, Lopatin, Margarita, Liu, Hai, Zhang, Nan, Zhang, Lori, Wu, Tony, Allen, Brian, Hartman, Anne-Renee, Hubbell, Earl, Jamshidi, Arash, Aravanis, Alexander

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Pervasive functional translation of non-canonical human open reading frames by Chen, Jin, Brunner, Andreas-David, Cogan, J. Zachery, Nuñez, James K., Fields, Alexander P., Adamson, Britt, Itzhak, Daniel N., Li, Jason Y., Mann, Matthias, Leonetti, Manuel D., Weissman, Jonathan S.

“…Ribosome profiling has revealed pervasive but largely uncharacterized translation outside of canonical coding sequences (CDSs). Here, we exploit a systematic…”
Get full text