Featured Publications
Featured List
Assessment of Machine Learning Detection of Environmental Enteropathy and Celiac Disease in Children
Sana Syed, Mohammad Al-Boni, Marium N Khan, Kamran Sadiq, Najeeha T Iqbal, Christopher A Moskaluk, Paul Kelly, Beatrice Amadi, S Asad Ali, Sean R Moore, Donald E Brown
JAMA Network Open, June 2019
Mo1992–Solving the Stain Dilemma: Computational Image Analysis to Address Differential Tissue Staining Color Bias in Duodenal Biopsies
Sana Syed, Aman Shrivastava, Karan Kant, Saurav Sengupta, Luke Kang, Marium N Khan, Najeeha T Iqbal, Kamran Sadiq, Christopher A Moskaluk, Beatrice Amadi, Paul Kelly, Asad Ali, Sean Moore, Donald Brown
Gastronenterology
Deep Learning for Detecting Diseases in Gastrointestinal Biopsy Images
Aman Srivastava, Saurav Sengupta, Sung-Jun Kang, Karan Kant, Marium Khan, S Asad Ali, Sean R Moore, Beatrice C Amadi, Paul Kelly, Sana Syed, Donald E Brown
IEEE Xplore
Publications
- Machine Learning Predictive Outcomes Modeling in Inflammatory Bowel Diseases. Inflamm Bowel Dis. 2022 Jun 3;28(6):819-829. doi: 10.1093/ibd/izab187. Review. PubMed PMID: 34417815; PubMed Central PMCID: PMC9165557.
- Application of Artificial Intelligence to Clinical Practice in Inflammatory Bowel Disease – What the Clinician Needs to Know. J Crohns Colitis. 2022 Mar 14;16(3):460-471. doi: 10.1093/ecco-jcc/jjab169. PubMed PMID: 34558619; PubMed Central PMCID: PMC8919817.
- Bile Acid Profiling Reveals Distinct Signatures in Undernourished Children with Environmental Enteric Dysfunction. JNutr. 2021Dec3;151(12):3689-3700. doi: 10.1093/jn/nxab321. PubMed PMID: 34718665; PubMed Central PMCID: PMC8643614.
- Distance from Healthcare Facilities Is Associated with Increased Morbidity of Acute Infection in Pediatric Patients in Matiari, Pakistan. Int J Environ Res Public Health. 2021 Nov 7;18(21). doi:10.3390/ijerph182111691. PubMed PMID: 34770204; PubMed Central PMCID: PMC8583418.
- Dialing in Prevention of Childhood Stunting and Diarrhea in Low-Income Countries. Clin Infect Dis. 2021 Nov 2;73(9):e2569-e2570. doi: 10.1093/cid/ciaa1059. PubMed PMID: 32785660.
- Deep Learning Methods for Anatomical Landmark Detection in Video Capsule Endoscopy Images. Proc Future Technol Conf (2020). 2021 Nov;1288:426-434. doi: 10.1007/978-3-030-63128-4_32. Epub 2020 Oct 31. PubMed PMID: 34693407; PubMed Central PMCID: PMC8528446.
- Gut integrity and duodenal enteropathogen burden in undernourished children with environmental enteric dysfunction. PLoS Negl Trop Dis. 2021 Jul;15(7):e0009584. doi: 10.1371/journal.pntd.0009584. eCollection 2021 Jul. PubMed PMID: 34264936; PubMed Central PMCID: PMC8352064.
- Artificial Intelligence-based Analytics for Diagnosis of Small Bowel Enteropathies and Black Box Feature Detection. J Pediatr Gastroenterol Nutr. 2021 Jun 1;72(6):833-841. doi: 10.1097/MPG.0000000000003057. PubMed PMID: 33534362; PubMed Central PMCID: PMC8767179.
- Mucosal Genomics Implicate Lymphocyte Activation and Lipid Metabolism in Refractory Environmental Enteric Dysfunction. Gastroenterology. 2021 May;160(6):2055-2071.e0. doi: 10.1053/j.gastro.2021.01.221. Epub 2021 Jan 29. PubMed PMID: 33524399; PubMed Central PMCID: PMC8113748.
- Deep learning systems detect dysplasia with human-like accuracy using histopathology and probe-based confocal laser endomicroscopy. Sci Rep. 2021 Mar 3;11(1):5086. doi: 10.1038/s41598-021-84510-4. PubMed PMID: 33658592; PubMed Central PMCID: PMC7930108.
- Self-Attentive Adversarial Stain Normalization. Pattern Recognit (2021). 2021 Jan;12661:120-140. doi: 10.1007/978-3-030-68763-2_10. Epub 2021 Feb 21. PubMed PMID: 34693406; PubMed Central PMCID: PMC8528268.
- Ten simple rules for engaging with artificial intelligence in biomedicine. PLoS Comput Biol. 2021 Feb;17(2):e1008531. doi: 10.1371/journal.pcbi.1008531. eCollection 2021 Feb. PubMed PMID: 33571194; PubMed Central PMCID: PMC7877652.
- Advancing Eosinophilic Esophagitis Diagnosis and Phenotype Assessment with Deep Learning Computer Vision. Biomed Eng Syst Technol Int Jt Conf BIOSTEC Revis Sel Pap. 2021 Feb;2021:44-55. doi: 10.5220/0010241900440055. PubMed PMID: 34046649; PubMed Central PMCID: PMC8144887.
- Semi-Supervised Classification of Noisy, Gigapixel Histology Images. Proc IEEE Int Symp Bioinformatics Bioeng. 2020 Oct;2020:563-568. doi: 10.1109/BIBE50027.2020.00097. Epub 2020 Dec 16. PubMed PMID: 34046246; PubMed Central PMCID: PMC8144886.
- Artificial Intelligence and Its Role in Identifying Esophageal Neoplasia. Dig Dis Sci. 2020 Dec;65(12):3448-3455. doi: 10.1007/s10620-020-06643-2. Epub 2020 Oct 15. Review. PubMed PMID: 33057945; PubMed Central PMCID: PMC8139616.
- Machine learning model demonstrates stunting at birth and systemic inflammatory biomarkers as predictors of subsequent infant growth – a four-year prospective study. BMC Pediatr. 2020 Oct 30;20(1):498. doi: 10.1186/s12887-020-02392-3. PubMed PMID: 33126871; PubMed Central PMCID: PMC7597024.
- Deep Learning for Whole-Slide Tissue Histopathology Classification: A Comparative Study in the Identification of Dysplastic and Non-Dysplastic Barrett’s Esophagus. J Pers Med. 2020 Sep 23;10(4). doi: 10.3390/jpm10040141. PubMed PMID: 32977465; PubMed Central PMCID: PMC7711456.
- Potential for Standardization and Automation for Pathology and Endoscopy in Inflammatory Bowel Disease. Inflamm Bowel Dis. 2020 Sep 18;26(10):1490-1497. doi: 10.1093/ibd/izaa211. Review. PubMed PMID: 32869844; PubMed Central PMCID: PMC7749192.
- Time to regain birth weight predicts neonatal growth velocity: A single-center experience. Clin Nutr ESPEN. 2020 Aug;38:165-171. doi: 10.1016/j.clnesp.2020.05.010. Epub 2020 Jun 20. PubMed PMID: 32690152; PubMed Central PMCID: PMC8144885.
- HMIC: Hierarchical Medical Image Classification, A Deep Learning Approach. Information (Basel). 2020 Jun;11(6). doi: 10.3390/info11060318. Epub 2020 Jun 12. PubMed PMID: 34367687; PubMed Central PMCID: PMC8346231.
- SCREENING FOR BARRETT’S ESOPHAGUS WITH PROBE-BASED CONFOCAL LASER ENDOMICROSCOPY VIDEOS. Proc IEEE Int Symp Biomed Imaging. 2020 Apr;2020:1659-1663. doi: 10.1109/isbi45749.2020.9098630. Epub 2020 May 22. PubMed PMID: 34040694; PubMed Central PMCID: PMC8144884.
- CeliacNet: Celiac Disease Severity Diagnosis on Duodenal Histopathological Images Using Deep Residual Networks. Proceedings (IEEE Int Conf Bioinformatics Biomed). 2019 Nov;2019:962-967. doi: 10.1109/bibm47256.2019.8983270. Epub 2020 Feb 6. PubMed PMID: 35003830; PubMed Central PMCID: PMC8740775.
- A novel histological index for evaluation of environmental enteric dysfunction identifies geographic-specific features of enteropathy among children with suboptimal growth. PLoS Negl Trop Dis. 2020 Jan;14(1):e0007975. doi: 10.1371/journal.pntd.0007975. eCollection 2020 Jan. PubMed PMID: 31929525; PubMed Central PMCID: PMC6980693.
- Artificial Intelligence Applied to Gastrointestinal Diagnostics: A Review. J Pediatr Gastroenterol Nutr. 2020 Jan;70(1):4-11. doi: 10.1097/MPG.0000000000002507. Review. PubMed PMID: 31567886; PubMed Central PMCID: PMC6934912.
- Diagnosis of Celiac Disease and Environmental Enteropathy on Biopsy Images Using Color Balancing on Convolutional Neural Networks. Proc Futur Technol Conf FTC (2019). 2020;1069:750-65. doi: 10.1007/978-3-030-32520-6_55. Epub 2019 Oct 13. PubMed PMID: 34726364; PubMed Central PMCID: PMC8536862.
- Mo1175 USE OF MACHINE LEARNING AND COMPUTER VISION TO LINK EOSINOPHILIC ESOPHAGITIS CELLULAR PATTERNS WITH CLINICAL PHENOTYPES AND DISEASE LOCATION. Proceedings of the Future Technologies Conference (FTC). 2020; 1.
- Exploring Themes and Bias in Art using Machine Learning Image Analysis. 2020 Systems and Information Engineering Design Symposium (SIEDS). 2020; :1-6. NIHMSID: NIHMS1696491.
- Pathobiome driven gut inflammation in Pakistani children with Environmental Enteric Dysfunction. PLoS One. 2019;14(8):e0221095. doi: 10.1371/journal.pone.0221095. eCollection 2019. PubMed PMID: 31442248; PubMed Central PMCID: PMC6707605.
- Study of Environmental Enteropathy and Malnutrition (SEEM) in Pakistan: protocols for biopsy based biomarker discovery and validation. BMC Pediatr. 2019 Jul 22;19(1):247. doi: 10.1186/s12887-019-1564-x. PubMed PMID: 31331393; PubMed Central PMCID: PMC6643315.
- Assessment of Machine Learning Detection of Environmental Enteropathy and Celiac Disease in Children. JAMA Netw Open. 2019 Jun 5;2(6):e195822. doi: 10.1001/jamanetworkopen.2019.5822. PubMed PMID: 31199451; PubMed Central PMCID: PMC6575155.
- Duodenal Biopsies Classification and Understanding using Convolutional Neural Networks. AMIA Jt Summits Transl Sci Proc. 2019;2019:453-461. eCollection 2019. PubMed PMID: 31258999; PubMed Central PMCID: PMC6568096.
- Cholestasis affects enteral tolerance and prospective weight gain in the NICU. Clin Nutr ESPEN. 2019 Apr;30:119-125. doi: 10.1016/j.clnesp.2019.01.006. Epub 2019 Feb 4. PubMed PMID: 30904211; PubMed Central PMCID: PMC8375631.
- Celiacnet: Celiac disease severity diagnosis on duodenal histopathological images using deep residual networks. 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). 2019; :962-967.
- Biomarkers of Systemic Inflammation and Growth in Early Infancy are Associated with Stunting in Young Tanzanian Children. Nutrients. 2018 Aug 24;10(9). doi: 10.3390/nu10091158. PubMed PMID: 30149537; PubMed Central PMCID: PMC6164697.
- Environmental Enteropathy in Undernourished Pakistani Children: Clinical and Histomorphometric Analyses. Am J Trop Med Hyg. 2018 Jun;98(6):1577-1584. doi: 10.4269/ajtmh.17-0306. Epub 2018 Mar 29. PubMed PMID: 29611507; PubMed Central PMCID: PMC6086170.
- Serum anti-flagellin and anti-lipopolysaccharide immunoglobulins as predictors of linear growth faltering in Pakistani infants at risk for environmental enteric dysfunction. PLoS One. 2018;13(3):e0193768. doi: 10.1371/journal.pone.0193768. eCollection 2018. PubMed PMID: 29509790; PubMed Central PMCID: PMC5839587.
- Promising Biomarkers of Environmental Enteric Dysfunction: A Prospective Cohort study in Pakistani Children. Sci Rep. 2018 Feb 14;8(1):2966. doi: 10.1038/s41598-018-21319-8. PubMed PMID: 29445110; PubMed Central PMCID: PMC5813024.
- High SMAD7 and p-SMAD2,3 expression is associated with environmental enteropathy in children. PLoS Negl Trop Dis. 2018 Feb;12(2):e0006224. doi: 10.1371/journal.pntd.0006224. eCollection 2018 Feb. PubMed PMID: 29415065; PubMed Central PMCID: PMC5819826.
- Vitamin D Status Is Associated with Hepcidin and Hemoglobin Concentrations in Children with Inflammatory Bowel Disease. Inflamm Bowel Dis. 2017 Sep;23(9):1650-1658. doi: 10.1097/MIB.0000000000001178. PubMed PMID: 28700535; PubMed Central PMCID: PMC5716347.
- Tissue is the Issue: Duodenal Biopsies to Elucidate Gut Structure and Function Among Undernourished Children in Low-Resource Settings. EBioMedicine. 2017 Sep;23:10-11. doi: 10.1016/j.ebiom.2017.08.003. Epub 2017 Aug 4. PubMed PMID: 28801237; PubMed Central PMCID: PMC5605323.
- Use of Reticulocyte Hemoglobin Content in the Assessment of Iron Deficiency in Children With Inflammatory Bowel Disease. J Pediatr Gastroenterol Nutr. 2017 May;64(5):713-720. doi: 10.1097/MPG.0000000000001335. PubMed PMID: 27429427; PubMed Central PMCID: PMC5239765.
- Environmental Enteric Dysfunction in Children. J Pediatr Gastroenterol Nutr. 2016 Jul;63(1):6-14. doi: 10.1097/MPG.0000000000001147. Review. PubMed PMID: 26974416; PubMed Central PMCID: PMC4920693.
- Determinants of Anemia among School-Aged Children in Mexico, the United States and Colombia. Nutrients. 2016 Jun 23;8(7). doi: 10.3390/nu8070387. PubMed PMID: 27347992; PubMed Central PMCID: PMC4963863.
- Pilot Study Evaluating Efficacy of 2 Regimens for Hypovitaminosis D Repletion in Pediatric Inflammatory Bowel Disease. J Pediatr Gastroenterol Nutr. 2016 Feb;62(2):252-8. doi: 10.1097/MPG.0000000000000915. PubMed PMID: 26196201; PubMed Central PMCID: PMC4863642.
- Authorship Concerns and Who Truly Owns a Research Idea?. Pediatrics. 2015 Nov;136(5):969-73. doi: 10.1542/peds.2015-1421. Epub 2015 Oct 12. PubMed PMID: 26459651; PubMed Central PMCID: PMC4621797.
- Estimates of possible severe bacterial infection in neonates in sub-Saharan Africa, south Asia, and Latin America for 2012: a systematic review and meta-analysis. Lancet Infect Dis. 2014 Aug;14(8):731-741. doi: 10.1016/S1473-3099(14)70804-7. Epub 2014 Jun 25. Review. PubMed PMID: 24974250; PubMed Central PMCID: PMC4123782.
- Neonatal severe bacterial infection impairment estimates in South Asia, sub-Saharan Africa, and Latin America for 2010. Pediatr Res. 2013 Dec;74 Suppl 1:73-85. doi: 10.1038/pr.2013.207. Review. PubMed PMID: 24366464; PubMed Central PMCID: PMC3873707.
- Years lived with disability (YLDs) for 1160 sequelae of 289 diseases and injuries 1990-2010: a systematic analysis for the Global Burden of Disease Study 2010. Lancet. 2012 Dec 15;380(9859):2163-96. doi: 10.1016/S0140-6736(12)61729-2. PubMed PMID: 23245607; PubMed Central PMCID: PMC6350784.
- Disability-adjusted life years (DALYs) for 291 diseases and injuries in 21 regions, 1990-2010: a systematic analysis for the Global Burden of Disease Study 2010. Lancet. 2012 Dec 15;380(9859):2197-223. doi: 10.1016/S0140-6736(12)61689-4. PubMed PMID: 23245608; NIHMSID:NIHMS1005030.
- Effect of case management on neonatal mortality due to sepsis and pneumonia. BMC Public Health. 2011 Apr 13;11 Suppl 3:S13. doi: 10.1186/1471-2458-11-S3-13. Review. PubMed PMID: 21501430; PubMed Central PMCID: PMC3231886.