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144 results on '"Sullivan, Brendan P."'

1. Author Correction: Divergent landscapes of A-to-I editing in postmortem and living human brain

Author

Rodriguez de los Santos, Miguel, Kopell, Brian H., Buxbaum Grice, Ariela, Ganesh, Gauri, Yang, Andy, Amini, Pardis, Liharska, Lora E., Vornholt, Eric, Fullard, John F., Dong, Pengfei, Park, Eric, Zipkowitz, Sarah, Kaji, Deepak A., Thompson, Ryan C., Liu, Donjing, Park, You Jeong, Cheng, Esther, Ziafat, Kimia, Moya, Emily, Fennessy, Brian, Wilkins, Lillian, Silk, Hannah, Linares, Lisa M., Sullivan, Brendan, Cohen, Vanessa, Kota, Prashant, Feng, Claudia, Johnson, Jessica S., Rieder, Marysia-Kolbe, Scarpa, Joseph, Nadkarni, Girish N., Wang, Minghui, Zhang, Bin, Sklar, Pamela, Beckmann, Noam D., Schadt, Eric E., Roussos, Panos, Charney, Alexander W., and Breen, Michael S.

Published
2024
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2. Divergent landscapes of A-to-I editing in postmortem and living human brain

Author

Rodriguez de los Santos, Miguel, Kopell, Brian H., Buxbaum Grice, Ariela, Ganesh, Gauri, Yang, Andy, Amini, Pardis, Liharska, Lora E., Vornholt, Eric, Fullard, John F., Dong, Pengfei, Park, Eric, Zipkowitz, Sarah, Kaji, Deepak A., Thompson, Ryan C., Liu, Donjing, Park, You Jeong, Cheng, Esther, Ziafat, Kimia, Moya, Emily, Fennessy, Brian, Wilkins, Lillian, Silk, Hannah, Linares, Lisa M., Sullivan, Brendan, Cohen, Vanessa, Kota, Prashant, Feng, Claudia, Johnson, Jessica S., Rieder, Marysia-Kolbe, Scarpa, Joseph, Nadkarni, Girish N., Wang, Minghui, Zhang, Bin, Sklar, Pamela, Beckmann, Noam D., Schadt, Eric E., Roussos, Panos, Charney, Alexander W., and Breen, Michael S.

Published
2024
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5. Developing a Technology Readiness Level Template for Model-Based Design Methods and Tools in a Collaborative Environment

Author

Santacruz, Roman F. Bastidas, Sullivan, Brendan P., Terzi, Sergio, Sassanelli, Claudio, Rannenberg, Kai, Editor-in-Chief, Soares Barbosa, Luís, Editorial Board Member, Goedicke, Michael, Editorial Board Member, Tatnall, Arthur, Editorial Board Member, Neuhold, Erich J., Editorial Board Member, Stiller, Burkhard, Editorial Board Member, Tröltzsch, Fredi, Editorial Board Member, Pries-Heje, Jan, Editorial Board Member, Kreps, David, Editorial Board Member, Reis, Ricardo, Editorial Board Member, Furnell, Steven, Editorial Board Member, Mercier-Laurent, Eunika, Editorial Board Member, Winckler, Marco, Editorial Board Member, Malaka, Rainer, Editorial Board Member, Noël, Frédéric, editor, Nyffenegger, Felix, editor, Rivest, Louis, editor, and Bouras, Abdelaziz, editor

Published
2023
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6. MBSE-PLM Integration: Initiatives and Future Outlook

Author

Gerhard, Detlef, Cordero, Sophia Salas, Vingerhoeds, Rob, Sullivan, Brendan P., Rossi, Monica, Brovar, Yana, Menshenin, Yaroslav, Fortin, Clement, Eynard, Benoit, Rannenberg, Kai, Editor-in-Chief, Soares Barbosa, Luís, Editorial Board Member, Goedicke, Michael, Editorial Board Member, Tatnall, Arthur, Editorial Board Member, Neuhold, Erich J., Editorial Board Member, Stiller, Burkhard, Editorial Board Member, Tröltzsch, Fredi, Editorial Board Member, Pries-Heje, Jan, Editorial Board Member, Kreps, David, Editorial Board Member, Reis, Ricardo, Editorial Board Member, Furnell, Steven, Editorial Board Member, Mercier-Laurent, Eunika, Editorial Board Member, Winckler, Marco, Editorial Board Member, Malaka, Rainer, Editorial Board Member, Noël, Frédéric, editor, Nyffenegger, Felix, editor, Rivest, Louis, editor, and Bouras, Abdelaziz, editor

Published
2023
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7. The structure of a potassium-selective ion channel reveals a hydrophobic gate regulating ion permeation

Author

Langan, Patricia S, Vandavasi, Venu Gopal, Kopec, Wojciech, Sullivan, Brendan, Afonne, Pavel V, Weiss, Kevin L, de Groot, Bert L, and Coates, Leighton

Subjects
Physical Sciences, Condensed Matter Physics, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, X-ray crystallography, conformational transitions, gating, potassium ion channels, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Physical Chemistry (incl. Structural), Physical chemistry, Condensed matter physics
Abstract

Protein dynamics are essential to function. One example of this is the various gating mechanisms within ion channels, which are transmembrane proteins that act as gateways into the cell. Typical ion channels switch between an open and closed state via a conformational transition which is often triggered by an external stimulus, such as ligand binding or pH and voltage differences. The atomic resolution structure of a potassium-selective ion channel named NaK2K has allowed us to observe that a hydro-phobic residue at the bottom of the selectivity filter, Phe92, appears in dual conformations. One of the two conformations of Phe92 restricts the diameter of the exit pore around the selectivity filter, limiting ion flow through the channel, while the other conformation of Phe92 provides a larger-diameter exit pore from the selectivity filter. Thus, it can be concluded that Phe92 acts as a hydro-phobic gate, regulating the flow of ions through the selectivity filter.

Published
2020

11. MBSE-PLM Integration: Initiatives and Future Outlook

Author

Gerhard, Detlef, primary, Cordero, Sophia Salas, additional, Vingerhoeds, Rob, additional, Sullivan, Brendan P., additional, Rossi, Monica, additional, Brovar, Yana, additional, Menshenin, Yaroslav, additional, Fortin, Clement, additional, and Eynard, Benoit, additional

Published
2023
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13. Reconfigurable Manufacturing: An Investigation of Diagnosability Requirements, Enabling Technologies and Applications in Industry

Author

Napoleone, Alessia, Sullivan, Brendan P., Arias-Nava, Elias, Andersen, Ann-Louise, Cavas-Martínez, Francisco, Series Editor, Chaari, Fakher, Series Editor, di Mare, Francesca, Series Editor, Gherardini, Francesco, Series Editor, Haddar, Mohamed, Series Editor, Ivanov, Vitalii, Series Editor, Kwon, Young W., Series Editor, Trojanowska, Justyna, Series Editor, Andersen, Ann-Louise, editor, Andersen, Rasmus, editor, Brunoe, Thomas Ditlev, editor, Larsen, Maria Stoettrup Schioenning, editor, Nielsen, Kjeld, editor, Napoleone, Alessia, editor, and Kjeldgaard, Stefan, editor

Published
2022
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14. Population‐based identity‐by‐descent mapping combined with exome sequencing to detect rare risk variants for schizophrenia

Author

Harold, Denise, Connolly, Siobhan, Riley, Brien P, Kendler, Kenneth S, McCarthy, Shane E, McCombie, William R, Richards, Alex, Owen, Michael J, O'Donovan, Michael C, Walters, James, Donnelly, Peter, Bates, Lesley, Barroso, Ines, Blackwell, Jenefer M, Bramon, Elvira, Brown, Matthew A, Casas, Juan P, Corvin, Aiden, Deloukas, Panos, Duncanson, Audrey, Jankowski, Janusz, Markus, Hugh S, Mathew, Christopher G, Palmer, Colin NA, Plomin, Robert, Rautanen, Anna, Sawcer, Stephen J, Trembath, Richard C, Viswanathan, Ananth C, Wood, Nicholas W, Spencer, Chris CA, Band, Gavin, Bellenguez, Céline, Freeman, Colin, Hellenthal, Garrett, Giannoulatou, Eleni, Hopkins, Lucinda, Pirinen, Matti, Pearson, Richard, Strange, Amy, Su, Zhan, Vukcevic, Damjan, Langford, Cordelia, Hunt, Sarah E, Edkins, Sarah, Gwilliam, Rhian, Blackburn, Hannah, Bumpstead, Suzannah J, Dronov, Serge, Gillman, Matthew, Gray, Emma, Hammond, Naomi, Jayakumar, Alagurevathi, McCann, Owen T, Liddle, Jennifer, Potter, Simon C, Ravindrarajah, Radhi, Ricketts, Michelle, Waller, Matthew, Weston, Paul, Widaa, Sara, Whittaker, Pamela, Ripke, Stephan, Neale, Benjamin M, Walters, James TR, Farh, Kai‐How, Holmans, Peter A, Lee, Phil, Bulik‐Sullivan, Brendan, Collier, David A, Huang, Hailiang, Pers, Tune H, Agartz, Ingrid, Agerbo, Esben, Albus, Margot, Alexander, Madeline, Amin, Farooq, Bacanu, Silviu A, Begemann, Martin, Belliveau, Richard A, Bene, Judit, Bergen, Sarah E, Bevilacqua, Elizabeth, Bigdeli, Tim B, Black, Donald W, Bruggeman, Richard, Buccola, Nancy G, Buckner, Randy L, Byerley, William, Cahn, Wiepke, Cai, Guiqing, Campion, Dominique, Cantor, Rita M, Carr, Vaughan J, Carrera, Noa, Catts, Stanley V, Chambert, Kimberley D, Chan, Raymond CK, and Chan, Ronald YL

Subjects
Biological Sciences, Genetics, Clinical Research, Schizophrenia, Brain Disorders, Human Genome, Prevention, Serious Mental Illness, Mental Health, Aetiology, 2.1 Biological and endogenous factors, Adult, Case-Control Studies, Chromosome Mapping, DNA Copy Number Variations, Databases, Genetic, Exome, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Genotype, Haplotypes, Humans, Male, Middle Aged, Risk Factors, Sequence Analysis, DNA, Exome Sequencing, GWAS, IBD mapping, rare variants, Wellcome Trust Case Control Consortium 2, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Clinical Sciences, Neurosciences, Clinical sciences
Abstract

Genome-wide association studies (GWASs) are highly effective at identifying common risk variants for schizophrenia. Rare risk variants are also important contributors to schizophrenia etiology but, with the exception of large copy number variants, are difficult to detect with GWAS. Exome and genome sequencing, which have accelerated the study of rare variants, are expensive so alternative methods are needed to aid detection of rare variants. Here we re-analyze an Irish schizophrenia GWAS dataset (n = 3,473) by performing identity-by-descent (IBD) mapping followed by exome sequencing of individuals identified as sharing risk haplotypes to search for rare risk variants in coding regions. We identified 45 rare haplotypes (>1 cM) that were significantly more common in cases than controls. By exome sequencing 105 haplotype carriers, we investigated these haplotypes for functional coding variants that could be tested for association in independent GWAS samples. We identified one rare missense variant in PCNT but did not find statistical support for an association with schizophrenia in a replication analysis. However, IBD mapping can prioritize both individual samples and genomic regions for follow-up analysis but genome rather than exome sequencing may be more effective at detecting risk variants on rare haplotypes.

Published
2019

15. Through the Lens of Social Studies, What Has Changed for Refugees to the U.S. Since the COVID-19 Pandemic Began? An Inquiry Lesson for Secondary Education

Author

Elbih, Randa N., Ciccone, Michelangelo, and Sullivan, Brendan

Abstract

As the COVID-19 pandemic unfolds, every aspect of daily life is being altered in response to the virus. The pandemic has altered secondary education. Classes online, teachers struggling to learn Zoom and make lessons meaningful and relevant to students. Students struggling to make sense of this moment, struggling with mental health issues due to the loss of routine and in many cases contact with adult role models. Unfortunately, in times of crisis such as these some of the most disenfranchized people in society are completely overlooked and forgotten, such as refugees. However, if more teachers were to leverage the social studies potential of current events such as the Coronavirus, greater empathy would be felt for marginalized people more starkly impacted by the pandemic, leading ultimately to a heightened sense of civic engagement among the next generation. The purpose of this paper is to assist teachers in guiding their students through analyzing current events, such as COVID-19's impact on refugees, toward developing civic mindedness. In addition to this, the paper will discuss some of the broader societal impacts the virus is having within the United States, as well as ways in which this event may be viewed as a historical subject in the future. The paper will begin by building the content knowledge of high school social studies teachers through addressing the following question: "What is the difference between a refugee entering the United States now versus one year ago before the COVID-19 pandemic?" Following this, the authors will present an inquiry-based learning segment designed to teach the History correlated to the COVID-19 pandemic to a classroom of secondary education students. The inquiry template follows the standard C3 format utilized by the State of Connecticut.

Published
2021
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16. Extending Value in Legacy Production Systems: Insights from the Liquid Food Processing

Author

Sullivan, Brendan P., Rossi, Monica, Ward, David, Leardi, Carlo, Rannenberg, Kai, Editor-in-Chief, Soares Barbosa, Luís, Editorial Board Member, Goedicke, Michael, Editorial Board Member, Tatnall, Arthur, Editorial Board Member, Neuhold, Erich J., Editorial Board Member, Stiller, Burkhard, Editorial Board Member, Tröltzsch, Fredi, Editorial Board Member, Pries-Heje, Jan, Editorial Board Member, Kreps, David, Editorial Board Member, Reis, Ricardo, Editorial Board Member, Furnell, Steven, Editorial Board Member, Mercier-Laurent, Eunika, Editorial Board Member, Winckler, Marco, Editorial Board Member, Malaka, Rainer, Editorial Board Member, Camarinha-Matos, Luis M., editor, Boucher, Xavier, editor, and Afsarmanesh, Hamideh, editor

Published
2021
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21. Analysis of shared heritability in common disorders of the brain

Author

Consortium, The Brainstorm, Anttila, Verneri, Bulik-Sullivan, Brendan, Finucane, Hilary K, Walters, Raymond K, Bras, Jose, Duncan, Laramie, Escott-Price, Valentina, Falcone, Guido J, Gormley, Padhraig, Malik, Rainer, Patsopoulos, Nikolaos A, Ripke, Stephan, Wei, Zhi, Yu, Dongmei, Lee, Phil H, Turley, Patrick, Grenier-Boley, Benjamin, Chouraki, Vincent, Kamatani, Yoichiro, Berr, Claudine, Letenneur, Luc, Hannequin, Didier, Amouyel, Philippe, Boland, Anne, Deleuze, Jean-François, Duron, Emmanuelle, Vardarajan, Badri N, Reitz, Christiane, Goate, Alison M, Huentelman, Matthew J, Kamboh, M Ilyas, Larson, Eric B, Rogaeva, Ekaterina, St George-Hyslop, Peter, Hakonarson, Hakon, Kukull, Walter A, Farrer, Lindsay A, Barnes, Lisa L, Beach, Thomas G, Demirci, F Yesim, Head, Elizabeth, Hulette, Christine M, Jicha, Gregory A, Kauwe, John SK, Kaye, Jeffrey A, Leverenz, James B, Levey, Allan I, Lieberman, Andrew P, Pankratz, Vernon S, Poon, Wayne W, Quinn, Joseph F, Saykin, Andrew J, Schneider, Lon S, Smith, Amanda G, Sonnen, Joshua A, Stern, Robert A, Van Deerlin, Vivianna M, Van Eldik, Linda J, Harold, Denise, Russo, Giancarlo, Rubinsztein, David C, Bayer, Anthony, Tsolaki, Magda, Proitsi, Petra, Fox, Nick C, Hampel, Harald, Owen, Michael J, Mead, Simon, Passmore, Peter, Morgan, Kevin, Nöthen, Markus M, Schott, Jonathan M, Rossor, Martin, Lupton, Michelle K, Hoffmann, Per, Kornhuber, Johannes, Lawlor, Brian, McQuillin, Andrew, Al-Chalabi, Ammar, Bis, Joshua C, Ruiz, Agustin, Boada, Mercè, Seshadri, Sudha, Beiser, Alexa, Rice, Kenneth, van der Lee, Sven J, De Jager, Philip L, Geschwind, Daniel H, Riemenschneider, Matthias, Riedel-Heller, Steffi, Rotter, Jerome I, Ransmayr, Gerhard, Hyman, Bradley T, Cruchaga, Carlos, Alegret, Montserrat, Winsvold, Bendik, Palta, Priit, Farh, Kai-How, and Cuenca-Leon, Ester

Subjects
Biological Sciences, Genetics, Biological Psychology, Health Sciences, Psychology, Clinical Research, Mental Health, Human Genome, Brain Disorders, Neurosciences, Mental Illness, 2.1 Biological and endogenous factors, Neurological, Mental health, Brain Diseases, Genetic Variation, Genome-Wide Association Study, Humans, Mental Disorders, Phenotype, Quantitative Trait, Heritable, Risk Factors, Brainstorm Consortium, General Science & Technology
Abstract

Disorders of the brain can exhibit considerable epidemiological comorbidity and often share symptoms, provoking debate about their etiologic overlap. We quantified the genetic sharing of 25 brain disorders from genome-wide association studies of 265,218 patients and 784,643 control participants and assessed their relationship to 17 phenotypes from 1,191,588 individuals. Psychiatric disorders share common variant risk, whereas neurological disorders appear more distinct from one another and from the psychiatric disorders. We also identified significant sharing between disorders and a number of brain phenotypes, including cognitive measures. Further, we conducted simulations to explore how statistical power, diagnostic misclassification, and phenotypic heterogeneity affect genetic correlations. These results highlight the importance of common genetic variation as a risk factor for brain disorders and the value of heritability-based methods in understanding their etiology.

Published
2018

22. Genomic Dissection of Bipolar Disorder and Schizophrenia, Including 28 Subphenotypes

Author

Consortium, Bipolar Disorder and Schizophrenia Working Group of the Psychiatric Genomics, Ruderfer, Douglas M, Ripke, Stephan, McQuillin, Andrew, Boocock, James, Stahl, Eli A, Pavlides, Jennifer M Whitehead, Mullins, Niamh, Charney, Alexander W, Ori, Anil PS, Loohuis, Loes M Olde, Domenici, Enrico, Di Florio, Arianna, Papiol, Sergi, Kalman, Janos L, Trubetskoy, Vassily, Adolfsson, Rolf, Agartz, Ingrid, Agerbo, Esben, Akil, Huda, Albani, Diego, Albus, Margot, Alda, Martin, Alexander, Madeline, Alliey-Rodriguez, Ney, Als, Thomas D, Amin, Farooq, Anjorin, Adebayo, Arranz, Maria J, Awasthi, Swapnil, Bacanu, Silviu A, Badner, Judith A, Baekvad-Hansen, Marie, Bakker, Steven, Band, Gavin, Barchas, Jack D, Barroso, Ines, Bass, Nicholas, Bauer, Michael, Baune, Bernhard T, Begemann, Martin, Bellenguez, Celine, Belliveau, Richard A, Bellivier, Frank, Bender, Stephan, Bene, Judit, Bergen, Sarah E, Berrettini, Wade H, Bevilacqua, Elizabeth, Biernacka, Joanna M, Bigdeli, Tim B, Black, Donald W, Blackburn, Hannah, Blackwell, Jenefer M, Blackwood, Douglas HR, Pedersen, Carsten Bocker, Boehnke, Michael, Boks, Marco, Borglum, Anders D, Bramon, Elvira, Breen, Gerome, Brown, Matthew A, Bruggeman, Richard, Buccola, Nancy G, Buckner, Randy L, Budde, Monika, Bulik-Sullivan, Brendan, Bumpstead, Suzannah J, Bunney, William, Burmeister, Margit, Buxbaum, Joseph D, Bybjerg-Grauholm, Jonas, Byerley, William, Cahn, Wiepke, Cai, Guiqing, Cairns, Murray J, Campion, Dominique, Cantor, Rita M, Carr, Vaughan J, Carrera, Noa, Casas, Juan P, Casas, Miquel, Catts, Stanley V, Cervantes, Pablo, Chambert, Kimberley D, Chan, Raymond CK, Chen, Eric YH, Chen, Ronald YL, Cheng, Wei, Cheung, Eric FC, Chong, Siow Ann, Clarke, Toni-Kim, Cloninger, C Robert, Cohen, David, Cohen, Nadine, Coleman, Jonathan RI, Collier, David A, Cormican, Paul, Coryell, William, and Craddock, Nicholas

Subjects
Human Genome, Neurosciences, Serious Mental Illness, Bipolar Disorder, Biotechnology, Schizophrenia, Brain Disorders, Genetics, Mental Health, Mental health, Good Health and Well Being, Case-Control Studies, Genetic Loci, Genome-Wide Association Study, Humans, Multifactorial Inheritance, Odds Ratio, Phenotype, Risk, White People, Bipolar Disorder and Schizophrenia Working Group of the Psychiatric Genomics Consortium. Electronic address: douglas.ruderfer@vanderbilt.edu, Bipolar Disorder and Schizophrenia Working Group of the Psychiatric Genomics Consortium, bipolar disorder, polygenic risk, psychosis, schizophrenia, subphenotypes, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Schizophrenia and bipolar disorder are two distinct diagnoses that share symptomology. Understanding the genetic factors contributing to the shared and disorder-specific symptoms will be crucial for improving diagnosis and treatment. In genetic data consisting of 53,555 cases (20,129 bipolar disorder [BD], 33,426 schizophrenia [SCZ]) and 54,065 controls, we identified 114 genome-wide significant loci implicating synaptic and neuronal pathways shared between disorders. Comparing SCZ to BD (23,585 SCZ, 15,270 BD) identified four genomic regions including one with disorder-independent causal variants and potassium ion response genes as contributing to differences in biology between the disorders. Polygenic risk score (PRS) analyses identified several significant correlations within case-only phenotypes including SCZ PRS with psychotic features and age of onset in BD. For the first time, we discover specific loci that distinguish between BD and SCZ and identify polygenic components underlying multiple symptom dimensions. These results point to the utility of genetics to inform symptomology and potential treatment.

Published
2018

23. Analysis of shared heritability in common disorders of the brain.

Author

Brainstorm Consortium, Anttila, Verneri, Bulik-Sullivan, Brendan, Finucane, Hilary K, Walters, Raymond K, Bras, Jose, Duncan, Laramie, Escott-Price, Valentina, Falcone, Guido J, Gormley, Padhraig, Malik, Rainer, Patsopoulos, Nikolaos A, Ripke, Stephan, Wei, Zhi, Yu, Dongmei, Lee, Phil H, Turley, Patrick, Grenier-Boley, Benjamin, Chouraki, Vincent, Kamatani, Yoichiro, Berr, Claudine, Letenneur, Luc, Hannequin, Didier, Amouyel, Philippe, Boland, Anne, Deleuze, Jean-François, Duron, Emmanuelle, Vardarajan, Badri N, Reitz, Christiane, Goate, Alison M, Huentelman, Matthew J, Kamboh, M Ilyas, Larson, Eric B, Rogaeva, Ekaterina, St George-Hyslop, Peter, Hakonarson, Hakon, Kukull, Walter A, Farrer, Lindsay A, Barnes, Lisa L, Beach, Thomas G, Demirci, F Yesim, Head, Elizabeth, Hulette, Christine M, Jicha, Gregory A, Kauwe, John SK, Kaye, Jeffrey A, Leverenz, James B, Levey, Allan I, Lieberman, Andrew P, Pankratz, Vernon S, Poon, Wayne W, Quinn, Joseph F, Saykin, Andrew J, Schneider, Lon S, Smith, Amanda G, Sonnen, Joshua A, Stern, Robert A, Van Deerlin, Vivianna M, Van Eldik, Linda J, Harold, Denise, Russo, Giancarlo, Rubinsztein, David C, Bayer, Anthony, Tsolaki, Magda, Proitsi, Petra, Fox, Nick C, Hampel, Harald, Owen, Michael J, Mead, Simon, Passmore, Peter, Morgan, Kevin, Nöthen, Markus M, Rossor, Martin, Lupton, Michelle K, Hoffmann, Per, Kornhuber, Johannes, Lawlor, Brian, McQuillin, Andrew, Al-Chalabi, Ammar, Bis, Joshua C, Ruiz, Agustin, Boada, Mercè, Seshadri, Sudha, Beiser, Alexa, Rice, Kenneth, van der Lee, Sven J, De Jager, Philip L, Geschwind, Daniel H, Riemenschneider, Matthias, Riedel-Heller, Steffi, Rotter, Jerome I, Ransmayr, Gerhard, Hyman, Bradley T, Cruchaga, Carlos, Alegret, Montserrat, Winsvold, Bendik, Palta, Priit, Farh, Kai-How, Cuenca-Leon, Ester, and Furlotte, Nicholas

Subjects
Brainstorm Consortium, Humans, Brain Diseases, Risk Factors, Mental Disorders, Quantitative Trait, Heritable, Phenotype, Genetic Variation, Genome-Wide Association Study, Clinical Research, Neurosciences, Rare Diseases, Human Genome, Brain Disorders, Genetics, Mental Health, 2.1 Biological and endogenous factors, Mental health, Neurological, General Science & Technology
Abstract

Disorders of the brain can exhibit considerable epidemiological comorbidity and often share symptoms, provoking debate about their etiologic overlap. We quantified the genetic sharing of 25 brain disorders from genome-wide association studies of 265,218 patients and 784,643 control participants and assessed their relationship to 17 phenotypes from 1,191,588 individuals. Psychiatric disorders share common variant risk, whereas neurological disorders appear more distinct from one another and from the psychiatric disorders. We also identified significant sharing between disorders and a number of brain phenotypes, including cognitive measures. Further, we conducted simulations to explore how statistical power, diagnostic misclassification, and phenotypic heterogeneity affect genetic correlations. These results highlight the importance of common genetic variation as a risk factor for brain disorders and the value of heritability-based methods in understanding their etiology.

Published
2018

24. Maritime Design Process Improvement Through a Lean Transformation

Author

Sullivan, Brendan P., Rossi, Monica, Ramundo, Lucia, Terzi, Sergio, Kacprzyk, Janusz, Series Editor, Gomide, Fernando, Advisory Editor, Kaynak, Okyay, Advisory Editor, Liu, Derong, Advisory Editor, Pedrycz, Witold, Advisory Editor, Polycarpou, Marios M., Advisory Editor, Rudas, Imre J., Advisory Editor, Wang, Jun, Advisory Editor, Rossi, Monica, editor, Rossini, Matteo, editor, and Terzi, Sergio, editor

Published
2020
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25. Correction to: MBSE-PLM Integration: Initiatives and Future Outlook

Author

Gerhard, Detlef, Salas Cordero, Sophia, Vingerhoeds, Rob, Sullivan, Brendan P., Rossi, Monica, Brovar, Yana, Menshenin, Yaroslav, Fortin, Clement, Eynard, Benoit, Rannenberg, Kai, Editor-in-Chief, Soares Barbosa, Luís, Editorial Board Member, Goedicke, Michael, Editorial Board Member, Tatnall, Arthur, Editorial Board Member, Neuhold, Erich J., Editorial Board Member, Stiller, Burkhard, Editorial Board Member, Tröltzsch, Fredi, Editorial Board Member, Pries-Heje, Jan, Editorial Board Member, Kreps, David, Editorial Board Member, Reis, Ricardo, Editorial Board Member, Furnell, Steven, Editorial Board Member, Mercier-Laurent, Eunika, Editorial Board Member, Winckler, Marco, Editorial Board Member, Malaka, Rainer, Editorial Board Member, Noël, Frédéric, editor, Nyffenegger, Felix, editor, Rivest, Louis, editor, and Bouras, Abdelaziz, editor

Published
2023
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26. The 3x3 rooks graph is the unique smallest graph with lazy cop number 3

Author

Sullivan, Brendan W., Townsend, Nikolas, and Werzanski, Mikayla

Subjects
Mathematics - Combinatorics, Computer Science - Discrete Mathematics, 05C57
Abstract

In the ordinary version of the pursuit-evasion game "cops and robbers", a team of cops and a robber occupy vertices of a graph and alternately move along the graph's edges, with perfect information about each other. If a cop lands on the robber, the cops win; if the robber can evade the cops indefinitely, he wins. In the variant "lazy cops and robbers", the cops may only choose one member of their squad to make a move when it's their turn. The minimum number of cops (respectively lazy cops) required to catch the robber is called the "cop number" (resp. "lazy cop number") of G and is denoted $c(G)$ (resp. $c_L(G)$). Previous work by Beveridge at al. has shown that the Petersen graph is the unique graph on ten vertices with $c(G)=3$, and all graphs on nine or fewer vertices have $c(G)\leq 2$. (This was a self-contained mathematical proof of a result found by computational search by Baird and Bonato.) In this article, we prove a similar result for lazy cops, namely that the 3x3 rooks graph ($K_3\square K_3$) is the unique graph on nine vertices which requires three lazy cops, and a graph on eight or fewer vertices requires at most two lazy cops., Comment: 24 pages, 14 figures

Published
2016

27. Significant Locus and Metabolic Genetic Correlations Revealed in Genome-Wide Association Study of Anorexia Nervosa

Author

Duncan, Laramie, Yilmaz, Zeynep, Gaspar, Helena, Walters, Raymond, Goldstein, Jackie, Anttila, Verneri, Bulik-Sullivan, Brendan, Ripke, Stephan, Thornton, Laura, Hinney, Anke, Daly, Mark, Sullivan, Patrick F, Zeggini, Eleftheria, Breen, Gerome, Bulik, Cynthia M, Gaspar, Héléna, Adan, Roger, Alfredsson, Lars, Ando, Tetsuya, Andreassen, Ole, Aschauer, Harald, Baker, Jessica, Barrett, Jeffrey, Bencko, Vladimir, Bergen, Andrew, Berrettini, Wade, Birgegård, Andreas, Boni, Claudette, Perica, Vesna Boraska, Brandt, Harry, Burghardt, Roland, Carlberg, Laura, Cassina, Matteo, Cesta, Carolyn, Cichon, Sven, Clementi, Maurizio, Cohen-Woods, Sarah, Coleman, Joni, Cone, Roger, Courtet, Philippe, Crawford, Steven, Crow, Scott, Crowley, Jim, Danner, Unna, Davis, Oliver, de Zwaan, Martina, Dedoussis, George, Degortes, Daniela, DeSocio, Janiece, Dick, Danielle, Dikeos, Dimitris, Dina, Christian, Ding, Bo, Dmitrzak-Weglarz, Monika, Docampo, Elisa, Egberts, Karin, Ehrlich, Stefan, Escaramís, Geòrgia, Esko, Tõnu, Espeseth, Thomas, Estivill, Xavier, Favaro, Angela, Fernández-Aranda, Fernando, Fichter, Manfred, Finan, Chris, Fischer, Krista, Floyd, James, Föcker, Manuel, Foretova, Lenka, Forzan, Monica, Fox, Caroline, Franklin, Christopher, Gaborieau, Valerie, Gallinger, Steven, Gambaro, Giovanni, Giegling, Ina, Gonidakis, Fragiskos, Gorwood, Philip, Gratacos, Monica, Guillaume, Sébastien, Guo, Yiran, Hakonarson, Hakon, Halmi, Katherine, Harrison, Rebecca, Hatzikotoulas, Konstantinos, Hauser, Joanna, Hebebrand, Johannes, Helder, Sietske, Hendriks, Judith, Herms, Stefan, Herpertz-Dahlmann, Beate, Herzog, Wolfgang, and Hilliard, Christopher

Subjects
Serious Mental Illness, Mental Health, Anorexia, Eating Disorders, Brain Disorders, Nutrition, Human Genome, Genetics, Prevention, Pediatric, Mental health, Anorexia Nervosa, Case-Control Studies, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Linkage Disequilibrium, Phenotype, Polymorphism, Single Nucleotide, Eating Disorders Working Group of the Psychiatric Genomics Consortium, Diabetes, GWAS, Metabolism, Medical and Health Sciences, Psychology and Cognitive Sciences, Psychiatry
Abstract

ObjectiveThe authors conducted a genome-wide association study of anorexia nervosa and calculated genetic correlations with a series of psychiatric, educational, and metabolic phenotypes.MethodFollowing uniform quality control and imputation procedures using the 1000 Genomes Project (phase 3) in 12 case-control cohorts comprising 3,495 anorexia nervosa cases and 10,982 controls, the authors performed standard association analysis followed by a meta-analysis across cohorts. Linkage disequilibrium score regression was used to calculate genome-wide common variant heritability (single-nucleotide polymorphism [SNP]-based heritability [h2SNP]), partitioned heritability, and genetic correlations (rg) between anorexia nervosa and 159 other phenotypes.ResultsResults were obtained for 10,641,224 SNPs and insertion-deletion variants with minor allele frequencies >1% and imputation quality scores >0.6. The h2SNP of anorexia nervosa was 0.20 (SE=0.02), suggesting that a substantial fraction of the twin-based heritability arises from common genetic variation. The authors identified one genome-wide significant locus on chromosome 12 (rs4622308) in a region harboring a previously reported type 1 diabetes and autoimmune disorder locus. Significant positive genetic correlations were observed between anorexia nervosa and schizophrenia, neuroticism, educational attainment, and high-density lipoprotein cholesterol, and significant negative genetic correlations were observed between anorexia nervosa and body mass index, insulin, glucose, and lipid phenotypes.ConclusionsAnorexia nervosa is a complex heritable phenotype for which this study has uncovered the first genome-wide significant locus. Anorexia nervosa also has large and significant genetic correlations with both psychiatric phenotypes and metabolic traits. The study results encourage a reconceptualization of this frequently lethal disorder as one with both psychiatric and metabolic etiology.

Published
2017

28. Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects

Author

Marshall, Christian R, Howrigan, Daniel P, Merico, Daniele, Thiruvahindrapuram, Bhooma, Wu, Wenting, Greer, Douglas S, Antaki, Danny, Shetty, Aniket, Holmans, Peter A, Pinto, Dalila, Gujral, Madhusudan, Brandler, William M, Malhotra, Dheeraj, Wang, Zhouzhi, Fajarado, Karin V Fuentes, Maile, Michelle S, Ripke, Stephan, Agartz, Ingrid, Albus, Margot, Alexander, Madeline, Amin, Farooq, Atkins, Joshua, Bacanu, Silviu A, Belliveau, Richard A, Bergen, Sarah E, Bertalan, Marcelo, Bevilacqua, Elizabeth, Bigdeli, Tim B, Black, Donald W, Bruggeman, Richard, Buccola, Nancy G, Buckner, Randy L, Bulik-Sullivan, Brendan, Byerley, William, Cahn, Wiepke, Cai, Guiqing, Cairns, Murray J, Campion, Dominique, Cantor, Rita M, Carr, Vaughan J, Carrera, Noa, Catts, Stanley V, Chambert, Kimberley D, Cheng, Wei, Cloninger, C Robert, Cohen, David, Cormican, Paul, Craddock, Nick, Crespo-Facorro, Benedicto, Crowley, James J, Curtis, David, Davidson, Michael, Davis, Kenneth L, Degenhardt, Franziska, Del Favero, Jurgen, DeLisi, Lynn E, Dikeos, Dimitris, Dinan, Timothy, Djurovic, Srdjan, Donohoe, Gary, Drapeau, Elodie, Duan, Jubao, Dudbridge, Frank, Eichhammer, Peter, Eriksson, Johan, Escott-Price, Valentina, Essioux, Laurent, Fanous, Ayman H, Farh, Kai-How, Farrell, Martilias S, Frank, Josef, Franke, Lude, Freedman, Robert, Freimer, Nelson B, Friedman, Joseph I, Forstner, Andreas J, Fromer, Menachem, Genovese, Giulio, Georgieva, Lyudmila, Gershon, Elliot S, Giegling, Ina, Giusti-Rodríguez, Paola, Godard, Stephanie, Goldstein, Jacqueline I, Gratten, Jacob, de Haan, Lieuwe, Hamshere, Marian L, Hansen, Mark, Hansen, Thomas, Haroutunian, Vahram, Hartmann, Annette M, Henskens, Frans A, Herms, Stefan, Hirschhorn, Joel N, Hoffmann, Per, Hofman, Andrea, Huang, Hailiang, Ikeda, Masashi, Joa, Inge, and Kähler, Anna K

Subjects
Serious Mental Illness, Human Genome, Schizophrenia, Genetics, Biotechnology, Prevention, Mental Health, Brain Disorders, 2.1 Biological and endogenous factors, Aetiology, Mental health, Case-Control Studies, DNA Copy Number Variations, Female, Genetic Loci, Genetic Markers, Genetic Predisposition to Disease, Genome-Wide Association Study, Genotype, Humans, Male, Risk Factors, Psychosis Endophenotypes International Consortium, CNV and Schizophrenia Working Groups of the Psychiatric Genomics Consortium, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Copy number variants (CNVs) have been strongly implicated in the genetic etiology of schizophrenia (SCZ). However, genome-wide investigation of the contribution of CNV to risk has been hampered by limited sample sizes. We sought to address this obstacle by applying a centralized analysis pipeline to a SCZ cohort of 21,094 cases and 20,227 controls. A global enrichment of CNV burden was observed in cases (odds ratio (OR) = 1.11, P = 5.7 × 10-15), which persisted after excluding loci implicated in previous studies (OR = 1.07, P = 1.7 × 10-6). CNV burden was enriched for genes associated with synaptic function (OR = 1.68, P = 2.8 × 10-11) and neurobehavioral phenotypes in mouse (OR = 1.18, P = 7.3 × 10-5). Genome-wide significant evidence was obtained for eight loci, including 1q21.1, 2p16.3 (NRXN1), 3q29, 7q11.2, 15q13.3, distal 16p11.2, proximal 16p11.2 and 22q11.2. Suggestive support was found for eight additional candidate susceptibility and protective loci, which consisted predominantly of CNVs mediated by nonallelic homologous recombination.

Published
2017

29. Rapid Evolution of the Photosystem II Electronic Structure during Water Splitting

Author

Davis, Katherine M., Sullivan, Brendan T., Palenik, Mark, Yan, Lifen, Purohit, Vatsal, Robison, Gregory, Kosheleva, Irina, Henning, Robert W., Seidler, Gerald T., and Pushkar, Yulia

Subjects
Physics - Biological Physics, Physics - Chemical Physics
Abstract

Photosynthetic water oxidation is a fundamental process that sustains the biosphere. A Mn$_{4}$Ca cluster embedded in the photosystem II protein environment is responsible for the production of atmospheric oxygen. Here, time-resolved x-ray emission spectroscopy (XES) was used to observe the process of oxygen formation in real time. These experiments reveal that the oxygen evolution step, initiated by three sequential laser flashes, is accompanied by rapid (within 50 $\mu$s) changes to the Mn K$\beta$ XES spectrum. However, no oxidation of the Mn$_{4}$Ca core above the all Mn$^{\text{IV}}$ state was detected to precede O-O bond formation. A new mechanism featuring Mn$^{\text{IV}}$=O formation in the S$_{3}$ state is proposed to explain the spectroscopic results. This chemical formulation is consistent with the unique reactivity of the S$_{3}$ state and explains facilitation of the following S$_{3}$ to S$_{0}$ transition, resolving in part the kinetic limitations associated with O-O bond formation. In the proposed mechanism, O-O bond formation precedes transfer of the final (4$^{\text{th}}$) electron from the Mn$_{4}$Ca cluster, in agreement with experiment., Comment: 49 pages, includes main text (pgs. 1-16) and supplementary material (pgs. 17-49), 13 figures (4 main text, and 9 supplementary), 12 tables (2 main text, 10 supplementary)

Published
2015
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31. Simulation and value stream map generated using real-time location system.

Author

Nava, Elias Arias and Sullivan, Brendan P.

Subjects
*VALUE stream mapping, *VALUE chains, *MANUFACTURING processes, *INDUSTRIALISM
Abstract

Value stream mapping (VSM) is a valuable practice employed by industry experts to identify inefficiencies in the value chain due to its visual representation capability and general ease of use. Enabled by a shift towards digitalization and smart connected systems, this project investigates the possibilities of transitioning VSM from a manual to digital process through the utilization of data generated from a Real-Time Location System (RTLS). This study focuses on merging the aspects of RTLS and VSM such that their advantages are combined to form a more robust and effective VSM process. Two simulated experiments and an initial validation test were conducted to demonstrate the capability of the system to function in an industrial environment by replicating an actual production process. The two experiments represent the current state of conditions of the company in two different instances of time. These outputs from the tracking system are then modified and converted into inputs for VSM. A VSM application was modified and utilized to create a digital value stream map with relevant performance parameters. Finally, a stochastic simulation was carried out to compare and extrapolate the results to a 16hrs shift to measure, among other outputs, the utilization of the machines with the two RTLS scenarios. [ABSTRACT FROM AUTHOR]

Published
2024
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32. Human in the loop: revolutionizing industry 5.0 with design thinking and systems thinking.

Author

Dehbozorgi, Mohammad Hossein, Postell, James, Ward, David, Leardi, Carlo, Sullivan, Brendan P., and Rossi, Monica

Subjects
DESIGN thinking, SYSTEMS theory, SUSTAINABILITY, MANUFACTURING industries, PHILOSOPHY of science
Abstract

This study delves into Industry 5.0's Human Centric Manufacturing and Systems (HCM and HCS), emphasizing worker welfare and sustainability. Industry 5.0 advocates a human-centric approach, built upon three foundational pillars safety, inclusivity, and empowerment. The paper highlights the successful integration of Design and Systems Thinking in HCM and proposes a workshop at MADE COMPETENCE CENTRE proving the effectiveness in raising awareness and promoting Human-Centric principles throughout the system life cycle and in achieving Human-Centric Systems (HCS). [ABSTRACT FROM AUTHOR]

Published
2024
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33. Exploring space manufacturing: designing a lunar factory for space-bound products in the new space economy.

Author

Francesco, Eva De, Ettorre, Anna, Acerbi, Federica, and Sullivan, Brendan P.

Subjects
SPACE industrialization, THREE-dimensional printing, SYSTEMS engineering, INDUSTRIAL engineering, ECONOMIC development
Abstract

This study proposes a Moon-based factory for space-bound products, aiming to revolutionize space exploration through In-Space Manufacturing (ISM). It defines key elements for lunar manufacturing by adapting Earth-based factory models to lunar conditions. [ABSTRACT FROM AUTHOR]

Published
2024
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34. Large-scale genomic analyses link reproductive aging to hypothalamic signaling, breast cancer susceptibility and BRCA1-mediated DNA repair.

Author

Day, Felix R, Ruth, Katherine S, Thompson, Deborah J, Lunetta, Kathryn L, Pervjakova, Natalia, Chasman, Daniel I, Stolk, Lisette, Finucane, Hilary K, Sulem, Patrick, Bulik-Sullivan, Brendan, Esko, Tõnu, Johnson, Andrew D, Elks, Cathy E, Franceschini, Nora, He, Chunyan, Altmaier, Elisabeth, Brody, Jennifer A, Franke, Lude L, Huffman, Jennifer E, Keller, Margaux F, McArdle, Patrick F, Nutile, Teresa, Porcu, Eleonora, Robino, Antonietta, Rose, Lynda M, Schick, Ursula M, Smith, Jennifer A, Teumer, Alexander, Traglia, Michela, Vuckovic, Dragana, Yao, Jie, Zhao, Wei, Albrecht, Eva, Amin, Najaf, Corre, Tanguy, Hottenga, Jouke-Jan, Mangino, Massimo, Smith, Albert V, Tanaka, Toshiko, Abecasis, Goncalo, Andrulis, Irene L, Anton-Culver, Hoda, Antoniou, Antonis C, Arndt, Volker, Arnold, Alice M, Barbieri, Caterina, Beckmann, Matthias W, Beeghly-Fadiel, Alicia, Benitez, Javier, Bernstein, Leslie, Bielinski, Suzette J, Blomqvist, Carl, Boerwinkle, Eric, Bogdanova, Natalia V, Bojesen, Stig E, Bolla, Manjeet K, Borresen-Dale, Anne-Lise, Boutin, Thibaud S, Brauch, Hiltrud, Brenner, Hermann, Brüning, Thomas, Burwinkel, Barbara, Campbell, Archie, Campbell, Harry, Chanock, Stephen J, Chapman, J Ross, Chen, Yii-Der Ida, Chenevix-Trench, Georgia, Couch, Fergus J, Coviello, Andrea D, Cox, Angela, Czene, Kamila, Darabi, Hatef, De Vivo, Immaculata, Demerath, Ellen W, Dennis, Joe, Devilee, Peter, Dörk, Thilo, Dos-Santos-Silva, Isabel, Dunning, Alison M, Eicher, John D, Fasching, Peter A, Faul, Jessica D, Figueroa, Jonine, Flesch-Janys, Dieter, Gandin, Ilaria, Garcia, Melissa E, García-Closas, Montserrat, Giles, Graham G, Girotto, Giorgia G, Goldberg, Mark S, González-Neira, Anna, Goodarzi, Mark O, Grove, Megan L, Gudbjartsson, Daniel F, Guénel, Pascal, Guo, Xiuqing, Haiman, Christopher A, Hall, Per, and Hamann, Ute

Subjects
PRACTICAL consortium, kConFab Investigators, AOCS Investigators, Generation Scotland, EPIC-InterAct Consortium, LifeLines Cohort Study, Hypothalamus, Humans, Breast Neoplasms, Genetic Predisposition to Disease, BRCA1 Protein, Genomics, Age Factors, Signal Transduction, DNA Repair, Aging, Reproduction, Menopause, Genotype, Phenotype, Models, Genetic, Adult, Middle Aged, Female, Gene Regulatory Networks, Genetic Variation, Genome-Wide Association Study, Models, Genetic, Developmental Biology, Medical and Health Sciences, Biological Sciences
Abstract

Menopause timing has a substantial impact on infertility and risk of disease, including breast cancer, but the underlying mechanisms are poorly understood. We report a dual strategy in ∼70,000 women to identify common and low-frequency protein-coding variation associated with age at natural menopause (ANM). We identified 44 regions with common variants, including two regions harboring additional rare missense alleles of large effect. We found enrichment of signals in or near genes involved in delayed puberty, highlighting the first molecular links between the onset and end of reproductive lifespan. Pathway analyses identified major association with DNA damage response (DDR) genes, including the first common coding variant in BRCA1 associated with any complex trait. Mendelian randomization analyses supported a causal effect of later ANM on breast cancer risk (∼6% increase in risk per year; P = 3 × 10(-14)), likely mediated by prolonged sex hormone exposure rather than DDR mechanisms.

Published
2015

35. Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores

Author

Vilhjálmsson, Bjarni J, Yang, Jian, Finucane, Hilary K, Gusev, Alexander, Lindström, Sara, Ripke, Stephan, Genovese, Giulio, Loh, Po-Ru, Bhatia, Gaurav, Do, Ron, Hayeck, Tristan, Won, Hong-Hee, Consortium, Schizophrenia Working Group of the Psychiatric Genomics, Neale, Benjamin M, Corvin, Aiden, Walters, James TR, Farh, Kai-How, Holmans, Peter A, Lee, Phil, Bulik-Sullivan, Brendan, Collier, David A, Huang, Hailiang, Pers, Tune H, Agartz, Ingrid, Agerbo, Esben, Albus, Margot, Alexander, Madeline, Amin, Farooq, Bacanu, Silviu A, Begemann, Martin, Belliveau, Richard A, Bene, Judit, Bergen, Sarah E, Bevilacqua, Elizabeth, Bigdeli, Tim B, Black, Donald W, Bruggeman, Richard, Buccola, Nancy G, Buckner, Randy L, Byerley, William, Cahn, Wiepke, Cai, Guiqing, Campion, Dominique, Cantor, Rita M, Carr, Vaughan J, Carrera, Noa, Catts, Stanley V, Chambert, Kimberly D, Chan, Raymond CK, Chen, Ronald YL, Chen, Eric YH, Cheng, Wei, Cheung, Eric FC, Chong, Siow Ann, Cloninger, C Robert, Cohen, David, Cohen, Nadine, Cormican, Paul, Craddock, Nick, Crowley, James J, Curtis, David, Davidson, Michael, Davis, Kenneth L, Degenhardt, Franziska, Del Favero, Jurgen, DeLisi, Lynn E, Demontis, Ditte, Dikeos, Dimitris, Dinan, Timothy, Djurovic, Srdjan, Donohoe, Gary, Drapeau, Elodie, Duan, Jubao, Dudbridge, Frank, Durmishi, Naser, Eichhammer, Peter, Eriksson, Johan, Escott-Price, Valentina, Essioux, Laurent, Fanous, Ayman H, Farrell, Martilias S, Frank, Josef, Franke, Lude, Freedman, Robert, Freimer, Nelson B, Friedl, Marion, Friedman, Joseph I, Fromer, Menachem, Georgieva, Lyudmila, Gershon, Elliot S, Giegling, Ina, Giusti-Rodrguez, Paola, Godard, Stephanie, Goldstein, Jacqueline I, Golimbet, Vera, Gopal, Srihari, Gratten, Jacob, and Grove, Jakob

Subjects
Epidemiology, Biological Sciences, Health Sciences, Genetics, Schizophrenia, Mental Health, Brain Disorders, Serious Mental Illness, Genome-Wide Association Study, Genotype, Humans, Linkage Disequilibrium, Models, Theoretical, Multifactorial Inheritance, Multiple Sclerosis, Phenotype, Polymorphism, Single Nucleotide, Prognosis, Quantitative Trait Loci, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Discovery, Biology, and Risk of Inherited Variants in Breast Cancer (DRIVE) study, Medical and Health Sciences, Genetics & Heredity, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Polygenic risk scores have shown great promise in predicting complex disease risk and will become more accurate as training sample sizes increase. The standard approach for calculating risk scores involves linkage disequilibrium (LD)-based marker pruning and applying a p value threshold to association statistics, but this discards information and can reduce predictive accuracy. We introduce LDpred, a method that infers the posterior mean effect size of each marker by using a prior on effect sizes and LD information from an external reference panel. Theory and simulations show that LDpred outperforms the approach of pruning followed by thresholding, particularly at large sample sizes. Accordingly, predicted R(2) increased from 20.1% to 25.3% in a large schizophrenia dataset and from 9.8% to 12.0% in a large multiple sclerosis dataset. A similar relative improvement in accuracy was observed for three additional large disease datasets and for non-European schizophrenia samples. The advantage of LDpred over existing methods will grow as sample sizes increase.

Published
2015

36. Efficient Bayesian mixed-model analysis increases association power in large cohorts

Author

Loh, Po-Ru, Tucker, George, Bulik-Sullivan, Brendan K, Vilhjálmsson, Bjarni J, Finucane, Hilary K, Salem, Rany M, Chasman, Daniel I, Ridker, Paul M, Neale, Benjamin M, Berger, Bonnie, Patterson, Nick, and Price, Alkes L

Subjects
Algorithms, Bayes Theorem, Female, Genetic Association Studies, Genome, Human, Genotyping Techniques, Humans, Linear Models, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Linear mixed models are a powerful statistical tool for identifying genetic associations and avoiding confounding. However, existing methods are computationally intractable in large cohorts and may not optimize power. All existing methods require time cost O(MN(2)) (where N is the number of samples and M is the number of SNPs) and implicitly assume an infinitesimal genetic architecture in which effect sizes are normally distributed, which can limit power. Here we present a far more efficient mixed-model association method, BOLT-LMM, which requires only a small number of O(MN) time iterations and increases power by modeling more realistic, non-infinitesimal genetic architectures via a Bayesian mixture prior on marker effect sizes. We applied BOLT-LMM to 9 quantitative traits in 23,294 samples from the Women's Genome Health Study (WGHS) and observed significant increases in power, consistent with simulations. Theory and simulations show that the boost in power increases with cohort size, making BOLT-LMM appealing for genome-wide association studies in large cohorts.

Published
2015

37. LD Score regression distinguishes confounding from polygenicity in genome-wide association studies.

Author

Bulik-Sullivan, Brendan K, Loh, Po-Ru, Finucane, Hilary K, Ripke, Stephan, Yang, Jian, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Patterson, Nick, Daly, Mark J, Price, Alkes L, and Neale, Benjamin M

Subjects
Schizophrenia Working Group of the Psychiatric Genomics Consortium, Humans, Regression Analysis, Sample Size, Linkage Disequilibrium, Polymorphism, Single Nucleotide, Genome, Human, Computer Simulation, Genome-Wide Association Study, Polymorphism, Single Nucleotide, Genome, Human, Developmental Biology, Medical and Health Sciences, Biological Sciences
Abstract

Both polygenicity (many small genetic effects) and confounding biases, such as cryptic relatedness and population stratification, can yield an inflated distribution of test statistics in genome-wide association studies (GWAS). However, current methods cannot distinguish between inflation from a true polygenic signal and bias. We have developed an approach, LD Score regression, that quantifies the contribution of each by examining the relationship between test statistics and linkage disequilibrium (LD). The LD Score regression intercept can be used to estimate a more powerful and accurate correction factor than genomic control. We find strong evidence that polygenicity accounts for the majority of the inflation in test statistics in many GWAS of large sample size.

Published
2015

38. A Customizable Lean Design Methodology for Maritime

Author

Sullivan, Brendan P., Rossi, Monica, Terzi, Sergio, Rannenberg, Kai, Editor-in-Chief, Sakarovitch, Jacques, Series Editor, Goedicke, Michael, Series Editor, Tatnall, Arthur, Series Editor, Neuhold, Erich J., Series Editor, Pras, Aiko, Series Editor, Tröltzsch, Fredi, Series Editor, Pries-Heje, Jan, Series Editor, Whitehouse, Diane, Series Editor, Reis, Ricardo, Series Editor, Furnell, Steven, Series Editor, Furbach, Ulrich, Series Editor, Winckler, Marco, Series Editor, Rauterberg, Matthias, Series Editor, Chiabert, Paolo, editor, Bouras, Abdelaziz, editor, Noël, Frédéric, editor, and Ríos, José, editor

Published
2018
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39. Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases

Author

Gusev, Alexander, Lee, S Hong, Trynka, Gosia, Finucane, Hilary, Vilhjálmsson, Bjarni J, Xu, Han, Zang, Chongzhi, Ripke, Stephan, Bulik-Sullivan, Brendan, Stahl, Eli, Kähler, Anna K, Hultman, Christina M, Purcell, Shaun M, McCarroll, Steven A, Daly, Mark J, Pasaniuc, Bogdan, Sullivan, Patrick F, Neale, Benjamin M, Wray, Naomi R, Raychaudhuri, Soumya, Price, Alkes, Corvin, Aiden, Walters, James TR, Farh, Kai-How, Holmans, Peter A, Lee, Phil, Collier, David A, Huang, Hailiang, Pers, Tune H, Agartz, Ingrid, Agerbo, Esben, Albus, Margot, Alexander, Madeline, Amin, Farooq, Bacanu, Silviu A, Begemann, Martin, Belliveau, Richard A, Bene, Judit, Bergen, Sarah E, Bevilacqua, Elizabeth, Bigdeli, Tim B, Black, Donald W, Børglum, Anders D, Bruggeman, Richard, Buccola, Nancy G, Buckner, Randy L, Byerley, William, Cahn, Wiepke, Cai, Guiqing, Campion, Dominique, Cantor, Rita M, Carr, Vaughan J, Carrera, Noa, Catts, Stanley V, Chambert, Kimberly D, Chan, Raymond CK, Chen, Ronald YL, Chen, Eric YH, Cheng, Wei, Cheung, Eric FC, Chong, Siow Ann, Cloninger, C Robert, Cohen, David, Cohen, Nadine, Cormican, Paul, Craddock, Nick, Crowley, James J, Curtis, David, Davidson, Michael, Davis, Kenneth L, Degenhardt, Franziska, Del Favero, Jurgen, DeLisi, Lynn E, Demontis, Ditte, Dikeos, Dimitris, Dinan, Timothy, Djurovic, Srdjan, Donohoe, Gary, Drapeau, Elodie, Duan, Jubao, Dudbridge, Frank, Durmishi, Naser, Eichhammer, Peter, Eriksson, Johan, Escott-Price, Valentina, Essioux, Laurent, Fanous, Ayman H, Farrell, Martilias S, Frank, Josef, Franke, Lude, Freedman, Robert, Freimer, Nelson B, Friedl, Marion, Friedman, Joseph I, Fromer, Menachem, Genovese, Giulio, and Georgieva, Lyudmila

Subjects
Epidemiology, Biological Sciences, Health Sciences, Genetics, Human Genome, Prevention, Computer Simulation, Genetic Diseases, Inborn, Genetic Variation, Genome-Wide Association Study, Humans, Inheritance Patterns, Models, Genetic, Open Reading Frames, Regulatory Elements, Transcriptional, Schizophrenia Working Group of the Psychiatric Genomics Consortium, SWE-SCZ Consortium, Medical and Health Sciences, Genetics & Heredity, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Regulatory and coding variants are known to be enriched with associations identified by genome-wide association studies (GWASs) of complex disease, but their contributions to trait heritability are currently unknown. We applied variance-component methods to imputed genotype data for 11 common diseases to partition the heritability explained by genotyped SNPs (hg(2)) across functional categories (while accounting for shared variance due to linkage disequilibrium). Extensive simulations showed that in contrast to current estimates from GWAS summary statistics, the variance-component approach partitions heritability accurately under a wide range of complex-disease architectures. Across the 11 diseases DNaseI hypersensitivity sites (DHSs) from 217 cell types spanned 16% of imputed SNPs (and 24% of genotyped SNPs) but explained an average of 79% (SE = 8%) of hg(2) from imputed SNPs (5.1× enrichment; p = 3.7 × 10(-17)) and 38% (SE = 4%) of hg(2) from genotyped SNPs (1.6× enrichment, p = 1.0 × 10(-4)). Further enrichment was observed at enhancer DHSs and cell-type-specific DHSs. In contrast, coding variants, which span 1% of the genome, explained

Published
2014

40. Biological insights from 108 schizophrenia-associated genetic loci

Author

Ripke, Stephan, Neale, Benjamin M, Corvin, Aiden, Walters, James TR, Farh, Kai-How, Holmans, Peter A, Lee, Phil, Bulik-Sullivan, Brendan, Collier, David A, Huang, Hailiang, Pers, Tune H, Agartz, Ingrid, Agerbo, Esben, Albus, Margot, Alexander, Madeline, Amin, Farooq, Bacanu, Silviu A, Begemann, Martin, Belliveau, Richard A Jr, Bene, Judit, Bergen, Sarah E, Bevilacqua, Elizabeth, Bigdeli, Tim B, Black, Donald W, Bruggeman, Richard, Buccola, Nancy G, Buckner, Randy L, Byerley, William, Cahn, Wiepke, Cai, Guiqing, Campion, Dominique, Cantor, Rita M, Carr, Vaughan J, Carrera, Noa, Catts, Stanley V, Chambert, Kimberly D, Chan, Raymond CK, Chen, Ronald YL, Chen, Eric YH, Cheng, Wei, Cheung, Eric FC, Chong, Siow Ann, Cloninger, C Robert, Cohen, David, Cohen, Nadine, Cormican, Paul, Craddock, Nick, Crowley, James J, Curtis, David, Davidson, Michael, Davis, Kenneth L, Degenhardt, Franziska, Del Favero, Jurgen, Demontis, Ditte, Dikeos, Dimitris, Dinan, Timothy, Djurovic, Srdjan, Donohoe, Gary, Drapeau, Elodie, Duan, Jubao, Dudbridge, Frank, Durmishi, Naser, Eichhammer, Peter, Eriksson, Johan, Escott-Price, Valentina, Essioux, Laurent, Fanous, Ayman H, Farrell, Martilias S, Frank, Josef, Franke, Lude, Freedman, Robert, Freimer, Nelson B, Friedl, Marion, Friedman, Joseph I, Fromer, Menachem, Genovese, Giulio, Georgieva, Lyudmila, Giegling, Ina, Giusti-Rodriguez, Paola, Godard, Stephanie, Goldstein, Jacqueline I, Golimbet, Vera, Gopal, Srihari, Gratten, Jacob, de Haan, Lieuwe, Hammer, Christian, Hamshere, Marian L, Hansen, Mark, Hansen, Thomas, Haroutunian, Vahram, Hartmann, Annette M, Henskens, Frans A, Herms, Stefan, Hirschhorn, Joel N, Hoffmann, Per, Hofman, Andrea, Hollegaard, Mads V, Hougaard, David M, Ikeda, Masashi, and Joa, Inge

Subjects
Human Genome, Brain Disorders, Serious Mental Illness, Prevention, Schizophrenia, Genetics, Neurosciences, Mental Health, 2.1 Biological and endogenous factors, Aetiology, Mental health, Alleles, Brain, Enhancer Elements, Genetic, Genetic Loci, Genetic Predisposition to Disease, Genome-Wide Association Study, Glutamic Acid, Humans, Immunity, Multifactorial Inheritance, Mutation, Odds Ratio, Polymorphism, Single Nucleotide, Synaptic Transmission, Schizophrenia Working Group of the Psychiatric Genomics Consortium, General Science & Technology
Abstract

Schizophrenia is a highly heritable disorder. Genetic risk is conferred by a large number of alleles, including common alleles of small effect that might be detected by genome-wide association studies. Here we report a multi-stage schizophrenia genome-wide association study of up to 36,989 cases and 113,075 controls. We identify 128 independent associations spanning 108 conservatively defined loci that meet genome-wide significance, 83 of which have not been previously reported. Associations were enriched among genes expressed in brain, providing biological plausibility for the findings. Many findings have the potential to provide entirely new insights into aetiology, but associations at DRD2 and several genes involved in glutamatergic neurotransmission highlight molecules of known and potential therapeutic relevance to schizophrenia, and are consistent with leading pathophysiological hypotheses. Independent of genes expressed in brain, associations were enriched among genes expressed in tissues that have important roles in immunity, providing support for the speculated link between the immune system and schizophrenia.

Published
2014

44. Genome-wide association analysis identifies 13 new risk loci for schizophrenia.

Author

Ripke, Stephan, O'Dushlaine, Colm, Chambert, Kimberly, Moran, Jennifer L, Kähler, Anna K, Akterin, Susanne, Bergen, Sarah E, Collins, Ann L, Crowley, James J, Fromer, Menachem, Kim, Yunjung, Lee, Sang Hong, Magnusson, Patrik KE, Sanchez, Nick, Stahl, Eli A, Williams, Stephanie, Wray, Naomi R, Xia, Kai, Bettella, Francesco, Borglum, Anders D, Bulik-Sullivan, Brendan K, Cormican, Paul, Craddock, Nick, de Leeuw, Christiaan, Durmishi, Naser, Gill, Michael, Golimbet, Vera, Hamshere, Marian L, Holmans, Peter, Hougaard, David M, Kendler, Kenneth S, Lin, Kuang, Morris, Derek W, Mors, Ole, Mortensen, Preben B, Neale, Benjamin M, O'Neill, Francis A, Owen, Michael J, Milovancevic, Milica Pejovic, Posthuma, Danielle, Powell, John, Richards, Alexander L, Riley, Brien P, Ruderfer, Douglas, Rujescu, Dan, Sigurdsson, Engilbert, Silagadze, Teimuraz, Smit, August B, Stefansson, Hreinn, Steinberg, Stacy, Suvisaari, Jaana, Tosato, Sarah, Verhage, Matthijs, Walters, James T, Multicenter Genetic Studies of Schizophrenia Consortium, Levinson, Douglas F, Gejman, Pablo V, Laurent, Claudine, Mowry, Bryan J, O'Donovan, Michael C, Pulver, Ann E, Schwab, Sibylle G, Wildenauer, Dieter B, Dudbridge, Frank, Shi, Jianxin, Albus, Margot, Alexander, Madeline, Campion, Dominique, Cohen, David, Dikeos, Dimitris, Duan, Jubao, Eichhammer, Peter, Godard, Stephanie, Hansen, Mark, Lerer, F Bernard, Liang, Kung-Yee, Maier, Wolfgang, Mallet, Jacques, Nertney, Deborah A, Nestadt, Gerald, Norton, Nadine, Papadimitriou, George N, Ribble, Robert, Sanders, Alan R, Silverman, Jeremy M, Walsh, Dermot, Williams, Nigel M, Wormley, Brandon, Psychosis Endophenotypes International Consortium, Arranz, Maria J, Bakker, Steven, Bender, Stephan, Bramon, Elvira, and Collier, David

Subjects
Multicenter Genetic Studies of Schizophrenia Consortium, Psychosis Endophenotypes International Consortium, Wellcome Trust Case Control Consortium 2, Humans, Genetic Predisposition to Disease, Case-Control Studies, Schizophrenia, Polymorphism, Single Nucleotide, Sweden, Female, Male, Genome-Wide Association Study, Polymorphism, Single Nucleotide, Developmental Biology, Biological Sciences, Medical and Health Sciences
Abstract

Schizophrenia is an idiopathic mental disorder with a heritable component and a substantial public health impact. We conducted a multi-stage genome-wide association study (GWAS) for schizophrenia beginning with a Swedish national sample (5,001 cases and 6,243 controls) followed by meta-analysis with previous schizophrenia GWAS (8,832 cases and 12,067 controls) and finally by replication of SNPs in 168 genomic regions in independent samples (7,413 cases, 19,762 controls and 581 parent-offspring trios). We identified 22 loci associated at genome-wide significance; 13 of these are new, and 1 was previously implicated in bipolar disorder. Examination of candidate genes at these loci suggests the involvement of neuronal calcium signaling. We estimate that 8,300 independent, mostly common SNPs (95% credible interval of 6,300-10,200 SNPs) contribute to risk for schizophrenia and that these collectively account for at least 32% of the variance in liability. Common genetic variation has an important role in the etiology of schizophrenia, and larger studies will allow more detailed understanding of this disorder.

Published
2013

45. Deep learning using tumor HLA peptide mass spectrometry datasets improves neoantigen identification

Author

Bulik-Sullivan, Brendan, Busby, Jennifer, Palmer, Christine D, Davis, Matthew J, Murphy, Tyler, Clark, Andrew, Busby, Michele, Duke, Fujiko, Yang, Aaron, Young, Lauren, Ojo, Noelle C, Caldwell, Kamilah, Abhyankar, Jesse, Boucher, Thomas, Hart, Meghan G, Makarov, Vladimir, De Montpreville, Vincent Thomas, Mercier, Olaf, Chan, Timothy A, Scagliotti, Giorgio, Bironzo, Paolo, Novello, Silvia, Karachaliou, Niki, Rosell, Rafael, Anderson, Ian, Gabrail, Nashat, Hrom, John, Limvarapuss, Chainarong, Choquette, Karin, Spira, Alexander, Rousseau, Raphael, Voong, Cynthia, Rizvi, Naiyer A, Fadel, Elie, Frattini, Mark, Jooss, Karin, Skoberne, Mojca, Francis, Joshua, and Yelensky, Roman

Published
2019
Full Text
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46. Simulation of the harvesting scheduling of red chile peppers in New Mexico.

Author

Arias-Nava, Elias, Valles-Rosales, Delia, Sullivan, Brendan P., and Sohn, Hansuk

Subjects
HOT peppers, PEPPERS, HARVESTING, FARM produce, CAPSICUM annuum, HARVESTING time
Abstract

Dried red chile peppers [Capsicum annuum (L.)] are an important agricultural product grown throughout the Southwestern United States and is extensively used in food and for commercial application. Given the high, broad demand for chile attention to the methods of harvesting, storage, transport, and packaging are critical for profitability. Currently, chile should be stored no more than 24 to 36 hours at ambient temperatures from the time of harvest due to the potential for natural fermentation to destroy the crop. The rate for calculating and determining the amount of useable/destroyed chile in ambient conditions is determined by several variables that include the harvesting method (hand-picked, mechanized), time of harvest following the optimal harvesting point (season), weather variations (moisture). In this work, a stochastic simulation-based model is presented to forecast optimal harvesting scenarios capable of supporting farmers and chile processors better plan/manage planting and growth acceleration programs. The tool developed allows for the economic feasibility of storage/stabilization systems, advanced mechanical harvesters, and other future advances based on the amount increase in chile yield to be analyzed. We used described simulation as an analysis tool to obtain the expected coverage and the estimation of the mean and quantile. [ABSTRACT FROM AUTHOR]

Published
2023
Full Text
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49. Textbook and Course Materials for 21-127 'Concepts of Mathematics'

Author

Sullivan, Brendan W.

Abstract

Concepts of Mathematics (21-127 at CMU) is a course designed to introduce students to the world of abstract mathematics, guiding them from more calculation-based math (that one learns in high school) to higher mathematics, which focuses more on abstract thinking, problem solving, and writing "proofs." This transition tends to be a shock: new notation, terminology, and expectations (particularly the requirement of "writing" mathematical thoughts formally) give students much trouble. Many standard texts for this course are found to be too dense, dry and formal by the students. Ultimately, this means these texts are unhelpful for student learning, despite their intentions. For this project, I have written a new textbook designed specifically for this course and the way it has been taught. My emphases--writing more informal prose, properly motivating all new material, and including a wider variety of exercises and questions for the reader--all reflect the goal of increasing the reader's interest and potential for learning. The selection of material, examples, explanations, and problems has been supported by in-classroom experience, and their presentation has been influenced greatly by educational research. I have also included accompanying class notes, meant to supplement the teaching of this course, as well as assignments and exams, and their corresponding solutions and grading rubrics. Ultimately, this project constitutes a standalone packet for future instructors of this course and similar ones. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]

Published
2013

50. American Business Meets American Gothic: Professional Development in the Art Museum

Author

Sullivan, Brendan and Morse, Annie

Abstract

Professional development in the art museum setting represents an opportunity for corporate and for-profit enterprises to enhance employees' skills in observation, creative thinking, teamwork, and sensitivity in diversity. Using original works of art as a point of departure for in-depth discussion of what appears as narrative content, participants gain insight into alternative interpretations and approaches to a problem or circumstance. In all-day sessions, staff from the Art Institute and consultants from creative meeting and event space Catalyst Ranch lead clients through interactive exercises designed to be of practical use in everyday problem-solving. (Contains 4 notes.)

Published
2011

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