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140 results on '"Goldberg, Arthur P."'

1. BioSimulators: a central registry of simulation engines and services for recommending specific tools

Author

Shaikh, Bilal, Smith, Lucian P., Vasilescu, Dan, Marupilla, Gnaneswara, Wilson, Michael, Agmon, Eran, Agnew, Henry, Andrews, Steven S., Anwar, Azraf, Beber, Moritz E., Bergmann, Frank T., Brooks, David, Brusch, Lutz, Calzone, Laurence, Choi, Kiri, Cooper, Joshua, Detloff, John, Drawert, Brian, Dumontier, Michel, Ermentrout, G. Bard, Faeder, James R., Freiburger, Andrew P., Fröhlich, Fabian, Funahashi, Akira, Garny, Alan, Gennari, John H., Gleeson, Padraig, Goelzer, Anne, Haiman, Zachary, Hellerstein, Joseph L., Hoops, Stefan, Ison, Jon C., Jahn, Diego, Jakubowski, Henry V., Jordan, Ryann, Kalaš, Matúš, König, Matthias, Liebermeister, Wolfram, Mandal, Synchon, McDougal, Robert, Medley, J. Kyle, Mendes, Pedro, Müller, Robert, Myers, Chris J., Naldi, Aurelien, Nguyen, Tung V. N., Nickerson, David P., Olivier, Brett G., Patoliya, Drashti, Paulevé, Loïc, Petzold, Linda R., Priya, Ankita, Rampadarath, Anand K., Rohwer, Johann M., Saglam, Ali S., Singh, Dilawar, Sinha, Ankur, Snoep, Jacky, Sorby, Hugh, Spangler, Ryan, Starruß, Jörn, Thomas, Payton J., van Niekerk, David, Weindl, Daniel, Zhang, Fengkai, Zhukova, Anna, Goldberg, Arthur P., Blinov, Michael L., Sauro, Herbert M., Moraru, Ion I., and Karr, Jonathan R.

Subjects
Quantitative Biology - Quantitative Methods, Computer Science - Computational Engineering, Finance, and Science, Quantitative Biology - Molecular Networks
Abstract

Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various subsystems and scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface. To help investigators find and use simulation tools, we developed BioSimulators (https://biosimulators.org), a central registry of the capabilities of simulation tools and consistent Python, command-line, and containerized interfaces to each version of each tool. The foundation of BioSimulators is standards, such as CellML, SBML, SED-ML, and the COMBINE archive format, and validation tools for simulation projects and simulation tools that ensure these standards are used consistently. To help modelers find tools for particular projects, we have also used the registry to develop recommendation services. We anticipate that BioSimulators will help modelers exchange, reproduce, and combine simulations., Comment: 6 pages, 2 figures

Published
2022

2. Exact Parallelization of the Stochastic Simulation Algorithm for Scalable Simulation of Large Biochemical Networks

Author

Goldberg, Arthur P., Jefferson, David R., Sekar, John A. P., and Karr, Jonathan R.

Subjects
Quantitative Biology - Molecular Networks, Computer Science - Distributed, Parallel, and Cluster Computing, Computer Science - Data Structures and Algorithms, Quantitative Biology - Quantitative Methods
Abstract

Comprehensive simulations of the entire biochemistry of cells have great potential to help physicians treat disease and help engineers design biological machines. But such simulations must model networks of millions of molecular species and reactions. The Stochastic Simulation Algorithm (SSA) is widely used for simulating biochemistry, especially systems with species populations small enough that discreteness and stochasticity play important roles. However, existing serial SSA methods are prohibitively slow for comprehensive networks, and existing parallel SSA methods, which use periodic synchronization, sacrifice accuracy. To enable fast, accurate, and scalable simulations of biochemistry, we present an exact parallel algorithm for SSA that partitions a biochemical network into many SSA processes that simulate in parallel. Our parallel SSA algorithm exactly coordinates the interactions among these SSA processes and the species state they share by structuring the algorithm as a parallel discrete event simulation (DES) application and using an optimistic parallel DES simulator to synchronize the interactions. We anticipate that our method will enable unprecedented biochemical simulations., Comment: 21 pages, 4 figures; 2020-05-20 submission: updated authors, affiliations, emails, acknowledgments and layout

Published
2020

3. ObjTables: structured spreadsheets that promote data quality, reuse, and integration

Author

Karr, Jonathan R., Liebermeister, Wolfram, Goldberg, Arthur P., Sekar, John A. P., and Shaikh, Bilal

Subjects
Computer Science - Databases, Quantitative Biology - Quantitative Methods
Abstract

A central challenge in science is to understand how systems behaviors emerge from complex networks. This often requires aggregating, reusing, and integrating heterogeneous information. Supplementary spreadsheets to articles are a key data source. Spreadsheets are popular because they are easy to read and write. However, spreadsheets are often difficult to reanalyze because they capture data ad hoc without schemas that define the objects, relationships, and attributes that they represent. To help researchers reuse and compose spreadsheets, we developed ObjTables, a toolkit that makes spreadsheets human- and machine-readable by combining spreadsheets with schemas and an object-relational mapping system. ObjTables includes a format for schemas; markup for indicating the class and attribute represented by each spreadsheet and column; numerous data types for scientific information; and high-level software for using schemas to read, write, validate, compare, merge, revision, and analyze spreadsheets. By making spreadsheets easier to reuse, ObjTables could enable unprecedented secondary meta-analyses. By making it easy to build new formats and associated software for new types of data, ObjTables can also accelerate emerging scientific fields., Comment: 5 pages, 1 figures, 18 pages of supplementary information, 3 supplementary datasets

Published
2020

4. Publisher Correction: Rates, distribution and implications of postzygotic mosaic mutations in autism spectrum disorder

Author

Lim, Elaine T, Uddin, Mohammed, De Rubeis, Silvia, Chan, Yingleong, Kamumbu, Anne S, Zhang, Xiaochang, D’Gama, Alissa M, Kim, Sonia N, Hill, Robert Sean, Goldberg, Arthur P, Poultney, Christopher, Minshew, Nancy J, Kushima, Itaru, Aleksic, Branko, Ozaki, Norio, Parellada, Mara, Arango, Celso, Penzol, Maria J, Carracedo, Angel, Kolevzon, Alexander, Hultman, Christina M, Weiss, Lauren A, Fromer, Menachem, Chiocchetti, Andreas G, Freitag, Christine M, Church, George M, Scherer, Stephen W, Buxbaum, Joseph D, and Walsh, Christopher A

Subjects
Biological Psychology, Biomedical and Clinical Sciences, Neurosciences, Psychology, Autism Sequencing Consortium, Cognitive Sciences, Neurology & Neurosurgery, Biological psychology
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

5. Emerging whole-cell modeling principles and methods

Author

Goldberg, Arthur P., Szigeti, Balázs, Chew, Yin Hoon, Sekar, John A. P., Roth, Yosef D., and Karr, Jonathan R.

Subjects
Quantitative Biology - Quantitative Methods
Abstract

Whole-cell computational models aim to predict cellular phenotypes from genotype by representing the entire genome, the structure and concentration of each molecular species, each molecular interaction, and the extracellular environment. Whole-cell models have great potential to transform bioscience, bioengineering, and medicine. However, numerous challenges remain to achieve whole-cell models. Nevertheless, researchers are beginning to leverage recent progress in measurement technology, bioinformatics, data sharing, rule-based modeling, and multi-algorithmic simulation to build the first whole-cell models. We anticipate that ongoing efforts to develop scalable whole-cell modeling tools will enable dramatically more comprehensive and more accurate models, including models of human cells., Comment: 10 pages, 2 figures, 7 supplementary tables

Published
2017
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6. Rates, distribution and implications of postzygotic mosaic mutations in autism spectrum disorder

Author

Lim, Elaine T, Uddin, Mohammed, De Rubeis, Silvia, Chan, Yingleong, Kamumbu, Anne S, Zhang, Xiaochang, D'Gama, Alissa M, Kim, Sonia N, Hill, Robert Sean, Goldberg, Arthur P, Poultney, Christopher, Minshew, Nancy J, Kushima, Itaru, Aleksic, Branko, Ozaki, Norio, Parellada, Mara, Arango, Celso, Penzol, Maria J, Carracedo, Angel, Kolevzon, Alexander, Hultman, Christina M, Weiss, Lauren A, Fromer, Menachem, Chiocchetti, Andreas G, Freitag, Christine M, Church, George M, Scherer, Stephen W, Buxbaum, Joseph D, and Walsh, Christopher A

Subjects
Biological Psychology, Biomedical and Clinical Sciences, Neurosciences, Psychology, Brain Disorders, Autism, Genetics, Pediatric, Mental Health, Intellectual and Developmental Disabilities (IDD), 2.1 Biological and endogenous factors, Aetiology, Mental health, Autism Spectrum Disorder, Databases, Genetic, Genetic Predisposition to Disease, Genetic Variation, Humans, Mosaicism, Mutation, Missense, Zygote, Autism Sequencing Consortium, Cognitive Sciences, Neurology & Neurosurgery, Biological psychology
Abstract

We systematically analyzed postzygotic mutations (PZMs) in whole-exome sequences from the largest collection of trios (5,947) with autism spectrum disorder (ASD) available, including 282 unpublished trios, and performed resequencing using multiple independent technologies. We identified 7.5% of de novo mutations as PZMs, 83.3% of which were not described in previous studies. Damaging, nonsynonymous PZMs within critical exons of prenatally expressed genes were more common in ASD probands than controls (P < 1 × 10-6), and genes carrying these PZMs were enriched for expression in the amygdala (P = 5.4 × 10-3). Two genes (KLF16 and MSANTD2) were significantly enriched for PZMs genome-wide, and other PZMs involved genes (SCN2A, HNRNPU and SMARCA4) whose mutation is known to cause ASD or other neurodevelopmental disorders. PZMs constitute a significant proportion of de novo mutations and contribute importantly to ASD risk.

Published
2017

7. Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci

Author

Sanders, Stephan J, He, Xin, Willsey, A Jeremy, Ercan-Sencicek, A Gulhan, Samocha, Kaitlin E, Cicek, A Ercument, Murtha, Michael T, Bal, Vanessa H, Bishop, Somer L, Dong, Shan, Goldberg, Arthur P, Jinlu, Cai, Keaney, John F, Klei, Lambertus, Mandell, Jeffrey D, Moreno-De-Luca, Daniel, Poultney, Christopher S, Robinson, Elise B, Smith, Louw, Solli-Nowlan, Tor, Su, Mack Y, Teran, Nicole A, Walker, Michael F, Werling, Donna M, Beaudet, Arthur L, Cantor, Rita M, Fombonne, Eric, Geschwind, Daniel H, Grice, Dorothy E, Lord, Catherine, Lowe, Jennifer K, Mane, Shrikant M, Martin, Donna M, Morrow, Eric M, Talkowski, Michael E, Sutcliffe, James S, Walsh, Christopher A, Yu, Timothy W, Consortium, Autism Sequencing, Ledbetter, David H, Martin, Christa Lese, Cook, Edwin H, Buxbaum, Joseph D, Daly, Mark J, Devlin, Bernie, Roeder, Kathryn, and State, Matthew W

Subjects
Biological Psychology, Biomedical and Clinical Sciences, Neurosciences, Psychology, Pediatric, Prevention, Biotechnology, Brain Disorders, Genetics, Mental Health, Intellectual and Developmental Disabilities (IDD), Human Genome, Autism, 2.1 Biological and endogenous factors, Aetiology, Mental health, Autism Spectrum Disorder, Female, Genetic Loci, Genetic Variation, Humans, Male, Protein Interaction Maps, Autism Sequencing Consortium, Cognitive Sciences, Neurology & Neurosurgery, Biological psychology
Abstract

Analysis of de novo CNVs (dnCNVs) from the full Simons Simplex Collection (SSC) (N = 2,591 families) replicates prior findings of strong association with autism spectrum disorders (ASDs) and confirms six risk loci (1q21.1, 3q29, 7q11.23, 16p11.2, 15q11.2-13, and 22q11.2). The addition of published CNV data from the Autism Genome Project (AGP) and exome sequencing data from the SSC and the Autism Sequencing Consortium (ASC) shows that genes within small de novo deletions, but not within large dnCNVs, significantly overlap the high-effect risk genes identified by sequencing. Alternatively, large dnCNVs are found likely to contain multiple modest-effect risk genes. Overall, we find strong evidence that de novo mutations are associated with ASD apart from the risk for intellectual disability. Extending the transmission and de novo association test (TADA) to include small de novo deletions reveals 71 ASD risk loci, including 6 CNV regions (noted above) and 65 risk genes (FDR ≤ 0.1).

Published
2015

9. BioSimulators: a central registry of simulation engines and services for recommending specific tools

Author

Shaikh, Bilal, primary, Smith, Lucian P, additional, Vasilescu, Dan, additional, Marupilla, Gnaneswara, additional, Wilson, Michael, additional, Agmon, Eran, additional, Agnew, Henry, additional, Andrews, Steven S, additional, Anwar, Azraf, additional, Beber, Moritz E, additional, Bergmann, Frank T, additional, Brooks, David, additional, Brusch, Lutz, additional, Calzone, Laurence, additional, Choi, Kiri, additional, Cooper, Joshua, additional, Detloff, John, additional, Drawert, Brian, additional, Dumontier, Michel, additional, Ermentrout, G Bard, additional, Faeder, James R, additional, Freiburger, Andrew P, additional, Fröhlich, Fabian, additional, Funahashi, Akira, additional, Garny, Alan, additional, Gennari, John H, additional, Gleeson, Padraig, additional, Goelzer, Anne, additional, Haiman, Zachary, additional, Hasenauer, Jan, additional, Hellerstein, Joseph L, additional, Hermjakob, Henning, additional, Hoops, Stefan, additional, Ison, Jon C, additional, Jahn, Diego, additional, Jakubowski, Henry V, additional, Jordan, Ryann, additional, Kalaš, Matúš, additional, König, Matthias, additional, Liebermeister, Wolfram, additional, Sheriff, Rahuman S Malik, additional, Mandal, Synchon, additional, McDougal, Robert, additional, Medley, J Kyle, additional, Mendes, Pedro, additional, Müller, Robert, additional, Myers, Chris J, additional, Naldi, Aurelien, additional, Nguyen, Tung V N, additional, Nickerson, David P, additional, Olivier, Brett G, additional, Patoliya, Drashti, additional, Paulevé, Loïc, additional, Petzold, Linda R, additional, Priya, Ankita, additional, Rampadarath, Anand K, additional, Rohwer, Johann M, additional, Saglam, Ali S, additional, Singh, Dilawar, additional, Sinha, Ankur, additional, Snoep, Jacky, additional, Sorby, Hugh, additional, Spangler, Ryan, additional, Starruß, Jörn, additional, Thomas, Payton J, additional, van Niekerk, David, additional, Weindl, Daniel, additional, Zhang, Fengkai, additional, Zhukova, Anna, additional, Goldberg, Arthur P, additional, Schaff, James C, additional, Blinov, Michael L, additional, Sauro, Herbert M, additional, Moraru, Ion I, additional, and Karr, Jonathan R, additional

Published
2022
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12. Synaptic, transcriptional and chromatin genes disrupted in autism

Author

De Rubeis, Silvia, He, Xin, Goldberg, Arthur P., Poultney, Christopher S., Samocha, Kaitlin, Cicek, Ercument A., Kou, Yan, Liu, Li, Fromer, Menachem, Walker, Susan, Singh, Tarjinder, Klei, Lambertus, Kosmicki, Jack, Fu, Shih-Chen, Aleksic, Branko, Biscaldi, Monica, Bolton, Patrick F., Brownfeld, Jessica M., Cai, Jinlu, Campbell, Nicholas G., Carracedo, Angel, Chahrour, Maria H., Chiocchetti, Andreas G., Coon, Hilary, Crawford, Emily L., Crooks, Lucy, Curran, Sarah R., Dawson, Geraldine, Duketis, Eftichia, Fernandez, Bridget A., Gallagher, Louise, Geller, Evan, Guter, Stephen J., Hill, Sean R., Ionita-Laza, Iuliana, Gonzalez, Patricia Jimenez, Kilpinen, Helena, Klauck, Sabine M., Kolevzon, Alexander, Lee, Irene, Lei, Jing, Lehtimäki, Terho, Lin, Chiao-Feng, Maʼayan, Avi, Marshall, Christian R., McInnes, Alison L., Neale, Benjamin, Owen, Michael J., Ozaki, Norio, Parellada, Mara, Parr, Jeremy R., Purcell, Shaun, Puura, Kaija, Rajagopalan, Deepthi, Rehnström, Karola, Reichenberg, Abraham, Sabo, Aniko, Sachse, Michael, Sanders, Stephan J., Schafer, Chad, Schulte-Rüther, Martin, Skuse, David, Stevens, Christine, Szatmari, Peter, Tammimies, Kristiina, Valladares, Otto, Voran, Annette, Wang, Li-San, Weiss, Lauren A., Willsey, Jeremy A., Yu, Timothy W., Yuen, Ryan K. C., Cook, Edwin H., Freitag, Christine M., Gill, Michael, Hultman, Christina M., Lehner, Thomas, Palotie, Aarno, Schellenberg, Gerard D., Sklar, Pamela, State, Matthew W., Sutcliffe, James S., Walsh, Christopher A., Scherer, Stephen W., Zwick, Michael E., Barrett, Jeffrey C., Cutler, David J., Roeder, Kathryn, Devlin, Bernie, Daly, Mark J., and Buxbaum, Joseph D.

Published
2014
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14. Comprehensive molecular characterization of human colon and rectal cancer

Author

Muzny, Donna M., Bainbridge, Matthew N., Chang, Kyle, Dinh, Huyen H., Drummond, Jennifer A., Fowler, Gerald, Kovar, Christie L., Lewis, Lora R., Morgan, Margaret B., Newsham, Irene F., Reid, Jeffrey G., Santibanez, Jireh, Shinbrot, Eve, Trevino, Lisa R., Wu, Yuan-Qing, Wang, Min, Gunaratne, Preethi, Donehower, Lawrence A., Creighton, Chad J., Wheeler, David A., Gibbs, Richard A., Lawrence, Michael S., Voet, Douglas, Jing, Rui, Cibulskis, Kristian, Sivachenko, Andrey, Stojanov, Petar, McKenna, Aaron, Lander, Eric S., Gabriel, Stacey, Getz, Gad, Ding, Li, Fulton, Robert S., Koboldt, Daniel C., Wylie, Todd, Walker, Jason, Dooling, David J., Fulton, Lucinda, Delehaunty, Kim D., Fronick, Catrina C., Demeter, Ryan, Mardis, Elaine R., Wilson, Richard K., Chu, Andy, Chun, Hye-Jung E., Mungall, Andrew J., Pleasance, Erin, Robertson, Gordon A., Stoll, Dominik, Balasundaram, Miruna, Birol, Inanc, Butterfield, Yaron S. N., Chuah, Eric, Coope, Robin J. N., Dhalla, Noreen, Guin, Ranabir, Hirst, Carrie, Hirst, Martin, Holt, Robert A., Lee, Darlene, Li, Haiyan I., Mayo, Michael, Moore, Richard A., Schein, Jacqueline E., Slobodan, Jared R., Tam, Angela, Thiessen, Nina, Varhol, Richard, Zeng, Thomas, Zhao, Yongjun, Jones, Steven J. M., Marra, Marco A., Bass, Adam J., Ramos, Alex H., Saksena, Gordon, Cherniack, Andrew D., Schumacher, Stephen E., Tabak, Barbara, Carter, Scott L., Pho, Nam H., Nguyen, Huy, Onofrio, Robert C., Crenshaw, Andrew, Ardlie, Kristin, Beroukhim, Rameen, Winckler, Wendy, Meyerson, Matthew, Protopopov, Alexei, Zhang, Juinhua, Hadjipanayis, Angela, Lee, Eunjung, Xi, Ruibin, Yang, Lixing, Ren, Xiaojia, Zhang, Hailei, Sathiamoorthy, Narayanan, Shukla, Sachet, Chen, Peng-Chieh, Haseley, Psalm, Xiao, Yonghong, Lee, Semin, Seidman, Jonathan, Chin, Lynda, Park, Peter J., Kucherlapati, Raju, Auman, Todd J., Hoadley, Katherine A., Du, Ying, Wilkerson, Matthew D., Shi, Yan, Liquori, Christina, Meng, Shaowu, Li, Ling, Turman, Yidi J., Topal, Michael D., Tan, Donghui, Waring, Scot, Buda, Elizabeth, Walsh, Jesse, Jones, Corbin D., Mieczkowski, Piotr A., Singh, Darshan, Wu, Junyuan, Gulabani, Anisha, Dolina, Peter, Bodenheimer, Tom, Hoyle, Alan P., Simons, Janae V., Soloway, Matthew, Mose, Lisle E., Jefferys, Stuart R., Balu, Saianand, O’Connor, Brian D., Prins, Jan F., Chiang, Derek Y., Hayes, Neil D., Perou, Charles M., Hinoue, Toshinori, Weisenberger, Daniel J., Maglinte, Dennis T., Pan, Fei, Berman, Benjamin P., Van Den Berg, David J., Shen, Hui, Triche, Timothy, Jr, Baylin, Stephen B., Laird, Peter W., Noble, Michael, Voet, Doug, Gehlenborg, Nils, DiCara, Daniel, Wu, Chang-Jiun, Yingchun Liu, Spring, Zhou, Lihua, Lin, Pei, Park, Richard W., Nazaire, Marc-Danie, Robinson, Jim, Thorvaldsdottir, Helga, Mesirov, Jill, Thorsson, Vesteinn, Reynolds, Sheila M., Bernard, Brady, Kreisberg, Richard, Lin, Jake, Iype, Lisa, Bressler, Ryan, Erkkilä, Timo, Gundapuneni, Madhumati, Liu, Yuexin, Norberg, Adam, Robinson, Tom, Yang, Da, Zhang, Wei, Shmulevich, Ilya, de Ronde, Jorma J., Schultz, Nikolaus, Cerami, Ethan, Ciriello, Giovanni, Goldberg, Arthur P., Gross, Benjamin, Jacobsen, Anders, Gao, Jianjiong, Kaczkowski, Bogumil, Sinha, Rileen, Aksoy, Arman B., Antipin, Yevgeniy, Reva, Boris, Shen, Ronglai, Taylor, Barry S., Chan, Timothy A., Ladanyi, Marc, Sander, Chris, Akbani, Rehan, Zhang, Nianxiang, Broom, Bradley M., Casasent, Tod, Unruh, Anna, Wakefield, Chris, Hamilton, Stanley R., Cason, Craig R., Baggerly, Keith A., Weinstein, John N., Haussler, David, Benz, Christopher C., Stuart, Joshua M., Benz, Stephen C., Sanborn, Zachary J., Vaske, Charles J., Zhu, Jingchun, Szeto, Christopher, Scott, Gary K., Yau, Christina, Ng, Sam, Goldstein, Ted, Ellrott, Kyle, Collisson, Eric, Cozen, Aaron E., Zerbino, Daniel, Wilks, Christopher, Craft, Brian, Spellman, Paul, Penny, Robert, Shelton, Troy, Hatfield, Martha, Morris, Scott, Yena, Peggy, Shelton, Candace, Sherman, Mark, Paulauskis, Joseph, Gastier-Foster, Julie M., Bowen, Jay, Ramirez, Nilsa C., Black, Aaron, Pyatt, Robert, Wise, Lisa, White, Peter, Bertagnolli, Monica, Brown, Jen, Chu, Gerald C., Czerwinski, Christine, Denstman, Fred, Dhir, Rajiv, Dörner, Arnulf, Fuchs, Charles S., Guillem, Jose G., Iacocca, Mary, Juhl, Hartmut, Kaufman, Andrew, Kohl, Bernard, III, Van Le, Xuan, Mariano, Maria C., Medina, Elizabeth N., Meyers, Michael, Nash, Garrett M., Paty, Phillip B., Petrelli, Nicholas, Rabeno, Brenda, Richards, William G., Solit, David, Swanson, Pat, Temple, Larissa, Tepper, Joel E., Thorp, Richard, Vakiani, Efsevia, Weiser, Martin R., Willis, Joseph E., Witkin, Gary, Zeng, Zhaoshi, Zinner, Michael J., Zornig, Carsten, Jensen, Mark A., Sfeir, Robert, Kahn, Ari B., Chu, Anna L., Kothiyal, Prachi, Wang, Zhining, Snyder, Eric E., Pontius, Joan, Pihl, Todd D., Ayala, Brenda, Backus, Mark, Walton, Jessica, Whitmore, Jon, Baboud, Julien, Berton, Dominique L., Nicholls, Matthew C., Srinivasan, Deepak, Raman, Rohini, Girshik, Stanley, Kigonya, Peter A., Alonso, Shelley, Sanbhadti, Rashmi N., Barletta, Sean P., Greene, John M., Pot, David A., Mills Shaw, Kenna R., Dillon, Laura A. L., Buetow, Ken, Davidsen, Tanja, Demchok, John A., Eley, Greg, Ferguson, Martin, Fielding, Peter, Schaefer, Carl, Sheth, Margi, Yang, Liming, Guyer, Mark S., Ozenberger, Bradley A., Palchik, Jacqueline D., Peterson, Jane, Sofia, Heidi J., and Thomson, Elizabeth

Published
2012
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23. Rates, distribution and implications of postzygotic mosaic mutations in autism spectrum disorder

Author

Lim, Elaine T., Uddin, Mohammed, De Rubeis, Silvia, Chan, Yingleong, Kamumbu, Anne S., Zhang, Xiaochang, D'Gama, Alissa M., Kim, Sonia N., Hill, Robert Sean, Goldberg, Arthur P., Poultney, Christopher, Minshew, Nancy J., Kushima, Itaru, Aleksic, Branko, Ozaki, Norio, Parellada, Mara, Arango, Celso, Penzol, Maria J., Carracedo, Angel, Kolevzon, Alexander, Hultman, Christina M., Weiss, Lauren A., Fromer, Menachem, Chiocchetti, Andreas G., Freitag, Christine M., Church, George M., Scherer, Stephen W., Buxbaum, Joseph D., Walsh, Christopher A, Aleksic, B, Anney, R, Barbosa, M, Barrett, J, Betancur, C, Bishop, S, Brusco, A, Buxbaum, Jd, Carracedo, A, Chiocchetti, Ag, Chung, Bhy, Cook, E, Coon, H, Cutler, Dj, Daly, M, De Rubeis, S, Doan, R, Fernández-Prieto, M, Ferrero, Gb, Freitag, Cm, Fromer, M, Gargus, J, Geschwind, D, Gill, M, Gómez-Guerrero, L, Hansen-Kiss, E, He, X, Herman, G, Hertz-Picciotto, I, Hultman, C, Iliadou, B, Ionita-Laza, I, Jugessur, A, Knudsen, Gp, Kolevzon, A, Kosmicki, J, Kushima, I, Lee, Sl, Lehner, T, Lennertz, S, Lim, E, Maciel, P, Magnus, P, Manoach, D, Minshew, N, Morrow, E, Mulle, J, Neale, B, Ozaki, N, Palotie, A, Parellada, M, Passos-Bueno, Mr, Pericak-Vance, M, Persico, A, Pessah, I, Reichenberg, A, Reichert, J, Renieri, A, Robinson, E, Samocha, K, Sanders, S, Sandin, S, Santangelo, Sl, Satterstrom, K, Schafer, C, Schellenberg, G, Scherer, S, Senthil, G, Silva, M, Singh, T, Siper, Pm, Soares, G, Stevens, C, Stoltenberg, C, Surén, P, Sutcliffe, Js, Szatmari, P, Tassone, F, Thurm, A, Walsh, C, Weiss, L, Werling, D, Willsey, J, Xu, X, Yu, Tw, Yuen, R, Zwick, Me., Howard Hughes Medical Institute [Boston] (HHMI), Howard Hughes Medical Institute (HHMI)-Harvard Medical School [Boston] (HMS), Boston Children's Hospital, Harvard Medical School [Boston] (HMS), Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Harvard University [Cambridge], Mohammed Bin Rashid University of Medicine and Health Sciences (MBRU), Icahn School of Medicine at Mount Sinai [New York] (MSSM), University of Pittsburgh (PITT), Pennsylvania Commonwealth System of Higher Education (PCSHE), Nagoya University, Hospital General Universitario 'Gregorio Marañón' [Madrid], Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Centro de Investigación Biomédica en Red Salud Mental [Madrid] (CIBER-SAM), Universidade de Santiago de Compostela [Spain] (USC ), CIBER de Enfermedades Raras (CIBERER), Fundación Pública Galega Medicina Xenómica - SERGAS [Santiago de Compostela, Spain] (Grupo de Medicina Xenómica), CIBER de Enfermedades Raras (CIBERER)-Universidade de Santiago de Compostela [Spain] (USC ), King Abdulaziz University, Karolinska Institutet [Stockholm], University of California [San Francisco] (UCSF), University of California, Goethe-University Frankfurt am Main, Génétique de l'autisme = Genetics of Autism (NPS-01), Neurosciences Paris Seine (NPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), The Hospital for sick children [Toronto] (SickKids), University of Toronto, McLaughlin Centre for Population Health Risk Assessment, University of Ottawa [Ottawa], Autism Sequencing Consortium: Branko Aleksic, Richard Anney, Mafalda Barbosa, Jeffrey Barrett, Catalina Betancur, Somer Bishop, Alfredo Brusco, Joseph D Buxbaum, Angel Carracedo, Andreas G Chiocchetti, Brian H Y Chung, Edwin Cook, Hilary Coon, David J Cutler, Mark Daly, Silvia De Rubeis, Ryan Doan, Montserrat Fernández-Prieto, Giovanni Battista Ferrero, Christine M Freitag, Menachem Fromer, Jay Gargus, Dan Geschwind, Michael Gill, Lorena Gómez-Guerrero, Emily Hansen-Kiss, Xin He, Gail Herman, Irva Hertz-Picciotto, Christina Hultman, Bozenna Iliadou, Iuliana Ionita-Laza, Anil Jugessur, Gun Peggy Knudsen, Alexander Kolevzon, Jack Kosmicki, Itaru Kushima, S L Lee, Thomas Lehner, Savannah Lennertz, Elaine Lim, Patricia Maciel, Per Magnus, Dara Manoach, Nancy Minshew, Eric Morrow, Jennifer Mulle, Benjamin Neale, Norio Ozaki, Aarno Palotie, Mara Parellada, Maria Rita Passos-Bueno, Margaret Pericak-Vance, Antonio Persico, Isaac Pessah, Avi Reichenberg, Jennifer Reichert, Alessandra Renieri, Elise Robinson, Kaitlin Samocha, Stephan Sanders, Sven Sandin, Susan L Santangelo, Kyle Satterstrom, Chad Schafer, Gerry Schellenberg, Stephen Scherer, Geetha Senthil, Marisol Silva, Tarjinder Singh, Paige M Siper, Gabriela Soares, Christine Stevens, Camilla Stoltenberg, Pål Surén, James S Sutcliffe, Peter Szatmari, Flora Tassone, Audrey Thurm, Christopher Walsh, Lauren Weiss, Donna Werling, Jeremy Willsey, Xinyi Xu, Timothy W Yu, Ryan Yuen, Michael E Zwick., University of California [San Francisco] (UC San Francisco), University of California (UC), Neuroscience Paris Seine (NPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Betancur, Catalina

Subjects
0301 basic medicine, Proband, Nonsynonymous substitution, Autism Spectrum Disorder, Databases, Genetic, Genetic Predisposition to Disease, Genetic Variation, Humans, Mosaicism, Mutation, Missense, Zygote, Neuroscience (all), Mutation, Missense, Epigenetics of autism, Biology, [SDV.GEN.GH] Life Sciences [q-bio]/Genetics/Human genetics, medicine.disease_cause, Article, 03 medical and health sciences, Genetic variation, mental disorders, Databases, Genetic, medicine, Missense mutation, Heritability of autism, MESH: Genetic Variation, MESH: Databases, Genetic, Genetics, MESH: Autism Spectrum Disorder, MESH: Mutation, Missense, [SDV.GEN]Life Sciences [q-bio]/Genetics, MESH: Humans, General Neuroscience, MESH: Genetic Predisposition to Disease, medicine.disease, 030104 developmental biology, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Autism spectrum disorder, MESH: Zygote, MESH: Mosaicism
Abstract

International audience; We systematically analyzed postzygotic mutations (PZMs) in whole-exome sequences from the largest collection of trios (5,947) with autism spectrum disorder (ASD) available, including 282 unpublished trios, and performed resequencing using multiple independent technologies. We identified 7.5% of de novo mutations as PZMs, 83.3% of which were not described in previous studies. Damaging, nonsynonymous PZMs within critical exons of prenatally expressed genes were more common in ASD probands than controls (P < 1 × 10-6), and genes carrying these PZMs were enriched for expression in the amygdala (P = 5.4 × 10-3). Two genes (KLF16 and MSANTD2) were significantly enriched for PZMs genome-wide, and other PZMs involved genes (SCN2A, HNRNPU and SMARCA4) whose mutation is known to cause ASD or other neurodevelopmental disorders. PZMs constitute a significant proportion of de novo mutations and contribute importantly to ASD risk.

Published
2017

24. The Realities of Justice for Today's Education

Author

Goldberg, Arthur J.

Abstract

This keynote address delivered at the Law in American Society Foundation's Fourth National Conference on Law-Focused Education stresses that law-oriented education programs need to candid about both the failure and succcesses of the legal system. (Author/SM)

Published
1975

26. 6-4-4+: The Ultimate Structure

Author

Goldberg, Arthur

Abstract

An educational architecture based on six years of elementary school, four years of high school, four years of college, and whatever years of university work that may be necessary for a Masters, Doctorate, or professional degree is described. (DB)

Published
1971

27. Reflections Of A Two Year College Dean

Author

Goldberg, Arthur

Abstract

A dean of students looks at the need to streamline services of a two-year college to make them responsive to student needs and to make them financially feasible. (CJ)

Published
1973

28. Meta-analysis of GWAS of over 16,000 individuals with autism spectrum disorder highlights a novel locus at 10q24.32 and a significant overlap with schizophrenia

Author

Anney, Richard J.L., Ripke, Stephan, Anttila, Verneri, Grove, Jakob, Holmans, Peter, Huang, Hailiang, Klei, Lambertus, Lee, Phil H., Medland, Sarah E., Neale, Benjamin, Robinson, Elise, Weiss, Lauren A., Zwaigenbaum, Lonnie, Yu, Timothy W., Wittemeyer, Kerstin, Willsey, A. Jeremy, Wijsman, Ellen M., Werge, Thomas, Wassink, Thomas H., Waltes, Regina, Walsh, Christopher A., Wallace, Simon, Vorstman, Jacob A.S., Vieland, Veronica J., Vicente, Astrid M., Vanengeland, Herman, Tsang, Kathryn, Thompson, Ann P., Szatmari, Peter, Svantesson, Oscar, Steinberg, Stacy, Stefansson, Kari, Stefansson, Hreinn, State, Matthew W., Soorya, Latha, Silagadze, Teimuraz, Scherer, Stephen W., Schellenberg, Gerard D., Sandin, Sven, Sanders, Stephan J., Saemundsen, Evald, Rouleau, Guy A., Rogé, Bernadette, Roeder, Kathryn, Roberts, Wendy, Reichert, Jennifer, Reichenberg, Abraham, Rehnström, Karola, Regan, Regina, Poustka, Fritz, Poultney, Christopher S., Piven, Joseph, Pinto, Dalila, Pericak-Vance, Margaret A., Pejovic-Milovancevic, Milica, Pedersen, Marianne Giørtz, Pedersen, Carsten Bøcker, Paterson, Andrew D., Parr, Jeremy R., Pagnamenta, Alistair T., Oliveira, Guiomar, Nurnberger, John I., Nordentoft, Merete, Murtha, Michael T., Mouga, Susana, Mortensen, Preben Bo, Mors, Ole, Morrow, Eric M., Moreno-De-Luca, Daniel, Monaco, Anthony P., Minshew, Nancy, Merikangas, Alison, McMahon, William M., McGrew, Susan G., Mattheisen, Manuel, Martsenkovsky, Igor, Martin, Donna M., Mane, Shrikant M., Magnusson, Pall, Magalhaes, Tiago, Maestrini, Elena, Lowe, Jennifer K., Lord, Catherine, Levitt, Pat, Martin, Christa Lese, Ledbetter, David H., Leboyer, Marion, Lecouteur, Ann S., Ladd-Acosta, Christine, Kolevzon, Alexander, Klauck, Sabine M., Jacob, Suma, Iliadou, Bozenna, Hultman, Christina M., Hougaard, David M., Hertz-Picciotto, Irva, Hendren, Robert, Hansen, Christine Søholm, Haines, Jonathan L., Guter, Stephen J., Grice, Dorothy E., Green, Jonathan M., Green, Andrew, Goldberg, Arthur P., Gillberg, Christopher, Gilbert, John, Gallagher, Louise, Freitag, Christine M., Fombonne, Eric, Folstein, Susan E., Fernandez, Bridget, Fallin, M. Daniele, Ercan-Sencicek, A. Gulhan, Ennis, Sean, Duque, Frederico, Duketis, Eftichia, Delorme, Richard, Derubeis, Silvia, Dejonge, Maretha V., Dawson, Geraldine, Cuccaro, Michael L., Correia, Catarina T., Conroy, Judith, Conceição, Ines C., Chiocchetti, Andreas G., Celestino-Soper, Patrícia B.S., Casey, Jillian, Cantor, Rita M., Café, Cátia, Bybjerg-Grauholm, Jonas, Brennan, Sean, Bourgeron, Thomas, Bolton, Patrick F., Bölte, Sven, Bolshakova, Nadia, Betancur, Catalina, Bernier, Raphael, Beaudet, Arthur L., Battaglia, Agatino, Bal, Vanessa H., Baird, Gillian, Bailey, Anthony J., Bækvad-Hansen, Marie, Bader, Joel S., Bacchelli, Elena, Anagnostou, Evdokia, Amaral, David, Almeida, Joana, Børglum, Anders D., Buxbaum, Joseph D., Chakravarti, Aravinda, Cook, Edwin H., Coon, Hilary, Geschwind, Daniel H., Gill, Michael, Hakonarson, Hakon, Hallmayer, Joachim, Palotie, Aarno, Santangelo, Susan, Sutcliffe, James S., Arking, Dan E., Devlin, Bernie, Daly, Mark J., Anney, Richard J.L., Ripke, Stephan, Anttila, Verneri, Grove, Jakob, Holmans, Peter, Huang, Hailiang, Klei, Lambertus, Lee, Phil H., Medland, Sarah E., Neale, Benjamin, Robinson, Elise, Weiss, Lauren A., Zwaigenbaum, Lonnie, Yu, Timothy W., Wittemeyer, Kerstin, Willsey, A. Jeremy, Wijsman, Ellen M., Werge, Thomas, Wassink, Thomas H., Waltes, Regina, Walsh, Christopher A., Wallace, Simon, Vorstman, Jacob A.S., Vieland, Veronica J., Vicente, Astrid M., Vanengeland, Herman, Tsang, Kathryn, Thompson, Ann P., Szatmari, Peter, Svantesson, Oscar, Steinberg, Stacy, Stefansson, Kari, Stefansson, Hreinn, State, Matthew W., Soorya, Latha, Silagadze, Teimuraz, Scherer, Stephen W., Schellenberg, Gerard D., Sandin, Sven, Sanders, Stephan J., Saemundsen, Evald, Rouleau, Guy A., Rogé, Bernadette, Roeder, Kathryn, Roberts, Wendy, Reichert, Jennifer, Reichenberg, Abraham, Rehnström, Karola, Regan, Regina, Poustka, Fritz, Poultney, Christopher S., Piven, Joseph, Pinto, Dalila, Pericak-Vance, Margaret A., Pejovic-Milovancevic, Milica, Pedersen, Marianne Giørtz, Pedersen, Carsten Bøcker, Paterson, Andrew D., Parr, Jeremy R., Pagnamenta, Alistair T., Oliveira, Guiomar, Nurnberger, John I., Nordentoft, Merete, Murtha, Michael T., Mouga, Susana, Mortensen, Preben Bo, Mors, Ole, Morrow, Eric M., Moreno-De-Luca, Daniel, Monaco, Anthony P., Minshew, Nancy, Merikangas, Alison, McMahon, William M., McGrew, Susan G., Mattheisen, Manuel, Martsenkovsky, Igor, Martin, Donna M., Mane, Shrikant M., Magnusson, Pall, Magalhaes, Tiago, Maestrini, Elena, Lowe, Jennifer K., Lord, Catherine, Levitt, Pat, Martin, Christa Lese, Ledbetter, David H., Leboyer, Marion, Lecouteur, Ann S., Ladd-Acosta, Christine, Kolevzon, Alexander, Klauck, Sabine M., Jacob, Suma, Iliadou, Bozenna, Hultman, Christina M., Hougaard, David M., Hertz-Picciotto, Irva, Hendren, Robert, Hansen, Christine Søholm, Haines, Jonathan L., Guter, Stephen J., Grice, Dorothy E., Green, Jonathan M., Green, Andrew, Goldberg, Arthur P., Gillberg, Christopher, Gilbert, John, Gallagher, Louise, Freitag, Christine M., Fombonne, Eric, Folstein, Susan E., Fernandez, Bridget, Fallin, M. Daniele, Ercan-Sencicek, A. Gulhan, Ennis, Sean, Duque, Frederico, Duketis, Eftichia, Delorme, Richard, Derubeis, Silvia, Dejonge, Maretha V., Dawson, Geraldine, Cuccaro, Michael L., Correia, Catarina T., Conroy, Judith, Conceição, Ines C., Chiocchetti, Andreas G., Celestino-Soper, Patrícia B.S., Casey, Jillian, Cantor, Rita M., Café, Cátia, Bybjerg-Grauholm, Jonas, Brennan, Sean, Bourgeron, Thomas, Bolton, Patrick F., Bölte, Sven, Bolshakova, Nadia, Betancur, Catalina, Bernier, Raphael, Beaudet, Arthur L., Battaglia, Agatino, Bal, Vanessa H., Baird, Gillian, Bailey, Anthony J., Bækvad-Hansen, Marie, Bader, Joel S., Bacchelli, Elena, Anagnostou, Evdokia, Amaral, David, Almeida, Joana, Børglum, Anders D., Buxbaum, Joseph D., Chakravarti, Aravinda, Cook, Edwin H., Coon, Hilary, Geschwind, Daniel H., Gill, Michael, Hakonarson, Hakon, Hallmayer, Joachim, Palotie, Aarno, Santangelo, Susan, Sutcliffe, James S., Arking, Dan E., Devlin, Bernie, and Daly, Mark J.

Abstract

Background: Over the past decade genome-wide association studies (GWAS) have been applied to aid in the understanding of the biology of traits. The success of this approach is governed by the underlying effect sizes carried by the true risk variants and the corresponding statistical power to observe such effects given the study design and sample size under investigation. Previous ASD GWAS have identified genome-wide significant (GWS) risk loci; however, these studies were of only of low statistical power to identify GWS loci at the lower effect sizes (odds ratio (OR) <1.15). Methods: We conducted a large-scale coordinated international collaboration to combine independent genotyping data to improve the statistical power and aid in robust discovery of GWS loci. This study uses genome-wide genotyping data from a discovery sample (7387 ASD cases and 8567 controls) followed by meta-analysis of summary statistics from two replication sets (7783 ASD cases and 11359 controls; and 1369 ASD cases and 137308 controls). Results: We observe a GWS locus at 10q24.32 that overlaps several genes including PITX3, which encodes a transcription factor identified as playing a role in neuronal differentiation and CUEDC2 previously reported to be associated with social skills in an independent population cohort. We also observe overlap with regions previously implicated in schizophrenia which was further supported by a strong genetic correlation between these disorders (Rg = 0.23; P = 9 × 10-6). We further combined these Psychiatric Genomics Consortium (PGC) ASD GWAS data with the recent PGC schizophrenia GWAS to identify additional regions which may be important in a common neurodevelopmental phenotype and identified 12 novel GWS loci. These include loci previously implicated in ASD such as FOXP1 at 3p13, ATP2B2 at 3p25.3, and a 'neurodevelopmental hub' on chromosome 8p11.23. Conclusions: This study is an important step in the ongoing endeavour to identify the loci whic

Published
2017

30. Whole-cell model simulations for medicine and bioengineering

Author

Karr, Jonathan R and Goldberg, Arthur P

Subjects
computational biology, dynamical modeling, systems biology
Abstract

Whole-cell models predict cell behaviors by modeling all molecular components and their interactions. Recently, we and other developed the first whole-cell model. The model represents the functionality of all 409 characterized genes and 725 metabolites throughout one life cycle of the reduced bacterium Mycoplasma genitalium. This model was validated against a broad range of data and provided insights into many previously unobserved cellular behaviors. Simulating the behavior of a single cell required modest computing resources – 1 core-day of an Intel E5520 CPU, capable of 3.3×1015 double-precision floating-point operations during the computation. Sampling the organism’s behavior required 128 simulations. Nevertheless, we anticipate that exascale computing resources will be required to use more comprehensive and more accurate whole-cell models to personalize medicine and engineer bacteria.

Published
2015
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32. Toward Community Standards and Software for Whole-Cell Modeling

Author

Waltemath, Dagmar, primary, Karr, Jonathan R., additional, Bergmann, Frank T., additional, Chelliah, Vijayalakshmi, additional, Hucka, Michael, additional, Krantz, Marcus, additional, Liebermeister, Wolfram, additional, Mendes, Pedro, additional, Myers, Chris J., additional, Pir, Pinar, additional, Alaybeyoglu, Begum, additional, Aranganathan, Naveen K, additional, Baghalian, Kambiz, additional, Bittig, Arne T., additional, Burke, Paulo E. Pinto, additional, Cantarelli, Matteo, additional, Chew, Yin Hoon, additional, Costa, Rafael S., additional, Cursons, Joseph, additional, Czauderna, Tobias, additional, Goldberg, Arthur P., additional, Gomez, Harold F., additional, Hahn, Jens, additional, Hameri, Tuure, additional, Gardiol, Daniel F. Hernandez, additional, Kazakiewicz, Denis, additional, Kiselev, Ilya, additional, Knight-Schrijver, Vincent, additional, Knupfer, Christian, additional, Konig, Matthias, additional, Lee, Daewon, additional, Lloret-Villas, Audald, additional, Mandrik, Nikita, additional, Medley, J. Kyle, additional, Moreau, Bertrand, additional, Naderi-Meshkin, Hojjat, additional, Palaniappan, Sucheendra K., additional, Priego-Espinosa, Daniel, additional, Scharm, Martin, additional, Sharma, Mahesh, additional, Smallbone, Kieran, additional, Stanford, Natalie J., additional, Song, Je-Hoon, additional, Theile, Tom, additional, Tokic, Milenko, additional, Tomar, Namrata, additional, Toure, Vasundra, additional, Uhlendorf, Jannis, additional, Varusai, Thawfeek M, additional, Watanabe, Leandro H., additional, Wendland, Florian, additional, Wolfien, Markus, additional, Yurkovich, James T., additional, Zhu, Yan, additional, Zardilis, Argyris, additional, Zhukova, Anna, additional, and Schreiber, Falk, additional

Published
2016
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35. Most genetic risk for autism resides with common variation

Author

Gaugler, Trent, primary, Klei, Lambertus, additional, Sanders, Stephan J, additional, Bodea, Corneliu A, additional, Goldberg, Arthur P, additional, Lee, Ann B, additional, Mahajan, Milind, additional, Manaa, Dina, additional, Pawitan, Yudi, additional, Reichert, Jennifer, additional, Ripke, Stephan, additional, Sandin, Sven, additional, Sklar, Pamela, additional, Svantesson, Oscar, additional, Reichenberg, Abraham, additional, Hultman, Christina M, additional, Devlin, Bernie, additional, Roeder, Kathryn, additional, and Buxbaum, Joseph D, additional

Published
2014
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36. Identification of Small Exonic CNV from Whole-Exome Sequence Data and Application to Autism Spectrum Disorder

Author

Poultney, Christopher S., primary, Goldberg, Arthur P., additional, Drapeau, Elodie, additional, Kou, Yan, additional, Harony-Nicolas, Hala, additional, Kajiwara, Yuji, additional, De Rubeis, Silvia, additional, Durand, Simon, additional, Stevens, Christine, additional, Rehnström, Karola, additional, Palotie, Aarno, additional, Daly, Mark J., additional, Ma’ayan, Avi, additional, Fromer, Menachem, additional, and Buxbaum, Joseph D., additional

Published
2013
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37. The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data

Author

Cerami, Ethan, primary, Gao, Jianjiong, additional, Dogrusoz, Ugur, additional, Gross, Benjamin E., additional, Sumer, Selcuk Onur, additional, Aksoy, Bülent Arman, additional, Jacobsen, Anders, additional, Byrne, Caitlin J., additional, Heuer, Michael L., additional, Larsson, Erik, additional, Antipin, Yevgeniy, additional, Reva, Boris, additional, Goldberg, Arthur P., additional, Sander, Chris, additional, and Schultz, Nikolaus, additional

Published
2012
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38. The Expanding Legacy of the Enslaved Potter-Poet David Drake

Author

Goldberg, Arthur F. and Goldberg, Deborah A.

Abstract

ABSTRACTThis article focuses on a number of important events in the ongoing legacies of David (Dave) Drake, an African-American potter who lived and worked in Edgefield, South Carolina. Dave’s creativity was expressed in writing poetry and as a conceptual artist. His inspirations have been recognized by efforts today in advancing literacy and improving education. This study examines an array of interactive museum programs, educational initiatives, films, theater and dance productions, poetry readings, and publications for young and old readers alike that have conveyed Dave’s accomplishments to broad audiences and students. Archaeological engagements, scholarly publications, and Dave’s induction into the South Carolina Hall of Fame are also considered. His legacies are discussed in their historical contexts and in regard to their impacts on facets of our contemporary society and culture. From limited recognition decades ago to broad acclaim today, Edgefield alkaline-glazed stoneware is now seen as the genesis of an artisan tradition of Southern stoneware.

Published
2017
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39. VirtualPlant: A Software Platform to Support Systems Biology Research

Author

Katari, Manpreet S., primary, Nowicki, Steve D., additional, Aceituno, Felipe F., additional, Nero, Damion, additional, Kelfer, Jonathan, additional, Thompson, Lee Parnell, additional, Cabello, Juan M., additional, Davidson, Rebecca S., additional, Goldberg, Arthur P., additional, Shasha, Dennis E., additional, Coruzzi, Gloria M., additional, and Gutieݩrrez, Rodrigo A., additional

Published
2009
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43. Intervention and Human Rights.

Author

Goldberg, Arthur J.

Abstract

Defends the right of nations to criticize human rights violations within other nations. Pointing out that the human rights protections cannot be left to domestic jurisdiction, Goldberg cites numerous treaties and declarations which make human rights protection a matter of international law. (GEA)

Published
1988

44. The Helsinki Final Act and the Madrid Review Conference: A Case Study of Political Non-Communication.

Author

Goldberg, Arthur J.

Subjects
CONFERENCES & conventions, HUMAN rights violations
Abstract

Abstract The article is the first authoritative published account of the two Follow-up Helsinki Act Conferences, at Belgrade 1977-1978 and at Madrid 1980 and still underway. The article describes what occurred at the Belgrade Conference. With the United States taking the lead, the West criticized the Soviet Union and other Eastern-bloc countries for their violations of the human rights provisions of the Helsinki Final Act. The article points out that the contention of the Soviet Union and its allies that such criticism constituted intervention in their internal affairs is without legal foundation. The author points out that the Concluding Document of the Belgrade Conference, noting the differences between the parties and fixing the date for the next Follow-up Conference at Madrid commencing in November 1980, was appropriate and preserved the Helsinki process, without compromising its principles. The article reviews the preparatory meeting before the convening of the Madrid Conference in November 1980. It then reviews the proceedings of the substantive Madrid meeting during the past two years. The article is critical of a proposal of the neutral and nonaligned countries for the Concluding Document of the Madrid Conference. [ABSTRACT FROM AUTHOR]

Published
1982
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45. Implementing a fee system based on appropriate subsidy.

Author

Goldberg, Arthur and Kovac, David C.

Abstract

This article focuses on implementation of a fee system based on appropriate subsidy related to the field of social service. Late in 1968 the board of directors of Jewish Family and Children's Service of St. Louis requested the traditional and periodic review of the agency's fee-charging practices. Since the system had not been reviewed for several years, it was decided by the administration to embark upon a major study, not only of its own practice but also of the current practice in the field. A consideration in the initial process was about a new approach to fee-charging, based upon the belief that prior practice had no visible rationale and that most attempts at reviewing fees resuited only in an increase in existing scales without any change in the basic concept. In almost every case of fee adjustment by professional staff, fees were adjusted downward, in contradiction to the frequent practice of private practitioners who adjusted their fees upward to match the increased capacity of some clients to pay.

Published
1973
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46. A new concept of subsidy in determining fees for service.

Author

Goldberg, Arthur and Kovac, David C.

Abstract

Clearly the way in which one perceives structure or creates it is determined by the way in which one perceives his world. The way current fee systems have evolved from the social work past is consistent with that past. This article oilers the suggestion that, along with the newly emerging views of service by clients and agency, a fresh appraisal be made of the basic assumption from which fee policies and procedures are created. This article has attempted to provide a new perspective. For the Jewish Family and Children's Service of St. Louis, it has provided the basis for revisions in practice that will have direct implications for the future. [ABSTRACT FROM AUTHOR]

Published
1971
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47. FOREWORD -- THE BURGER COURT 1971 TERM: ONE STEP FORWARD, TWO STEPS BACKWARD?

Author

Goldberg, Arthur J.

Subjects
AMISH, CRIMINAL law, FREEDOM of religion, EDUCATION policy, LEGAL judgments
Abstract

This article focuses on Burger Court's criminal law decisions. The Burger Court, in its criminal law decisions of the October 1971 Term, on occasion confounded both its critics and protagonists. This is equally true of its decisions in other areas. Thus, by way of example, in the criminal law area it struck down the Administration's domestic wiretapping program. In dealing with the first amendment's safeguard of the free exercise of religion, the Court held that the Amish need not comply with Wisconsin's compulsory formal education requirement after the eighth grade; compliance, in the Court's view, was inconsistent with the free exercise of their religious beliefs. An analysis of these and other decisions of the 1971 Term shows that it is conceivable if another vacancy on the Court should occur during President Nixon's tenure, that his five appointees-- then a majority of the Court--might join to over rule significant criminal law and other forward looking decisions of the Warren Court.

Published
1972
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48. SECTARIAN VERSUS NON-SECTARIAN INTAKE POLICIES.

Author

Peyser, Hedy and Goldberg, Arthur

Subjects
RESEARCH, JEWISH community centers, SOCIAL services, JEWISH families, JEWISH children
Abstract

The article presents a study that examined the intake policies, practices, and experiences of other Jewish agencies in the U.S. The Jewish Family and Children's Service of Saint Louis, Missouri, undertook a critical examination of its non-sectarian intake policies. A questionnaire was sent to all 38 Jewish social service agencies. The questionnaire comprised of three parts: the first part, filled out by agencies who do not serve non-Jewish customers; the second to be completed by those serving non-Jewish customers; and the third part by all agencies.

Published
1970

49. Marine Biochemistry: A New Interdisciplinary Course for the Interim

Author

Goldberg, Arthur S.

Abstract

Discusses an undergraduate course which includes lectures, laboratory, and field trips and is designed for the interim winter semester. The course is interdisciplinary, involving a study of the biochemistry, pharmacology, and physiological significance of compounds from marine flora and fauna. (MLH)

Published
1976

50. Intranasal Absorption of Flurazepam, Midazolam, and Triazolam in Dogs

Author

Lui, Chung Y., Amidon, Gordon L., and Goldberg, Arthur

Abstract

Intranasal delivery of flurazepam, midazolam, and triazolam was studied in a dog model as a possible alternate route of drug administration for treatment of insomnia. Four beagles received each hypnotic by both intranasal and oral routes on two separate occasions. Plasma concentrations for each hypnotic after dosing were measured by electron-capture gas-liquid chromatography. The mean intranasal absorption rates (tmax) of flurazepam, midazolam, and triazolam were 1.7, 2.0, and 2.6 times faster, respectively, compared with oral dosing. The mean dose-normalized peak concentrations (Cmax) after intranasal delivery were 16.4, 2.9, and 3.4 times higher, respectively, versus oral administration. The mean dose-normalized AUCs estimated for these compounds after nasal administration were 2.4−, 2.5−, and at least 2-fold larger than after oral administration for midazolam, triazolam, and flurazepam, respectively. If these observations can be extrapolated to humans, the faster absorption achieved by the intranasal route would appear to benefit insomniacs characterized by difficulty in falling asleep because of an anticipated faster sedative effect onset. The higher peak concentrations and larger amounts absorbed in the case of intranasal midazolam and triazolam delivery may lead to dose reduction.

Published
1991
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