The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms

Walker, Kimberly; Kalra, Divya; Lowdon, Rebecca F.; Chen, Guangyi; Molik, David; Soto, Daniela C.; Dabbaghie, Fawaz; Khleifat, Ahmad Al; Mahmoud, Medhat; Paulin, Luis F; Raza, Muhammad Sohail; Pfeifer, Susanne; Agustinho, Daniel Paiva; Aliyev, Elbay; Avdeyev, Pavel; Barrozo, Enrico R.; Behera, Sairam; Billingsley, Kimberley; Li, Chong; Choubey, Deepak; Coster, Wouter De; Fu, Yilei; Gener, Alejandro Rafael; Hefferon, Timothy; Henke, David; Höps, Wolfram; Illarionova, Anastasia; Jochum, Michael D.; María, José; Kesharwani, Rupesh K.; Kolora, Sree Rohit Raj; Kubica, Jędrzej; Lakra, Priya; Lattimer, Damaris; Liew, Chia-Sin; Lo, Bai-Wei; Lo, Chunhsuan; Lötter, Anneri; Majidian, Sina; Mendem, Suresh Kumar; Mondal, Rajarshi; Ohmiya, Hiroko; Parvin, Nasrin; Peralta, Carolina M; Poon, Chi-Lam; Prabhakaran, Ramanandan; Saitou, Marie; Sammi, Aditi; Sanio, Philippe; Sapoval, Nicolae; Syed, Najeeb; Treangen, Todd J.; Wang, Gaojianyong; Xu, Tiancheng; Yang, Jianzhi; Zhang, Shangzhe; Zhou, Weiyu; Sedlazeck, Fritz J.; Busby, Ben

doi:10.12688/f1000research.110194.1

Cited by 2 publications

(1 citation statement)

References 142 publications

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“…Многие исследователи практики проведения хакатонов по медицинской тематике отмечают, что, во-первых, это прекрасная возможность участия в междисциплинарных проектах, объединяющих компетенции ИТ-специалистов и медицинских работников, что способствует межпрофессиональному обучению (например, [5]), во-вторых, возможность выращивания поколения новаторов, способных использовать инновационные и предпринимательские подходы для решения сложных задач современной системы здравоохранения [6], в-третьих, возможность внедрения новых методик активного обучения в области медицины, способствующих развитию навыков постановки и решения задач в области цифровизации системы здравоохранения [7]. Причём темы проведения хакатонов в области медицины могут быть различны: от эпидемиологических исследований и вирусологии, до геномики и биоинформатики [8]. Однако проведение хакатонов по медицинской тематике сопряжено с рядом возникающих проблем у организаторов.…”

Section: Experience Of Conducting the First Russian Cardiology Hackat...unclassified

Experience of conducting the first Russian cardiology hackathon Cardio data hack

et al. 2023

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This article is about the experience in organizing and conducting the first Russian cardiology hackathon Cardio data hack UFA 2022 which took place in Ufa in November 2022. It describes the preparation stages and organizational conditions of the hackathon conducting, the ways of interacting between the event organizer and participants, and the methods of evaluating the tasks. The first hackathon case was the recognition of ventricular bigeminy in patients with 24-hour ECG recording; the second case was performing a meta-analysis of the studies which assessed efficacy and safety of oral anticoagulants in atrial fibrillation and chronic renal failure stages IV and V. The hackathon attracted 179 registered participants who formed 42 teams, but further only 37 of them confirmed their participation and formed 8 teams. 7 teams gave the final solution of the tasks, and 5 of them presented their results with 3 of them giving solutions for both cases. Eventually, there were obtained the prototypes of solution for bigeminy recognition during Holter monitoring and high-quality meta-analyses evaluating the efficacy and safety of oral anticoagulants.

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Section: Experience Of Conducting the First Russian Cardiology Hackat...unclassified

Experience of conducting the first Russian cardiology hackathon Cardio data hack

et al. 2023

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Identification of potential SARS-CoV-2 genetic markers resulting from host domestication

Wiśniewski,

Chen

2024

Preprint

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We developed a k-mer-based pipeline, namely the Pathogen Origin Recognition Tool using Enriched K-mers (PORT-EK) to identify genomic regions enriched in the respective hosts after the comparison of metagenomes of isolates between two host species. Using it we identified thousands of k-mers enriched in US white-tailed deer and betacoronaviruses in bat reservoirs while comparing them with human isolates. We demonstrated different coverage landscapes of k-mers enriched in deer and bats and unraveled 148 mutations in enriched k-mers yielded from the comparison of viral metagenomes between bat and human isolates. We observed that the third position within a genetic codon is prone to mutations, resulting in a high frequency of synonymous mutations of amino acids harboring the same physicochemical properties as unaltered amino acids. Finally, we classified and predicted the likelihood of host species based on the enriched k-mer counts. Altogether, PORT-EK showcased its feasibility for identifying enriched viral genomic regions, illuminating the different intrinsic tropisms of coronavirus after host domestication.

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The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms

Cited by 2 publications

References 142 publications

Experience of conducting the first Russian cardiology hackathon Cardio data hack

Experience of conducting the first Russian cardiology hackathon Cardio data hack

Identification of potential SARS-CoV-2 genetic markers resulting from host domestication

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