exRNA-eCLIP intersection analysis reveals a map of extracellular RNA binding proteins and associated RNAs across major human biofluids and carriers

Authors: 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

Source: In Cell Genomics 10 May 2023 3(5)

Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation

Authors: 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.

Source: In Cell 4 April 2019 177(2):446-462

exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids

Authors: Murillo, Oscar D., Thistlethwaite, William, Rozowsky, Joel, Subramanian, Sai Lakshmi, Lucero, Rocco, Shah, Neethu, Jackson, Andrew R., Srinivasan, Srimeenakshi, Chung, Allen, Laurent, Clara D., Kitchen, Robert R., Galeev, Timur, Warrell, Jonathan, Diao, James A., Welsh, Joshua A., Hanspers, Kristina, Riutta, Anders, Burgstaller-Muehlbacher, Sebastian, Shah, Ravi V., Yeri, Ashish, Jenkins, Lisa M., Ahsen, Mehmet E., Cordon-Cardo, Carlos, Dogra, Navneet, Gifford, Stacey M., Smith, Joshua T., Stolovitzky, Gustavo, Tewari, Ashutosh K., Wunsch, Benjamin H., Yadav, Kamlesh K., Danielson, Kirsty M., Filant, Justyna, Moeller, Courtney, Nejad, Parham, Paul, Anu, Simonson, Bridget, Wong, David K., Zhang, Xuan, Balaj, Leonora, Gandhi, Roopali, Sood, Anil K., Alexander, Roger P., Wang, Liang, Wu, Chunlei, Wong, David T.W., Galas, David J., Van Keuren-Jensen, Kendall, Patel, Tushar, Jones, Jennifer C., Das, Saumya, Cheung, Kei-Hoi, Pico, Alexander R., Su, Andrew I., Raffai, Robert L., Laurent, Louise C., Roth, Matthew E., Gerstein, Mark B., Milosavljevic, Aleksandar

Source: In Cell 4 April 2019 177(2):463-477

The EV antibody database: An interactive database of curated antibodies for extracellular vesicle and nanoparticle research

Authors: 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., De Hoff, Peter, Franklin, Jeffrey L., Raffai, Robert L., Das, Saumya, Routenberg, David A., Nolan, John P., Charest, Al, Laurent, Louise C., Alexander, Roger P.

Source: In Extracellular Vesicle June 2024 3

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

Authors: modENCODE Consortium, Gerstein, Mark B., Lu, Zhi John, Van Nostrand, Eric L., Cheng, Chao, Arshinoff, Bradley I., Liu, Tao, Yip, Kevin Y., Robilotto, Rebecca, Rechtsteiner, Andreas, Ikegami, Kohta, Alves, Pedro, Chateigner, Aurelien, Perry, Marc, Morris, Mitzi, Auerbach, Raymond K., Feng, Xin, Leng, Jing, Vielle, Anne, Niu, Wei, Rhrissorrakrai, Kahn, Agarwal, Ashish, Alexander, Roger P., Barber, Galt, Brdlik, Cathleen M., Brennan, Jennifer, Brouillet, Jeremy Jean, Carr, Adrian, Cheung, Ming-Sin, Clawson, Hiram, Contrino, Sergio, Dannenberg, Luke O., Dernburg, Abby F., Desai, Arshad, Dick, Lindsay, Dosé, Andréa C., Du, Jiang, Egelhofer, Thea, Ercan, Sevinc, Euskirchen, Ghia, Ewing, Brent, Feingold, Elise A., Gassmann, Reto, Good, Peter J., Green, Phil, Gullier, Francois, Gutwein, Michelle, Guyer, Mark S., Habegger, Lukas, Han, Ting, Henikoff, Jorja G., Henz, Stefan R., Hinrichs, Angie, Holster, Heather, Hyman, Tony, Iniguez, A. Leo, Janette, Judith, Jensen, Morten, Kato, Masaomi, Kent, W. James, Kephart, Ellen, Khivansara, Vishal, Khurana, Ekta, Kim, John K., Kolasinska-Zwierz, Paulina, Lai, Eric C., Latorre, Isabel, Leahey, Amber, Lewis, Suzanna, Lloyd, Paul, Lochovsky, Lucas, Lowdon, Rebecca F., Lubling, Yaniv, Lyne, Rachel, MacCoss, Michael, Mackowiak, Sebastian D., Mangone, Marco, McKay, Sheldon, Mecenas, Desirea, Merrihew, Gennifer, Miller, David M., Muroyama, Andrew, Murray, John I., Ooi, Siew-Loon, Pham, Hoang, Phippen, Taryn, Preston, Elica A., Rajewsky, Nikolaus, Rätsch, Gunnar, Rosenbaum, Heidi, Rozowsky, Joel, Rutherford, Kim, Ruzanov, Peter, Sarov, Mihail, Sasidharan, Rajkumar, Sboner, Andrea, Scheid, Paul, Segal, Eran, Shin, Hyunjin, Shou, Chong, Slack, Frank J., Slightam, Cindie, Smith, Richard, Spencer, William C., Stinson, E. O., Taing, Scott, Takasaki, Teruaki, Vafeados, Dionne, Voronina, Ksenia, Wang, Guilin, Washington, Nicole L., Whittle, Christina M., Wu, Beijing, Yan, Koon-Kiu, Zeller, Georg, Zha, Zheng, Zhong, Mei, Zhou, Xingliang, Ahringer, Julie, Strome, Susan, Gunsalus, Kristin C., Micklem, Gos, Liu, X. Shirley, Reinke, Valerie, Kim, Stuart K., Hillier, LaDeana W., Henikoff, Steven, Piano, Fabio, Snyder, Michael, Stein, Lincoln, Lieb, Jason D., Waterston, Robert H.

Source: Science, 2010 Dec . 330(6012), 1775-1787.

Access URL: https://www.jstor.org/stable/40986581

Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks

Authors: Yan, Koon-Kiu, Fang, Gang, Bhardwaj, Nitin, Alexander, Roger P., Gerstein, Mark, Petsko, Gregory A.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2010 May . 107(20), 9186-9191.

Access URL: https://www.jstor.org/stable/25681568

Evolutionary Genomics Reveals Conserved Structural Determinants of Signaling and Adaptation in Microbial Chemoreceptors

Authors: Alexander, Roger P., Zhulin, Igor B.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2007 Feb . 104(8), 2885-2890.

Access URL: https://www.jstor.org/stable/25426569

CheV: CheW-like coupling proteins at the core of the chemotaxis signaling network

Authors: Alexander, Roger P., Lowenthal, Andrew C., Harshey, Rasika M., Ottemann, Karen M.

Source: In Trends in Microbiology 2010 18(11):494-503

Open Problems in Extracellular RNA Data Analysis: Insights From an ERCC Online Workshop.

Authors: 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.

Source: Frontiers in Genetics; 1/3/2022, Vol. 12, p1-7, 7p

Subject Terms: RNA analysis, RNA-binding proteins, DATA analysis, VIDEO recording

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Annotating non-coding regions of the genome.

Authors: Alexander, Roger P.^1,2, Fang, Gang^1,2, Rozowsky, Joel², Snyder, Michael³, Gerstein, Mark B.^1,2,4 mark.gerstein@yale.edu

Source: Nature Reviews Genetics. Aug2010, Vol. 11 Issue 8, p559-571. 13p. 2 Diagrams, 4 Charts, 1 Graph.

Subject Terms: *HUMAN genome, *DNA, *PROTEINS, *GENOMICS, *NUCLEOTIDE sequence, *GENETIC transcription

Improved Reconstruction of In Silico Gene Regulatory Networks by Integrating Knockout and Perturbation Data.

Authors: Yip, Kevin Y.¹, Alexander, Roger P.², Koon-Kiu Yan², Gerstein, Mark^1,2,3 mark.gerstein@yale.edu

Source: PLoS ONE. 2010, Vol. 5 Issue 1, p1-9. 9p. 1 Diagram, 7 Charts, 1 Graph.

Subject Terms: *GENE expression, *DIFFERENTIAL equations, *HEREDITY, *BESSEL functions, *GENETIC regulation, *TRANSCENDENTAL functions, *BESSEL polynomials

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Comparative analysis of the transcriptome across distant species.

Authors: Gerstein, Mark B., Rozowsky, Joel, Yan, Koon-Kiu, Wang, Daifeng, Cheng, Chao, Brown, James B., Davis, Carrie A., Hillier, LaDeana, Sisu, Cristina, Li, Jingyi Jessica, Pei, Baikang, Harmanci, Arif O., Duff, Michael O., Djebali, Sarah, Alexander, Roger P., Alver, Burak H., Auerbach, Raymond, Bell, Kimberly, Bickel, Peter J., Boeck, Max E.

Source: Nature. 8/28/2014, Vol. 512 Issue 7515, p445-448. 4p. 2 Diagrams, 9 Graphs.

Subjects: RNA sequencing, GENOMICS, DEVELOPMENTAL genetics, ENCODE Project, COMPARATIVE studies, GENE expression