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1,812 results on '"Omenn, Gilbert S."'

3. To do no harm — and the most good — with AI in health care

Author

Goldberg, Carey Beth, Adams, Laura, Blumenthal, David, Brennan, Patricia Flatley, Brown, Noah, Butte, Atul J., Cheatham, Morgan, deBronkart, Dave, Dixon, Jennifer, Drazen, Jeffrey, Evans, Barbara J., Hoffman, Sara M., Holmes, Chris, Lee, Peter, Manrai, Arjun Kumar, Omenn, Gilbert S., Perlin, Jonathan B., Ramoni, Rachel, Sapiro, Guillermo, Sarkar, Rupa, Sood, Harpreet, Vayena, Effy, and Kohane, Isaac S.

Published
2024
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4. Comprehensive proteogenomic characterization of rare kidney tumors

Author

Lazar, Alexander J., Paulovich, Amanda G., Antczak, Andrzej, Green, Anthony, Ma’ayan, Avi, Pruetz, Barb, Zhang, Bing, Reva, Boris, Druker, Brian J., Goldthwaite, Charles A., Jr., Birger, Chet, Mani, D.R., Chesla, David, Fenyö, David, Schadt, Eric E., Wilson, George, Kołodziejczak, Iga, John, Ivy, Hafron, Jason, Vo, Josh, Zaalishvili, Kakhaber, Ketchum, Karen A., Rodland, Karin D., Nyce, Kristen, Wiznerowicz, Maciej, Domagalski, Marcin J., Anurag, Meenakshi, Borucki, Melissa, Gillette, Michael A., Birrer, Michael J., Edwards, Nathan J., Vatanian, Negin, VanderKolk, Pamela, McGarvey, Peter B., Dhir, Rajiv, Thangudu, Ratna R., Crispen, Reese, Smith, Richard D., Payne, Samuel H., Cottingham, Sandra, Cai, Shuang, Carr, Steven A., Liu, Tao, Le, Toan, Ma, Weiping, Zhang, Xu, Lu, Yin, Shutack, Yvonne, Zhang, Zhen, Li, Ginny Xiaohe, Chen, Lijun, Hsiao, Yi, Mannan, Rahul, Zhang, Yuping, Luo, Jie, Petralia, Francesca, Cho, Hanbyul, Hosseini, Noshad, Leprevost, Felipe da Veiga, Calinawan, Anna, Li, Yize, Anand, Shankara, Dagar, Aniket, Geffen, Yifat, Kumar-Sinha, Chandan, Chugh, Seema, Le, Anne, Ponce, Sean, Guo, Shenghao, Zhang, Cissy, Schnaubelt, Michael, Al Deen, Nataly Naser, Chen, Feng, Caravan, Wagma, Houston, Andrew, Hopkins, Alex, Newton, Chelsea J., Wang, Xiaoming, Polasky, Daniel A., Haynes, Sarah, Yu, Fengchao, Jing, Xiaojun, Chen, Siqi, Robles, Ana I., Mesri, Mehdi, Thiagarajan, Mathangi, An, Eunkyung, Getz, Gad A., Linehan, W. Marston, Hostetter, Galen, Jewell, Scott D., Chan, Daniel W., Wang, Pei, Omenn, Gilbert S., Mehra, Rohit, Ricketts, Christopher J., Ding, Li, Chinnaiyan, Arul M., Cieslik, Marcin P., Dhanasekaran, Saravana M., Zhang, Hui, and Nesvizhskii, Alexey I.

Published
2024
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5. International comparisons of laboratory values from the 4CE collaborative to predict COVID-19 mortality

Author

Weber, Griffin M, Hong, Chuan, Xia, Zongqi, Palmer, Nathan P, Avillach, Paul, L’Yi, Sehi, Keller, Mark S, Murphy, Shawn N, Gutiérrez-Sacristán, Alba, Bonzel, Clara-Lea, Serret-Larmande, Arnaud, Neuraz, Antoine, Omenn, Gilbert S, Visweswaran, Shyam, Klann, Jeffrey G, South, Andrew M, Loh, Ne Hooi Will, Cannataro, Mario, Beaulieu-Jones, Brett K, Bellazzi, Riccardo, Agapito, Giuseppe, Alessiani, Mario, Aronow, Bruce J, Bell, Douglas S, Benoit, Vincent, Bourgeois, Florence T, Chiovato, Luca, Cho, Kelly, Dagliati, Arianna, DuVall, Scott L, Barrio, Noelia García, Hanauer, David A, Ho, Yuk-Lam, Holmes, John H, Issitt, Richard W, Liu, Molei, Luo, Yuan, Lynch, Kristine E, Maidlow, Sarah E, Malovini, Alberto, Mandl, Kenneth D, Mao, Chengsheng, Matheny, Michael E, Moore, Jason H, Morris, Jeffrey S, Morris, Michele, Mowery, Danielle L, Ngiam, Kee Yuan, Patel, Lav P, Pedrera-Jimenez, Miguel, Ramoni, Rachel B, Schriver, Emily R, Schubert, Petra, Balazote, Pablo Serrano, Spiridou, Anastasia, Tan, Amelia LM, Tan, Byorn WL, Tibollo, Valentina, Torti, Carlo, Trecarichi, Enrico M, Wang, Xuan, Kohane, Isaac S, Cai, Tianxi, and Brat, Gabriel A

Subjects
Health Services and Systems, Health Sciences, Basic Behavioral and Social Science, Behavioral and Social Science, Good Health and Well Being, Consortium for Clinical Characterization of COVID-19 by EHR, Health services and systems
Abstract

Given the growing number of prediction algorithms developed to predict COVID-19 mortality, we evaluated the transportability of a mortality prediction algorithm using a multi-national network of healthcare systems. We predicted COVID-19 mortality using baseline commonly measured laboratory values and standard demographic and clinical covariates across healthcare systems, countries, and continents. Specifically, we trained a Cox regression model with nine measured laboratory test values, standard demographics at admission, and comorbidity burden pre-admission. These models were compared at site, country, and continent level. Of the 39,969 hospitalized patients with COVID-19 (68.6% male), 5717 (14.3%) died. In the Cox model, age, albumin, AST, creatine, CRP, and white blood cell count are most predictive of mortality. The baseline covariates are more predictive of mortality during the early days of COVID-19 hospitalization. Models trained at healthcare systems with larger cohort size largely retain good transportability performance when porting to different sites. The combination of routine laboratory test values at admission along with basic demographic features can predict mortality in patients hospitalized with COVID-19. Importantly, this potentially deployable model differs from prior work by demonstrating not only consistent performance but also reliable transportability across healthcare systems in the US and Europe, highlighting the generalizability of this model and the overall approach.

Published
2022

6. Functional organization of the maternal and paternal human 4D Nucleome

Author

Lindsly, Stephen, Jia, Wenlong, Chen, Haiming, Liu, Sijia, Ronquist, Scott, Chen, Can, Wen, Xingzhao, Stansbury, Cooper, Dotson, Gabrielle A, Ryan, Charles, Rehemtulla, Alnawaz, Omenn, Gilbert S, Wicha, Max, Li, Shuai Cheng, Muir, Lindsey, and Rajapakse, Indika

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Bioinformatics, Genomic analysis, Genomics
Abstract

Every human somatic cell inherits a maternal and a paternal genome, which work together to give rise to cellular phenotypes. However, the allele-specific relationship between gene expression and genome structure through the cell cycle is largely unknown. By integrating haplotype-resolved genome-wide chromosome conformation capture, mature and nascent mRNA, and protein binding data from a B lymphoblastoid cell line, we investigate this relationship both globally and locally. We introduce the maternal and paternal 4D Nucleome, enabling detailed analysis of the mechanisms and dynamics of genome structure and gene function for diploid organisms. Our analyses find significant coordination between allelic expression biases and local genome conformation, and notably absent expression bias in universally essential cell cycle and glycolysis genes. We propose a model in which coordinated biallelic expression reflects prioritized preservation of essential gene sets.

Published
2021

7. Pan-cancer proteogenomics characterization of tumor immunity

Author

Abelin, Jennifer, Aguet, François, Akiyama, Yo, An, Eunkyung, Anand, Shankara, Anurag, Meenakshi, Babur, Özgün, Bavarva, Jasmin, Birger, Chet, Birrer, Michael J., Cao, Song, Carr, Steven A., Chan, Daniel W., Chinnaiyan, Arul M., Cho, Hanbyul, Clauser, Karl, Colaprico, Antonio, Zhou, Daniel Cui, da Veiga Leprevost, Felipe, Day, Corbin, Dhanasekaran, Saravana M., Ding, Li, Domagalski, Marcin J., Dou, Yongchao, Druker, Brian J., Edwards, Nathan, Ellis, Matthew J., Foltz, Steven M., Francis, Alicia, Geffen, Yifat, Getz, Gad, Heiman, David I., Hong, Runyu, Hu, Yingwei, Huang, Chen, Jaehnig, Eric J., Jewell, Scott D., Ji, Jiayi, Jiang, Wen, Katsnelson, Lizabeth, Ketchum, Karen A., Kolodziejczak, Iga, Krug, Karsten, Kumar-Sinha, Chandan, Lei, Jonathan T., Liang, Wen-Wei, Liao, Yuxing, Lindgren, Caleb M., Liu, Tao, Liu, Wenke, McDermott, Jason, McKerrow, Wilson, Mesri, Mehdi, Mumphrey, Michael Brodie, Newton, Chelsea J., Oldroyd, Robert, Payne, Samuel H., Pugliese, Pietro, Rodland, Karin D., Rodrigues, Fernanda Martins, Ruggles, Kelly V., Savage, Sara R., Schadt, Eric E., Schnaubelt, Michael, Schraink, Tobias, Schürer, Stephan, Shi, Zhiao, Smith, Richard D., Song, Feng, Song, Yizhe, Stathias, Vasileios, Storrs, Erik P., Tan, Jimin, Terekhanova, Nadezhda V., Thangudu, Ratna R., Thiagarajan, Mathangi, Wang, Liang-Bo, Wen, Bo, Wu, Yige, Wyczalkowski, Matthew A., Yao, Lijun, Li, Qing Kay, Zhang, Hui, Zhang, Qing, Zhang, Xu, Zhang, Zhen, Petralia, Francesca, Ma, Weiping, Yaron, Tomer M., Caruso, Francesca Pia, Tignor, Nicole, Wang, Joshua M., Charytonowicz, Daniel, Johnson, Jared L., Huntsman, Emily M., Marino, Giacomo B., Calinawan, Anna, Evangelista, John Erol, Selvan, Myvizhi Esai, Chowdhury, Shrabanti, Rykunov, Dmitry, Krek, Azra, Song, Xiaoyu, Turhan, Berk, Christianson, Karen E., Lewis, David A., Deng, Eden Z., Clarke, Daniel J.B., Whiteaker, Jeffrey R., Kennedy, Jacob J., Zhao, Lei, Segura, Rossana Lazcano, Batra, Harsh, Raso, Maria Gabriela, Parra, Edwin Roger, Soundararajan, Rama, Tang, Ximing, Li, Yize, Yi, Xinpei, Satpathy, Shankha, Wang, Ying, Wiznerowicz, Maciej, González-Robles, Tania J., Iavarone, Antonio, Gosline, Sara J.C., Reva, Boris, Robles, Ana I., Nesvizhskii, Alexey I., Mani, D.R., Gillette, Michael A., Klein, Robert J., Cieslik, Marcin, Zhang, Bing, Paulovich, Amanda G., Sebra, Robert, Gümüş, Zeynep H., Hostetter, Galen, Fenyö, David, Omenn, Gilbert S., Cantley, Lewis C., Ma'ayan, Avi, Lazar, Alexander J., Ceccarelli, Michele, and Wang, Pei

Published
2024
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9. Ontology-based systematic classification and analysis of coronaviruses, hosts, and host-coronavirus interactions towards deep understanding of COVID-19

Author

Yu, Hong, Li, Li, Huang, Hsin-hui, Wang, Yang, Liu, Yingtong, Ong, Edison, Huffman, Anthony, Zeng, Tao, Zhang, Jingsong, Li, Pengpai, Liu, Zhiping, Zhang, Xiangyan, Ye, Xianwei, Handelman, Samuel K., Higgins, Gerry, Omenn, Gilbert S., Athey, Brian, Hur, Junguk, Chen, Luonan, and He, Yongqun

Subjects
Quantitative Biology - Other Quantitative Biology
Abstract

Given the existing COVID-19 pandemic worldwide, it is critical to systematically study the interactions between hosts and coronaviruses including SARS-Cov, MERS-Cov, and SARS-CoV-2 (cause of COVID-19). We first created four host-pathogen interaction (HPI)-Outcome postulates, and generated a HPI-Outcome model as the basis for understanding host-coronavirus interactions (HCI) and their relations with the disease outcomes. We hypothesized that ontology can be used as an integrative platform to classify and analyze HCI and disease outcomes. Accordingly, we annotated and categorized different coronaviruses, hosts, and phenotypes using ontologies and identified their relations. Various COVID-19 phenotypes are hypothesized to be caused by the backend HCI mechanisms. To further identify the causal HCI-outcome relations, we collected 35 experimentally-verified HCI protein-protein interactions (PPIs), and applied literature mining to identify additional host PPIs in response to coronavirus infections. The results were formulated in a logical ontology representation for integrative HCI-outcome understanding. Using known PPIs as baits, we also developed and applied a domain-inferred prediction method to predict new PPIs and identified their pathological targets on multiple organs. Overall, our proposed ontology-based integrative framework combined with computational predictions can be used to support fundamental understanding of the intricate interactions between human patients and coronaviruses (including SARS-CoV-2) and their association with various disease outcomes., Comment: 32 pages, 1 table, 6 figures

Published
2020

10. Validation of an internationally derived patient severity phenotype to support COVID-19 analytics from electronic health record data

Author

Klann, Jeffrey G, Estiri, Hossein, Weber, Griffin M, Moal, Bertrand, Avillach, Paul, Hong, Chuan, Tan, Amelia LM, Beaulieu-Jones, Brett K, Castro, Victor, Maulhardt, Thomas, Geva, Alon, Malovini, Alberto, South, Andrew M, Visweswaran, Shyam, Morris, Michele, Samayamuthu, Malarkodi J, Omenn, Gilbert S, Ngiam, Kee Yuan, Mandl, Kenneth D, Boeker, Martin, Olson, Karen L, Mowery, Danielle L, Follett, Robert W, Hanauer, David A, Bellazzi, Riccardo, Moore, Jason H, Loh, Ne-Hooi Will, Bell, Douglas S, Wagholikar, Kavishwar B, Chiovato, Luca, Tibollo, Valentina, Rieg, Siegbert, Li, Anthony LLJ, Jouhet, Vianney, Schriver, Emily, Xia, Zongqi, Hutch, Meghan, Luo, Yuan, Kohane, Isaac S, EHR, The Consortium for Clinical Characterization of COVID-19 by, Brat, Gabriel A, and Murphy, Shawn N

Subjects
Health Services and Systems, Health Sciences, Patient Safety, HIV/AIDS, Good Health and Well Being, COVID-19, Electronic Health Records, Hospitalization, Humans, Machine Learning, Prognosis, ROC Curve, Sensitivity and Specificity, Severity of Illness Index, novel coronavirus, disease severity, computable phenotype, medical informatics, data networking, data interoperability, Consortium for Clinical Characterization of COVID-19 by EHR (4CE), Information and Computing Sciences, Engineering, Medical and Health Sciences, Medical Informatics, Biomedical and clinical sciences, Health sciences, Information and computing sciences
Abstract

ObjectiveThe Consortium for Clinical Characterization of COVID-19 by EHR (4CE) is an international collaboration addressing coronavirus disease 2019 (COVID-19) with federated analyses of electronic health record (EHR) data. We sought to develop and validate a computable phenotype for COVID-19 severity.Materials and methodsTwelve 4CE sites participated. First, we developed an EHR-based severity phenotype consisting of 6 code classes, and we validated it on patient hospitalization data from the 12 4CE clinical sites against the outcomes of intensive care unit (ICU) admission and/or death. We also piloted an alternative machine learning approach and compared selected predictors of severity with the 4CE phenotype at 1 site.ResultsThe full 4CE severity phenotype had pooled sensitivity of 0.73 and specificity 0.83 for the combined outcome of ICU admission and/or death. The sensitivity of individual code categories for acuity had high variability-up to 0.65 across sites. At one pilot site, the expert-derived phenotype had mean area under the curve of 0.903 (95% confidence interval, 0.886-0.921), compared with an area under the curve of 0.956 (95% confidence interval, 0.952-0.959) for the machine learning approach. Billing codes were poor proxies of ICU admission, with as low as 49% precision and recall compared with chart review.DiscussionWe developed a severity phenotype using 6 code classes that proved resilient to coding variability across international institutions. In contrast, machine learning approaches may overfit hospital-specific orders. Manual chart review revealed discrepancies even in the gold-standard outcomes, possibly owing to heterogeneous pandemic conditions.ConclusionsWe developed an EHR-based severity phenotype for COVID-19 in hospitalized patients and validated it at 12 international sites.

Published
2021

11. Clinical phenotypes and outcomes in children with multisystem inflammatory syndrome across SARS-CoV-2 variant eras: a multinational study from the 4CE consortium

Author

Aaron, James R., Adam, Atif, Agapito, Giuseppe, Albayrak, Adem, Albi, Giuseppe, Alessiani, Mario, Alloni, Anna, Amendola, Danilo F., Angoulvant, François, Anthony, Li LLJ., Aronow, Bruce J., Ashraf, Fatima, Atz, Andrew, Avillach, Paul, Panickan, Vidul Ayakulangara, Azevedo, Paula S., Badenes, Rafael, Balshi, James, Batugo, Ashley, Beaulieu-Jones, Brendin R., Beaulieu-Jones, Brett K., Bell, Douglas S., Bellasi, Antonio, Bellazzi, Riccardo, Benoit, Vincent, Beraghi, Michele, Bernal-Sobrino, José Luis, Bernaux, Mélodie, Bey, Romain, Bhatnagar, Surbhi, Blanco-Martínez, Alvar, Boeker, Martin, Bonzel, Clara-Lea, Booth, John, Bosari, Silvano, Bourgeois, Florence T., Bradford, Robert L., Brat, Gabriel A., Bréant, Stéphane, Brown, Nicholas W., Bruno, Raffaele, Bryant, William A., Bucalo, Mauro, Bucholz, Emily, Burgun, Anita, Cai, Tianxi, Cannataro, Mario, Carmona, Aldo, Cattelan, Anna Maria, Caucheteux, Charlotte, Champ, Julien, Chen, Jin, Chen, Krista Y., Chiovato, Luca, Chiudinelli, Lorenzo, Cho, Kelly, Cimino, James J., Colicchio, Tiago K., Cormont, Sylvie, Cossin, Sébastien, Craig, Jean B., Cruz-Bermúdez, Juan Luis, Cruz-Rojo, Jaime, Dagliati, Arianna, Daniar, Mohamad, Daniel, Christel, Das, Priyam, Devkota, Batsal, Dionne, Audrey, Duan, Rui, Dubiel, Julien, DuVall, Scott L., Esteve, Loic, Estiri, Hossein, Fan, Shirley, Follett, Robert W., Ganslandt, Thomas, García-Barrio, Noelia, Garmire, Lana X., Gehlenborg, Nils, Getzen, Emily J., Geva, Alon, Goh, Rachel SJ., González, Tomás González, Gradinger, Tobias, Gramfort, Alexandre, Griffier, Romain, Griffon, Nicolas, Grisel, Olivier, Gutiérrez-Sacristán, Alba, Guzzi, Pietro H., Han, Larry, Hanauer, David A., Haverkamp, Christian, Hazard, Derek Y., He, Bing, Henderson, Darren W., Hilka, Martin, Ho, Yuk-Lam, Holmes, John H., Honerlaw, Jacqueline P., Hong, Chuan, Huling, Kenneth M., Hutch, Meghan R., Issitt, Richard W., Jannot, Anne Sophie, Jouhet, Vianney, Kainth, Mundeep K., Kate, Kernan F., Kavuluru, Ramakanth, Keller, Mark S., Kennedy, Chris J., Kernan, Kate F., Key, Daniel A., Kirchoff, Katie, Klann, Jeffrey G., Kohane, Isaac S., Krantz, Ian D., Kraska, Detlef, Krishnamurthy, Ashok K., L'Yi, Sehi, Leblanc, Judith, Lemaitre, Guillaume, Lenert, Leslie, Leprovost, Damien, Liu, Molei, Will Loh, Ne Hooi, Long, Qi, Lozano-Zahonero, Sara, Luo, Yuan, Lynch, Kristine E., Mahmood, Sadiqa, Maidlow, Sarah E., Makoudjou, Adeline, Makwana, Simran, Malovini, Alberto, Mandl, Kenneth D., Mao, Chengsheng, Maram, Anupama, Maripuri, Monika, Martel, Patricia, Martins, Marcelo R., Marwaha, Jayson S., Masino, Aaron J., Mazzitelli, Maria, Mazzotti, Diego R., Mensch, Arthur, Milano, Marianna, Minicucci, Marcos F., Moal, Bertrand, Ahooyi, Taha Mohseni, Moore, Jason H., Moraleda, Cinta, Morris, Jeffrey S., Morris, Michele, Moshal, Karyn L., Mousavi, Sajad, Mowery, Danielle L., Murad, Douglas A., Murphy, Shawn N., Naughton, Thomas P., Breda Neto, Carlos Tadeu, Neuraz, Antoine, Newburger, Jane, Ngiam, Kee Yuan, Njoroge, Wanjiku FM., Norman, James B., Obeid, Jihad, Okoshi, Marina P., Olson, Karen L., Omenn, Gilbert S., Orlova, Nina, Ostasiewski, Brian D., Palmer, Nathan P., Paris, Nicolas, Patel, Lav P., Pedrera-Jiménez, Miguel, Pfaff, Ashley C., Pfaff, Emily R., Pillion, Danielle, Pizzimenti, Sara, Priya, Tanu, Prokosch, Hans U., Prudente, Robson A., Prunotto, Andrea, Quirós-González, Víctor, Ramoni, Rachel B., Raskin, Maryna, Rieg, Siegbert, Roig-Domínguez, Gustavo, Rojo, Pablo, Romero-Garcia, Nekane, Rubio-Mayo, Paula, Sacchi, Paolo, Sáez, Carlos, Salamanca, Elisa, Samayamuthu, Malarkodi Jebathilagam, Sanchez-Pinto, L. Nelson, Sandrin, Arnaud, Santhanam, Nandhini, Santos, Janaina C.C., Sanz Vidorreta, Fernando J., Savino, Maria, Schriver, Emily R., Schubert, Petra, Schuettler, Juergen, Scudeller, Luigia, Sebire, Neil J., Serrano-Balazote, Pablo, Serre, Patricia, Serret-Larmande, Arnaud, Shah, Mohsin A., Hossein Abad, Zahra Shakeri, Silvio, Domenick, Sliz, Piotr, Son, Jiyeon, Sonday, Charles, South, Andrew M., Sperotto, Francesca, Spiridou, Anastasia, Strasser, Zachary H., Tan, Amelia LM., Tan, Bryce W.Q., Tan, Byorn W.L., Tanni, Suzana E., Taylor, Deanne M., Terriza-Torres, Ana I., Tibollo, Valentina, Tippmann, Patric, Toh, Emma MS., Torti, Carlo, Trecarichi, Enrico M., Vallejos, Andrew K., Varoquaux, Gael, Vella, Margaret E., Verdy, Guillaume, Vie, Jill-Jênn, Visweswaran, Shyam, Vitacca, Michele, Wagholikar, Kavishwar B., Waitman, Lemuel R., Wang, Xuan, Wassermann, Demian, Weber, Griffin M., Wolkewitz, Martin, Wong, Scott, Xia, Zongqi, Xiong, Xin, Ye, Ye, Yehya, Nadir, Yuan, William, Zachariasse, Joany M., Zahner, Janet J., Zambelli, Alberto, Zhang, Harrison G., Zöller, Daniela, Zuccaro, Valentina, Zucco, Chiara, Li, Xiudi, Rofeberg, Valerie N., Elias, Matthew D., Laird-Gion, Jessica, and Newburger, Jane W.

Published
2023
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12. Characterization of long COVID temporal sub-phenotypes by distributed representation learning from electronic health record data: a cohort study

Author

Aaron, James R., Agapito, Giuseppe, Albayrak, Adem, Albi, Giuseppe, Alessiani, Mario, Alloni, Anna, Amendola, Danilo F., François Angoulvant, Anthony, Li L.L.J., Aronow, Bruce J., Ashraf, Fatima, Atz, Andrew, Avillach, Paul, Azevedo, Paula S., Balshi, James, Beaulieu-Jones, Brett K., Bell, Douglas S., Bellasi, Antonio, Bellazzi, Riccardo, Benoit, Vincent, Beraghi, Michele, Bernal-Sobrino, José Luis, Bernaux, Mélodie, Bey, Romain, Bhatnagar, Surbhi, Blanco-Martínez, Alvar, Bonzel, Clara-Lea, Booth, John, Bosari, Silvano, Bourgeois, Florence T., Bradford, Robert L., Brat, Gabriel A., Bréant, Stéphane, Brown, Nicholas W., Bruno, Raffaele, Bryant, William A., Bucalo, Mauro, Bucholz, Emily, Burgun, Anita, Cai, Tianxi, Cannataro, Mario, Carmona, Aldo, Caucheteux, Charlotte, Champ, Julien, Chen, Jin, Chen, Krista Y., Chiovato, Luca, Chiudinelli, Lorenzo, Cho, Kelly, Cimino, James J., Colicchio, Tiago K., Cormont, Sylvie, Cossin, Sébastien, Craig, Jean B., Cruz-Bermúdez, Juan Luis, Cruz-Rojo, Jaime, Dagliati, Arianna, Daniar, Mohamad, Daniel, Christel, Das, Priyam, Devkota, Batsal, Dionne, Audrey, Duan, Rui, Dubiel, Julien, DuVall, Scott L., Esteve, Loic, Estiri, Hossein, Fan, Shirley, Follett, Robert W., Ganslandt, Thomas, Barrio, Noelia García, Garmire, Lana X., Gehlenborg, Nils, Getzen, Emily J., Geva, Alon, Gradinger, Tobias, Gramfort, Alexandre, Griffier, Romain, Griffon, Nicolas, Grisel, Olivier, Gutiérrez-Sacristán, Alba, Han, Larry, Hanauer, David A., Haverkamp, Christian, Hazard, Derek Y., He, Bing, Henderson, Darren W., Hilka, Martin, Ho, Yuk-Lam, Holmes, John H., Hong, Chuan, Huling, Kenneth M., Hutch, Meghan R., Issitt, Richard W., Jannot, Anne Sophie, Jouhet, Vianney, Kavuluru, Ramakanth, Keller, Mark S., Kennedy, Chris J., Key, Daniel A., Kirchoff, Katie, Klann, Jeffrey G., Kohane, Isaac S., Krantz, Ian D., Kraska, Detlef, Krishnamurthy, Ashok K., L'Yi, Sehi, Le, Trang T., Leblanc, Judith, Lemaitre, Guillaume, Lenert, Leslie, Leprovost, Damien, Liu, Molei, Will Loh, Ne Hooi, Long, Qi, Lozano-Zahonero, Sara, Luo, Yuan, Lynch, Kristine E., Mahmood, Sadiqa, Maidlow, Sarah E., Makoudjou, Adeline, Malovini, Alberto, Mandl, Kenneth D., Mao, Chengsheng, Maram, Anupama, Martel, Patricia, Martins, Marcelo R., Marwaha, Jayson S., Masino, Aaron J., Mazzitelli, Maria, Mensch, Arthur, Milano, Marianna, Minicucci, Marcos F., Moal, Bertrand, Ahooyi, Taha Mohseni, Moore, Jason H., Moraleda, Cinta, Morris, Jeffrey S., Morris, Michele, Moshal, Karyn L., Mousavi, Sajad, Mowery, Danielle L., Murad, Douglas A., Murphy, Shawn N., Naughton, Thomas P., Breda Neto, Carlos Tadeu, Neuraz, Antoine, Newburger, Jane, Ngiam, Kee Yuan, Njoroge, Wanjiku F.M., Norman, James B., Obeid, Jihad, Okoshi, Marina P., Olson, Karen L., Omenn, Gilbert S., Orlova, Nina, Ostasiewski, Brian D., Palmer, Nathan P., Paris, Nicolas, Patel, Lav P., Pedrera-Jiménez, Miguel, Pfaff, Emily R., Pfaff, Ashley C., Pillion, Danielle, Pizzimenti, Sara, Prokosch, Hans U., Prudente, Robson A., Prunotto, Andrea, Quirós-González, Víctor, Ramoni, Rachel B., Raskin, Maryna, Rieg, Siegbert, Roig-Domínguez, Gustavo, Rojo, Pablo, Rubio-Mayo, Paula, Sacchi, Paolo, Sáez, Carlos, Salamanca, Elisa, Samayamuthu, Malarkodi Jebathilagam, Sanchez-Pinto, L. Nelson, Sandrin, Arnaud, Santhanam, Nandhini, Santos, Janaina C.C., Sanz Vidorreta, Fernando J., Savino, Maria, Schriver, Emily R., Schubert, Petra, Schuettler, Juergen, Scudeller, Luigia, Sebire, Neil J., Serrano-Balazote, Pablo, Serre, Patricia, Serret-Larmande, Arnaud, Shah, Mohsin, Hossein Abad, Zahra Shakeri, Silvio, Domenick, Sliz, Piotr, Son, Jiyeon, Sonday, Charles, South, Andrew M., Spiridou, Anastasia, Strasser, Zachary H., Tan, Amelia L.M., Tan, Bryce W.Q., Tan, Byorn W.L., Tanni, Suzana E., Taylor, Deanne M., Terriza-Torres, Ana I., Tibollo, Valentina, Tippmann, Patric, Toh, Emma M.S., Torti, Carlo, Trecarichi, Enrico M., Tseng, Yi-Ju, Vallejos, Andrew K., Varoquaux, Gael, Vella, Margaret E., Verdy, Guillaume, Vie, Jill-Jênn, Visweswaran, Shyam, Vitacca, Michele, Wagholikar, Kavishwar B., Waitman, Lemuel R., Wang, Xuan, Wassermann, Demian, Weber, Griffin M., Wolkewitz, Martin, Wong, Scott, Xia, Zongqi, Xiong, Xin, Ye, Ye, Yehya, Nadir, Yuan, William, Zambelli, Alberto, Zhang, Harrison G., Zo¨ller, Daniela, Zuccaro, Valentina, Zucco, Chiara, Mesa, Rebecca, and Verdy, Guillame

Published
2023
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13. Deep learning integrates histopathology and proteogenomics at a pan-cancer level

Author

Aguet, François, Akiyama, Yo, Anand, Shankara, Anurag, Meenakshi, Babur, Özgün, Bavarva, Jasmin, Birger, Chet, Birrer, Michael J., Cantley, Lewis C., Cao, Song, Carr, Steven A., Ceccarelli, Michele, Chan, Daniel W., Chinnaiyan, Arul M., Cho, Hanbyul, Chowdhury, Shrabanti, Cieslik, Marcin P., Clauser, Karl R., Colaprico, Antonio, Zhou, Daniel Cui, da Veiga Leprevost, Felipe, Day, Corbin, Dhanasekaran, Saravana M., Domagalski, Marcin J., Dou, Yongchao, Druker, Brian J., Edwards, Nathan, Ellis, Matthew J., Selvan, Myvizhi Esai, Foltz, Steven M., Francis, Alicia, Geffen, Yifat, Getz, Gad, Gonzalez Robles, Tania J., Gosline, Sara J.C., Gümüş, Zeynep H., Heiman, David I., Hiltke, Tara, Hostetter, Galen, Hu, Yingwei, Huang, Chen, Huntsman, Emily, Iavarone, Antonio, Jaehnig, Eric J., Jewell, Scott D., Ji, Jiayi, Jiang, Wen, Johnson, Jared L., Katsnelson, Lizabeth, Ketchum, Karen A., Kolodziejczak, Iga, Krug, Karsten, Kumar-Sinha, Chandan, Lei, Jonathan T., Liang, Wen-Wei, Liao, Yuxing, Lindgren, Caleb M., Liu, Tao, Ma, Weiping, Rodrigues, Fernanda Martins, McKerrow, Wilson, Mesri, Mehdi, Nesvizhskii, Alexey I., Newton, Chelsea J., Oldroyd, Robert, Paulovich, Amanda G., Payne, Samuel H., Petralia, Francesca, Pugliese, Pietro, Reva, Boris, Rykunov, Dmitry, Satpathy, Shankha, Savage, Sara R., Schadt, Eric E., Schnaubelt, Michael, Schürer, Stephan, Shi, Zhiao, Smith, Richard D., Song, Xiaoyu, Song, Yizhe, Stathias, Vasileios, Storrs, Erik P., Terekhanova, Nadezhda V., Thangudu, Ratna R., Thiagarajan, Mathangi, Tignor, Nicole, Wang, Liang-Bo, Wang, Pei, Wang, Ying, Wen, Bo, Wiznerowicz, Maciej, Wu, Yige, Wyczalkowski, Matthew A., Yao, Lijun, Yaron, Tomer M., Yi, Xinpei, Zhang, Bing, Zhang, Hui, Zhang, Qing, Zhang, Xu, Zhang, Zhen, Wang, Joshua M., Hong, Runyu, Demicco, Elizabeth G., Tan, Jimin, Lazcano, Rossana, Moreira, Andre L., Li, Yize, Calinawan, Anna, Razavian, Narges, Schraink, Tobias, Gillette, Michael A., Omenn, Gilbert S., An, Eunkyung, Rodriguez, Henry, Tsirigos, Aristotelis, Ruggles, Kelly V., Ding, Li, Robles, Ana I., Mani, D.R., Rodland, Karin D., Lazar, Alexander J., Liu, Wenke, and Fenyö, David

Published
2023
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14. Proteogenomic insights suggest druggable pathways in endometrial carcinoma

Author

Antczak, Andrzej, Anurag, Meenakshi, Bauer, Thomas, Birger, Chet, Birrer, Michael J., Borucki, Melissa, Cai, Shuang, Calinawan, Anna, Carr, Steven A., Castro, Patricia, Cerda, Sandra, Chan, Daniel W., Chesla, David, Cieslik, Marcin P., Cottingham, Sandra, Dhir, Rajiv, Domagalski, Marcin J., Druker, Brian J., Duffy, Elizabeth, Edwards, Nathan J., Edwards, Robert, Ellis, Matthew J., Eschbacher, Jennifer, Fam, Mina, Fevrier-Sullivan, Brenda, Francis, Jesse, Freymann, John, Gabriel, Stacey, Getz, Gad, Gillette, Michael A., Godwin, Andrew K., Goldthwaite, Charles A., Grady, Pamela, Hafron, Jason, Hariharan, Pushpa, Hindenach, Barbara, Hoadley, Katherine A., Huang, Jasmine, Ittmann, Michael M., Johnson, Ashlie, Jones, Corbin D., Ketchum, Karen A., Kirby, Justin, Le, Toan, Ma'ayan, Avi, Madan, Rashna, Mareedu, Sailaja, McGarvey, Peter B., Modugno, Francesmary, Montgomery, Rebecca, Nyce, Kristen, Paulovich, Amanda G., Pruetz, Barbara L., Qi, Liqun, Richey, Shannon, Schadt, Eric E., Shutack, Yvonne, Singh, Shilpi, Smith, Michael, Tansil, Darlene, Thangudu, Ratna R., Tobin, Matt, Um, Ki Sung, Vatanian, Negin, Webster, Alex, Wilson, George D., Wright, Jason, Zaalishvili, Kakhaber, Zhang, Zhen, Zhao, Grace, Dou, Yongchao, Katsnelson, Lizabeth, Gritsenko, Marina A., Hu, Yingwei, Reva, Boris, Hong, Runyu, Wang, Yi-Ting, Kolodziejczak, Iga, Lu, Rita Jui-Hsien, Tsai, Chia-Feng, Bu, Wen, Liu, Wenke, Guo, Xiaofang, An, Eunkyung, Arend, Rebecca C., Bavarva, Jasmin, Chen, Lijun, Chu, Rosalie K., Czekański, Andrzej, Davoli, Teresa, Demicco, Elizabeth G., DeLair, Deborah, Devereaux, Kelly, Dhanasekaran, Saravana M., Dottino, Peter, Dover, Bailee, Fillmore, Thomas L., Foxall, McKenzie, Hermann, Catherine E., Hiltke, Tara, Hostetter, Galen, Jędryka, Marcin, Jewell, Scott D., Johnson, Isabelle, Kahn, Andrea G., Ku, Amy T., Kumar-Sinha, Chandan, Kurzawa, Paweł, Lazar, Alexander J., Lazcano, Rossana, Lei, Jonathan T., Li, Yi, Liao, Yuxing, Lih, Tung-Shing M., Lin, Tai-Tu, Martignetti, John A., Masand, Ramya P., Matkowski, Rafał, McKerrow, Wilson, Mesri, Mehdi, Monroe, Matthew E., Moon, Jamie, Moore, Ronald J., Nestor, Michael D., Newton, Chelsea, Omelchenko, Tatiana, Omenn, Gilbert S., Payne, Samuel H., Petyuk, Vladislav A., Robles, Ana I., Rodriguez, Henry, Ruggles, Kelly V., Rykunov, Dmitry, Savage, Sara R., Schepmoes, Athena A., Shi, Tujin, Shi, Zhiao, Tan, Jimin, Taylor, Mason, Thiagarajan, Mathangi, Wang, Joshua M., Weitz, Karl K., Wen, Bo, Williams, C.M., Wu, Yige, Wyczalkowski, Matthew A., Yi, Xinpei, Zhang, Xu, Zhao, Rui, Mutch, David, Chinnaiyan, Arul M., Smith, Richard D., Nesvizhskii, Alexey I., Wang, Pei, Wiznerowicz, Maciej, Ding, Li, Mani, D.R., Zhang, Hui, Anderson, Matthew L., Rodland, Karin D., Zhang, Bing, Liu, Tao, and Fenyö, David

Published
2023
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15. Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation

Author

An, Eunkyung, Anurag, Meenakshi, Bavarva, Jasmin, Birrer, Michael J., Babur, Özgün, Cao, Song, Ceccarelli, Michele, Chan, Daniel W., Chinnaiyan, Arul M., Cho, Hanbyul, Chowdhury, Shrabanti, Cieslik, Marcin P., Colaprico, Antonio, Carr, Steven A., da Veiga Leprevost, Felipe, Day, Corbin, Domagalski, Marcin J., Dou, Yongchao, Druker, Brian J., Edwards, Nathan, Ellis, Matthew J., Fenyo, David, Foltz, Steven M., Francis, Alicia, Gonzalez Robles, Tania J., Gosline, Sara J.C., Gümüş, Zeynep H., Hiltke, Tara, Hong, Runyu, Hostetter, Galen, Hu, Yingwei, Huang, Chen, Iavarone, Antonio, Jaehnig, Eric J., Jewel, Scott D., Ji, Jiayi, Jiang, Wen, Katsnelson, Lizabeth, Ketchum, Karen A., Kolodziejczak, Iga, Kumar-Sinha, Chandan, Krug, Karsten, Lei, Jonathan T., Liang, Wen-Wei, Liao, Yuxing, Lindgren, Caleb M., Liu, Tao, Liu, Wenke, Ma, Weiping, McKerrow, Wilson, Mesri, Mehdi, Mani, D.R., Nesvizhskii, Alexey I., Newton, Chelsea, Oldroyd, Robert, Omenn, Gilbert S., Paulovich, Amanda G., Petralia, Francesca, Pugliese, Pietro, Reva, Boris, Rodland, Karin D., Ruggles, Kelly V., Rykunov, Dmitry, Rodrigues, Fernanda Martins, Savage, Sara R., Schadt, Eric E., Schnaubelt, Michael, Schraink, Tobias, Shi, Zhiao, Smith, Richard D., Song, Xiaoyu, Stathias, Vasileios, Storrs, Erik P., Schürer, Stephan, Selvan, Myvizhi Esai, Tan, Jimin, Terekhanova, Nadezhda V., Thangudu, Ratna R., Tignor, Nicole, Thiagarajan, Mathangi, Wang, Joshua M., Wang, Pei, Wang, Ying (Cindy), Wen, Bo, Wiznerowicz, Maciej, Wu, Yige, Wyczalkowski, Matthew A., Yao, Lijun, Yi, Xinpei, Zhang, Bing, Zhang, Hui, Zhang, Xu, Zhang, Zhen, Zhou, Daniel Cui, Geffen, Yifat, Anand, Shankara, Akiyama, Yo, Yaron, Tomer M., Song, Yizhe, Johnson, Jared L., Govindan, Akshay, Li, Yize, Huntsman, Emily, Wang, Liang-Bo, Birger, Chet, Heiman, David I., Zhang, Qing, Miller, Mendy, Maruvka, Yosef E., Haradhvala, Nicholas J., Calinawan, Anna, Belkin, Saveliy, Kerelsky, Alexander, Clauser, Karl R., Satpathy, Shankha, Payne, Samuel H., Gillette, Michael A., Dhanasekaran, Saravana M., Rodriguez, Henry, Robles, Ana I., Lazar, Alexander J., Aguet, François, Cantley, Lewis C., Ding, Li, and Getz, Gad

Published
2023
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16. Pan-cancer proteogenomics connects oncogenic drivers to functional states

Author

An, Eunkyung, Anurag, Meenakshi, Bavarva, Jasmin, Birrer, Michael J., Calinawan, Anna, Ceccarelli, Michele, Chan, Daniel W., Chinnaiyan, Arul M., Cho, Hanbyul, Chowdhury, Shrabanti, Cieslik, Marcin P., da Veiga Leprevost, Felipe, Day, Corbin, Domagalski, Marcin J., Dou, Yongchao, Druker, Brian J., Edwards, Nathan, Ellis, Matthew J., Selvan, Myvizhi Esai, Foltz, Steven M., Francis, Alicia, Gonzalez Robles, Tania J., Gosline, Sara J.C., Gümüş, Zeynep H., Hiltke, Tara, Hong, Runyu, Hostetter, Galen, Hu, Yingwei, Huang, Chen, Huntsman, Emily, Jaehnig, Eric J., Jewel, Scott D., Ji, Jiayi, Jiang, Wen, Katsnelson, Lizabeth, Ketchum, Karen A., Kolodziejczak, Iga, Lei, Jonathan T., Liao, Yuxing, Lindgren, Caleb M., Liu, Tao, Ma, Weiping, McKerrow, Wilson, Nesvizhskii, Alexey I., Newton, Chelsea, Oldroyd, Robert, Omenn, Gilbert S., Paulovich, Amanda G., Petralia, Francesca, Reva, Boris, Rodland, Karin D., Ruggles, Kelly V., Rykunov, Dmitry, Savage, Sara R., Schadt, Eric E., Schnaubelt, Michael, Schraink, Tobias, Shi, Zhiao, Smith, Richard D., Song, Xiaoyu, Tan, Jimin, Thangudu, Ratna R., Tignor, Nicole, Wang, Joshua M., Wang, Pei, Wang, Ying (Cindy), Wen, Bo, Wiznerowicz, Maciej, Yi, Xinpei, Zhang, Bing, Zhang, Hui, Zhang, Xu, Zhang, Zhen, Li, Yize, Porta-Pardo, Eduard, Tokheim, Collin, Bailey, Matthew H., Yaron, Tomer M., Stathias, Vasileios, Geffen, Yifat, Imbach, Kathleen J., Cao, Song, Anand, Shankara, Akiyama, Yo, Liu, Wenke, Wyczalkowski, Matthew A., Song, Yizhe, Storrs, Erik P., Wendl, Michael C., Zhang, Wubing, Sibai, Mustafa, Ruiz-Serra, Victoria, Liang, Wen-Wei, Terekhanova, Nadezhda V., Rodrigues, Fernanda Martins, Clauser, Karl R., Heiman, David I., Zhang, Qing, Aguet, Francois, Calinawan, Anna P., Dhanasekaran, Saravana M., Birger, Chet, Satpathy, Shankha, Zhou, Daniel Cui, Wang, Liang-Bo, Baral, Jessika, Johnson, Jared L., Huntsman, Emily M., Pugliese, Pietro, Colaprico, Antonio, Iavarone, Antonio, Chheda, Milan G., Ricketts, Christopher J., Fenyö, David, Payne, Samuel H., Rodriguez, Henry, Robles, Ana I., Gillette, Michael A., Kumar-Sinha, Chandan, Lazar, Alexander J., Cantley, Lewis C., Getz, Gad, and Ding, Li

Published
2023
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17. Proteogenomic data and resources for pan-cancer analysis

Author

Lazar, Alexander J., Paulovich, Amanda G., Colaprico, Antonio, Iavarone, Antonio, Chinnaiyan, Arul M., Druker, Brian J., Kumar-Sinha, Chandan, Newton, Chelsea J., Huang, Chen, Mani, D.R., Smith, Richard D., Huntsman, Emily, Schadt, Eric E., An, Eunkyung, Petralia, Francesca, Hostetter, Galen, Omenn, Gilbert S., Cho, Hanbyul, Rodriguez, Henry, Zhang, Hui, Kolodziejczak, Iga, Johnson, Jared L., Bavarva, Jasmin, Tan, Jimin, Rodland, Karin D., Clauser, Karl R., Krug, Karsten, Cantley, Lewis C., Wiznerowicz, Maciej, Ellis, Matthew J., Anurag, Meenakshi, Mesri, Mehdi, Gillette, Michael A., Birrer, Michael J., Ceccarelli, Michele, Dhanasekaran, Saravana M., Edwards, Nathan, Tignor, Nicole, Babur, Özgün, Pugliese, Pietro, Gosline, Sara J.C., Jewell, Scott D., Satpathy, Shankha, Chowdhury, Shrabanti, Schürer, Stephan, Carr, Steven A., Liu, Tao, Hiltke, Tara, Yaron, Tomer M., Stathias, Vasileios, Liu, Wenke, Zhang, Xu, Song, Yizhe, Zhang, Zhen, Li, Yize, Dou, Yongchao, Da Veiga Leprevost, Felipe, Geffen, Yifat, Calinawan, Anna P., Aguet, François, Akiyama, Yo, Anand, Shankara, Birger, Chet, Cao, Song, Chaudhary, Rekha, Chilappagari, Padmini, Cieslik, Marcin, Zhou, Daniel Cui, Day, Corbin, Domagalski, Marcin J., Esai Selvan, Myvizhi, Fenyö, David, Foltz, Steven M., Francis, Alicia, Gonzalez-Robles, Tania, Gümüş, Zeynep H., Heiman, David, Holck, Michael, Hong, Runyu, Hu, Yingwei, Jaehnig, Eric J., Ji, Jiayi, Jiang, Wen, Katsnelson, Lizabeth, Ketchum, Karen A., Klein, Robert J., Lei, Jonathan T., Liang, Wen-Wei, Liao, Yuxing, Lindgren, Caleb M., Ma, Weiping, Ma, Lei, MacCoss, Michael J., Martins Rodrigues, Fernanda, McKerrow, Wilson, Nguyen, Ngoc, Oldroyd, Robert, Pilozzi, Alexander, Reva, Boris, Rudnick, Paul, Ruggles, Kelly V., Rykunov, Dmitry, Savage, Sara R., Schnaubelt, Michael, Schraink, Tobias, Shi, Zhiao, Singhal, Deepak, Song, Xiaoyu, Storrs, Erik, Terekhanova, Nadezhda V., Thangudu, Ratna R., Thiagarajan, Mathangi, Wang, Liang-Bo, Wang, Joshua M., Wang, Ying, Wen, Bo, Wu, Yige, Wyczalkowski, Matthew A., Xin, Yi, Yao, Lijun, Yi, Xinpei, Zhang, Qing, Zuhl, Maya, Getz, Gad, Ding, Li, Nesvizhskii, Alexey I., Wang, Pei, Robles, Ana I., Zhang, Bing, and Payne, Samuel H.

Published
2023
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18. International electronic health record-derived COVID-19 clinical course profiles: the 4CE consortium

Author

Brat, Gabriel A, Weber, Griffin M, Gehlenborg, Nils, Avillach, Paul, Palmer, Nathan P, Chiovato, Luca, Cimino, James, Waitman, Lemuel R, Omenn, Gilbert S, Malovini, Alberto, Moore, Jason H, Beaulieu-Jones, Brett K, Tibollo, Valentina, Murphy, Shawn N, Yi, Sehi L’, Keller, Mark S, Bellazzi, Riccardo, Hanauer, David A, Serret-Larmande, Arnaud, Gutierrez-Sacristan, Alba, Holmes, John J, Bell, Douglas S, Mandl, Kenneth D, Follett, Robert W, Klann, Jeffrey G, Murad, Douglas A, Scudeller, Luigia, Bucalo, Mauro, Kirchoff, Katie, Craig, Jean, Obeid, Jihad, Jouhet, Vianney, Griffier, Romain, Cossin, Sebastien, Moal, Bertrand, Patel, Lav P, Bellasi, Antonio, Prokosch, Hans U, Kraska, Detlef, Sliz, Piotr, Tan, Amelia LM, Ngiam, Kee Yuan, Zambelli, Alberto, Mowery, Danielle L, Schiver, Emily, Devkota, Batsal, Bradford, Robert L, Daniar, Mohamad, Daniel, Christel, Benoit, Vincent, Bey, Romain, Paris, Nicolas, Serre, Patricia, Orlova, Nina, Dubiel, Julien, Hilka, Martin, Jannot, Anne Sophie, Breant, Stephane, Leblanc, Judith, Griffon, Nicolas, Burgun, Anita, Bernaux, Melodie, Sandrin, Arnaud, Salamanca, Elisa, Cormont, Sylvie, Ganslandt, Thomas, Gradinger, Tobias, Champ, Julien, Boeker, Martin, Martel, Patricia, Esteve, Loic, Gramfort, Alexandre, Grisel, Olivier, Leprovost, Damien, Moreau, Thomas, Varoquaux, Gael, Vie, Jill-Jênn, Wassermann, Demian, Mensch, Arthur, Caucheteux, Charlotte, Haverkamp, Christian, Lemaitre, Guillaume, Bosari, Silvano, Krantz, Ian D, South, Andrew, Cai, Tianxi, and Kohane, Isaac S

Subjects
Health Services and Systems, Health Sciences, Good Health and Well Being, Databases, Outcomes research, Viral infection, Health services and systems
Abstract

We leveraged the largely untapped resource of electronic health record data to address critical clinical and epidemiological questions about Coronavirus Disease 2019 (COVID-19). To do this, we formed an international consortium (4CE) of 96 hospitals across five countries (www.covidclinical.net). Contributors utilized the Informatics for Integrating Biology and the Bedside (i2b2) or Observational Medical Outcomes Partnership (OMOP) platforms to map to a common data model. The group focused on temporal changes in key laboratory test values. Harmonized data were analyzed locally and converted to a shared aggregate form for rapid analysis and visualization of regional differences and global commonalities. Data covered 27,584 COVID-19 cases with 187,802 laboratory tests. Case counts and laboratory trajectories were concordant with existing literature. Laboratory tests at the time of diagnosis showed hospital-level differences equivalent to country-level variation across the consortium partners. Despite the limitations of decentralized data generation, we established a framework to capture the trajectory of COVID-19 disease in patients and their response to interventions.

Published
2020

19. Informative missingness: What can we learn from patterns in missing laboratory data in the electronic health record?

Author

Tan, Amelia L.M., Getzen, Emily J., Hutch, Meghan R., Strasser, Zachary H., Gutiérrez-Sacristán, Alba, Le, Trang T., Dagliati, Arianna, Morris, Michele, Hanauer, David A., Moal, Bertrand, Bonzel, Clara-Lea, Yuan, William, Chiudinelli, Lorenzo, Das, Priam, Zhang, Harrison G., Aronow, Bruce J., Avillach, Paul, Brat, Gabriel.A., Cai, Tianxi, Hong, Chuan, La Cava, William G., Hooi Will Loh, He, Luo, Yuan, Murphy, Shawn N., Yuan Hgiam, Kee, Omenn, Gilbert S., Patel, Lav P., Jebathilagam Samayamuthu, Malarkodi, Shriver, Emily R., Shakeri Hossein Abad, Zahra, Tan, Byorn W.L., Visweswaran, Shyam, Wang, Xuan, Weber, Griffin M., Xia, Zongqi, Verdy, Bertrand, Long, Qi, Mowery, Danielle L., and Holmes, John H.

Published
2023
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21. SurvMaximin: Robust federated approach to transporting survival risk prediction models

Author

Wang, Xuan, Zhang, Harrison G., Xiong, Xin, Hong, Chuan, Weber, Griffin M., Brat, Gabriel A., Bonzel, Clara-Lea, Luo, Yuan, Duan, Rui, Palmer, Nathan P., Hutch, Meghan R., Gutiérrez-Sacristán, Alba, Bellazzi, Riccardo, Chiovato, Luca, Cho, Kelly, Dagliati, Arianna, Estiri, Hossein, García-Barrio, Noelia, Griffier, Romain, Hanauer, David A., Ho, Yuk-Lam, Holmes, John H., Keller, Mark S., Klann MEng, Jeffrey G., L'Yi, Sehi, Lozano-Zahonero, Sara, Maidlow, Sarah E., Makoudjou, Adeline, Malovini, Alberto, Moal, Bertrand, Moore, Jason H., Morris, Michele, Mowery, Danielle L., Murphy, Shawn N, Neuraz, Antoine, Yuan Ngiam, Kee, Omenn, Gilbert S., Patel, Lav P., Pedrera-Jiménez, Miguel, Prunotto, Andrea, Jebathilagam Samayamuthu, Malarkodi, Sanz Vidorreta, Fernando J, Schriver, Emily R., Schubert, Petra, Serrano-Balazote, Pablo, South, Andrew M., Tan, Amelia L.M., Tan, Byorn W.L., Tibollo, Valentina, Tippmann, Patric, Visweswaran, Shyam, Xia, Zongqi, Yuan, William, Zöller, Daniela, Kohane, Isaac S., Avillach, Paul, Guo, Zijian, and Cai, Tianxi

Published
2022
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22. International electronic health record-derived post-acute sequelae profiles of COVID-19 patients

Author

Zhang, Harrison G., Dagliati, Arianna, Shakeri Hossein Abad, Zahra, Xiong, Xin, Bonzel, Clara-Lea, Xia, Zongqi, Tan, Bryce W. Q., Avillach, Paul, Brat, Gabriel A., Hong, Chuan, Morris, Michele, Visweswaran, Shyam, Patel, Lav P., Gutiérrez-Sacristán, Alba, Hanauer, David A., Holmes, John H., Samayamuthu, Malarkodi Jebathilagam, Bourgeois, Florence T., L’Yi, Sehi, Maidlow, Sarah E., Moal, Bertrand, Murphy, Shawn N., Strasser, Zachary H., Neuraz, Antoine, Ngiam, Kee Yuan, Loh, Ne Hooi Will, Omenn, Gilbert S., Prunotto, Andrea, Dalvin, Lauren A., Klann, Jeffrey G., Schubert, Petra, Vidorreta, Fernando J. Sanz, Benoit, Vincent, Verdy, Guillaume, Kavuluru, Ramakanth, Estiri, Hossein, Luo, Yuan, Malovini, Alberto, Tibollo, Valentina, Bellazzi, Riccardo, Cho, Kelly, Ho, Yuk-Lam, Tan, Amelia L. M., Tan, Byorn W. L., Gehlenborg, Nils, Lozano-Zahonero, Sara, Jouhet, Vianney, Chiovato, Luca, Aronow, Bruce J., Toh, Emma M. S., Wong, Wei Gen Scott, Pizzimenti, Sara, Wagholikar, Kavishwar B., Bucalo, Mauro, Cai, Tianxi, South, Andrew M., Kohane, Isaac S., and Weber, Griffin M.

Published
2022
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23. A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology

Author

He, Yongqun, Yu, Hong, Huffman, Anthony, Lin, Asiyah Yu, Natale, Darren A., Beverley, John, Zheng, Ling, Perl, Yehoshua, Wang, Zhigang, Liu, Yingtong, Ong, Edison, Wang, Yang, Huang, Philip, Tran, Long, Du, Jinyang, Shah, Zalan, Shah, Easheta, Desai, Roshan, Huang, Hsin-hui, Tian, Yujia, Merrell, Eric, Duncan, William D., Arabandi, Sivaram, Schriml, Lynn M., Zheng, Jie, Masci, Anna Maria, Wang, Liwei, Liu, Hongfang, Smaili, Fatima Zohra, Hoehndorf, Robert, Pendlington, Zoë May, Roncaglia, Paola, Ye, Xianwei, Xie, Jiangan, Tang, Yi-Wei, Yang, Xiaolin, Peng, Suyuan, Zhang, Luxia, Chen, Luonan, Hur, Junguk, Omenn, Gilbert S., Athey, Brian, and Smith, Barry

Published
2022
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27. Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework.

Author

Glusman, Gustavo, Rose, Peter W, Prlić, Andreas, Dougherty, Jennifer, Duarte, José M, Hoffman, Andrew S, Barton, Geoffrey J, Bendixen, Emøke, Bergquist, Timothy, Bock, Christian, Brunk, Elizabeth, Buljan, Marija, Burley, Stephen K, Cai, Binghuang, Carter, Hannah, Gao, JianJiong, Godzik, Adam, Heuer, Michael, Hicks, Michael, Hrabe, Thomas, Karchin, Rachel, Leman, Julia Koehler, Lane, Lydie, Masica, David L, Mooney, Sean D, Moult, John, Omenn, Gilbert S, Pearl, Frances, Pejaver, Vikas, Reynolds, Sheila M, Rokem, Ariel, Schwede, Torsten, Song, Sicheng, Tilgner, Hagen, Valasatava, Yana, Zhang, Yang, and Deutsch, Eric W

Subjects
Humans, Sequence Analysis, Protein, Protein Conformation, Polymorphism, Genetic, Algorithms, Congresses as Topic, Genome-Wide Association Study, Networking and Information Technology R&D, Human Genome, Biotechnology, Genetics, Generic health relevance, Clinical Sciences
Abstract

The translation of personal genomics to precision medicine depends on the accurate interpretation of the multitude of genetic variants observed for each individual. However, even when genetic variants are predicted to modify a protein, their functional implications may be unclear. Many diseases are caused by genetic variants affecting important protein features, such as enzyme active sites or interaction interfaces. The scientific community has catalogued millions of genetic variants in genomic databases and thousands of protein structures in the Protein Data Bank. Mapping mutations onto three-dimensional (3D) structures enables atomic-level analyses of protein positions that may be important for the stability or formation of interactions; these may explain the effect of mutations and in some cases even open a path for targeted drug development. To accelerate progress in the integration of these data types, we held a two-day Gene Variation to 3D (GVto3D) workshop to report on the latest advances and to discuss unmet needs. The overarching goal of the workshop was to address the question: what can be done together as a community to advance the integration of genetic variants and 3D protein structures that could not be done by a single investigator or laboratory? Here we describe the workshop outcomes, review the state of the field, and propose the development of a framework with which to promote progress in this arena. The framework will include a set of standard formats, common ontologies, a common application programming interface to enable interoperation of the resources, and a Tool Registry to make it easy to find and apply the tools to specific analysis problems. Interoperability will enable integration of diverse data sources and tools and collaborative development of variant effect prediction methods.

Published
2017

28. The 2023 Report on the Proteome from the HUPO Human Proteome Project

Author

Omenn, Gilbert S., Lane, Lydie, Overall, Christopher M., Lindskog, Cecilia, Pineau, Charles, Packer, Nicolle H., Cristea, Ileana M., Weintraub, Susan T., Orchard, Sandra, Roehrl, Michael H. A., Nice, Edouard, Guo, Tiannan, Van Eyk, Jennifer E., Liu, Siqi, Bandeira, Nuno, Aebersold, Ruedi, Moritz, Robert L., Deutsch, Eric W., Omenn, Gilbert S., Lane, Lydie, Overall, Christopher M., Lindskog, Cecilia, Pineau, Charles, Packer, Nicolle H., Cristea, Ileana M., Weintraub, Susan T., Orchard, Sandra, Roehrl, Michael H. A., Nice, Edouard, Guo, Tiannan, Van Eyk, Jennifer E., Liu, Siqi, Bandeira, Nuno, Aebersold, Ruedi, Moritz, Robert L., and Deutsch, Eric W.

Abstract

Since 2010, the Human Proteome Project (HPP), the flagship initiative of the Human Proteome Organization (HUPO), has pursued two goals: (1) to credibly identify the protein parts list and (2) to make proteomics an integral part of multiomics studies of human health and disease. The HPP relies on international collaboration, data sharing, standardized reanalysis of MS data sets by PeptideAtlas and MassIVE-KB using HPP Guidelines for quality assurance, integration and curation of MS and non-MS protein data by neXtProt, plus extensive use of antibody profiling carried out by the Human Protein Atlas. According to the neXtProt release 2023-04-18, protein expression has now been credibly detected (PE1) for 18,397 of the 19,778 neXtProt predicted proteins coded in the human genome (93%). Of these PE1 proteins, 17,453 were detected with mass spectrometry (MS) in accordance with HPP Guidelines and 944 by a variety of non-MS methods. The number of neXtProt PE2, PE3, and PE4 missing proteins now stands at 1381. Achieving the unambiguous identification of 93% of predicted proteins encoded from across all chromosomes represents remarkable experimental progress on the Human Proteome parts list. Meanwhile, there are several categories of predicted proteins that have proved resistant to detection regardless of protein-based methods used. Additionally there are some PE1–4 proteins that probably should be reclassified to PE5, specifically 21 LINC entries and ∼30 HERV entries; these are being addressed in the present year. Applying proteomics in a wide array of biological and clinical studies ensures integration with other omics platforms as reported by the Biology and Disease-driven HPP teams and the antibody and pathology resource pillars. Current progress has positioned the HPP to transition to its Grand Challenge Project focused on determining the primary function(s) of every protein itself and in networks and pathways within the context of human health and disease.

Published
2024
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31. Pan-cancer proteogenomics characterization of tumor immunity

Author

Petralia, Francesca, primary, Ma, Weiping, additional, Yaron, Tomer M., additional, Caruso, Francesca Pia, additional, Tignor, Nicole, additional, Wang, Joshua M., additional, Charytonowicz, Daniel, additional, Johnson, Jared L., additional, Huntsman, Emily M., additional, Marino, Giacomo B., additional, Calinawan, Anna, additional, Evangelista, John Erol, additional, Selvan, Myvizhi Esai, additional, Chowdhury, Shrabanti, additional, Rykunov, Dmitry, additional, Krek, Azra, additional, Song, Xiaoyu, additional, Turhan, Berk, additional, Christianson, Karen E., additional, Lewis, David A., additional, Deng, Eden Z., additional, Clarke, Daniel J.B., additional, Whiteaker, Jeffrey R., additional, Kennedy, Jacob J., additional, Zhao, Lei, additional, Segura, Rossana Lazcano, additional, Batra, Harsh, additional, Raso, Maria Gabriela, additional, Parra, Edwin Roger, additional, Soundararajan, Rama, additional, Tang, Ximing, additional, Li, Yize, additional, Yi, Xinpei, additional, Satpathy, Shankha, additional, Wang, Ying, additional, Wiznerowicz, Maciej, additional, González-Robles, Tania J., additional, Iavarone, Antonio, additional, Gosline, Sara J.C., additional, Reva, Boris, additional, Robles, Ana I., additional, Nesvizhskii, Alexey I., additional, Mani, D.R., additional, Gillette, Michael A., additional, Klein, Robert J., additional, Cieslik, Marcin, additional, Zhang, Bing, additional, Paulovich, Amanda G., additional, Sebra, Robert, additional, Gümüş, Zeynep H., additional, Hostetter, Galen, additional, Fenyö, David, additional, Omenn, Gilbert S., additional, Cantley, Lewis C., additional, Ma'ayan, Avi, additional, Lazar, Alexander J., additional, Ceccarelli, Michele, additional, Wang, Pei, additional, Abelin, Jennifer, additional, Aguet, François, additional, Akiyama, Yo, additional, An, Eunkyung, additional, Anand, Shankara, additional, Anurag, Meenakshi, additional, Babur, Özgün, additional, Bavarva, Jasmin, additional, Birger, Chet, additional, Birrer, Michael J., additional, Cao, Song, additional, Carr, Steven A., additional, Chan, Daniel W., additional, Chinnaiyan, Arul M., additional, Cho, Hanbyul, additional, Clauser, Karl, additional, Colaprico, Antonio, additional, Zhou, Daniel Cui, additional, da Veiga Leprevost, Felipe, additional, Day, Corbin, additional, Dhanasekaran, Saravana M., additional, Ding, Li, additional, Domagalski, Marcin J., additional, Dou, Yongchao, additional, Druker, Brian J., additional, Edwards, Nathan, additional, Ellis, Matthew J., additional, Foltz, Steven M., additional, Francis, Alicia, additional, Geffen, Yifat, additional, Getz, Gad, additional, Heiman, David I., additional, Hong, Runyu, additional, Hu, Yingwei, additional, Huang, Chen, additional, Jaehnig, Eric J., additional, Jewell, Scott D., additional, Ji, Jiayi, additional, Jiang, Wen, additional, Katsnelson, Lizabeth, additional, Ketchum, Karen A., additional, Kolodziejczak, Iga, additional, Krug, Karsten, additional, Kumar-Sinha, Chandan, additional, Lei, Jonathan T., additional, Liang, Wen-Wei, additional, Liao, Yuxing, additional, Lindgren, Caleb M., additional, Liu, Tao, additional, Liu, Wenke, additional, McDermott, Jason, additional, McKerrow, Wilson, additional, Mesri, Mehdi, additional, Mumphrey, Michael Brodie, additional, Newton, Chelsea J., additional, Oldroyd, Robert, additional, Payne, Samuel H., additional, Pugliese, Pietro, additional, Rodland, Karin D., additional, Rodrigues, Fernanda Martins, additional, Ruggles, Kelly V., additional, Savage, Sara R., additional, Schadt, Eric E., additional, Schnaubelt, Michael, additional, Schraink, Tobias, additional, Schürer, Stephan, additional, Shi, Zhiao, additional, Smith, Richard D., additional, Song, Feng, additional, Song, Yizhe, additional, Stathias, Vasileios, additional, Storrs, Erik P., additional, Tan, Jimin, additional, Terekhanova, Nadezhda V., additional, Thangudu, Ratna R., additional, Thiagarajan, Mathangi, additional, Wang, Liang-Bo, additional, Wen, Bo, additional, Wu, Yige, additional, Wyczalkowski, Matthew A., additional, Yao, Lijun, additional, Li, Qing Kay, additional, Zhang, Hui, additional, Zhang, Qing, additional, Zhang, Xu, additional, and Zhang, Zhen, additional

Published
2024
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32. The 2023 Report on the Proteome from the HUPO Human Proteome Project

Author

Omenn, Gilbert S., primary, Lane, Lydie, additional, Overall, Christopher M., additional, Lindskog, Cecilia, additional, Pineau, Charles, additional, Packer, Nicolle H., additional, Cristea, Ileana M., additional, Weintraub, Susan T., additional, Orchard, Sandra, additional, Roehrl, Michael H. A., additional, Nice, Edouard, additional, Guo, Tiannan, additional, Van Eyk, Jennifer E., additional, Liu, Siqi, additional, Bandeira, Nuno, additional, Aebersold, Ruedi, additional, Moritz, Robert L., additional, and Deutsch, Eric W., additional

Published
2024
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33. Assessing the Potential of GPT-4 to Annotate Medical Notes Across Different Languages and Countries: A Model Evaluation Study

Author

Saad Menezes, Maria Clara, primary, Hoffmann, Alexander F., additional, Tan, Amelia LM, additional, Nalbandyan, Marine, additional, Omenn, Gilbert S., additional, Mazzotti, Diego, additional, Hernández-Arango, Alejandro, additional, Visweswaran, Shyam, additional, Venkatesh, Shruthi, additional, Mandl, Kenneth D., additional, Bourgeois, Florence T., additional, Lee, James WK, additional, Makmur, Andrew, additional, Hanauer, David A., additional, Semanik, Michael G., additional, Kerivan, Lauren T., additional, Hill, Terra, additional, Forero, Julian, additional, Restrepo Castro, Carlos Andrés CR, additional, Vigna, Matteo, additional, Ceriana, Piero, additional, Abu-el-rub, Noor, additional, Avillach, Paul, additional, Bellazzi, Riccardo, additional, Callaci, Thomas, additional, Gutiérrez-Sacristán, Alba, additional, Malovini, Alberto, additional, Mathew, Jomol P., additional, Morris, Michele, additional, Murthy, Venkatesh, additional, Parimbelli, Enea, additional, Patel, Lav P., additional, Sáez, Carlos, additional, Samayamuthu, Malarkodi Jebathilagam, additional, Thompson, Jeffrey, additional, Tibollo, Valentina, additional, Xia, Zongqi, additional, Kohane, Isaac, additional, and anon, The Consortium for Clinical, additional

Published
2024
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36. Clinical phenotypes and outcomes in children with multisystem inflammatory syndrome across SARS-CoV-2 variant eras: a multinational study from the 4CE consortium

Author

Sperotto, Francesca, primary, Gutiérrez-Sacristán, Alba, additional, Makwana, Simran, additional, Li, Xiudi, additional, Rofeberg, Valerie N., additional, Cai, Tianxi, additional, Bourgeois, Florence T., additional, Omenn, Gilbert S., additional, Hanauer, David A., additional, Sáez, Carlos, additional, Bonzel, Clara-Lea, additional, Bucholz, Emily, additional, Dionne, Audrey, additional, Elias, Matthew D., additional, García-Barrio, Noelia, additional, González, Tomás González, additional, Issitt, Richard W., additional, Kernan, Kate F., additional, Laird-Gion, Jessica, additional, Maidlow, Sarah E., additional, Mandl, Kenneth D., additional, Ahooyi, Taha Mohseni, additional, Moraleda, Cinta, additional, Morris, Michele, additional, Moshal, Karyn L., additional, Pedrera-Jiménez, Miguel, additional, Shah, Mohsin A., additional, South, Andrew M., additional, Spiridou, Anastasia, additional, Taylor, Deanne M., additional, Verdy, Guillaume, additional, Visweswaran, Shyam, additional, Wang, Xuan, additional, Xia, Zongqi, additional, Zachariasse, Joany M., additional, Newburger, Jane W., additional, Avillach, Paul, additional, Aaron, James R., additional, Adam, Atif, additional, Agapito, Giuseppe, additional, Albayrak, Adem, additional, Albi, Giuseppe, additional, Alessiani, Mario, additional, Alloni, Anna, additional, Amendola, Danilo F., additional, Angoulvant, François, additional, Anthony, Li LLJ., additional, Aronow, Bruce J., additional, Ashraf, Fatima, additional, Atz, Andrew, additional, Panickan, Vidul Ayakulangara, additional, Azevedo, Paula S., additional, Badenes, Rafael, additional, Balshi, James, additional, Batugo, Ashley, additional, Beaulieu-Jones, Brendin R., additional, Beaulieu-Jones, Brett K., additional, Bell, Douglas S., additional, Bellasi, Antonio, additional, Bellazzi, Riccardo, additional, Benoit, Vincent, additional, Beraghi, Michele, additional, Bernal-Sobrino, José Luis, additional, Bernaux, Mélodie, additional, Bey, Romain, additional, Bhatnagar, Surbhi, additional, Blanco-Martínez, Alvar, additional, Boeker, Martin, additional, Booth, John, additional, Bosari, Silvano, additional, Bradford, Robert L., additional, Brat, Gabriel A., additional, Bréant, Stéphane, additional, Brown, Nicholas W., additional, Bruno, Raffaele, additional, Bryant, William A., additional, Bucalo, Mauro, additional, Burgun, Anita, additional, Cannataro, Mario, additional, Carmona, Aldo, additional, Cattelan, Anna Maria, additional, Caucheteux, Charlotte, additional, Champ, Julien, additional, Chen, Jin, additional, Chen, Krista Y., additional, Chiovato, Luca, additional, Chiudinelli, Lorenzo, additional, Cho, Kelly, additional, Cimino, James J., additional, Colicchio, Tiago K., additional, Cormont, Sylvie, additional, Cossin, Sébastien, additional, Craig, Jean B., additional, Cruz-Bermúdez, Juan Luis, additional, Cruz-Rojo, Jaime, additional, Dagliati, Arianna, additional, Daniar, Mohamad, additional, Daniel, Christel, additional, Das, Priyam, additional, Devkota, Batsal, additional, Duan, Rui, additional, Dubiel, Julien, additional, DuVall, Scott L., additional, Esteve, Loic, additional, Estiri, Hossein, additional, Fan, Shirley, additional, Follett, Robert W., additional, Ganslandt, Thomas, additional, Garmire, Lana X., additional, Gehlenborg, Nils, additional, Getzen, Emily J., additional, Geva, Alon, additional, Goh, Rachel SJ., additional, Gradinger, Tobias, additional, Gramfort, Alexandre, additional, Griffier, Romain, additional, Griffon, Nicolas, additional, Grisel, Olivier, additional, Guzzi, Pietro H., additional, Han, Larry, additional, Haverkamp, Christian, additional, Hazard, Derek Y., additional, He, Bing, additional, Henderson, Darren W., additional, Hilka, Martin, additional, Ho, Yuk-Lam, additional, Holmes, John H., additional, Honerlaw, Jacqueline P., additional, Hong, Chuan, additional, Huling, Kenneth M., additional, Hutch, Meghan R., additional, Jannot, Anne Sophie, additional, Jouhet, Vianney, additional, Kainth, Mundeep K., additional, Kate, Kernan F., additional, Kavuluru, Ramakanth, additional, Keller, Mark S., additional, Kennedy, Chris J., additional, Key, Daniel A., additional, Kirchoff, Katie, additional, Klann, Jeffrey G., additional, Kohane, Isaac S., additional, Krantz, Ian D., additional, Kraska, Detlef, additional, Krishnamurthy, Ashok K., additional, L'Yi, Sehi, additional, Leblanc, Judith, additional, Lemaitre, Guillaume, additional, Lenert, Leslie, additional, Leprovost, Damien, additional, Liu, Molei, additional, Will Loh, Ne Hooi, additional, Long, Qi, additional, Lozano-Zahonero, Sara, additional, Luo, Yuan, additional, Lynch, Kristine E., additional, Mahmood, Sadiqa, additional, Makoudjou, Adeline, additional, Malovini, Alberto, additional, Mao, Chengsheng, additional, Maram, Anupama, additional, Maripuri, Monika, additional, Martel, Patricia, additional, Martins, Marcelo R., additional, Marwaha, Jayson S., additional, Masino, Aaron J., additional, Mazzitelli, Maria, additional, Mazzotti, Diego R., additional, Mensch, Arthur, additional, Milano, Marianna, additional, Minicucci, Marcos F., additional, Moal, Bertrand, additional, Moore, Jason H., additional, Morris, Jeffrey S., additional, Mousavi, Sajad, additional, Mowery, Danielle L., additional, Murad, Douglas A., additional, Murphy, Shawn N., additional, Naughton, Thomas P., additional, Breda Neto, Carlos Tadeu, additional, Neuraz, Antoine, additional, Newburger, Jane, additional, Ngiam, Kee Yuan, additional, Njoroge, Wanjiku FM., additional, Norman, James B., additional, Obeid, Jihad, additional, Okoshi, Marina P., additional, Olson, Karen L., additional, Orlova, Nina, additional, Ostasiewski, Brian D., additional, Palmer, Nathan P., additional, Paris, Nicolas, additional, Patel, Lav P., additional, Pfaff, Ashley C., additional, Pfaff, Emily R., additional, Pillion, Danielle, additional, Pizzimenti, Sara, additional, Priya, Tanu, additional, Prokosch, Hans U., additional, Prudente, Robson A., additional, Prunotto, Andrea, additional, Quirós-González, Víctor, additional, Ramoni, Rachel B., additional, Raskin, Maryna, additional, Rieg, Siegbert, additional, Roig-Domínguez, Gustavo, additional, Rojo, Pablo, additional, Romero-Garcia, Nekane, additional, Rubio-Mayo, Paula, additional, Sacchi, Paolo, additional, Salamanca, Elisa, additional, Samayamuthu, Malarkodi Jebathilagam, additional, Sanchez-Pinto, L. Nelson, additional, Sandrin, Arnaud, additional, Santhanam, Nandhini, additional, Santos, Janaina C.C., additional, Sanz Vidorreta, Fernando J., additional, Savino, Maria, additional, Schriver, Emily R., additional, Schubert, Petra, additional, Schuettler, Juergen, additional, Scudeller, Luigia, additional, Sebire, Neil J., additional, Serrano-Balazote, Pablo, additional, Serre, Patricia, additional, Serret-Larmande, Arnaud, additional, Hossein Abad, Zahra Shakeri, additional, Silvio, Domenick, additional, Sliz, Piotr, additional, Son, Jiyeon, additional, Sonday, Charles, additional, Sperotto, Francesca, additional, Strasser, Zachary H., additional, Tan, Amelia LM., additional, Tan, Bryce W.Q., additional, Tan, Byorn W.L., additional, Tanni, Suzana E., additional, Terriza-Torres, Ana I., additional, Tibollo, Valentina, additional, Tippmann, Patric, additional, Toh, Emma MS., additional, Torti, Carlo, additional, Trecarichi, Enrico M., additional, Vallejos, Andrew K., additional, Varoquaux, Gael, additional, Vella, Margaret E., additional, Vie, Jill-Jênn, additional, Vitacca, Michele, additional, Wagholikar, Kavishwar B., additional, Waitman, Lemuel R., additional, Wassermann, Demian, additional, Weber, Griffin M., additional, Wolkewitz, Martin, additional, Wong, Scott, additional, Xiong, Xin, additional, Ye, Ye, additional, Yehya, Nadir, additional, Yuan, William, additional, Zahner, Janet J., additional, Zambelli, Alberto, additional, Zhang, Harrison G., additional, Zöller, Daniela, additional, Zuccaro, Valentina, additional, and Zucco, Chiara, additional

Published
2023
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37. What Every Reader Should Know About Studies Using Electronic Health Record Data but May Be Afraid to Ask

Author

Kohane, Isaac S, Aronow, Bruce J, Avillach, Paul, Beaulieu-Jones, Brett K, Bellazzi, Riccardo, Bradford, Robert L, Brat, Gabriel A, Cannataro, Mario, Cimino, James J, García-Barrio, Noelia, Gehlenborg, Nils, Ghassemi, Marzyeh, Gutiérrez-Sacristán, Alba, Hanauer, David A, Holmes, John H, Hong, Chuan, Klann, Jeffrey G, Loh, Ne Hooi Will, Luo, Yuan, Mandl, Kenneth D, Daniar, Mohamad, Moore, Jason H, Murphy, Shawn N, Neuraz, Antoine, Ngiam, Kee Yuan, Omenn, Gilbert S, Palmer, Nathan, Patel, Lav P, Pedrera-Jiménez, Miguel, Sliz, Piotr, South, Andrew M, Tan, Amelia Li Min, Taylor, Deanne M, Taylor, Bradley W, Torti, Carlo, Vallejos, Andrew K, Wagholikar, Kavishwar B, Weber, Griffin M, and Cai, Tianxi

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Public aspects of medicine, RA1-1270
Abstract

Coincident with the tsunami of COVID-19–related publications, there has been a surge of studies using real-world data, including those obtained from the electronic health record (EHR). Unfortunately, several of these high-profile publications were retracted because of concerns regarding the soundness and quality of the studies and the EHR data they purported to analyze. These retractions highlight that although a small community of EHR informatics experts can readily identify strengths and flaws in EHR-derived studies, many medical editorial teams and otherwise sophisticated medical readers lack the framework to fully critically appraise these studies. In addition, conventional statistical analyses cannot overcome the need for an understanding of the opportunities and limitations of EHR-derived studies. We distill here from the broader informatics literature six key considerations that are crucial for appraising studies utilizing EHR data: data completeness, data collection and handling (eg, transformation), data type (ie, codified, textual), robustness of methods against EHR variability (within and across institutions, countries, and time), transparency of data and analytic code, and the multidisciplinary approach. These considerations will inform researchers, clinicians, and other stakeholders as to the recommended best practices in reviewing manuscripts, grants, and other outputs from EHR-data derived studies, and thereby promote and foster rigor, quality, and reliability of this rapidly growing field.

Published
2021
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40. New and improved proteomics technologies for understanding complex biological systems: Addressing a grand challenge in the life sciences

Author

Hood, Leroy E, Omenn, Gilbert S, Moritz, Robert L, Aebersold, Ruedi, Yamamoto, Keith R, Amos, Michael, Hunter‐Cevera, Jennie, Locascio, Laurie, and Participants, Workshop

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Bioengineering, Biotechnology, Agriculture, Animals, Biological Science Disciplines, Computational Biology, Ecology, Genome, Human Genome Project, Humans, Mass Spectrometry, Protein Folding, Proteins, Proteomics, Research, Systems Biology, United States, Complex systems, Democratization of proteomics, Economic growth, Grand challenges, Integration, Systems biology, Workshop Participants, Information and Computing Sciences, Medical and Health Sciences, Biochemistry & Molecular Biology, Biological sciences, Biomedical and clinical sciences
Abstract

This White Paper sets out a Life Sciences Grand Challenge for Proteomics Technologies to enhance our understanding of complex biological systems, link genomes with phenotypes, and bring broad benefits to the biosciences and the US economy. The paper is based on a workshop hosted by the National Institute of Standards and Technology (NIST) in Gaithersburg, MD, 14-15 February 2011, with participants from many federal R&D agencies and research communities, under the aegis of the US National Science and Technology Council (NSTC). Opportunities are identified for a coordinated R&D effort to achieve major technology-based goals and address societal challenges in health, agriculture, nutrition, energy, environment, national security, and economic development.

Published
2012

41. Functional proteogenomics reveals biomarkers and therapeutic targets in lymphomas

Author

Rolland, Delphine C.M., Basrur, Venkatesha, Jeon, Yoon-Kyung, McNeil-Schwalm, Carla, Fermin, Damian, Conlon, Kevin P., Zhou, Yeqiao, Ng, Samuel Y., Tsou, Chih-Chiang, Brown, Noah A., Thomas, Dafydd G., Bailey, Nathanael G., Omenn, Gilbert S., Nesvizhskii, Alexey I., Root, David E., Weinstock, David M., Faryabi, Robert B., Lim, Megan S., and Elenitoba-Johnson, Kojo S. J.

Published
2017

42. Deep learning integrates histopathology and proteogenomics at a pan-cancer level

Author

Wang, Joshua M., primary, Hong, Runyu, additional, Demicco, Elizabeth G., additional, Tan, Jimin, additional, Lazcano, Rossana, additional, Moreira, Andre L., additional, Li, Yize, additional, Calinawan, Anna, additional, Razavian, Narges, additional, Schraink, Tobias, additional, Gillette, Michael A., additional, Omenn, Gilbert S., additional, An, Eunkyung, additional, Rodriguez, Henry, additional, Tsirigos, Aristotelis, additional, Ruggles, Kelly V., additional, Ding, Li, additional, Robles, Ana I., additional, Mani, D.R., additional, Rodland, Karin D., additional, Lazar, Alexander J., additional, Liu, Wenke, additional, Fenyö, David, additional, Aguet, François, additional, Akiyama, Yo, additional, Anand, Shankara, additional, Anurag, Meenakshi, additional, Babur, Özgün, additional, Bavarva, Jasmin, additional, Birger, Chet, additional, Birrer, Michael J., additional, Cantley, Lewis C., additional, Cao, Song, additional, Carr, Steven A., additional, Ceccarelli, Michele, additional, Chan, Daniel W., additional, Chinnaiyan, Arul M., additional, Cho, Hanbyul, additional, Chowdhury, Shrabanti, additional, Cieslik, Marcin P., additional, Clauser, Karl R., additional, Colaprico, Antonio, additional, Zhou, Daniel Cui, additional, da Veiga Leprevost, Felipe, additional, Day, Corbin, additional, Dhanasekaran, Saravana M., additional, Domagalski, Marcin J., additional, Dou, Yongchao, additional, Druker, Brian J., additional, Edwards, Nathan, additional, Ellis, Matthew J., additional, Selvan, Myvizhi Esai, additional, Foltz, Steven M., additional, Francis, Alicia, additional, Geffen, Yifat, additional, Getz, Gad, additional, Gonzalez Robles, Tania J., additional, Gosline, Sara J.C., additional, Gümüş, Zeynep H., additional, Heiman, David I., additional, Hiltke, Tara, additional, Hostetter, Galen, additional, Hu, Yingwei, additional, Huang, Chen, additional, Huntsman, Emily, additional, Iavarone, Antonio, additional, Jaehnig, Eric J., additional, Jewell, Scott D., additional, Ji, Jiayi, additional, Jiang, Wen, additional, Johnson, Jared L., additional, Katsnelson, Lizabeth, additional, Ketchum, Karen A., additional, Kolodziejczak, Iga, additional, Krug, Karsten, additional, Kumar-Sinha, Chandan, additional, Lei, Jonathan T., additional, Liang, Wen-Wei, additional, Liao, Yuxing, additional, Lindgren, Caleb M., additional, Liu, Tao, additional, Ma, Weiping, additional, Rodrigues, Fernanda Martins, additional, McKerrow, Wilson, additional, Mesri, Mehdi, additional, Nesvizhskii, Alexey I., additional, Newton, Chelsea J., additional, Oldroyd, Robert, additional, Paulovich, Amanda G., additional, Payne, Samuel H., additional, Petralia, Francesca, additional, Pugliese, Pietro, additional, Reva, Boris, additional, Rykunov, Dmitry, additional, Satpathy, Shankha, additional, Savage, Sara R., additional, Schadt, Eric E., additional, Schnaubelt, Michael, additional, Schürer, Stephan, additional, Shi, Zhiao, additional, Smith, Richard D., additional, Song, Xiaoyu, additional, Song, Yizhe, additional, Stathias, Vasileios, additional, Storrs, Erik P., additional, Terekhanova, Nadezhda V., additional, Thangudu, Ratna R., additional, Thiagarajan, Mathangi, additional, Tignor, Nicole, additional, Wang, Liang-Bo, additional, Wang, Pei, additional, Wang, Ying, additional, Wen, Bo, additional, Wiznerowicz, Maciej, additional, Wu, Yige, additional, Wyczalkowski, Matthew A., additional, Yao, Lijun, additional, Yaron, Tomer M., additional, Yi, Xinpei, additional, Zhang, Bing, additional, Zhang, Hui, additional, Zhang, Qing, additional, Zhang, Xu, additional, and Zhang, Zhen, additional

Published
2023
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43. Proteogenomic insights suggest druggable pathways in endometrial carcinoma

Author

Dou, Yongchao, primary, Katsnelson, Lizabeth, additional, Gritsenko, Marina A., additional, Hu, Yingwei, additional, Reva, Boris, additional, Hong, Runyu, additional, Wang, Yi-Ting, additional, Kolodziejczak, Iga, additional, Lu, Rita Jui-Hsien, additional, Tsai, Chia-Feng, additional, Bu, Wen, additional, Liu, Wenke, additional, Guo, Xiaofang, additional, An, Eunkyung, additional, Arend, Rebecca C., additional, Bavarva, Jasmin, additional, Chen, Lijun, additional, Chu, Rosalie K., additional, Czekański, Andrzej, additional, Davoli, Teresa, additional, Demicco, Elizabeth G., additional, DeLair, Deborah, additional, Devereaux, Kelly, additional, Dhanasekaran, Saravana M., additional, Dottino, Peter, additional, Dover, Bailee, additional, Fillmore, Thomas L., additional, Foxall, McKenzie, additional, Hermann, Catherine E., additional, Hiltke, Tara, additional, Hostetter, Galen, additional, Jędryka, Marcin, additional, Jewell, Scott D., additional, Johnson, Isabelle, additional, Kahn, Andrea G., additional, Ku, Amy T., additional, Kumar-Sinha, Chandan, additional, Kurzawa, Paweł, additional, Lazar, Alexander J., additional, Lazcano, Rossana, additional, Lei, Jonathan T., additional, Li, Yi, additional, Liao, Yuxing, additional, Lih, Tung-Shing M., additional, Lin, Tai-Tu, additional, Martignetti, John A., additional, Masand, Ramya P., additional, Matkowski, Rafał, additional, McKerrow, Wilson, additional, Mesri, Mehdi, additional, Monroe, Matthew E., additional, Moon, Jamie, additional, Moore, Ronald J., additional, Nestor, Michael D., additional, Newton, Chelsea, additional, Omelchenko, Tatiana, additional, Omenn, Gilbert S., additional, Payne, Samuel H., additional, Petyuk, Vladislav A., additional, Robles, Ana I., additional, Rodriguez, Henry, additional, Ruggles, Kelly V., additional, Rykunov, Dmitry, additional, Savage, Sara R., additional, Schepmoes, Athena A., additional, Shi, Tujin, additional, Shi, Zhiao, additional, Tan, Jimin, additional, Taylor, Mason, additional, Thiagarajan, Mathangi, additional, Wang, Joshua M., additional, Weitz, Karl K., additional, Wen, Bo, additional, Williams, C.M., additional, Wu, Yige, additional, Wyczalkowski, Matthew A., additional, Yi, Xinpei, additional, Zhang, Xu, additional, Zhao, Rui, additional, Mutch, David, additional, Chinnaiyan, Arul M., additional, Smith, Richard D., additional, Nesvizhskii, Alexey I., additional, Wang, Pei, additional, Wiznerowicz, Maciej, additional, Ding, Li, additional, Mani, D.R., additional, Zhang, Hui, additional, Anderson, Matthew L., additional, Rodland, Karin D., additional, Zhang, Bing, additional, Liu, Tao, additional, Fenyö, David, additional, Antczak, Andrzej, additional, Anurag, Meenakshi, additional, Bauer, Thomas, additional, Birger, Chet, additional, Birrer, Michael J., additional, Borucki, Melissa, additional, Cai, Shuang, additional, Calinawan, Anna, additional, Carr, Steven A., additional, Castro, Patricia, additional, Cerda, Sandra, additional, Chan, Daniel W., additional, Chesla, David, additional, Cieslik, Marcin P., additional, Cottingham, Sandra, additional, Dhir, Rajiv, additional, Domagalski, Marcin J., additional, Druker, Brian J., additional, Duffy, Elizabeth, additional, Edwards, Nathan J., additional, Edwards, Robert, additional, Ellis, Matthew J., additional, Eschbacher, Jennifer, additional, Fam, Mina, additional, Fevrier-Sullivan, Brenda, additional, Francis, Jesse, additional, Freymann, John, additional, Gabriel, Stacey, additional, Getz, Gad, additional, Gillette, Michael A., additional, Godwin, Andrew K., additional, Goldthwaite, Charles A., additional, Grady, Pamela, additional, Hafron, Jason, additional, Hariharan, Pushpa, additional, Hindenach, Barbara, additional, Hoadley, Katherine A., additional, Huang, Jasmine, additional, Ittmann, Michael M., additional, Johnson, Ashlie, additional, Jones, Corbin D., additional, Ketchum, Karen A., additional, Kirby, Justin, additional, Le, Toan, additional, Ma'ayan, Avi, additional, Madan, Rashna, additional, Mareedu, Sailaja, additional, McGarvey, Peter B., additional, Modugno, Francesmary, additional, Montgomery, Rebecca, additional, Nyce, Kristen, additional, Paulovich, Amanda G., additional, Pruetz, Barbara L., additional, Qi, Liqun, additional, Richey, Shannon, additional, Schadt, Eric E., additional, Shutack, Yvonne, additional, Singh, Shilpi, additional, Smith, Michael, additional, Tansil, Darlene, additional, Thangudu, Ratna R., additional, Tobin, Matt, additional, Um, Ki Sung, additional, Vatanian, Negin, additional, Webster, Alex, additional, Wilson, George D., additional, Wright, Jason, additional, Zaalishvili, Kakhaber, additional, Zhang, Zhen, additional, and Zhao, Grace, additional

Published
2023
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44. Pan-cancer proteogenomics connects oncogenic drivers to functional states

Author

Li, Yize, primary, Porta-Pardo, Eduard, additional, Tokheim, Collin, additional, Bailey, Matthew H., additional, Yaron, Tomer M., additional, Stathias, Vasileios, additional, Geffen, Yifat, additional, Imbach, Kathleen J., additional, Cao, Song, additional, Anand, Shankara, additional, Akiyama, Yo, additional, Liu, Wenke, additional, Wyczalkowski, Matthew A., additional, Song, Yizhe, additional, Storrs, Erik P., additional, Wendl, Michael C., additional, Zhang, Wubing, additional, Sibai, Mustafa, additional, Ruiz-Serra, Victoria, additional, Liang, Wen-Wei, additional, Terekhanova, Nadezhda V., additional, Rodrigues, Fernanda Martins, additional, Clauser, Karl R., additional, Heiman, David I., additional, Zhang, Qing, additional, Aguet, Francois, additional, Calinawan, Anna P., additional, Dhanasekaran, Saravana M., additional, Birger, Chet, additional, Satpathy, Shankha, additional, Zhou, Daniel Cui, additional, Wang, Liang-Bo, additional, Baral, Jessika, additional, Johnson, Jared L., additional, Huntsman, Emily M., additional, Pugliese, Pietro, additional, Colaprico, Antonio, additional, Iavarone, Antonio, additional, Chheda, Milan G., additional, Ricketts, Christopher J., additional, Fenyö, David, additional, Payne, Samuel H., additional, Rodriguez, Henry, additional, Robles, Ana I., additional, Gillette, Michael A., additional, Kumar-Sinha, Chandan, additional, Lazar, Alexander J., additional, Cantley, Lewis C., additional, Getz, Gad, additional, Ding, Li, additional, An, Eunkyung, additional, Anurag, Meenakshi, additional, Bavarva, Jasmin, additional, Birrer, Michael J., additional, Calinawan, Anna, additional, Ceccarelli, Michele, additional, Chan, Daniel W., additional, Chinnaiyan, Arul M., additional, Cho, Hanbyul, additional, Chowdhury, Shrabanti, additional, Cieslik, Marcin P., additional, da Veiga Leprevost, Felipe, additional, Day, Corbin, additional, Domagalski, Marcin J., additional, Dou, Yongchao, additional, Druker, Brian J., additional, Edwards, Nathan, additional, Ellis, Matthew J., additional, Selvan, Myvizhi Esai, additional, Foltz, Steven M., additional, Francis, Alicia, additional, Gonzalez Robles, Tania J., additional, Gosline, Sara J.C., additional, Gümüş, Zeynep H., additional, Hiltke, Tara, additional, Hong, Runyu, additional, Hostetter, Galen, additional, Hu, Yingwei, additional, Huang, Chen, additional, Huntsman, Emily, additional, Jaehnig, Eric J., additional, Jewel, Scott D., additional, Ji, Jiayi, additional, Jiang, Wen, additional, Katsnelson, Lizabeth, additional, Ketchum, Karen A., additional, Kolodziejczak, Iga, additional, Lei, Jonathan T., additional, Liao, Yuxing, additional, Lindgren, Caleb M., additional, Liu, Tao, additional, Ma, Weiping, additional, McKerrow, Wilson, additional, Nesvizhskii, Alexey I., additional, Newton, Chelsea, additional, Oldroyd, Robert, additional, Omenn, Gilbert S., additional, Paulovich, Amanda G., additional, Petralia, Francesca, additional, Reva, Boris, additional, Rodland, Karin D., additional, Ruggles, Kelly V., additional, Rykunov, Dmitry, additional, Savage, Sara R., additional, Schadt, Eric E., additional, Schnaubelt, Michael, additional, Schraink, Tobias, additional, Shi, Zhiao, additional, Smith, Richard D., additional, Song, Xiaoyu, additional, Tan, Jimin, additional, Thangudu, Ratna R., additional, Tignor, Nicole, additional, Wang, Joshua M., additional, Wang, Pei, additional, Wang, Ying (Cindy), additional, Wen, Bo, additional, Wiznerowicz, Maciej, additional, Yi, Xinpei, additional, Zhang, Bing, additional, Zhang, Hui, additional, Zhang, Xu, additional, and Zhang, Zhen, additional

Published
2023
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45. Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation

Author

Geffen, Yifat, primary, Anand, Shankara, additional, Akiyama, Yo, additional, Yaron, Tomer M., additional, Song, Yizhe, additional, Johnson, Jared L., additional, Govindan, Akshay, additional, Babur, Özgün, additional, Li, Yize, additional, Huntsman, Emily, additional, Wang, Liang-Bo, additional, Birger, Chet, additional, Heiman, David I., additional, Zhang, Qing, additional, Miller, Mendy, additional, Maruvka, Yosef E., additional, Haradhvala, Nicholas J., additional, Calinawan, Anna, additional, Belkin, Saveliy, additional, Kerelsky, Alexander, additional, Clauser, Karl R., additional, Krug, Karsten, additional, Satpathy, Shankha, additional, Payne, Samuel H., additional, Mani, D.R., additional, Gillette, Michael A., additional, Dhanasekaran, Saravana M., additional, Thiagarajan, Mathangi, additional, Mesri, Mehdi, additional, Rodriguez, Henry, additional, Robles, Ana I., additional, Carr, Steven A., additional, Lazar, Alexander J., additional, Aguet, François, additional, Cantley, Lewis C., additional, Ding, Li, additional, Getz, Gad, additional, An, Eunkyung, additional, Anurag, Meenakshi, additional, Bavarva, Jasmin, additional, Birrer, Michael J., additional, Cao, Song, additional, Ceccarelli, Michele, additional, Chan, Daniel W., additional, Chinnaiyan, Arul M., additional, Cho, Hanbyul, additional, Chowdhury, Shrabanti, additional, Cieslik, Marcin P., additional, Colaprico, Antonio, additional, Zhou, Daniel Cui, additional, da Veiga Leprevost, Felipe, additional, Day, Corbin, additional, Domagalski, Marcin J., additional, Dou, Yongchao, additional, Druker, Brian J., additional, Edwards, Nathan, additional, Ellis, Matthew J., additional, Selvan, Myvizhi Esai, additional, Fenyo, David, additional, Foltz, Steven M., additional, Francis, Alicia, additional, Gonzalez Robles, Tania J., additional, Gosline, Sara J.C., additional, Gümüş, Zeynep H., additional, Hiltke, Tara, additional, Hong, Runyu, additional, Hostetter, Galen, additional, Hu, Yingwei, additional, Huang, Chen, additional, Iavarone, Antonio, additional, Jaehnig, Eric J., additional, Jewel, Scott D., additional, Ji, Jiayi, additional, Jiang, Wen, additional, Katsnelson, Lizabeth, additional, Ketchum, Karen A., additional, Kolodziejczak, Iga, additional, Kumar-Sinha, Chandan, additional, Lei, Jonathan T., additional, Liang, Wen-Wei, additional, Liao, Yuxing, additional, Lindgren, Caleb M., additional, Liu, Tao, additional, Liu, Wenke, additional, Ma, Weiping, additional, Rodrigues, Fernanda Martins, additional, McKerrow, Wilson, additional, Nesvizhskii, Alexey I., additional, Newton, Chelsea, additional, Oldroyd, Robert, additional, Omenn, Gilbert S., additional, Paulovich, Amanda G., additional, Petralia, Francesca, additional, Pugliese, Pietro, additional, Reva, Boris, additional, Rodland, Karin D., additional, Ruggles, Kelly V., additional, Rykunov, Dmitry, additional, Savage, Sara R., additional, Schadt, Eric E., additional, Schnaubelt, Michael, additional, Schraink, Tobias, additional, Shi, Zhiao, additional, Smith, Richard D., additional, Song, Xiaoyu, additional, Stathias, Vasileios, additional, Storrs, Erik P., additional, Tan, Jimin, additional, Terekhanova, Nadezhda V., additional, Thangudu, Ratna R., additional, Tignor, Nicole, additional, Wang, Joshua M., additional, Wang, Pei, additional, Wang, Ying (Cindy), additional, Wen, Bo, additional, Wiznerowicz, Maciej, additional, Wu, Yige, additional, Wyczalkowski, Matthew A., additional, Yao, Lijun, additional, Yi, Xinpei, additional, Zhang, Bing, additional, Zhang, Hui, additional, Zhang, Xu, additional, and Zhang, Zhen, additional

Published
2023
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46. Proteogenomic data and resources for pan-cancer analysis

Author

Li, Yize, primary, Dou, Yongchao, additional, Da Veiga Leprevost, Felipe, additional, Geffen, Yifat, additional, Calinawan, Anna P., additional, Aguet, François, additional, Akiyama, Yo, additional, Anand, Shankara, additional, Birger, Chet, additional, Cao, Song, additional, Chaudhary, Rekha, additional, Chilappagari, Padmini, additional, Cieslik, Marcin, additional, Colaprico, Antonio, additional, Zhou, Daniel Cui, additional, Day, Corbin, additional, Domagalski, Marcin J., additional, Esai Selvan, Myvizhi, additional, Fenyö, David, additional, Foltz, Steven M., additional, Francis, Alicia, additional, Gonzalez-Robles, Tania, additional, Gümüş, Zeynep H., additional, Heiman, David, additional, Holck, Michael, additional, Hong, Runyu, additional, Hu, Yingwei, additional, Jaehnig, Eric J., additional, Ji, Jiayi, additional, Jiang, Wen, additional, Katsnelson, Lizabeth, additional, Ketchum, Karen A., additional, Klein, Robert J., additional, Lei, Jonathan T., additional, Liang, Wen-Wei, additional, Liao, Yuxing, additional, Lindgren, Caleb M., additional, Ma, Weiping, additional, Ma, Lei, additional, MacCoss, Michael J., additional, Martins Rodrigues, Fernanda, additional, McKerrow, Wilson, additional, Nguyen, Ngoc, additional, Oldroyd, Robert, additional, Pilozzi, Alexander, additional, Pugliese, Pietro, additional, Reva, Boris, additional, Rudnick, Paul, additional, Ruggles, Kelly V., additional, Rykunov, Dmitry, additional, Savage, Sara R., additional, Schnaubelt, Michael, additional, Schraink, Tobias, additional, Shi, Zhiao, additional, Singhal, Deepak, additional, Song, Xiaoyu, additional, Storrs, Erik, additional, Terekhanova, Nadezhda V., additional, Thangudu, Ratna R., additional, Thiagarajan, Mathangi, additional, Wang, Liang-Bo, additional, Wang, Joshua M., additional, Wang, Ying, additional, Wen, Bo, additional, Wu, Yige, additional, Wyczalkowski, Matthew A., additional, Xin, Yi, additional, Yao, Lijun, additional, Yi, Xinpei, additional, Zhang, Hui, additional, Zhang, Qing, additional, Zuhl, Maya, additional, Getz, Gad, additional, Ding, Li, additional, Nesvizhskii, Alexey I., additional, Wang, Pei, additional, Robles, Ana I., additional, Zhang, Bing, additional, Payne, Samuel H., additional, Lazar, Alexander J., additional, Paulovich, Amanda G., additional, Iavarone, Antonio, additional, Chinnaiyan, Arul M., additional, Druker, Brian J., additional, Kumar-Sinha, Chandan, additional, Newton, Chelsea J., additional, Huang, Chen, additional, Mani, D.R., additional, Smith, Richard D., additional, Huntsman, Emily, additional, Schadt, Eric E., additional, An, Eunkyung, additional, Petralia, Francesca, additional, Hostetter, Galen, additional, Omenn, Gilbert S., additional, Cho, Hanbyul, additional, Rodriguez, Henry, additional, Kolodziejczak, Iga, additional, Johnson, Jared L., additional, Bavarva, Jasmin, additional, Tan, Jimin, additional, Rodland, Karin D., additional, Clauser, Karl R., additional, Krug, Karsten, additional, Cantley, Lewis C., additional, Wiznerowicz, Maciej, additional, Ellis, Matthew J., additional, Anurag, Meenakshi, additional, Mesri, Mehdi, additional, Gillette, Michael A., additional, Birrer, Michael J., additional, Ceccarelli, Michele, additional, Dhanasekaran, Saravana M., additional, Edwards, Nathan, additional, Tignor, Nicole, additional, Babur, Özgün, additional, Gosline, Sara J.C., additional, Jewell, Scott D., additional, Satpathy, Shankha, additional, Chowdhury, Shrabanti, additional, Schürer, Stephan, additional, Carr, Steven A., additional, Liu, Tao, additional, Hiltke, Tara, additional, Yaron, Tomer M., additional, Stathias, Vasileios, additional, Liu, Wenke, additional, Zhang, Xu, additional, Song, Yizhe, additional, and Zhang, Zhen, additional

Published
2023
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48. A high-stringency blueprint of the human proteome

Author

Adhikari, Subash, Nice, Edouard C., Deutsch, Eric W., Lane, Lydie, Omenn, Gilbert S., Pennington, Stephen R., Paik, Young-Ki, Overall, Christopher M., Corrales, Fernando J., Cristea, Ileana M., Van Eyk, Jennifer E., Uhlén, Mathias, Lindskog, Cecilia, Chan, Daniel W., Bairoch, Amos, Waddington, James C., Justice, Joshua L., LaBaer, Joshua, Rodriguez, Henry, He, Fuchu, Kostrzewa, Markus, Ping, Peipei, Gundry, Rebekah L., Stewart, Peter, Srivastava, Sanjeeva, Srivastava, Sudhir, Nogueira, Fabio C. S., Domont, Gilberto B., Vandenbrouck, Yves, Lam, Maggie P. Y., Wennersten, Sara, Vizcaino, Juan Antonio, Wilkins, Marc, Schwenk, Jochen M., Lundberg, Emma, Bandeira, Nuno, Marko-Varga, Gyorgy, Weintraub, Susan T., Pineau, Charles, Kusebauch, Ulrike, Moritz, Robert L., Ahn, Seong Beom, Palmblad, Magnus, Snyder, Michael P., Aebersold, Ruedi, and Baker, Mark S.

Published
2020
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