Search Results - "Alexander, Roger P"

Evolutionary genomics reveals conserved structural determinants of signaling and adaptation in microbial chemoreceptors by Alexander, Roger P, Zhulin, Igor B

“…As an important model for transmembrane signaling, methyl-accepting chemotaxis proteins (MCPs) have been extensively studied by using genetic, biochemical, and…”
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Improved reconstruction of in silico gene regulatory networks by integrating knockout and perturbation data by Yip, Kevin Y, Alexander, Roger P, Yan, Koon-Kiu, Gerstein, Mark

“…We performed computational reconstruction of the in silico gene regulatory networks in the DREAM3 Challenges. Our task was to learn the networks from two types…”
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Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks by Yan, Koon-Kiu, Fang, Gang, Bhardwaj, Nitin, Alexander, Roger P, Gerstein, Mark

“…The genome has often been called the operating system (OS) for a living organism. A computer OS is described by a regulatory control network termed the call…”
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Open Problems in Extracellular RNA Data Analysis: Insights From an ERCC Online Workshop by Alexander, Roger P, Kitchen, Robert R, Tosar, Juan Pablo, Roth, Matthew, Mestdagh, Pieter, Max, Klaas E A, Rozowsky, Joel, Kaczor-Urbanowicz, Karolina Elżbieta, Chang, Justin, Balaj, Leonora, Losic, Bojan, Van Nostrand, Eric L, LaPlante, Emily, Mateescu, Bogdan, White, Brian S, Yu, Rongshan, Milosavljevic, Aleksander, Stolovitzky, Gustavo, Spengler, Ryan M

“…We now know RNA can survive the harsh environment of biofluids when encapsulated in vesicles or by associating with lipoproteins or RNA binding proteins. These…”
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Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation by Srinivasan, Srimeenakshi, Yeri, Ashish, Cheah, Pike See, Chung, Allen, Danielson, Kirsty, De Hoff, Peter, Filant, Justyna, Laurent, Clara D., Laurent, Lucie D., Magee, Rogan, Moeller, Courtney, Murthy, Venkatesh L., Nejad, Parham, Paul, Anu, Rigoutsos, Isidore, Rodosthenous, Rodosthenis, Shah, Ravi V., Simonson, Bridget, To, Cuong, Wong, David, Yan, Irene K., Zhang, Xuan, Balaj, Leonora, Breakefield, Xandra O., Daaboul, George, Gandhi, Roopali, Lapidus, Jodi, Londin, Eric, Patel, Tushar, Raffai, Robert L., Sood, Anil K., Alexander, Roger P., Das, Saumya, Laurent, Louise C.

“…Poor reproducibility within and across studies arising from lack of knowledge regarding the performance of extracellular RNA (exRNA) isolation methods has…”
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Identification of genes critical for resistance to infection by West Nile virus using RNA-Seq analysis by Qian, Feng, Chung, Lisa, Zheng, Wei, Bruno, Vincent, Alexander, Roger P, Wang, Zhong, Wang, Xiaomei, Kurscheid, Sebastian, Zhao, Hongyu, Fikrig, Erol, Gerstein, Mark, Snyder, Michael, Montgomery, Ruth R

“…The West Nile virus (WNV) is an emerging infection of biodefense concern and there are no available treatments or vaccines. Here we used a high-throughput…”
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Annotating non-coding regions of the genome by Gerstein, Mark B, Alexander, Roger P, Fang, Gang, Rozowsky, Joel, Snyder, Michael

“…Key Points Most of the human genome consists of DNA that does not code for proteins. Annotating functional regions in the non-coding genome involves two…”
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Comparative genomic and protein sequence analyses of a complex system controlling bacterial chemotaxis by Wuichet, Kristin, Alexander, Roger P, Zhulin, Igor B

“…Molecular machinery governing bacterial chemotaxis consists of the CheA-CheY two-component system, an array of specialized chemoreceptors, and several…”
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Understanding modularity in molecular networks requires dynamics by Alexander, Roger P, Kim, Philip M, Emonet, Thierry, Gerstein, Mark B

“…The era of genome sequencing has produced long lists of the molecular parts from which cellular machines are constructed. A fundamental goal in systems biology…”
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CheV: CheW-like coupling proteins at the core of the chemotaxis signaling network by Alexander, Roger P, Lowenthal, Andrew C, Harshey, Rasika M, Ottemann, Karen M

“…Microbes have chemotactic signaling systems that enable them to detect and follow chemical gradients in their environments. The core of these sensory systems…”
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The EV antibody database: An interactive database of curated antibodies for extracellular vesicle and nanoparticle research by Morey, Amber, Ng, Martin, Spanos, Michail, Zhang, Piyan, Xu, Tuoye, Cheung, Willi, Chatterjee, Emeli, Gokulnath, Priyanka, Carnel-Amar, Natacha, Soares Chiaretti, Ana Luisa, Nelson, Collin, George, Jubin, Luo, Michelle, Chakraborty, Abhik, Perucci, Luiza, Jones, Jennifer C, Hoff, Peter De, Franklin, Jeffrey L, Raffai, Robert L, Das, Saumya, Routenberg, David A, Nolan, John P, Charest, Al, Laurent, Louise C, Alexander, Roger P

“…Antibodies are critical tools for research into extracellular vesicles (EVs) and other extracellular nanoparticles (ENPs), where they can be used for their…”
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exRNA-eCLIP intersection analysis reveals a map of extracellular RNA binding proteins and associated RNAs across major human biofluids and carriers by LaPlante, Emily L., Stürchler, Alessandra, Fullem, Robert, Chen, David, Starner, Anne C., Esquivel, Emmanuel, Alsop, Eric, Jackson, Andrew R., Ghiran, Ionita, Pereira, Getulio, Rozowsky, Joel, Chang, Justin, Gerstein, Mark B., Alexander, Roger P., Roth, Matthew E., Franklin, Jeffrey L., Coffey, Robert J., Raffai, Robert L., Mansuy, Isabelle M., Stavrakis, Stavros, deMello, Andrew J., Laurent, Louise C., Wang, Yi-Ting, Tsai, Chia-Feng, Liu, Tao, Jones, Jennifer, Van Keuren-Jensen, Kendall, Van Nostrand, Eric, Mateescu, Bogdan, Milosavljevic, Aleksandar

“…Although the role of RNA binding proteins (RBPs) in extracellular RNA (exRNA) biology is well established, their exRNA cargo and distribution across biofluids…”
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ExRNA Atlas analysis provides an exRNA census and reveals six types of vesicular and non-vesicular exRNA carrier profiles detectable across human body fluids by Murillo, Oscar D, Thistlethwaite, William, Lucero, Rocco, Subramanian, Sai Lakshmi, Shah, Neethu, Jackson, Andrew R, Rozowsky, Joel, Kitchen, Robert R, Diao, James, Galeev, Timur, Warrell, Jonathan, Hanspers, Kristina, Riutta, Anders, Pico, Alexander, Alexander, Roger P, Galas, David, Su, Andrew I, Laurent, Louise C, Jensen, Kendall, Roth, Matthew, Gerstein, Mark B, Milosavljevic, Aleksandar

“…Background: To gain insights into exRNA communication, the NIH Extracellular RNA Communication Consortium created the Extracellular RNA Atlas including 5309…”
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