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1,756 results on '"Ananthakrishnan, A. N."'

3. Reverse metabolomics for the discovery of chemical structures from humans

Author

Gentry, Emily C, Collins, Stephanie L, Panitchpakdi, Morgan, Belda-Ferre, Pedro, Stewart, Allison K, Carrillo Terrazas, Marvic, Lu, Hsueh-han, Zuffa, Simone, Yan, Tingting, Avila-Pacheco, Julian, Plichta, Damian R, Aron, Allegra T, Wang, Mingxun, Jarmusch, Alan K, Hao, Fuhua, Syrkin-Nikolau, Mashette, Vlamakis, Hera, Ananthakrishnan, Ashwin N, Boland, Brigid S, Hemperly, Amy, Vande Casteele, Niels, Gonzalez, Frank J, Clish, Clary B, Xavier, Ramnik J, Chu, Hiutung, Baker, Erin S, Patterson, Andrew D, Knight, Rob, Siegel, Dionicio, and Dorrestein, Pieter C

Subjects
Medical Biochemistry and Metabolomics, Analytical Chemistry, Biomedical and Clinical Sciences, Chemical Sciences, Inflammatory Bowel Disease, Digestive Diseases, Crohn's Disease, Autoimmune Disease, Animals, Humans, Bifidobacterium, Bile Acids and Salts, CD4-Positive T-Lymphocytes, Clostridium, Cohort Studies, Crohn Disease, Enterococcus, Esters, Fatty Acids, Inflammatory Bowel Diseases, Metabolomics, Phenotype, Pregnane X Receptor, Reproducibility of Results, Tandem Mass Spectrometry, Amides, General Science & Technology
Abstract

Determining the structure and phenotypic context of molecules detected in untargeted metabolomics experiments remains challenging. Here we present reverse metabolomics as a discovery strategy, whereby tandem mass spectrometry spectra acquired from newly synthesized compounds are searched for in public metabolomics datasets to uncover phenotypic associations. To demonstrate the concept, we broadly synthesized and explored multiple classes of metabolites in humans, including N-acyl amides, fatty acid esters of hydroxy fatty acids, bile acid esters and conjugated bile acids. Using repository-scale analysis1,2, we discovered that some conjugated bile acids are associated with inflammatory bowel disease (IBD). Validation using four distinct human IBD cohorts showed that cholic acids conjugated to Glu, Ile/Leu, Phe, Thr, Trp or Tyr are increased in Crohn's disease. Several of these compounds and related structures affected pathways associated with IBD, such as interferon-γ production in CD4+ T cells3 and agonism of the pregnane X receptor4. Culture of bacteria belonging to the Bifidobacterium, Clostridium and Enterococcus genera produced these bile amidates. Because searching repositories with tandem mass spectrometry spectra has only recently become possible, this reverse metabolomics approach can now be used as a general strategy to discover other molecules from human and animal ecosystems.

Published
2024

5. Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution

Author

Kang, Joyce B., Shen, Amber Z., Gurajala, Saisriram, Nathan, Aparna, Rumker, Laurie, Aguiar, Vitor R. C., Valencia, Cristian, Lagattuta, Kaitlyn A., Zhang, Fan, Jonsson, Anna Helena, Yazar, Seyhan, Alquicira-Hernandez, Jose, Khalili, Hamed, Ananthakrishnan, Ashwin N., Jagadeesh, Karthik, Dey, Kushal, Daly, Mark J., Xavier, Ramnik J., Donlin, Laura T., Anolik, Jennifer H., Powell, Joseph E., Rao, Deepak A., Brenner, Michael B., Gutierrez-Arcelus, Maria, Luo, Yang, Sakaue, Saori, and Raychaudhuri, Soumya

Published
2023
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8. Comprehensive Association Analyses of Extraintestinal Manifestations in Inflammatory Bowel Disease

Author

Khrom, Michelle, Long, Millie, Dube, Shishir, Robbins, Lori, Botwin, Gregory J., Yang, Shaohong, Mengesha, Emebet, Li, Dalin, Naito, Takeo, Bonthala, Nirupama N., Ha, Christina, Melmed, Gil, Rabizadeh, Shervin, Syal, Gaurav, Vasiliauskas, Eric, Ziring, David, Brant, Steven R., Cho, Judy, Duerr, Richard H., Rioux, John, Schumm, Phil, Silverberg, Mark, Ananthakrishnan, Ashwin N., Faubion, William A., Jabri, Bana, Lira, Sergio A., Newberry, Rodney D., Sandler, Robert S., Xavier, Ramnik J., Kugathasan, Subra, Hercules, David, Targan, Stephan R., Sartor, R. Balfour, Haritunians, Talin, and McGovern, Dermot P.B.

Published
2024
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10. Leveraging polygenic enrichments of gene features to predict genes underlying complex traits and diseases

Author

Weeks, Elle M., Ulirsch, Jacob C., Cheng, Nathan Y., Trippe, Brian L., Fine, Rebecca S., Miao, Jenkai, Patwardhan, Tejal A., Kanai, Masahiro, Nasser, Joseph, Fulco, Charles P., Tashman, Katherine C., Aguet, Francois, Li, Taibo, Ordovas-Montanes, Jose, Smillie, Christopher S., Biton, Moshe, Shalek, Alex K., Ananthakrishnan, Ashwin N., Xavier, Ramnik J., Regev, Aviv, Gupta, Rajat M., Lage, Kasper, Ardlie, Kristin G., Hirschhorn, Joel N., Lander, Eric S., Engreitz, Jesse M., and Finucane, Hilary K.

Published
2023
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15. Semi-Supervised Off Policy Reinforcement Learning

Author

Sonabend-W, Aaron, Laha, Nilanjana, Ananthakrishnan, Ashwin N., Cai, Tianxi, and Mukherjee, Rajarshi

Subjects
Computer Science - Machine Learning, Computer Science - Artificial Intelligence, Statistics - Methodology, Statistics - Machine Learning
Abstract

Reinforcement learning (RL) has shown great success in estimating sequential treatment strategies which take into account patient heterogeneity. However, health-outcome information, which is used as the reward for reinforcement learning methods, is often not well coded but rather embedded in clinical notes. Extracting precise outcome information is a resource intensive task, so most of the available well-annotated cohorts are small. To address this issue, we propose a semi-supervised learning (SSL) approach that efficiently leverages a small sized labeled data with true outcome observed, and a large unlabeled data with outcome surrogates. In particular, we propose a semi-supervised, efficient approach to Q-learning and doubly robust off policy value estimation. Generalizing SSL to sequential treatment regimes brings interesting challenges: 1) Feature distribution for Q-learning is unknown as it includes previous outcomes. 2) The surrogate variables we leverage in the modified SSL framework are predictive of the outcome but not informative to the optimal policy or value function. We provide theoretical results for our Q-function and value function estimators to understand to what degree efficiency can be gained from SSL. Our method is at least as efficient as the supervised approach, and moreover safe as it robust to mis-specification of the imputation models.

Published
2020

16. Gut microbial metabolism of 5-ASA diminishes its clinical efficacy in inflammatory bowel disease

Author

Mehta, Raaj S., Mayers, Jared R., Zhang, Yancong, Bhosle, Amrisha, Glasser, Nathaniel R., Nguyen, Long H., Ma, Wenjie, Bae, Sena, Branck, Tobyn, Song, Kijun, Sebastian, Luke, Pacheco, Julian Avila, Seo, Hyuk-Soo, Clish, Clary, Dhe-Paganon, Sirano, Ananthakrishnan, Ashwin N., Franzosa, Eric A., Balskus, Emily P., Chan, Andrew T., and Huttenhower, Curtis

Published
2023
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21. HLA-DP on Epithelial Cells Enables Tissue Damage by NKp44+ Natural Killer Cells in Ulcerative Colitis

Author

Akar, Alaa, Flemming, Cornelius, Felix, Flomm, Flosbach, Markus, Jäger, Julia, Jeromin, Niklas, Jung, Johannes, Ohms, Mareike, Reinshagen, Konrad, Rische, Johann, Sagebiel, Adrian, Sandfort, Deborah, Steinert, Fenja, Tomuschat, Christian, Wesche, Jasmin, Shifteh Abedian, Abraham, Clara, Achkar, Jean-Paul, Ahmad, Tariq, Alberts, Rudi, Alizadeh, Behrooz, Amininejad, Leila, Ananthakrishnan, Ashwin N., Andersen, Vibeke, Anderson, Carl A., Andrews, Jane M., Annese, Vito, Aumais, Guy, Baidoo, Leonard, Baldassano, Robert N., Bampton, Peter A., Barclay, Murray, Barrett, Jeffrey C., Bethge, Johannes, Bewshea, Claire, Bis, Joshua C., Bitton, Alain, BK, Thelma, Boucher, Gabrielle, Brain, Oliver, Brand, Stephan, Brant, Steven R., Cheon, Jae Hee, Chew, Angela, Cho, Judy H., Cleynen, Isabelle, Cohain, Ariella, Cooney, Rachel, Croft, Anthony, Daly, Mark J., D'Amato, Mauro, Danese, Silvio, Daryani, Naser Ebrahim, Datta, Lisa Wu, Degenhardt, Frauke, Denapiene, Goda, Denson, Lee A., Devaney, Kathy L., Dewit, Olivier, D'Inca, Renata, Drummond, Hazel E., Dubinsky, Marla, Duerr, Richard H., Edwards, Cathryn, Ellinghaus, David, Ellul, Pierre, Esaki, Motohiro, Essers, Jonah, Ferguson, Lynnette R., Festen, Eleonora A., Fleshner, Philip, Florin, Tim, Franchimont, Denis, Franke, Andre, Fuyuno, Yuta, Gearry, Richard, Georges, Michel, Gieger, Christian, Glas, Jürgen, Goyette, Philippe, Green, Todd, Griffiths, Anne M., Guthery, Stephen L., Hakonarson, Hakon, Halfvarson, Jonas, Hanigan, Katherine, Haritunians, Talin, Hart, Ailsa, Hawkey, Chris, Hayward, Nicholas K., Hedl, Matija, Henderson, Paul, Hold, Georgina L., Hong, Myhunghee, Hu, Xinli, Huang, Hailiang, Hugot, Jean-Pierre, Hui, Ken Y., Imielinski, Marcin, Jazayeri, Omid, Jonaitis, Laimas, Jostins, Luke, Juyal, Garima, Chandra Juyal, Ramesh, Kalla, Rahul, Karlsen, Tom H., Kennedy, Nicholas A., Khan, Mohammed Azam, Kim, Won Ho, Kitazono, Takanari, Kiudelis, Gediminas, Kubo, Michiaki, Kugathasan, Subra, Kupcinskas, Limas, Lamb, Christopher A., de Lange, Katrina M., Latiano, Anna, Laukens, Debby, Lawrance, Ian C., Lee, James C., Lees, Charlie W., Leja, Marcis, Lewis, Nina, Van Limbergen, Johan, Lionetti, Paolo, Liu, Jimmy Z., Louis, Edouard, Luo, Yang, Mahy, Gillian, Malekzadeh, Masoud Mohammad, Malekzadeh, Reza, Mansfield, John, Marriott, Suzie, Massey, Dunecan, Mathew, Christopher G., Matsui, Toshiyuki, McGovern, Dermot P.B., van der Meulen, Andrea, Midha, Vandana, Milgrom, Raquel, Mirzaei, Samaneh, Mitrovic, Mitja, Montgomery, Grant W., Mowat, Craig, Müller, Christoph, Newman, William G., Ng, Aylwin, Ng, Siew C., Evelyn Ng, Sok Meng, Nikolaus, Susanna, Ning, Kaida, Nöthen, Markus, Oikonomou, Ioannis, Okou, David, Orchard, Timothy R., Palmieri, Orazio, Parkes, Miles, Phillips, Anne, Ponsioen, Cyriel Y., Potocnik, Urõs, Poustchi, Hossein, Prescott, Natalie J., Proctor, Deborah D., Radford-Smith, Graham, Rahier, Jean- Francois, Regueiro, Miguel, Reinisch, Walter, Rieder, Florian, Rioux, John D., Roberts, Rebecca, Rogler, Gerhard, Russell, Richard K., Sanderson, Jeremy D., Sans, Miquel, Satsangi, Jack, Schadt, Eric E., Scharl, Michael, Schembri, John, Schreiber, Stefan, Schumm, L. Philip, Scott, Regan, Seielstad, Mark, Shah, Tejas, Sharma, Yashoda, Silverberg, Mark S., Simmons, Alison, Simms, Lisa A., Singh, Abhey, Skieceviciene, Jurgita, van Sommeren, Suzanne, Song, Kyuyoung, Sood, Ajit, Spain, Sarah L., Steinhart, A. Hillary, Stempak, Joanne M., Stronati, Laura, Sung, Joseph J.Y., Targan, Stephan R., Taylor, Kirstin M., Theatre, Emilie, Torkvist, Leif, Torres, Esther A., Tremelling, Mark, Uhlig, Holm H., Umeno, Junji, Vahedi, Homayon, Vasiliauskas, Eric, Velde, Anje ter, Ventham, Nicholas T., Vermeire, Severine, Verspaget, Hein W., De Vos, Martine, Walters, Thomas, Wang, Kai, Wang, Ming-Hsi, Weersma, Rinse K., Wei, Zhi, Whiteman, David, Wijmenga, Cisca, Wilson, David C., Winkelmann, Juliane, Wong, Sunny H., Xavier, Ramnik J., Yamazaki, Keiko, Yang, Suk-Kyun, Ye, Byong Duk, Zeissig, Sebastian, Zhang, Bin, Zhang, Clarence K., Zhang, Hu, Zhang, Wei, Zhao, Hongyu, Zhao, Zhen Z., Baumdick, Martin E., Niehrs, Annika, Schwerk, Maria, Hinrichs, Ole, Jordan-Paiz, Ana, Padoan, Benedetta, Wegner, Lucy H.M., Schloer, Sebastian, Zecher, Britta F., Malsy, Jakob, Joshi, Vinita R., Illig, Christin, Schröder-Schwarz, Jennifer, Möller, Kimberly J., Martin, Maureen P., Yuki, Yuko, Ozawa, Mikki, Sauter, Jürgen, Schmidt, Alexander H., Perez, Daniel, Giannou, Anastasios D., Carrington, Mary, Davis, Randall S., Schumacher, Udo, Sauter, Guido, Huber, Samuel, Puelles, Victor G., Melling, Nathaniel, Altfeld, Marcus, and Bunders, Madeleine J.

Published
2023
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22. Frailty in inflammatory bowel diseases: an emerging concept

Author

Kochar, Bharati, Orkaby, Ariela R, Ananthakrishnan, Ashwin N, and Ritchie, Christine S

Subjects
Autoimmune Disease, Digestive Diseases, Crohn's Disease, Inflammatory Bowel Disease, Aging, 2.1 Biological and endogenous factors, Aetiology, Oral and gastrointestinal, Crohn’s disease, aging, frailty, geriatrics, inflammation, inflammatory bowel diseases, ulcerative colitis, Clinical Sciences, Pharmacology and Pharmaceutical Sciences
Abstract

Inflammatory bowel diseases (IBD), consisting of Crohn's disease and ulcerative colitis, are chronic remitting, relapsing inflammatory conditions of the gastrointestinal tract. While traditionally a disease of younger ages, the number of older adults with IBD is rising rapidly. Patients with IBD often experience geriatric syndromes at earlier ages. Older adults with IBD have poorer disease and treatment-related outcomes compared with younger adults with IBD. Applying the principles of geriatrics to understanding a chronic disease in older adults may improve health span. Better tools are needed to stratify IBD patients who are at high risk for adverse events. Frailty is a geriatric construct that may approximate biologic age. Frailty is a complex, multi-dimensional syndrome that leads to increased vulnerability to stress and decline of reserve across multiple physiologic systems. In this review, we present the leading conceptual models of frailty and discuss the applications of frailty in immune-mediated diseases. We also review chronic conditions where frailty has been applied successfully as a tool for risk stratification. Finally, we discuss in the detail the growing body of literature highlighting the relationship between frailty and IBD, the epidemiology of frailty in IBD, and ramifications of frailty in IBD.

Published
2021

30. Large-scale sequencing identifies multiple genes and rare variants associated with Crohn’s disease susceptibility

Author

Sazonovs, Aleksejs, Stevens, Christine R., Venkataraman, Guhan R., Yuan, Kai, Avila, Brandon, Abreu, Maria T., Ahmad, Tariq, Allez, Matthieu, Ananthakrishnan, Ashwin N., Atzmon, Gil, Baras, Aris, Barrett, Jeffrey C., Barzilai, Nir, Beaugerie, Laurent, Beecham, Ashley, Bernstein, Charles N., Bitton, Alain, Bokemeyer, Bernd, Chan, Andrew, Chung, Daniel, Cleynen, Isabelle, Cosnes, Jacques, Cutler, David J., Daly, Allan, Damas, Oriana M., Datta, Lisa W., Dawany, Noor, Devoto, Marcella, Dodge, Sheila, Ellinghaus, Eva, Fachal, Laura, Farkkila, Martti, Faubion, William, Ferreira, Manuel, Franchimont, Denis, Gabriel, Stacey B., Ge, Tian, Georges, Michel, Gettler, Kyle, Giri, Mamta, Glaser, Benjamin, Goerg, Siegfried, Goyette, Philippe, Graham, Daniel, Hämäläinen, Eija, Haritunians, Talin, Heap, Graham A., Hiltunen, Mikko, Hoeppner, Marc, Horowitz, Julie E., Irving, Peter, Iyer, Vivek, Jalas, Chaim, Kelsen, Judith, Khalili, Hamed, Kirschner, Barbara S., Kontula, Kimmo, Koskela, Jukka T., Kugathasan, Subra, Kupcinskas, Juozas, Lamb, Christopher A., Laudes, Matthias, Lévesque, Chloé, Levine, Adam P., Lewis, James D., Liefferinckx, Claire, Loescher, Britt-Sabina, Louis, Edouard, Mansfield, John, May, Sandra, McCauley, Jacob L., Mengesha, Emebet, Mni, Myriam, Moayyedi, Paul, Moran, Christopher J., Newberry, Rodney D., O’Charoen, Sirimon, Okou, David T., Oldenburg, Bas, Ostrer, Harry, Palotie, Aarno, Paquette, Jean, Pekow, Joel, Peter, Inga, Pierik, Marieke J., Ponsioen, Cyriel Y., Pontikos, Nikolas, Prescott, Natalie, Pulver, Ann E., Rahmouni, Souad, Rice, Daniel L., Saavalainen, Päivi, Sands, Bruce, Sartor, R. Balfour, Schiff, Elena R., Schreiber, Stefan, Schumm, L. Philip, Segal, Anthony W., Seksik, Philippe, Shawky, Rasha, Sheikh, Shehzad Z., Silverberg, Mark S., Simmons, Alison, Skeiceviciene, Jurgita, Sokol, Harry, Solomonson, Matthew, Somineni, Hari, Sun, Dylan, Targan, Stephan, Turner, Dan, Uhlig, Holm H., van der Meulen, Andrea E., Vermeire, Séverine, Verstockt, Sare, Voskuil, Michiel D., Winter, Harland S., Young, Justine, Duerr, Richard H., Franke, Andre, Brant, Steven R., Cho, Judy, Weersma, Rinse K., Parkes, Miles, Xavier, Ramnik J., Rivas, Manuel A., Rioux, John D., McGovern, Dermot P. B., Huang, Hailiang, Anderson, Carl A., and Daly, Mark J.

Published
2022
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32. Challenges in IBD Research 2024: Environmental Triggers

Author

Ananthakrishnan, Ashwin N, primary, Gerasimidis, Kostantinos, additional, Ho, Shuk-Mei, additional, Mayer, Emeran, additional, Pollock, Jennifer, additional, Soni, Shefali, additional, Wu, Gary D, additional, Benyacoub, Jalil, additional, Ali, Basmah, additional, Favreau, Alex, additional, Smith, Denise Elsbree, additional, Oh, Ji-eun, additional, Heller, Caren, additional, Hurtado-Lorenzo, Andres, additional, Moss, Alan, additional, and Croitoru, Ken, additional

Published
2024
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35. IOIBD Recommendations for Clinical Trials in Ulcerative Proctitis: The PROCTRIAL Consensus

Author

Caron, Bénédicte, Abreu, Maria T., Siegel, Corey A., Panaccione, Remo, Sands, Bruce E., Dignass, Axel, Turner, Dan, Dotan, Iris, Hart, Ailsa L., Ahuja, Vineet, Allez, Matthieu, Ananthakrishnan, Ashwin N., Ghosh, Subrata, Griffiths, Anne M., Halfvarson, Jonas, Kaser, Arthur, Kotze, Paulo G., Koutroubakis, Ioannis E., Lakatos, Peter L., Levine, Arie, Lewis, James D., Magro, Fernando, Mantzaris, Gerassimos J., O’Morain, Colm, Ran, Zhihua, Reinisch, Walter, Rogler, Gerhard, Sachar, David B., Siegmund, Britta, Silverberg, Mark S., Sood, Ajit, Spinelli, Antonino, Steinwurz, Flavio, Tysk, Curt, Yamamoto-Furusho, Jesus K., Schreiber, Stefan, Rubin, David T., Sandborn, William J., Danese, Silvio, and Peyrin-Biroulet, Laurent

Published
2022
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38. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases.

Author

Lloyd-Price, Jason, Arze, Cesar, Ananthakrishnan, Ashwin N, Schirmer, Melanie, Avila-Pacheco, Julian, Poon, Tiffany W, Andrews, Elizabeth, Ajami, Nadim J, Bonham, Kevin S, Brislawn, Colin J, Casero, David, Courtney, Holly, Gonzalez, Antonio, Graeber, Thomas G, Hall, A Brantley, Lake, Kathleen, Landers, Carol J, Mallick, Himel, Plichta, Damian R, Prasad, Mahadev, Rahnavard, Gholamali, Sauk, Jenny, Shungin, Dmitry, Vázquez-Baeza, Yoshiki, White, Richard A, IBDMDB Investigators, Braun, Jonathan, Denson, Lee A, Jansson, Janet K, Knight, Rob, Kugathasan, Subra, McGovern, Dermot PB, Petrosino, Joseph F, Stappenbeck, Thaddeus S, Winter, Harland S, Clish, Clary B, Franzosa, Eric A, Vlamakis, Hera, Xavier, Ramnik J, and Huttenhower, Curtis

Subjects
IBDMDB Investigators, Animals, Humans, Viruses, Fungi, Inflammatory Bowel Diseases, Phylogeny, Species Specificity, Health, Transcriptome, Gastrointestinal Microbiome, General Science & Technology
Abstract

Inflammatory bowel diseases, which include Crohn's disease and ulcerative colitis, affect several million individuals worldwide. Crohn's disease and ulcerative colitis are complex diseases that are heterogeneous at the clinical, immunological, molecular, genetic, and microbial levels. Individual contributing factors have been the focus of extensive research. As part of the Integrative Human Microbiome Project (HMP2 or iHMP), we followed 132 subjects for one year each to generate integrated longitudinal molecular profiles of host and microbial activity during disease (up to 24 time points each; in total 2,965 stool, biopsy, and blood specimens). Here we present the results, which provide a comprehensive view of functional dysbiosis in the gut microbiome during inflammatory bowel disease activity. We demonstrate a characteristic increase in facultative anaerobes at the expense of obligate anaerobes, as well as molecular disruptions in microbial transcription (for example, among clostridia), metabolite pools (acylcarnitines, bile acids, and short-chain fatty acids), and levels of antibodies in host serum. Periods of disease activity were also marked by increases in temporal variability, with characteristic taxonomic, functional, and biochemical shifts. Finally, integrative analysis identified microbial, biochemical, and host factors central to this dysregulation. The study's infrastructure resources, results, and data, which are available through the Inflammatory Bowel Disease Multi'omics Database ( http://ibdmdb.org ), provide the most comprehensive description to date of host and microbial activities in inflammatory bowel diseases.

Published
2019

39. Sugars and Gastrointestinal Health

Author

Arnone, Djésia, Chabot, Caroline, Heba, Anne-Charlotte, Kökten, Tunay, Caron, Bénédicte, Hansmannel, Franck, Dreumont, Natacha, Ananthakrishnan, Ashwin N., Quilliot, Didier, and Peyrin-Biroulet, Laurent

Published
2022
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40. Lifestyle, behaviour, and environmental modification for the management of patients with inflammatory bowel diseases: an International Organization for Study of Inflammatory Bowel Diseases consensus

Author

Abreu, M, Ahuja, V, Allez, M, Ananthakrishnan, A, Bemelman, W, Bernstein, C, Braun, J, Chowers, Y, Colombel, J-F, Danese, S, D'Haens, G, D'Hoore, A, Dignass, A, Dotan, I, Dubinsky, M, Ekbom, A, Fleshner, P, Gasche, C, Gassull, MA, Gearry, R, Ghosh, S, Gibson, P, Griffiths, A, Halfvarson, J, Hanauer, S, Harpaz, N, Hart, A, Hibi, T, Kamm, M, Kaplan, G, Kaser, A, Korelitz, B, Kotze, P, Koutroubakis, I, Kruis, W, Lakatos, P, Lewis, J, Lindsay, J, Loftus, E, Louis, E, Lukas, M, Magro, F, Mahadevan, U, Mantzaris, G, Mary, J-Y, McGovern, D, Moum, B, Munkholm, P, Neurath, M, Ng, S, O'Morain, C, Oresland, T, Panaccione, R, Panes, J, Panis, Y, Pemberton, J, Peyrin-Biroulet, L, Prantera, C, Rachmilewitz, D, Ran, Z, Reinisch, W, Remzi, F, Rhodes, J, Riddell, R, Rogler, G, Rubin, D, Sachar, D, Sandborn, W, Sands, B, Sartor, B, Schoelmerich, J, Schreiber, S, Siegel, C, Siegmund, B, Silverberg, M, Söderholm, J, Sood, A, Spinelli, A, Stange, E, Steinwurz, F, Targan, S, Travis, S, Turner, D, Tysk, C, Vatn, M, Vermeire, S, Watanabe, M, Yamamoto, T, Yamamoto-Furusho, J, Ananthakrishnan, Ashwin N, Kaplan, Gilaad G, Bernstein, Charles N, Burke, Kristin E, Lochhead, Paul J, Sasson, Alexa N, Agrawal, Manasi, Tiong, Jimmy Ho Tuan, Steinberg, Joshua, Kruis, Wolfgang, Steinwurz, Flavio, Ahuja, Vineet, Ng, Siew C, Rubin, David T, Colombel, Jean-Frederic, and Gearry, Richard

Published
2022
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45. Endpoints for extraintestinal manifestations in inflammatory bowel disease trials: the EXTRA consensus from the International Organization for the Study of Inflammatory Bowel Diseases

Author

Guillo, Lucas, Abreu, Maria, Panaccione, Remo, Sandborn, William J, Azevedo, Valderilio F, Gensler, Lianne, Moghaddam, Bahar, Ahuja, Vineet, Ali, Sabrina A, Allez, Matthieu, Ananthakrishnan, Ashwin N, Bhattacharya, Abhik, Dubinsky, Marla, Griffiths, Anne, Hart, Ailsa, Korelitz, Burton, Kotze, Paulo G, Koutroubakis, Ioannis E, Lakatos, Peter L, Lindsay, James O, Magro, Fernando, Mantzaris, Gerassimos J, Ng, Siew C, O'Morain, Colm, Panés, Julian, Parigi, Tommaso, Ran, Zhihua, Rogler, Gerhard, Rubin, David T, Sachar, David B, Siegmund, Britta, Steinwurz, Flavio, Tysk, Curt, Vavricka, Stephan, Verstraete, Sofia G, Brezin, Antoine P, Haemel, Anna K, Dignass, Axel, Sands, Bruce E, Danese, Silvio, and Peyrin-Biroulet, Laurent

Published
2022
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48. Estimating Average Treatment Effects with a Double-Index Propensity Score

Author

Cheng, David, Chakrabortty, Abhishek, Ananthakrishnan, Ashwin N., and Cai, Tianxi

Subjects
Statistics - Methodology
Abstract

We consider estimating average treatment effects (ATE) of a binary treatment in observational data when data-driven variable selection is needed to select relevant covariates from a moderately large number of available covariates $\mathbf{X}$. To leverage covariates among $\mathbf{X}$ predictive of the outcome for efficiency gain while using regularization to fit a parametric propensity score (PS) model, we consider a dimension reduction of $\mathbf{X}$ based on fitting both working PS and outcome models using adaptive LASSO. A novel PS estimator, the Double-index Propensity Score (DiPS), is proposed, in which the treatment status is smoothed over the linear predictors for $\mathbf{X}$ from both the initial working models. The ATE is estimated by using the DiPS in a normalized inverse probability weighting (IPW) estimator, which is found to maintain double-robustness and also local semiparametric efficiency with a fixed number of covariates $p$. Under misspecification of working models, the smoothing step leads to gains in efficiency and robustness over traditional doubly-robust estimators. These results are extended to the case where $p$ diverges with sample size and working models are sparse. Simulations show the benefits of the approach in finite samples. We illustrate the method by estimating the ATE of statins on colorectal cancer risk in an electronic medical record (EMR) study and the effect of smoking on C-reactive protein (CRP) in the Framingham Offspring Study., Comment: 48 pages, 1 figure; Finalized revised version

Published
2017
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