Analyzing historical diagnosis code data from NIH N3C and RECOVER Programs using deep learning to determine risk factors for Long Covid

Authors: Sengupta, Saurav, Loomba, Johanna, Sharma, Suchetha, Brown, Donald E., Thorpe, Lorna, Haendel, Melissa A, Chute, Christopher G, Hong, Stephanie

Source: 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Bioinformatics and Biomedicine (BIBM), 2022 IEEE International Conference on. :2797-2802 Dec, 2022

Relation: 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

A Simple Standard for Sharing Ontological Mappings (SSSOM)

Authors: Matentzoglu, Nicolas, Balhoff, James P., Bello, Susan M., Bizon, Chris, Brush, Matthew, Callahan, Tiffany J., Chute, Christopher G, Duncan, William D., Evelo, Chris T., Gabriel, Davera, Graybeal, John, Gray, Alasdair, Gyori, Benjamin M., Haendel, Melissa, Harmse, Henriette, Harris, Nomi L., Harrow, Ian, Hegde, Harshad, Hoyt, Amelia L., Hoyt, Charles T., Jiao, Dazhi, Jiménez-Ruiz, Ernesto, Jupp, Simon, Kim, Hyeongsik, Koehler, Sebastian, Liener, Thomas, Long, Qinqin, Malone, James, McLaughlin, James A., McMurry, Julie A., Moxon, Sierra, Munoz-Torres, Monica C., Osumi-Sutherland, David, Overton, James A., Peters, Bjoern, Putman, Tim, Queralt-Rosinach, Núria, Shefchek, Kent, Solbrig, Harold, Thessen, Anne, Tudorache, Tania, Vasilevsky, Nicole, Wagner, Alex H., Mungall, Christopher J.

Subject Terms: Computer Science - Databases

Access URL: http://arxiv.org/abs/2112.07051

An Open Natural Language Processing Development Framework for EHR-based Clinical Research: A case demonstration using the National COVID Cohort Collaborative (N3C)

Authors: Liu, Sijia, Wen, Andrew, Wang, Liwei, He, Huan, Fu, Sunyang, Miller, Robert, Williams, Andrew, Harris, Daniel, Kavuluru, Ramakanth, Liu, Mei, Abu-el-rub, Noor, Schutte, Dalton, Zhang, Rui, Rouhizadeh, Masoud, Osborne, John D., He, Yongqun, Topaloglu, Umit, Hong, Stephanie S, Saltz, Joel H, Schaffter, Thomas, Pfaff, Emily, Chute, Christopher G., Duong, Tim, Haendel, Melissa A., Fuentes, Rafael, Szolovits, Peter, Xu, Hua, Liu, Hongfang, Collaborative, National COVID Cohort, Processing, Natural Language, Subgroup

Subject Terms: Computer Science - Computation and Language, Computer Science - Information Retrieval

Access URL: http://arxiv.org/abs/2110.10780

Characterizing Design Patterns of EHR-Driven Phenotype Extraction Algorithms

Authors: Zhong, Yizhen, Rasmussen, Luke, Deng, Yu, Pacheco, Jennifer, Smith, Maureen, Starren, Justin, Wei, Wei-Qi, Speltz, Peter, Denny, Joshua, Walton, Nephi, Hripcsak, George, Chute, Christopher G, Luo, Yuan

Source: 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Bioinformatics and Biomedicine (BIBM), 2018 IEEE International Conference on. :1143-1146 Dec, 2018

Relation: 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

The Science of Precision Prevention: Research Opportunities and Clinical Applications to Reduce Cardiovascular Health Disparities

Authors: Pearson, Thomas A., Vitalis, Debbie, Pratt, Charlotte, Campo, Rebecca, Armoundas, Antonis A., Au, David, Beech, Bettina, Brazhnik, Olga, Chute, Christopher G., Davidson, Karina W., Diez-Roux, Ana V., Fine, Lawrence J., Gabriel, Davera, Groenveld, Peter, Hall, Jaclyn, Hamilton, Alison B., Hu, Hui, Ji, Heng, Kind, Amy, Kraus, William E., Krumholz, Harlan, Mensah, George A., Merchant, Raina M., Mozaffarian, Dariush, Murray, David M., Neumark-Sztainer, Dianne, Petersen, Maya, Goff, David

Source: In JACC: Advances January 2024 3(1)

COVID-19 outcomes in persons with hemophilia: results from a US-based national COVID-19 surveillance registry

Authors: Wilcox, Adam B., Lee, Adam M., Graves, Alexis, Anzalone, Alfred (Jerrod), Manna, Amin, Saha, Amit, Olex, Amy, Zhou, Andrea, Williams, Andrew E., Southerland, Andrew, Girvin, Andrew T., Walden, Anita, Sharathkumar, Anjali A., Amor, Benjamin, Bates, Benjamin, Hendricks, Brian, Patel, Brijesh, Alexander, Caleb, Bramante, Carolyn, Ward-Caviness, Cavin, Madlock-Brown, Charisse, Suver, Christine, Chute, Christopher, Dillon, Christopher, Wu, Chunlei, Schmitt, Clare, Takemoto, Cliff, Housman, Dan, Gabriel, Davera, Eichmann, David A., Mazzotti, Diego, Brown, Don, Boudreau, Eilis, Hill, Elaine, Zampino, Elizabeth, Marti, Emily Carlson, Pfaff, Emily R., French, Evan, Koraishy, Farrukh M., Mariona, Federico, Prior, Fred, Sokos, George, Martin, Greg, Lehmann, Harold, Spratt, Heidi, Mehta, Hemalkumar, Liu, Hongfang, Sidky, Hythem, Hayanga, J. W. Awori, Pincavitch, Jami, Clark, Jaylyn, Harper, Jeremy Richard, Islam, Jessica, Ge, Jin, Gagnier, Joel, Saltz, Joel H., Saltz, Joel, Loomba, Johanna, Buse, John, Mathew, Jomol, Rutter, Joni L., McMurry, Julie A., Guinney, Justin, Starren, Justin, Crowley, Karen, Bradwell, Katie Rebecca, Walters, Kellie M., Wilkins, Ken, Gersing, Kenneth R., Cato, Kenrick Dwain, Murray, Kimberly, Kostka, Kristin, Northington, Lavance, Pyles, Lee Allan, Misquitta, Leonie, Cottrell, Lesley, Portilla, Lili, Deacy, Mariam, Bissell, Mark M., Clark, Marshall, Emmett, Mary, Saltz, Mary Morrison, Palchuk, Matvey B., Haendel, Melissa A., Adams, Meredith, Temple-O’Connor, Meredith, Kurilla, Michael G., Morris, Michele, Qureshi, Nabeel, Safdar, Nasia, Garbarini, Nicole, Sharafeldin, Noha, Sadan, Ofer, Francis, Patricia A., Burgoon, Penny Wung, Robinson, Peter, Payne, Philip R.O., Fuentes, Rafael, Jawa, Randeep, Erwin-Cohen, Rebecca, Patel, Rena, Moffitt, Richard A., Zhu, Richard L., Kamaleswaran, Rishi, Hurley, Robert, Miller, Robert T., Pyarajan, Saiju, Michael, Sam G., Bozzette, Samuel, Mallipattu, Sandeep, Vedula, Satyanarayana, Chapman, Scott, O’Neil, Shawn T., Setoguchi, Soko, Hong, Stephanie S., Johnson, Steve, Bennett, Tellen D., Callahan, Tiffany, Topaloglu, Umit, Sheikh, Usman, Gordon, Valery, Subbian, Vignesh, Kibbe, Warren A., Hernandez, Wenndy, Beasley, Will, Cooper, Will, Hillegass, William, Zhang, Xiaohan Tanner, Sharathkumar, Anjali, Wendt, Linder, Ortman, Chris, Srinivasan, Ragha, Chute, Christopher G., Chrischilles, Elizabeth, Takemoto, Clifford M.

Source: In Journal of Thrombosis and Haemostasis January 2024 22(1):61-75

Outcomes of SARS-CoV-2 infection among patients with orthopaedic fracture surgery in the National COVID Cohort Collaborative (N3C)

Authors: Levitt, Eli B., Patch, David A., Hess, Matthew C., Terrero, Alfredo, Jaeger, Byron, Haendel, Melissa A., Chute, Christopher G., Yeager, Matthew T., Ponce, Brent A., Theiss, Steven M., Spitler, Clay A., Johnson, Joey P.

Source: In Injury December 2023 54(12)

Linking The Cancer Imaging Archive and GenBank to the National Clinical Cohort Collaborative.

Authors: Baghal, Ahmad¹, abaghal@uams.edu, Saltz, Joel², Kurc, Tahsin², Prasanna, Prateek², Baghal, Samantha³, Hajagos, Janos², Bremer, Erich², Al‐Shukri, Shaymaa¹, Kennedy, Joshua L.⁴, Rutherford, Michael¹, Nolan, Tracy¹, Smith, Kirk¹, Chute, Christopher G.⁵, Prior, Fred¹

Source: Learning Health Systems; Jan2025, Vol. 9 Issue 1, p1-7, 7p

Risk of severe acute respiratory syndrome coronavirus 2 infection among women with polycystic ovary syndrome

Authors: Haendel, Melissa A., Chute, Christopher G., Walden, Anita, Gersing, Kenneth R., Misquitta, Leonie, Burgoon, Penny Wung, Bozzette, Samuel, Deacy, Mariam, Dillon, Christopher, Erwin-Cohen, Rebecca, Garbarini, Nicole, Gordon, Valery, Kurilla, Michael G., Marti, Emily Carlson, Michael, Sam G., Portilla, Lili, Schmitt, Clare, Temple-O'Connor, Meredith, Bennett, Tellen D., Eichmann, David A., Guinney, Justin, Kibbe, Warren A., Liu, Hongfang, Payne, Philip R.O., Pfaff, Emily R., Robinson, Peter N., Saltz, Joel H., Spratt, Heidi, Starren, Justin, Suver, Christine, Wilcox, Adam B., Williams, Andrew E., Wu, Chunlei, Gabriel, Davera, Hong, Stephanie S., Kostka, Kristin, Lehmann, Harold P., Moffitt, Richard A., Morris, Michele, Palchuk, Matvey B., Zhang, Xiaohan Tanner, Zhu, Richard L., Clark, Marshall, Girvin, Andrew T., Lee, Adam M., Miller, Robert T., Walters, Kellie M., Cooper, Will, Francis, Patricia A., Fuentes, Rafael, Graves, Alexis, McMurry, Julie A., Neumann, Andrew J., O'Neil, Shawn T., Sheikh, Usman, Zampino, Elizabeth, Bissell, Mark M., Bradwell, Katie Rebecca, Manna, Amin, Qureshi, Nabeel, Saltz, Mary Morrison, Volz, Andréa M., Bramante, Carolyn, Harper, Jeremy Richard, Hernandez, Wenndy, Koraishy, Farrukh M., Mariona, Federico, Saha, Amit, Vedula, Satyanarayana, Alur-Gupta, Snigdha, Boland, Mary Regina, Dokras, Anuja

Source: In Fertility and Sterility May 2023 119(5):847-857

Generalisable long COVID subtypes: findings from the NIH N3C and RECOVER programmes

Authors: Spratt, Heidi, Visweswaran, Shyam, Flack, Joseph Eugene, IV, Yoo, Yun Jae, Gabriel, Davera, Alexander, G. Caleb, Mehta, Hemalkumar B., Liu, Feifan, Miller, Robert T., Wong, Rachel, Hill, Elaine L., Thorpe, Lorna E., Divers, Jasmin, Reese, Justin T., Blau, Hannah, Casiraghi, Elena, Bergquist, Timothy, Loomba, Johanna J., Callahan, Tiffany J., Laraway, Bryan, Antonescu, Corneliu, Coleman, Ben, Gargano, Michael, Wilkins, Kenneth J., Cappelletti, Luca, Fontana, Tommaso, Ammar, Nariman, Antony, Blessy, Murali, T.M., Caufield, J. Harry, Karlebach, Guy, McMurry, Julie A., Williams, Andrew, Moffitt, Richard, Banerjee, Jineta, Solomonides, Anthony E., Davis, Hannah, Kostka, Kristin, Valentini, Giorgio, Sahner, David, Chute, Christopher G., Madlock-Brown, Charisse, Haendel, Melissa A., Robinson, Peter N.

Source: In eBioMedicine January 2023 87

Genetic testing knowledge base (GTKB) towards individualized genetic test recommendation — An experimental study

Authors: Zhu, Qian, Liu, Hongfang, Chute, Christopher G., Ferber, Matthew

Source: 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Bioinformatics and Biomedicine (BIBM), 2014 IEEE International Conference on. :574-577 Nov, 2014

Relation: 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

Using semantic web technologies for quality measure phenotyping algorithm representation and automatic execution on EHR data

Authors: Shen, Feichen, Li, Dingcheng, Liu, Hongfang, Lee, Yugyung, Pathak, Jyotishman, Chute, Christopher G, Tao, Cui

Source: IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI) Biomedical and Health Informatics (BHI), 2014 IEEE-EMBS International Conference on. :531-534 Jun, 2014

Relation: 2014 IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI)

FHIR-Ontop-OMOP: Building clinical knowledge graphs in FHIR RDF with the OMOP Common data Model

Authors: Xiao, Guohui, Pfaff, Emily, Prud'hommeaux, Eric, Booth, David, Sharma, Deepak K., Huo, Nan, Yu, Yue, Zong, Nansu, Ruddy, Kathryn J., Chute, Christopher G., Jiang, Guoqian

Source: In Journal of Biomedical Informatics October 2022 134

Identifying who has long COVID in the USA: a machine learning approach using N3C data

Authors: Bramante, Carolyn, Dorr, David, Morris, Michele, Parker, Ann M, Sidky, Hythem, Gersing, Ken, Hong, Stephanie, Niehaus, Emily, Pfaff, Emily R ^{*, *}, Girvin, Andrew T ^*, Bennett, Tellen D, Bhatia, Abhishek, Brooks, Ian M, Deer, Rachel R, Dekermanjian, Jonathan P, Jolley, Sarah Elizabeth, Kahn, Michael G, Kostka, Kristin, McMurry, Julie A, Moffitt, Richard, Walden, Anita, Chute, Christopher G, Haendel, Melissa A

Source: In The Lancet Digital Health July 2022 4(7):e532-e541

Mining drug-drug interaction patterns from linked data: A case study for Warfarin, Clopidogrel, and Simvastatin

Authors: Pathak, Jyotishman, Kiefer, Richard C., Chute, Christopher G.

Source: 2013 IEEE International Conference on Bioinformatics and Biomedicine Bioinformatics and Biomedicine (BIBM), 2013 IEEE International Conference on. :23-30 Dec, 2013

Relation: 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

Developing an ETL tool for converting the PCORnet CDM into the OMOP CDM to facilitate the COVID-19 data integration

Authors: Yu, Yue, Zong, Nansu, Wen, Andrew, Liu, Sijia, Stone, Daniel J., Knaack, David, Chamberlain, Alanna M., Pfaff, Emily, Gabriel, Davera, Chute, Christopher G., Shah, Nilay, Jiang, Guoqian

Source: In Journal of Biomedical Informatics March 2022 127

Long-term use of immunosuppressive medicines and in-hospital COVID-19 outcomes: a retrospective cohort study using data from the National COVID Cohort Collaborative

Authors: Haendel, Melissa A, Chute, Christopher G, Andersen, Kathleen M, Bates, Benjamin A, Rashidi, Emaan S, Olex, Amy L, Mannon, Roslyn B, Patel, Rena C, Singh, Jasvinder, Sun, Jing, Auwaerter, Paul G, Ng, Derek K, Segal, Jodi B, Garibaldi, Brian T, Mehta, Hemalkumar B, Alexander, G Caleb ^*

Source: In The Lancet Rheumatology January 2022 4(1):e33-e41

Characterizing Long COVID: Deep Phenotype of a Complex Condition

Authors: Deer, Rachel R, Rock, Madeline A, Vasilevsky, Nicole, Carmody, Leigh, Rando, Halie, Anzalone, Alfred J, Basson, Marc D, Bennett, Tellen D, Bergquist, Timothy, Boudreau, Eilis A, Bramante, Carolyn T, Byrd, James Brian, Callahan, Tiffany J, Chan, Lauren E, Chu, Haitao, Chute, Christopher G, Coleman, Ben D, Davis, Hannah E, Gagnier, Joel, Greene, Casey S, Hillegass, William B, Kavuluru, Ramakanth, Kimble, Wesley D, Koraishy, Farrukh M, Köhler, Sebastian, Liang, Chen, Liu, Feifan, Liu, Hongfang, Madhira, Vithal, Madlock-Brown, Charisse R, Matentzoglu, Nicolas, Mazzotti, Diego R, McMurry, Julie A, McNair, Douglas S, Moffitt, Richard A, Monteith, Teshamae S, Parker, Ann M, Perry, Mallory A, Pfaff, Emily, Reese, Justin T, Saltz, Joel, Schuff, Robert A, Solomonides, Anthony E, Solway, Julian, Spratt, Heidi, Stein, Gary S, Sule, Anupam A, Topaloglu, Umit, Vavougios, George D., Wang, Liwei, Haendel, Melissa A, Robinson, Peter N

Source: In eBioMedicine December 2021 74

Associations between HIV infection and clinical spectrum of COVID-19: a population level analysis based on US National COVID Cohort Collaborative (N3C) data

Authors: Moffitt, Richard, Akelsrod, Hana, Crandall, Keith A, Francheschini, Nora, French, Evan, Po-Yu Chiang, Teresa, Caleb-Alexander, G, Andersen, Kathleen M, Vinson, Amanda J, Brown, Todd T, Mannon, Roslyn B, Yang, Xueying ^*, Sun, Jing, Patel, Rena C, Zhang, Jiajia, Guo, Siyuan, Zheng, Qulu, Olex, Amy L, Olatosi, Bankole, Weissman, Sharon B, Islam, Jessica Y, Chute, Christopher G, Haendel, Melissa, Kirk, Gregory D, Li, Xiaoming

Source: In The Lancet HIV November 2021 8(11):e690-e700

Outcomes of SARS-CoV-2 Infection in Patients With Chronic Liver Disease and Cirrhosis: A National COVID Cohort Collaborative Study

Authors: Harper, Jeremy R., Chute, Christopher G., Haendel, Melissa A., Ge, Jin, Pletcher, Mark J., Lai, Jennifer C.

Source: In Gastroenterology November 2021 161(5):1487-1501