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@ARTICLE{Wilkinson1975-vf,
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@INPROCEEDINGS{ICH_Expert_Working_Group2005-xb,
  title     = "The Clinical Evaluation of {QT/QTC} Interval Prolongation and
               Proarrhythmic Potential for Nonantiarrhythmic Drugs",
  booktitle = "{ICH} Harmonized Tripartite Guideline",
  author    = "{ICH Expert Working Group}",
  publisher = "ICH Expert Working Group",
  month     =  may,
  year      =  2005
}

@ARTICLE{Chae2018-tq,
  title    = "Mechanistic Model for Blood Pressure and Heart Rate Changes
              Produced by Telmisartan in Human Beings",
  author   = "Chae, Dongwoo and Son, Mijeong and Kim, Yukyung and Son, Hankil
              and Park, Kyungsoo",
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  language = "en"
}

@ARTICLE{Putter2006-gx,
  title    = "Estimation and prediction in a multi-state model for breast
              cancer",
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              Elgalta, Rachid and van de Velde, Cornelis J H",
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@ARTICLE{Le-Rademacher2018-eq,
  title    = "Application of multi-state models in cancer clinical trials",
  author   = "Le-Rademacher, Jennifer G and Peterson, Ryan A and Therneau,
              Terry M and Sanford, Ben L and Stone, Richard M and Mandrekar,
              Sumithra J",
  journal  = "Clin. Trials",
  volume   =  15,
  number   =  5,
  pages    = "489--498",
  month    =  oct,
  year     =  2018,
  keywords = "Multi-state model; cancer; clinical trials; survival analysis;
              time-to-event data",
  language = "en"
}

@ARTICLE{He2015-sr,
  title    = "Simultaneous variable selection for joint models of longitudinal
              and survival outcomes",
  author   = "He, Zangdong and Tu, Wanzhu and Wang, Sijian and Fu, Haoda and
              Yu, Zhangsheng",
  journal  = "Biometrics",
  volume   =  71,
  number   =  1,
  pages    = "178--187",
  month    =  mar,
  year     =  2015,
  keywords = "ALASSO; Cholesky decomposition; EM algorithm; Gaussian
              quadrature; Joint models; Mixed effect selection",
  language = "en"
}

@ARTICLE{Bai2019-ar,
  title   = "Translational Quantitative Systems Pharmacology in Drug
             Development: from Current Landscape to Good Practices",
  author  = "Bai, Jane P F and Earp, Justin C and Pillai, Venkateswaran C",
  journal = "AAPS J.",
  volume  =  21,
  number  =  4,
  pages   = "72",
  month   =  jun,
  year    =  2019
}

@MISC{Iooss2018-uu,
  title  = "sensitivity: Global Sensitivity Analysis of Model Outputs",
  author = "Iooss, Bertrand and Janon, Alexandre and Pujol, Gilles and from
            Khalid Boumhaout, With Contributions and Veiga, Sebastien Da and
            Delage, Thibault and Fruth, Jana and Gilquin, Laurent and
            Guillaume, Joseph and Le Gratiet, Loic and Lemaitre, Paul and
            Nelson, Barry L and Monari, Filippo and Oomen, Roelof and Rakovec,
            Oldrich and Ramos, Bernardo and Roustant, Olivier and Song, Eunhye
            and Staum, Jeremy and Sueur, Roman and Touati, Taieb and Weber,
            Frank",
  year   =  2018
}

@MISC{Bache2014-be,
  title  = "magrittr: A {Forward-Pipe} Operator for {R}",
  author = "Bache, Stefan Milton and Wickham, Hadley",
  year   =  2014
}

@MISC{R_Core_Team2018-mi,
  title       = "R: A Language and Environment for Statistical Computing",
  author      = "{R Core Team}",
  institution = "R Foundation for Statistical Computing",
  year        =  2018,
  address     = "Vienna, Austria"
}

@MISC{Chang2019-dc,
  title  = "shiny: Web Application Framework for {R}",
  author = "Chang, Winston and Cheng, Joe and Allaire, J J and Xie, Yihui and
            McPherson, Jonathan",
  year   =  2019
}

@MISC{Wickham2017-td,
  title  = "tidyverse: Easily Install and Load the 'Tidyverse'",
  author = "Wickham, Hadley",
  year   =  2017
}

@MISC{Pinheiro2019-cr,
  title  = "{nlme}: Linear and Nonlinear Mixed Effects Models",
  author = "Pinheiro, Jose and Bates, Douglas and DebRoy, Saikat and Sarkar,
            Deepayan and {R Core Team}",
  year   =  2019
}

@ARTICLE{Lee2019-on,
  title    = "Optimizing natural killer cell doses for heterogeneous cancer
              patients on the basis of multiple event times",
  author   = "Lee, Juhee and Thall, Peter F and Rezvani, Katy",
  journal  = "J. R. Stat. Soc. Ser. C Appl. Stat.",
  volume   =  68,
  number   =  2,
  pages    = "461--474",
  month    =  feb,
  year     =  2019,
  keywords = "Cellular Therapy; Dose Finding; Natural Killer Cells; Phase I--II
              Clinical Trial; Precision Medicine",
  language = "en"
}

@ARTICLE{Chang2019-ei,
  title    = "A translational platform {PBPK} model for antibody disposition in
              the brain",
  author   = "Chang, Hsueh-Yuan and Wu, Shengjia and Meno-Tetang, Guy and Shah,
              Dhaval K",
  journal  = "J. Pharmacokinet. Pharmacodyn.",
  month    =  may,
  year     =  2019,
  keywords = "Blood--CSF barrier; Blood--brain barrier; Brain; Interspecies
              scaling; Monoclonal antibody; PBPK model; Pharmacokinetics",
  language = "en"
}

@ARTICLE{Lai2019-zi,
  title    = "Towards personalized computer simulation of breast cancer
              treatment: a multi-scale pharmacokinetic and pharmacodynamic
              model informed by multi-type patient data",
  author   = "Lai, Xiaoran and Geier, Oliver M and Fleischer, Thomas and
              Garred, {\O}ystein and Borgen, Elin and Funke, Simon W and Kumar,
              Surendra and Rognes, Marie E and Seierstad, Therese and
              B{\o}rressen-Dale, Anne-Lise and Kristensen, Vessela N and
              Engebr{\aa}ten, Olav and K{\"o}hn-Luque, Alvaro and Frigessi,
              Arnoldo",
  journal  = "Cancer Res.",
  month    =  may,
  year     =  2019,
  language = "en"
}

@ARTICLE{Betts2019-bd,
  title    = "A Translational Quantitative Systems Pharmacology Model for {CD3}
              Bispecific Molecules: Application to Quantify {T} {Cell-Mediated}
              Tumor Cell Killing by {P-Cadherin} {LP} {DART\textregistered{}}",
  author   = "Betts, Alison and Haddish-Berhane, Nahor and Shah, Dhaval K and
              van der Graaf, Piet H and Barletta, Frank and King, Lindsay and
              Clark, Tracey and Kamperschroer, Cris and Root, Adam and Hooper,
              Andrea and Chen, Xiaoying",
  journal  = "AAPS J.",
  volume   =  21,
  number   =  4,
  pages    = "66",
  month    =  may,
  year     =  2019,
  keywords = "CD3 bispecific; PK/PD; immunotherapy; quantitative systems
              pharmacology; translational modeling",
  language = "en"
}

@ARTICLE{Ueckert2018-jt,
  title    = "Modeling Composite Assessment Data Using Item Response Theory",
  author   = "Ueckert, Sebastian",
  journal  = "CPT Pharmacometrics Syst Pharmacol",
  volume   =  7,
  number   =  4,
  pages    = "205--218",
  month    =  apr,
  year     =  2018,
  language = "en"
}

@ARTICLE{Ide2017-uf,
  title     = "Supervised Item Response Models for Informative Prediction",
  author    = "Id{\'e}, Tsuyoshi and Dhurandhar, Amit",
  journal   = "Knowl. Inf. Syst.",
  publisher = "Springer-Verlag New York, Inc.",
  volume    =  51,
  number    =  1,
  pages     = "235--257",
  month     =  apr,
  year      =  2017,
  address   = "New York, NY, USA",
  keywords  = "Item response theory, Metric learning, Questionnaire data"
}

@ARTICLE{LaRosa2019-jt,
  title   = "Iatrogenic Withdrawal Syndrome: a Review of Pathophysiology,
             Prevention, and Treatment",
  author  = "LaRosa, Jessica M and Aponte-Patel, Linda",
  journal = "Curr. Pediatr. Rep.",
  volume  =  7,
  number  =  1,
  pages   = "12--19",
  month   =  mar,
  year    =  2019
}

@ARTICLE{Goulooze2018-co,
  title    = "Covariates in Pharmacometric Repeated {Time-to-Event} Models: Old
              and New ({Pre)Selection} Tools",
  author   = "Goulooze, Sebastiaan C and Krekels, Elke H J and Hankemeier,
              Thomas and Knibbe, Catherijne A J",
  journal  = "AAPS J.",
  volume   =  21,
  number   =  1,
  pages    = "11",
  month    =  dec,
  year     =  2018,
  keywords = "covariate model building; empirical Bayes estimate; non-linear
              mixed effects modeling; repeated time-to-event",
  language = "en"
}

@ARTICLE{Xu2017-md,
  title    = "Further Evaluation of Covariate Analysis using Empirical Bayes
              Estimates in Population Pharmacokinetics: the Perception of
              Shrinkage and Likelihood Ratio Test",
  author   = "Xu, Xu Steven and Yuan, Min and Yang, Haitao and Feng, Yan and
              Xu, Jinfeng and Pinheiro, Jose",
  journal  = "AAPS J.",
  volume   =  19,
  number   =  1,
  pages    = "264--273",
  month    =  jan,
  year     =  2017,
  keywords = "covariate; empirical bayes estimates; likelihood ratio test;
              population pharmacokinetics; shrinkage",
  language = "en"
}

@ARTICLE{Levey2006-ab,
  title    = "Using standardized serum creatinine values in the modification of
              diet in renal disease study equation for estimating glomerular
              filtration rate",
  author   = "Levey, Andrew S and Coresh, Josef and Greene, Tom and Stevens,
              Lesley A and Zhang, Yaping Lucy and Hendriksen, Stephen and
              Kusek, John W and Van Lente, Frederick and {Chronic Kidney
              Disease Epidemiology Collaboration}",
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  volume   =  145,
  number   =  4,
  pages    = "247--254",
  month    =  aug,
  year     =  2006,
  language = "en"
}

@ARTICLE{Danieli2019-uu,
  title    = "Competing risks modeling of cumulative effects of time-varying
              drug exposures",
  author   = "Danieli, Coraline and Abrahamowicz, Michal",
  journal  = "Stat. Methods Med. Res.",
  volume   =  28,
  number   =  1,
  pages    = "248--262",
  month    =  jan,
  year     =  2019,
  keywords = "Survival analysis; competing risks; pharmaco-epidemiology;
              simulations; time-dependent covariates",
  language = "en"
}

@INCOLLECTION{Zink2018-xr,
  title     = "Detecting Safety Signals Among Adverse Events in Clinical Trials",
  booktitle = "Biopharmaceutical Applied Statistics Symposium : Volume 2
               Biostatistical Analysis of Clinical Trials",
  author    = "Zink, Richard C",
  editor    = "Peace, Karl E and Chen, Ding-Geng and Menon, Sandeep",
  publisher = "Springer Singapore",
  pages     = "107--125",
  year      =  2018,
  address   = "Singapore"
}

@ARTICLE{Allignol2016-js,
  title    = "Statistical issues in the analysis of adverse events in
              time-to-event data",
  author   = "Allignol, Arthur and Beyersmann, Jan and Schmoor, Claudia",
  journal  = "Pharm. Stat.",
  volume   =  15,
  number   =  4,
  pages    = "297--305",
  month    =  jul,
  year     =  2016,
  keywords = "Aalen-Johansen; competing risks; safety; survival",
  language = "en"
}

@ARTICLE{Proctor2016-wj,
  title    = "Analysing adverse events by time-to-event models: the {CLEOPATRA}
              study",
  author   = "Proctor, Tanja and Schumacher, Martin",
  journal  = "Pharm. Stat.",
  volume   =  15,
  number   =  4,
  pages    = "306--314",
  month    =  jul,
  year     =  2016,
  keywords = "adverse events; competing risks; incidence rate; multi-state
              models; time-to-event",
  language = "en"
}

@ARTICLE{Hengelbrock2016-bg,
  title    = "Safety data from randomized controlled trials: applying models
              for recurrent events",
  author   = "Hengelbrock, Johannes and Gillhaus, Johanna and Kloss, Sebastian
              and Leverkus, Friedhelm",
  journal  = "Pharm. Stat.",
  volume   =  15,
  number   =  4,
  pages    = "315--323",
  month    =  jul,
  year     =  2016,
  keywords = "adverse events; randomized controlled trials; recurrent events;
              safety data; survival analysis",
  language = "en"
}

@ARTICLE{Duke2015-lq,
  title    = "Seeing is believing: good graphic design principles for medical
              research",
  author   = "Duke, Susan P and Bancken, Fabrice and Crowe, Brenda and Soukup,
              Mat and Botsis, Taxiarchis and Forshee, Richard",
  journal  = "Stat. Med.",
  volume   =  34,
  number   =  22,
  pages    = "3040--3059",
  month    =  sep,
  year     =  2015,
  keywords = "communication; graphics; visual perception; visualization",
  language = "en"
}

@ARTICLE{Titze2017-wh,
  title    = "A generic viral dynamic model to systematically characterize the
              interaction between oncolytic virus kinetics and tumor growth",
  author   = "Titze, Melanie I and Frank, Julia and Ehrhardt, Michael and
              Smola, Sigrun and Graf, Norbert and Lehr, Thorsten",
  journal  = "Eur. J. Pharm. Sci.",
  volume   =  97,
  pages    = "38--46",
  month    =  jan,
  year     =  2017,
  keywords = "Glioblastoma; Mathematical model; Non-linear mixed effects
              modeling; Pharmacokinetic/pharmacodynamics modeling; Treatment
              score",
  language = "en"
}

@ARTICLE{Martinez-Reina2019-mp,
  title    = "Effects of long-term treatment of denosumab on bone mineral
              density: insights from an in-silico model of bone mineralization",
  author   = "Mart{\'\i}nez-Reina, Javier and Pivonka, Peter",
  journal  = "Bone",
  month    =  may,
  year     =  2019,
  keywords = "Bone mineral density; Bone mineralization; Bone remodeling;
              Denosumab; PK-PD modeling; Postmenopausal osteoporosis;
              RANK-RANKL-OPG pathway",
  language = "en"
}

@MISC{Peyrin-Biroulet2017-iv,
  title   = "{P369} Safety and lymphocyte-lowering properties of etrasimod
             ({APD334)}, an oral, potent, next-generation, selective {S1P}
             receptor modulator, after dose escalation in healthy volunteers",
  author  = "Peyrin-Biroulet, L and Christopher, R and Trokan, L and Lassen, C
             and Adams, J and K{\"u}hbacher, T",
  journal = "Journal of Crohn's and Colitis",
  volume  =  11,
  number  = "suppl\_1",
  pages   = "S265--S266",
  year    =  2017
}

@MISC{Sandborn2015-hh,
  title   = "445 The {TOUCHSTONE} Study: A Randomized, {Double-Blind},
             {Placebo-Controlled} Induction Trial of an Oral {S1P} Receptor
             Modulator ({RPC1063}) in Moderate to Severe Ulcerative Colitis",
  author  = "Sandborn, William and Feagan, Brian G and Wolf, Douglas C and
             D'Haens, Geert R and Vermeire, Severine and Hanauer, Stephen B and
             Ghosh, Subrata and Smith, Heather and Cravets, Matt and Frohna,
             Paul A and Gujrathi, Sheila and Olson, Allan",
  journal = "Gastroenterology",
  volume  =  148,
  number  =  4,
  pages   = "S--93",
  year    =  2015
}

@MISC{DAmbrosio2016-fm,
  title   = "Ponesimod, a selective {S1P1} receptor modulator: a potential
             treatment for multiple sclerosis and other immune-mediated
             diseases",
  author  = "D'Ambrosio, Daniele and Freedman, Mark S and Prinz, Joerg",
  journal = "Therapeutic Advances in Chronic Disease",
  volume  =  7,
  number  =  1,
  pages   = "18--33",
  year    =  2016
}

@ARTICLE{Subei2015-xw,
  title    = "Sphingosine 1-phosphate receptor modulators in multiple sclerosis",
  author   = "Subei, Adnan M and Cohen, Jeffrey A",
  journal  = "CNS Drugs",
  volume   =  29,
  number   =  7,
  pages    = "565--575",
  month    =  jul,
  year     =  2015,
  language = "en"
}

@ARTICLE{Baeyens2015-ay,
  title    = "Exit Strategies: {S1P} Signaling and {T} Cell Migration",
  author   = "Baeyens, Audrey and Fang, Victoria and Chen, Cynthia and Schwab,
              Susan R",
  journal  = "Trends Immunol.",
  volume   =  36,
  number   =  12,
  pages    = "778--787",
  month    =  dec,
  year     =  2015,
  language = "en"
}

@ARTICLE{Fang2008-he,
  title    = "Label-free cell-based assays for {GPCR} screening",
  author   = "Fang, Ye and Frutos, Anthony G and Verklereen, Ronald",
  journal  = "Comb. Chem. High Throughput Screen.",
  volume   =  11,
  number   =  5,
  pages    = "357--369",
  month    =  jun,
  year     =  2008,
  language = "en"
}

@MISC{Zhu2018-yv,
  title   = "Epithelial barrier dysfunctions in atopic dermatitis: a
             skin-gut-lung model linking microbiome alteration and immune
             dysregulation",
  author  = "Zhu, T H and Zhu, T R and Tran, K A and Sivamani, R K and Shi, V Y",
  journal = "British Journal of Dermatology",
  volume  =  179,
  number  =  3,
  pages   = "570--581",
  year    =  2018
}

@MISC{Burg2018-hr,
  title   = "Sphingosine 1-Phosphate Receptor 1 Signaling Maintains Endothelial
             Cell Barrier Function and Protects Against Immune
             {Complex-Induced} Vascular Injury",
  author  = "Burg, Nathalie and Swendeman, Steven and Worgall, Stefan and Hla,
             Timothy and Salmon, Jane E",
  journal = "Arthritis \& Rheumatology",
  volume  =  70,
  number  =  11,
  pages   = "1879--1889",
  year    =  2018
}

@ARTICLE{Brinkmann2010-ib,
  title    = "Fingolimod ({FTY720)}: discovery and development of an oral drug
              to treat multiple sclerosis",
  author   = "Brinkmann, Volker and Billich, Andreas and Baumruker, Thomas and
              Heining, Peter and Schmouder, Robert and Francis, Gordon and
              Aradhye, Shreeram and Burtin, Pascale",
  journal  = "Nat. Rev. Drug Discov.",
  volume   =  9,
  number   =  11,
  pages    = "883--897",
  month    =  nov,
  year     =  2010,
  language = "en"
}

@ARTICLE{Carbone2013-bq,
  title    = "Sex and age are determinants of the clinical phenotype of primary
              biliary cirrhosis and response to ursodeoxycholic acid",
  author   = "Carbone, Marco and Mells, George F and Pells, Greta and Dawwas,
              Muhammad F and Newton, Julia L and Heneghan, Michael A and
              Neuberger, James M and Day, Darren B and Ducker, Samantha J and
              {UK PBC Consortium} and Sandford, Richard N and Alexander, Graeme
              J and Jones, David E J",
  journal  = "Gastroenterology",
  volume   =  144,
  number   =  3,
  pages    = "560--569.e7; quiz e13--4",
  month    =  mar,
  year     =  2013,
  language = "en"
}

@ARTICLE{Boonstra2012-im,
  title    = "Epidemiology of primary sclerosing cholangitis and primary
              biliary cirrhosis: a systematic review",
  author   = "Boonstra, Kirsten and Beuers, Ulrich and Ponsioen, Cyriel Y",
  journal  = "J. Hepatol.",
  volume   =  56,
  number   =  5,
  pages    = "1181--1188",
  month    =  may,
  year     =  2012,
  language = "en"
}

@ARTICLE{Hirschfield2018-wy,
  title    = "The British Society of {Gastroenterology/UK-PBC} primary biliary
              cholangitis treatment and management guidelines",
  author   = "Hirschfield, Gideon M and Dyson, Jessica K and Alexander, Graeme
              J M and Chapman, Michael H and Collier, Jane and H{\"u}bscher,
              Stefan and Patanwala, Imran and Pereira, Stephen P and Thain,
              Collette and Thorburn, Douglas and Tiniakos, Dina and Walmsley,
              Martine and Webster, George and Jones, David E J",
  journal  = "Gut",
  volume   =  67,
  number   =  9,
  pages    = "1568--1594",
  month    =  sep,
  year     =  2018,
  keywords = "autoimmune liver disease; care pathway; guidelines; obeticholic
              acid; ursodeoxycholic acid",
  language = "en"
}

@MISC{Lindor2009-il,
  title   = "Primary biliary cirrhosis",
  author  = "Lindor, Keith D and Eric Gershwin, M and Poupon, Raoul and Kaplan,
             Marshall and Bergasa, Nora V and Jenny Heathcote, E",
  journal = "Hepatology",
  volume  =  50,
  number  =  1,
  pages   = "291--308",
  year    =  2009
}

@MISC{White2018-sl,
  title   = "Review article: novel oral-targeted therapies in inflammatory
             bowel disease",
  author  = "White, J R and Phillips, F and Monaghan, T and Fateen, W and
             Samuel, S and Ghosh, S and Moran, G W",
  journal = "Alimentary Pharmacology \& Therapeutics",
  volume  =  47,
  number  =  12,
  pages   = "1610--1622",
  year    =  2018
}

@ARTICLE{Kirchgesner2018-vy,
  title    = "Risk of Serious and Opportunistic Infections Associated With
              Treatment of Inflammatory Bowel Diseases",
  author   = "Kirchgesner, Julien and Lemaitre, Magali and Carrat, Fabrice and
              Zureik, Mahmoud and Carbonnel, Franck and Dray-Spira, Rosemary",
  journal  = "Gastroenterology",
  volume   =  155,
  number   =  2,
  pages    = "337--346.e10",
  month    =  aug,
  year     =  2018,
  keywords = "Anti-TNFs; Combination Therapy; Infection; Inflammatory Bowel
              Disease; Thiopurines",
  language = "en"
}

@MISC{Kornbluth2010-ql,
  title   = "Ulcerative Colitis Practice Guidelines in Adults: American College
             of Gastroenterology, Practice Parameters Committee",
  author  = "Kornbluth, Asher and Sachar, David B",
  journal = "American Journal of Gastroenterology",
  volume  =  105,
  number  =  3,
  pages   = "501--523",
  year    =  2010
}

@MISC{Rowe2017-cw,
  title        = "Inflammatory Bowel Disease",
  booktitle    = "Medscape",
  author       = "Rowe, William A and Lichtenstein, Gary R",
  month        =  oct,
  year         =  2017,
  howpublished = "\url{https://emedicine.medscape.com/article/179037-overview}",
  note         = "Accessed: 2019-5-13"
}

@MISC{Kaser2010-dy,
  title   = "Inflammatory Bowel Disease",
  author  = "Kaser, Arthur and Zeissig, Sebastian and Blumberg, Richard S",
  journal = "Annual Review of Immunology",
  volume  =  28,
  number  =  1,
  pages   = "573--621",
  year    =  2010
}

@ARTICLE{Van_der_Sloot2017-gi,
  title    = "Inflammatory Bowel Diseases: Review of Known Environmental
              Protective and Risk Factors Involved",
  author   = "van der Sloot, Kimberley W J and Amini, Marzyeh and Peters, Vera
              and Dijkstra, Gerard and Alizadeh, Behrooz Z",
  journal  = "Inflamm. Bowel Dis.",
  volume   =  23,
  number   =  9,
  pages    = "1499--1509",
  month    =  sep,
  year     =  2017,
  language = "en"
}

@MISC{Burisch2013-yd,
  title   = "The burden of inflammatory bowel disease in Europe",
  author  = "Burisch, Johan and Jess, Tine and Martinato, Matteo and Lakatos,
             Peter L",
  journal = "Journal of Crohn's and Colitis",
  volume  =  7,
  number  =  4,
  pages   = "322--337",
  year    =  2013
}

@ARTICLE{Weimers2018-wh,
  title    = "The Natural History of {IBD}: Lessons Learned",
  author   = "Weimers, Petra and Munkholm, Pia",
  journal  = "Curr. Treat. Options Gastroenterol.",
  volume   =  16,
  number   =  1,
  pages    = "101--111",
  month    =  mar,
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license: MIT

license_type: permissive

branch_name: refs/heads/master

extension: bib