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3. Genetic effects on gene expression across human tissues

Author

Aguet, François, Brown, Andrew A, Castel, Stephane E, Davis, Joe R, He, Yuan, Jo, Brian, Mohammadi, Pejman, Park, YoSon, Parsana, Princy, Segrè, Ayellet V, Strober, Benjamin J, Zappala, Zachary, Cummings, Beryl B, Gelfand, Ellen T, Hadley, Kane, Huang, Katherine H, Lek, Monkol, Li, Xiao, Nedzel, Jared L, Nguyen, Duyen Y, Noble, Michael S, Sullivan, Timothy J, Tukiainen, Taru, MacArthur, Daniel G, Getz, Gad, Addington, Anjene, Guan, Ping, Koester, Susan, Little, A Roger, Lockhart, Nicole C, Moore, Helen M, Rao, Abhi, Struewing, Jeffery P, Volpi, Simona, Brigham, Lori E, Hasz, Richard, Hunter, Marcus, Johns, Christopher, Johnson, Mark, Kopen, Gene, Leinweber, William F, Lonsdale, John T, McDonald, Alisa, Mestichelli, Bernadette, Myer, Kevin, Roe, Bryan, Salvatore, Michael, Shad, Saboor, Thomas, Jeffrey A, Walters, Gary, Washington, Michael, Wheeler, Joseph, Bridge, Jason, Foster, Barbara A, Gillard, Bryan M, Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T, Jewell, Scott D, Montroy, Robert G, Rohrer, Daniel C, Valley, Dana, Mash, Deborah C, Davis, David A, Sobin, Leslie, Barcus, Mary E, Branton, Philip A, Abell, Nathan S, Balliu, Brunilda, Delaneau, Olivier, Frésard, Laure, Gamazon, Eric R, Garrido-Martín, Diego, Gewirtz, Ariel DH, Gliner, Genna, Gloudemans, Michael J, Han, Buhm, He, Amy Z, Hormozdiari, Farhad, Li, Xin, Liu, Boxiang, Kang, Eun Yong, McDowell, Ian C, Ongen, Halit, Palowitch, John J, Peterson, Christine B, Quon, Gerald, Ripke, Stephan, Saha, Ashis, Shabalin, Andrey A, Shimko, Tyler C, Sul, Jae Hoon, Teran, Nicole A, Tsang, Emily K, Zhang, Hailei, Zhou, Yi-Hui, Bustamante, Carlos D, Cox, Nancy J, and Guigó, Roderic

Subjects
Human Genome, Genetics, Biotechnology, 1.1 Normal biological development and functioning, 2.1 Biological and endogenous factors, Aetiology, Underpinning research, Generic health relevance, Alleles, Chromosomes, Human, Disease, Female, Gene Expression Profiling, Gene Expression Regulation, Genetic Variation, Genome, Human, Genotype, Humans, Male, Organ Specificity, Quantitative Trait Loci, GTEx Consortium, Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group, Statistical Methods groups—Analysis Working Group, Enhancing GTEx (eGTEx) groups, NIH Common Fund, NIH/NCI, NIH/NHGRI, NIH/NIMH, NIH/NIDA, Biospecimen Collection Source Site—NDRI, Biospecimen Collection Source Site—RPCI, Biospecimen Core Resource—VARI, Brain Bank Repository—University of Miami Brain Endowment Bank, Leidos Biomedical—Project Management, ELSI Study, Genome Browser Data Integration &Visualization—EBI, Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz, Lead analysts:, Laboratory, Data Analysis &Coordinating Center (LDACC):, NIH program management:, Biospecimen collection:, Pathology:, eQTL manuscript working group:, General Science & Technology
Abstract

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of disease.

Published
2017

11. On Audre and Malcolm’s Advice

Author

Hunter, Marcus Anthony, McHale, Susan M., Series editor, King, Valarie, Series editor, Van Hook, Jennifer, Series editor, M. Burton, Linda, editor, Burton, Dorian, editor, and M. McHale, Susan, editor

Published
2016
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13. Us Versus Them: How California State Prisons Justify Solitary Confinement

Author

Williams, Anthony James, Hunter, Marcus A1, Williams, Anthony James, Williams, Anthony James, Hunter, Marcus A1, and Williams, Anthony James

Abstract

This dissertation examines how actors across the California state prison system use inconvenience as a strategy to harm incarcerated people through solitary confinement. Prison administration imbue prison staff with a frightening level of discretionary power over the lives of incarcerated people. Prison staff use safety, security, and punishment to justify the practice. Using their discretionary power, individual actors can and do take away days, weeks, years, and decades from the lives of those deemed inconvenient based on their identity (e.g., perceived ethno-racial identity), actions (e.g., political organizing), or even more arbitrary reasons (e.g., perceived disrespect). I argue that California state prisons knowingly rely on staff discretionary power to reify institutional racism on an individual level through routine decision-making. To substantiate this argument, I use a range of archival documents, unpublished quantitative administrative data, qualitative interviews from both sides of prison walls, and secondary academic sources. In so doing, I reveal the social costs of California state prisons’ continued justification of solitary confinement.

Published
2023

31. The impact of rare variation on gene expression across tissues

Author

Li, Xin, Kim, Yungil, Tsang, Emily K., Davis, Joe R., Damani, Farhan N., Chiang, Colby, Hess, Gaelen T., Zappala, Zachary, Strober, Benjamin J., Scott, Alexandra J., Li, Amy, Ganna, Andrea, Bassik, Michael C., Merker, Jason D., Aguet, Franois, Ardlie, Kristin G., Cummings, Beryl B., Gelfand, Ellen T., Getz, Gad, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Kashin, Seva, Karczewski, Konrad J., Lek, Monkol, Li, Xiao, MacArthur, Daniel G., Nedzel, Jared L., Nguyen, Duyen T., Noble, Michael S., Segr, Ayellet V., Trowbridge, Casandra A., Tukiainen, Taru, Abell, Nathan S., Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K., Brown, Andrew, Brown, Christopher D., Castel, Stephane E., Chen, Lin S., Conrad, Donald F., Cox, Nancy J., Delaneau, Olivier, Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Ferreira, Pedro G., Frsard, Laure, Gamazon, Eric R., Garrido-Martn, Diego, Gewirtz, Ariel D.H., Gliner, Genna, Gloudemans, Michael J., Guigo, Roderic, Hall, Ira M., Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Kyung Im, Hae, Jo, Brian, Yong Kang, Eun, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I., McDowell, Ian C., Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B., Muoz-Aguirre, Manuel, Ndungu, Anne W., Nicolae, Dan L., Nobel, Andrew B., Oliva, Meritxell, Ongen, Halit, Palowitch, John J., Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J., Peterson, Christine B., Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Shabalin, Andrey A., Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E., Sul, Jae Hoon, Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A., Xi, Hualin S., Yeger-Lotem, Esti, Zaugg, Judith B., Zhou, Yi-Hui, Akey, Joshua M., Bates, Daniel, Chan, Joanne, Claussnitzer, Melina, Demanelis, Kathryn, Diegel, Morgan, Doherty, Jennifer A., Feinberg, Andrew P., Fernando, Marian S., Halow, Jessica, Hansen, Kasper D., Haugen, Eric, Hickey, Peter F., Hou, Lei, Jasmine, Farzana, Jian, Ruiqi, Jiang, Lihua, Johnson, Audra, Kaul, Rajinder, Kellis, Manolis, Kibriya, Muhammad G., Lee, Kristen, Billy Li, Jin, Li, Qin, Lin, Jessica, Lin, Shin, Linder, Sandra, Linke, Caroline, Liu, Yaping, Maurano, Matthew T., Molinie, Benoit, Nelson, Jemma, Neri, Fidencio J., Park, Yongjin, Pierce, Brandon L., Rinaldi, Nicola J., Rizzardi, Lindsay F., Sandstrom, Richard, Skol, Andrew, Smith, Kevin S., Snyder, Michael P., Stamatoyannopoulos, John, Tang, Hua, Wang, Li, Wang, Meng, Van Wittenberghe, Nicholas, Wu, Fan, Zhang, Rui, Nierras, Concepcion R., Branton, Philip A., Carithers, Latarsha J., Guan, Ping, Moore, Helen M., Rao, Abhi, Vaught, Jimmie B., Gould, Sarah E., Lockart, Nicole C., Martin, Casey, Struewing, Jeffery P., Volpi, Simona, Addington, Anjene M., Koester, Susan E., Little, A. Roger, Brigham, Lori E., Hasz, Richard, Hunter, Marcus, Johns, Christopher, Johnson, Mark, Kopen, Gene, Leinweber, William F., Lonsdale, John T., McDonald, Alisa, Mestichelli, Bernadette, Myer, Kevin, Roe, Brian, Salvatore, Michael, Shad, Saboor, Thomas, Jeffrey A., Walters, Gary, Washington, Michael, Wheeler, Joseph, Bridge, Jason, Foster, Barbara A., Gillard, Bryan M., Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T., Jewell, Scott D., Montroy, Robert G., Rohrer, Daniel C., Valley, Dana R., Davis, David A., Mash, Deborah C., Undale, Anita H., Smith, Anna M., Tabor, David E., Roche, Nancy V., McLean, Jeffrey A., Vatanian, Negin, Robinson, Karna L., Sobin, Leslie, Barcus, Mary E., Valentino, Kimberly M., Qi, Liqun, Hunter, Steven, Hariharan, Pushpa, Singh, Shilpi, Um, Ki Sung, Matose, Takunda, Tomaszewski, Maria M., Barker, Laura K., Mosavel, Maghboeba, Siminoff, Laura A., Traino, Heather M., Flicek, Paul, Juettemann, Thomas, Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Craft, Brian, Goldman, Mary, Haeussler, Maximilian, Kent, W. James, Lee, Christopher M., Paten, Benedict, Rosenbloom, Kate R., Vivian, John, and Zhu, Jingchun

Subjects
Disease susceptibility -- Genetic aspects, Genetic variation -- Observations, Gene expression -- Observations, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Xin Li [1]; Yungil Kim [2]; Emily K. Tsang [1, 3]; Joe R. Davis [1, 4]; Farhan N. Damani [2]; Colby Chiang [5]; Gaelen T. Hess [4]; Zachary Zappala [...]

Published
2017
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32. Dynamic landscape and regulation of RNA editing in mammals

Author

Tan, Meng How, Li, Qin, Shanmugam, Raghuvaran, Piskol, Robert, Kohler, Jennefer, Young, Amy N., Liu, Kaiwen Ivy, Zhang, Rui, Ramaswami, Gokul, Ariyoshi, Kentaro, Gupte, Ankita, Keegan, Liam P., George, Cyril X., Ramu, Avinash, Huang, Ni, Pollina, Elizabeth A., Leeman, Dena S., Rustighi, Alessandra, Goh, Y. P. Sharon, Aguet, Franois, Ardlie, Kristin G., Cummings, Beryl B., Gelfand, Ellen T., Getz, Gad, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Kashin, Seva, Karczewski, Konrad J., Lek, Monkol, Li, Xiao, MacArthur, Daniel G., Nedzel, Jared L., Nguyen, Duyen T., Noble, Michael S., Segr, Ayellet V., Trowbridge, Casandra A., Tukiainen, Taru, Abell, Nathan S., Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K., Brown, Andrew, Brown, Christopher D., Castel, Stephane E., Chen, Lin S., Chiang, Colby, Conrad, Donald F., Cox, Nancy J., Damani, Farhan N., Davis, Joe R., Delaneau, Olivier, Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Ferreira, Pedro G., Frsard, Laure, Gamazon, Eric R., Garrido-Martn, Diego, Gewirtz, Ariel D. H., Gliner, Genna, Gloudemans, Michael J., Guigo, Roderic, Hall, Ira M., Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Kyung Im, Hae, Jo, Brian, Yong Kang, Eun, Kim, Yungil, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Li, Xin, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I., McDowell, Ian C., Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B., Muoz-Aguirre, Manuel, Ndungu, Anne W., Nicolae, Dan L., Nobel, Andrew B., Oliva, Meritxell, Ongen, Halit, Palowitch, John J., Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J., Peterson, Christine B., Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Scott, Alexandra J., Shabalin, Andrey A., Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E., Strober, Benjamin J., Sul, Jae Hoon, Tsang, Emily K., Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A., Xi, Hualin S., Yeger-Lotem, Esti, Zappala, Zachary, Zaugg, Judith B., Zhou, Yi-Hui, Akey, Joshua M., Bates, Daniel, Chan, Joanne, Claussnitzer, Melina, Demanelis, Kathryn, Diegel, Morgan, Doherty, Jennifer A., Feinberg, Andrew P., Fernando, Marian S., Halow, Jessica, Hansen, Kasper D., Haugen, Eric, Hickey, Peter F., Hou, Lei, Jasmine, Farzana, Jian, Ruiqi, Jiang, Lihua, Johnson, Audra, Kaul, Rajinder, Kellis, Manolis, Kibriya, Muhammad G., Lee, Kristen, Li, Jin Billy, Lin, Jessica, Lin, Shin, Linder, Sandra, Linke, Caroline, Liu, Yaping, Maurano, Matthew T., Molinie, Benoit, Nelson, Jemma, Neri, Fidencio J., Park, Yongjin, Pierce, Brandon L., Rinaldi, Nicola J., Rizzardi, Lindsay F., Sandstrom, Richard, Skol, Andrew, Smith, Kevin S., Snyder, Michael P., Stamatoyannopoulos, John, Tang, Hua, Wang, Li, Wang, Meng, Van Wittenberghe, Nicholas, Wu, Fan, Nierras, Concepcion R., Branton, Philip A., Carithers, Latarsha J., Guan, Ping, Moore, Helen M., Rao, Abhi, Vaught, Jimmie B., Gould, Sarah E., Lockart, Nicole C., Martin, Casey, Struewing, Jeffery P., Volpi, Simona, Addington, Anjene M., Koester, Susan E., Little, A. Roger, Brigham, Lori E., Hasz, Richard, Hunter, Marcus, Johns, Christopher, Johnson, Mark, Kopen, Gene, Leinweber, William F., Lonsdale, John T., McDonald, Alisa, Mestichelli, Bernadette, Myer, Kevin, Roe, Brian, Salvatore, Michael, Shad, Saboor, Thomas, Jeffrey A., Walters, Gary, Washington, Michael, Wheeler, Joseph, Bridge, Jason, Foster, Barbara A., Gillard, Bryan M., Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T., Jewell, Scott D., Montroy, Robert G., Rohrer, Daniel C., Valley, Dana R., Davis, David A., Mash, Deborah C., Undale, Anita H., Smith, Anna M., Tabor, David E., Roche, Nancy V., McLean, Jeffrey A., Vatanian, Negin, Robinson, Karna L., Sobin, Leslie, Barcus, Mary E., Valentino, Kimberly M., Qi, Liqun, Hunter, Steven, Hariharan, Pushpa, Singh, Shilpi, Um, Ki Sung, Matose, Takunda, Tomaszewski, Maria M., Barker, Laura K., Mosavel, Maghboeba, Siminoff, Laura A., Traino, Heather M., Flicek, Paul, Juettemann, Thomas, Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Craft, Brian, Goldman, Mary, Haeussler, Maximilian, Kent, W. James, Lee, Christopher M., Paten, Benedict, Rosenbloom, Kate R., Vivian, John, Zhu, Jingchun, Chawla, Ajay, Del Sal, Giannino, Peltz, Gary, Brunet, Anne, Samuel, Charles E., OConnell, Mary A., Walkley, Carl R., and Nishikura, Kazuko

Subjects
Genetic research, Mammals -- Genetic aspects, RNA processing -- Research, Genetic regulation, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Meng How Tan (corresponding author) [1, 2, 3]; Qin Li [1]; Raghuvaran Shanmugam [2, 3]; Robert Piskol [1]; Jennefer Kohler [1]; Amy N. Young [1]; Kaiwen Ivy Liu [3]; [...]

Published
2017
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33. Landscape of X chromosome inactivation across human tissues

Author

Tukiainen, Taru, Villani, Alexandra-Chlo, Yen, Angela, Rivas, Manuel A., Marshall, Jamie L., Satija, Rahul, Aguirre, Matt, Gauthier, Laura, Fleharty, Mark, Kirby, Andrew, Cummings, Beryl B., Castel, Stephane E., Karczewski, Konrad J., Aguet, Franois, Byrnes, Andrea, Ardlie, Kristin G., Gelfand, Ellen T., Getz, Gad, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Kashin, Seva, Lek, Monkol, Li, Xiao, MacArthur, Daniel G., Nedzel, Jared L., Nguyen, Duyen T., Noble, Michael S., Segr, Ayellet V., Trowbridge, Casandra A., Abell, Nathan S., Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K., Brown, Andrew, Brown, Christopher D., Chen, Lin S., Chiang, Colby, Conrad, Donald F., Cox, Nancy J., Damani, Farhan N., Davis, Joe R., Delaneau, Olivier, Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Ferreira, Pedro G., Frsard, Laure, Gamazon, Eric R., Garrido-Martn, Diego, Gewirtz, Ariel D. H., Gliner, Genna, Gloudemans, Michael J., Guigo, Roderic, Hall, Ira M., Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Kyung Im, Hae, Jo, Brian, Yong Kang, Eun, Kim, Yungil, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Li, Xin, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I., McDowell, Ian C., Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B., Muoz-Aguirre, Manuel, Ndungu, Anne W., Nicolae, Dan L., Nobel, Andrew B., Oliva, Meritxell, Ongen, Halit, Palowitch, John J., Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J., Peterson, Christine B., Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Scott, Alexandra J., Shabalin, Andrey A., Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E., Strober, Benjamin J., Sul, Jae Hoon, Tsang, Emily K., Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A., Xi, Hualin S., Yeger-Lotem, Esti, Zappala, Zachary, Zaugg, Judith B., Zhou, Yi-Hui, Akey, Joshua M., Bates, Daniel, Chan, Joanne, Claussnitzer, Melina, Demanelis, Kathryn, Diegel, Morgan, Doherty, Jennifer A., Feinberg, Andrew P., Fernando, Marian S., Halow, Jessica, Hansen, Kasper D., Haugen, Eric, Hickey, Peter F., Hou, Lei, Jasmine, Farzana, Jian, Ruiqi, Jiang, Lihua, Johnson, Audra, Kaul, Rajinder, Kellis, Manolis, Kibriya, Muhammad G., Lee, Kristen, Li, Jin Billy, Li, Qin, Lin, Jessica, Lin, Shin, Linder, Sandra, Linke, Caroline, Liu, Yaping, Maurano, Matthew T., Molinie, Benoit, Nelson, Jemma, Neri, Fidencio J., Park, Yongjin, Pierce, Brandon L., Rinaldi, Nicola J., Rizzardi, Lindsay F., Sandstrom, Richard, Skol, Andrew, Smith, Kevin S., Snyder, Michael P., Stamatoyannopoulos, John, Tang, Hua, Wang, Li, Wang, Meng, Van Wittenberghe, Nicholas, Wu, Fan, Zhang, Rui, Nierras, Concepcion R., Branton, Philip A., Carithers, Latarsha J., Guan, Ping, Moore, Helen M., Rao, Abhi, Vaught, Jimmie B., Gould, Sarah E., Lockart, Nicole C., Martin, Casey, Struewing, Jeffery P., Volpi, Simona, Addington, Anjene M., Koester, Susan E., Little, A. Roger, Brigham, Lori E., Hasz, Richard, Hunter, Marcus, Johns, Christopher, Johnson, Mark, Kopen, Gene, Leinweber, William F., Lonsdale, John T., McDonald, Alisa, Mestichelli, Bernadette, Myer, Kevin, Roe, Brian, Salvatore, Michael, Shad, Saboor, Thomas, Jeffrey A., Walters, Gary, Washington, Michael, Wheeler, Joseph, Bridge, Jason, Foster, Barbara A., Gillard, Bryan M., Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T., Jewell, Scott D., Montroy, Robert G., Rohrer, Daniel C., Valley, Dana R., Davis, David A., Mash, Deborah C., Undale, Anita H., Smith, Anna M., Tabor, David E., Roche, Nancy V., McLean, Jeffrey A., Vatanian, Negin, Robinson, Karna L., Sobin, Leslie, Barcus, Mary E., Valentino, Kimberly M., Qi, Liqun, Hunter, Steven, Hariharan, Pushpa, Singh, Shilpi, Um, Ki Sung, Matose, Takunda, Tomaszewski, Maria M., Barker, Laura K., Mosavel, Maghboeba, Siminoff, Laura A., Traino, Heather M., Flicek, Paul, Juettemann, Thomas, Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Craft, Brian, Goldman, Mary, Haeussler, Maximilian, Kent, W. James, Lee, Christopher M., Paten, Benedict, Rosenbloom, Kate R., Vivian, John, Zhu, Jingchun, Regev, Aviv, and Hacohen, Nir

Subjects
Chromosomes -- Physiological aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Taru Tukiainen (corresponding author) [1, 2]; Alexandra-Chlo Villani [2, 3]; Angela Yen [2, 4]; Manuel A. Rivas [1, 2, 5]; Jamie L. Marshall [1, 2]; Rahul Satija [2, 6, [...]

Published
2017
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37. Southside, We Outside: Policing and Placemaking in Historic Jamaica, Queens, New York

Author

Roychoudhury, Debanjan, Hunter, Marcus A1, Roychoudhury, Debanjan, Roychoudhury, Debanjan, Hunter, Marcus A1, and Roychoudhury, Debanjan

Abstract

The National Advisory Commission on Civil Disorders, commonly known as “The Kerner Commission” after its chair Otto Kerner, was assigned by U.S. President Lyndon Johnson in 1967 to report on the causes of urban uprisings over the course of four consecutive summers. ‘Rioting’ took place in 150 American cities and resulted directly from police violence against African Americans. The report concluded that the nation was moving toward two societies, one black, one white—separate and unequal. Fifty years later, urban (and suburban) uprisings following police murders again illuminate the trajectory that the Kerner Commission cautioned against. Protests over several summers challenging excessive police use of force, police violence, and the role of police in enforcing structural racism in the U.S., culminated in 2020, during the midst of the COVID-19 pandemic, and have since taken place around the world.Developing a qualitative study of policing in the Jamaica section of Queens County, New York seeks: 1) to better understand the ways in which policing and police violence in urban communities have been contested during the post-1968 era of massive demographic, political, economic, and cultural change and 2) to investigate how and why the American “War on Drugs” has emerged and police power has expanded and the ways this historic process has shaped Black American neighborhoods, politics, and subjectivity. The findings of this study deepen our understandings of the American police-community dialectic by centering Black agency, politics, and press. Guided by critical discourse analysis and “conceptual metaphor theory,” data is drawn from Black Press, White Press, the archives, and civic organization membership, to examine discourse on protests, civic, and political action, following the historic killings of 10-year-old Clifford Glover in 1973, and 23-year-old Sean Bell in 2006. This study’s recovery of the collective memory of Clifford Glover is the most extensive social scien

Published
2022

39. U.S. Truth, Racial Healing, and Transformation Funders' Briefing Program, January 19, 2021

Author

Christopher, Gail C., primary, Crow, La Quen Náay Liz Medicine, additional, Greenberg, Melanie, additional, Tabron, La June Montgomery, additional, Zeitz, Paul, additional, Pentikainen, Antti, additional, Rico, José A., additional, McNair, Tia Brown, additional, Austin, Angela Waters, additional, Chavis, Charles, additional, Oliver, Isaiah, additional, Hosey, Diane, additional, Hou, Grace, additional, Hipple, Andreas, additional, Gopal, Srikanth (Srik), additional, Hunter, Marcus Anthony, additional, and Adamson, Hannah, additional

Published
2021
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42. Population-scale tissue transcriptomics maps long non-coding RNAs to complex disease

Author

de Goede, Olivia M., primary, Nachun, Daniel C., additional, Ferraro, Nicole M., additional, Gloudemans, Michael J., additional, Rao, Abhiram S., additional, Smail, Craig, additional, Eulalio, Tiffany Y., additional, Aguet, François, additional, Ng, Bernard, additional, Xu, Jishu, additional, Barbeira, Alvaro N., additional, Castel, Stephane E., additional, Kim-Hellmuth, Sarah, additional, Park, YoSon, additional, Scott, Alexandra J., additional, Strober, Benjamin J., additional, Brown, Christopher D., additional, Wen, Xiaoquan, additional, Hall, Ira M., additional, Battle, Alexis, additional, Lappalainen, Tuuli, additional, Im, Hae Kyung, additional, Ardlie, Kristin G., additional, Mostafavi, Sara, additional, Quertermous, Thomas, additional, Kirkegaard, Karla, additional, Montgomery, Stephen B., additional, Anand, Shankara, additional, Gabriel, Stacey, additional, Getz, Gad A., additional, Graubert, Aaron, additional, Hadley, Kane, additional, Handsaker, Robert E., additional, Huang, Katherine H., additional, Li, Xiao, additional, MacArthur, Daniel G., additional, Meier, Samuel R., additional, Nedzel, Jared L., additional, Nguyen, Duyen T., additional, Segrè, Ayellet V., additional, Todres, Ellen, additional, Balliu, Brunilda, additional, Bonazzola, Rodrigo, additional, Brown, Andrew, additional, Conrad, Donald F., additional, Cotter, Daniel J., additional, Cox, Nancy, additional, Das, Sayantan, additional, Dermitzakis, Emmanouil T., additional, Einson, Jonah, additional, Engelhardt, Barbara E., additional, Eskin, Eleazar, additional, Flynn, Elise D., additional, Fresard, Laure, additional, Gamazon, Eric R., additional, Garrido-Martín, Diego, additional, Gay, Nicole R., additional, Guigó, Roderic, additional, Hamel, Andrew R., additional, He, Yuan, additional, Hoffman, Paul J., additional, Hormozdiari, Farhad, additional, Hou, Lei, additional, Jo, Brian, additional, Kasela, Silva, additional, Kashin, Seva, additional, Kellis, Manolis, additional, Kwong, Alan, additional, Li, Xin, additional, Liang, Yanyu, additional, Mangul, Serghei, additional, Mohammadi, Pejman, additional, Muñoz-Aguirre, Manuel, additional, Nobel, Andrew B., additional, Oliva, Meritxell, additional, Park, Yongjin, additional, Parsana, Princy, additional, Reverter, Ferran, additional, Rouhana, John M., additional, Sabatti, Chiara, additional, Saha, Ashis, additional, Stephens, Matthew, additional, Stranger, Barbara E., additional, Teran, Nicole A., additional, Viñuela, Ana, additional, Wang, Gao, additional, Wright, Fred, additional, Wucher, Valentin, additional, Zou, Yuxin, additional, Ferreira, Pedro G., additional, Li, Gen, additional, Melé, Marta, additional, Yeger-Lotem, Esti, additional, Bradbury, Debra, additional, Krubit, Tanya, additional, McLean, Jeffrey A., additional, Qi, Liqun, additional, Robinson, Karna, additional, Roche, Nancy V., additional, Smith, Anna M., additional, Tabor, David E., additional, Undale, Anita, additional, Bridge, Jason, additional, Brigham, Lori E., additional, Foster, Barbara A., additional, Gillard, Bryan M., additional, Hasz, Richard, additional, Hunter, Marcus, additional, Johns, Christopher, additional, Johnson, Mark, additional, Karasik, Ellen, additional, Kopen, Gene, additional, Leinweber, William F., additional, McDonald, Alisa, additional, Moser, Michael T., additional, Myer, Kevin, additional, Ramsey, Kimberley D., additional, Roe, Brian, additional, Shad, Saboor, additional, Thomas, Jeffrey A., additional, Walters, Gary, additional, Washington, Michael, additional, Wheeler, Joseph, additional, Jewell, Scott D., additional, Rohrer, Daniel C., additional, Valley, Dana R., additional, Davis, David A., additional, Mash, Deborah C., additional, Barcus, Mary E., additional, Branton, Philip A., additional, Sobin, Leslie, additional, Barker, Laura K., additional, Gardiner, Heather M., additional, Mosavel, Maghboeba, additional, Siminoff, Laura A., additional, Flicek, Paul, additional, Haeussler, Maximilian, additional, Juettemann, Thomas, additional, Kent, W. James, additional, Lee, Christopher M., additional, Powell, Conner C., additional, Rosenbloom, Kate R., additional, Ruffier, Magali, additional, Sheppard, Dan, additional, Taylor, Kieron, additional, Trevanion, Stephen J., additional, Zerbino, Daniel R., additional, Abell, Nathan S., additional, Akey, Joshua, additional, Chen, Lin, additional, Demanelis, Kathryn, additional, Doherty, Jennifer A., additional, Feinberg, Andrew P., additional, Hansen, Kasper D., additional, Hickey, Peter F., additional, Jasmine, Farzana, additional, Jiang, Lihua, additional, Kaul, Rajinder, additional, Kibriya, Muhammad G., additional, Li, Jin Billy, additional, Li, Qin, additional, Lin, Shin, additional, Linder, Sandra E., additional, Pierce, Brandon L., additional, Rizzardi, Lindsay F., additional, Skol, Andrew D., additional, Smith, Kevin S., additional, Snyder, Michael, additional, Stamatoyannopoulos, John, additional, Tang, Hua, additional, Wang, Meng, additional, Carithers, Latarsha J., additional, Guan, Ping, additional, Koester, Susan E., additional, Little, A. Roger, additional, Moore, Helen M., additional, Nierras, Concepcion R., additional, Rao, Abhi K., additional, Vaught, Jimmie B., additional, and Volpi, Simona, additional

Published
2021
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49. A Quantitative Proteome Map of the Human Body

Author

Jiang, Lihua, primary, Wang, Meng, additional, Lin, Shin, additional, Jian, Ruiqi, additional, Li, Xiao, additional, Chan, Joanne, additional, Dong, Guanlan, additional, Fang, Huaying, additional, Robinson, Aaron E., additional, Snyder, Michael P., additional, Aguet, François, additional, Anand, Shankara, additional, Ardlie, Kristin G., additional, Gabriel, Stacey, additional, Getz, Gad, additional, Graubert, Aaron, additional, Hadley, Kane, additional, Handsaker, Robert E., additional, Huang, Katherine H., additional, Kashin, Seva, additional, MacArthur, Daniel G., additional, Meier, Samuel R., additional, Nedzel, Jared L., additional, Nguyen, Duyen Y., additional, Segrè, Ayellet V., additional, Todres, Ellen, additional, Balliu, Brunilda, additional, Barbeira, Alvaro N., additional, Battle, Alexis, additional, Bonazzola, Rodrigo, additional, Brown, Andrew, additional, Brown, Christopher D., additional, Castel, Stephane E., additional, Conrad, Don, additional, Cotter, Daniel J., additional, Cox, Nancy, additional, Das, Sayantan, additional, de Goede, Olivia M., additional, Dermitzakis, Emmanouil T., additional, Engelhardt, Barbara E., additional, Eskin, Eleazar, additional, Eulalio, Tiffany Y., additional, Ferraro, Nicole M., additional, Flynn, Elise, additional, Fresard, Laure, additional, Gamazon, Eric R., additional, Garrido-Martín, Diego, additional, Gay, Nicole R., additional, Guigó, Roderic, additional, Hamel, Andrew R., additional, He, Yuan, additional, Hoffman, Paul J., additional, Hormozdiari, Farhad, additional, Hou, Lei, additional, Im, Hae Kyung, additional, Jo, Brian, additional, Kasela, Silva, additional, Kellis, Manolis, additional, Kim-Hellmuth, Sarah, additional, Kwong, Alan, additional, Lappalainen, Tuuli, additional, Li, Xin, additional, Liang, Yanyu, additional, Mangul, Serghei, additional, Mohammadi, Pejman, additional, Montgomery, Stephen B., additional, Muñoz-Aguirre, Manuel, additional, Nachun, Daniel C., additional, Nobel, Andrew B., additional, Oliva, Meritxell, additional, Park, YoSon, additional, Park, Yongjin, additional, Parsana, Princy, additional, Reverter, Ferran, additional, Rouhana, John M., additional, Sabatti, Chiara, additional, Saha, Ashis, additional, Skol, Andrew D., additional, Stephens, Matthew, additional, Stranger, Barbara E., additional, Strober, Benjamin J., additional, Teran, Nicole A., additional, Viñuela, Ana, additional, Wang, Gao, additional, Wen, Xiaoquan, additional, Wright, Fred, additional, Wucher, Valentin, additional, Zou, Yuxin, additional, Ferreira, Pedro G., additional, Li, Gen, additional, Melé, Marta, additional, Yeger-Lotem, Esti, additional, Barcus, Mary E., additional, Bradbury, Debra, additional, Krubit, Tanya, additional, McLean, Jeffrey A., additional, Qi, Liqun, additional, Robinson, Karna, additional, Roche, Nancy V., additional, Smith, Anna M., additional, Sobin, Leslie, additional, Tabor, David E., additional, Undale, Anita, additional, Bridge, Jason, additional, Brigham, Lori E., additional, Foster, Barbara A., additional, Gillard, Bryan M., additional, Hasz, Richard, additional, Hunter, Marcus, additional, Johns, Christopher, additional, Johnson, Mark, additional, Karasik, Ellen, additional, Kopen, Gene, additional, Leinweber, William F., additional, McDonald, Alisa, additional, Moser, Michael T., additional, Myer, Kevin, additional, Ramsey, Kimberley D., additional, Roe, Brian, additional, Shad, Saboor, additional, Thomas, Jeffrey A., additional, Walters, Gary, additional, Washington, Michael, additional, Wheeler, Joseph, additional, Jewell, Scott D., additional, Rohrer, Daniel C., additional, Valley, Dana R., additional, Davis, David A., additional, Mash, Deborah C., additional, Branton, Philip A., additional, Barker, Laura K., additional, Gardiner, Heather M., additional, Mosavel, Maghboeba, additional, Siminoff, Laura A., additional, Flicek, Paul, additional, Haeussler, Maximilian, additional, Juettemann, Thomas, additional, Kent, W. James, additional, Lee, Christopher M., additional, Powell, Conner C., additional, Rosenbloom, Kate R., additional, Ruffier, Magali, additional, Sheppard, Dan, additional, Taylor, Kieron, additional, Trevanion, Stephen J., additional, Zerbino, Daniel R., additional, Abell, Nathan S., additional, Akey, Joshua, additional, Chen, Lin, additional, Demanelis, Kathryn, additional, Doherty, Jennifer A., additional, Feinberg, Andrew P., additional, Hansen, Kasper D., additional, Hickey, Peter F., additional, Jasmine, Farzana, additional, Kaul, Rajinder, additional, Kibriya, Muhammad G., additional, Li, Jin Billy, additional, Li, Qin, additional, Linder, Sandra E., additional, Pierce, Brandon L., additional, Rizzardi, Lindsay F., additional, Smith, Kevin S., additional, Stamatoyannopoulos, John, additional, Tang, Hua, additional, Carithers, Latarsha J., additional, Guan, Ping, additional, Koester, Susan E., additional, Little, A. Roger, additional, Moore, Helen M., additional, Nierras, Concepcion R., additional, Rao, Abhi K., additional, Vaught, Jimmie B., additional, and Volpi, Simona, additional

Published
2020
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50. Structural aspects of the membrane and ultrastructural features of Sarcina flava and Sarcina morrhuae

Author

Hunter, Marcus Ian Stuart and Thirkell, David

Subjects
579.3, QR83.S3H8, Hydrogen bacteria
Abstract

1. The preparation, purification and properties of a water-soluble membrane component from S. flava using the synthetic detergent Lubrol L has been described. This fraction contained carotenoid, glucose and peptide, was highly stable to heat and pH extremes, and release of free carotenoid from it proved extremely difficult. The possible effect of the binding of the membrane components within detergent micelles is discussed and the dangers inherent, in the determination of molecular weights, by osmometry or ultracentrifugation, in the presence of detergent have been indicated. 2. The polar carotenoid subfractions from S. flava have been characterised and found to consist of carotenoid, glucose and peptide. The linkage between carotonoid and glucose is presumed to be glycosidic, and a model for the in vivo orientation of the carotenoid complex in the bacterial membrane has been proposed. A possible correlation between membrane stability and carotenoid content has been found, and this is discussed in relation to the model. 3. After complete removal of the free pigments from S. morrhuae by solvent extraction, a water soluble carotenoid fraction was isolated and characterised. The material, whose molecular weight is approximately 9,000 contains carotenoid, glucose and peptide. The bond between glucose and carotenoid is again presumed to be glycosidlc, and the peptide moiety contains high proportions of the acidic amino acids, the significance of which is discussed. This bound pigment is also thought to represent one form in which: carotenoid is bound in the bacterial membrane. 4. The effect of the age of the culture on the chemical composition of the total membrane fraction from S. flava has been investigated. Both protein and lipid contents decrease with age although there is little variation in carbohydrate content. It is suggested that the decreased lipid content is a reflection of the increased binding of lipid to protein with age. Considerable variation in the fatty acid composition with age was observed, which makes the use of the fatty acid profile as a taxonomic criterion for this species of doubtful value. The presence of a sterol in S. flava membrane lipids is indicated although from GLC data, it seems unlikely that this is cholesterol. Mono-saccharides detected in membrane hydrolysates were ribose, rhamnose, glucose, and mannose. The presence of glucosamine and galactosamine was also indicated. 5, The general ultrastructural features of whole cells of both S. flava and S. morrhuae have been described. S. flava exhibits many of the fine structural features common to Gram-positive organisms and was seen to form the packets of cells typical of the Sarcinae. Cell division in S. flava was shown to be of the cell membrane septation type, and a mechanism for this mode of division has been proposed. Preparation of protoplasts from S. flava using the method of Baird-Parker and Woodroffe (1967) was unsuccessful, but the treatment with lysozyme, revealed a layered appearance of the cell wall. Several intracytoplasmic membranous inclusions were seen in these cells and their relationship to mesosomes is discussed. Mesosomes as such were also present, but never in association with developing septa. The effect of varying conditions of fixation on the fine structure of S. flava was also studied. Evidence has been presented that, under certain conditions, sporulation may occur in S. flava. Good fixation of S. morrhuae cells proved difficult to achieve, and this may be due to insufficient concentration of salts in the fixation medium. Cells of S. morrhuae are approximately twice the size of S. flava cells, and division was seen to occur in a much more random fashion, producing irregular clumps of cells with common cell walls. Spherical or ovoid bodies of unknown composition were seen in association with the cytoplasmic membrane.

Published
1971

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