Conference Program

Reproducibility for AI in Predictive Medicine

  • * CHARME Speaker
  • ** CHARME Invited Speaker

Poster Session - Abstracts

P1. Timothy J. Peters, Terence P. Speed and Susan J. Clark. A general framework for evaluating cross-platform concordance in genomic studies

P2. Paolo Missier, Jacek Cała. Preserving value in large scale data analytics through selective re-computation: the ReComp framework in the P4NU Turing Institute initiative for preventive HealthCare

P3.Andrej Blejec, Špela Baebler, Anna Coll Rius, Marko Petek, Živa Ramšak, Maja Zagorščak, Kristina Gruden. pISA-tree - being FAIR on the institutional level

P4. Arvind Singh Mer, Wail Ba-alawi, Petr Smirnov, Ming-Sound Tsao, David Cescon, Anna Goldenberg, Benjamin Haibe-Kains. Systematic assessment of genomic biomarkers for anticancer drug sensitivity prediction in patient derived xenografts

P5. Jongsuk Chung, Yeon Jeong Kim, Eunjeong Cho, Ki-Wook Lee, Taeseob Lee, Dong Hyeong Sung, Donghyun Park, Dae-Soon Son, Woongyang Park. The manufacture method of reference materials for NGS proficiency test of somatic variants

P6. Susanne Hollmann, Domenica D’Elia, Kristina Gruden, Marcus Frohme. With CHARME towards Standardization - Making the Case to train Communication and Sharing of Data amongst Researchers in Life Science Research

P7. Jarnot Patryk, Grynberg Marcin, Gruca Aleksandra. Same data - different results. Performance of protein sequence comparison tools in case of low complexity regions

P8. Donghyeong Seong, Jongsuk Chung, Ki-Wook Lee, Taeseob Lee, Byung-Suk Kim, Byoung-Kee Yic, Woongyang Park, Dae-Soon Son, Quality control reference database for NGS panel sequencing

P9. Benjamin Lam, Paolo Missier, Michael Catt. P4@NU: Exploring the role of digital and genetic biomarkers to learn personalized predictive models of metabolic diseases

P10. Yen Hoang, Stefanie Gryzik, Detlef Groth, Ria Baumgrass, PRI - Pattern Recognition of Immune cells

P11. Riya Paul, Michael Czisch, Philipp G. Sämann, Bertram Müller-Myhsok, Morphological ICA: Exploiting across subjects covariance and independent component analysis to define volume based networks

P12. David Kreil and Paweł Łabaj. Processing pipeline calibration and confounder removal for accurate and reproducible patient profiling

P13. Jingcheng Yang, Yechao Huang, Jun Shang, Zhaojie Xia, Luyao Ren, Ying Yu, Yuanting Zheng, Li Guo, Leming Shi. Choppy: an integrated pipeline management platform for efficiently achieving computational reproducibility in omics
P14. Eran Elhaik, Why all Principal Component Analyses (PCA) in genetics are likely wrong?

P15. Malik Yousef, Loai Abddallah, Jens Allmer, maTE: Discovering Expressed MicroRNA - Target Interactions

P16. Veronica Tozzo, Annalisa Barla, Modeling of gene expression time series with the latent time-evolving graphical lasso

P17. Xin Shao, Jie Liao and Xiaohui Fan, Integrated analysis of cancer cell lines and tumor samples guides cell line selection for cancer research: a landscape study

P18. Colin Birkenbihl, Marc Jacobs, Martin Hofmann-Apitius. Laying the Foundation for Reproducible Machine Learning: Systematic Cross-sectional and Longitudinal Dataset Comparisons

P19. Jens Dörpinghaus, Marc Jacobs, Martin Hofmann-Apitius. Context graph for biomedical research data: A FAIR and open approach towards reproducible research in Medicine

P20. Giacomo Baruzzo, Ilaria Patuzzi, Barbara Di Camillo, SPARSim Single Cell: a count data simulator for scRNA-seq data

P21. Wendell Jones, A Pan-Cancer Analysis of the TME Shows Reproducibility but Tissue-Dependent Associations between RNA-based Immune Signatures, Tumor Mutational Burden, and Outcomes

P22. Chunlin Xiao, Huixiao Hong, Wenming Xiao. Evaluation of de novo assembly and structural variation detection in a paired tumor-normal samples

P23. Amrane Meriem, Oukid Salyha, Tolga Ensari. M-RNA lung Cancer Data Classification Using Feature selection

P24. Matías M. Falcó, Cankut Çubuk, Carlos Loucera, María Peña-Chilet, Marta R. Hidalgo, Joaquín Dopazo. Machine learning and mechanistic models of pathway activity to discover new therapeutic targets

P25. Kelci Miclaus, Meijian Guan, Eliver Ghosn. Analytic Opportunities and Challenges with Single-Cell RNA-Sequencing Data

P26. Agata Muszyńska, Ryszard Przewłocki, Paweł Łabaj. Improving reproducibility in RNA-seq data analysis with svaseq

P27. David Kreil, Paweł Łabaj and Anna Bergstrom Lucas. SEQC2 calibration benchmarks for reproducible accurate gene transcript profiling: A comprehensive onco-panel reference for gene structure variant identification
P28. Paula A. Marin Zapata, Stefan Prechtl, Sebastian Raese, Djork-Arne Clevert. Automating the analysis of high content screens by artificial intelligence

P29. Paula A. Marin Zapata, Sina Roth, Dirk Schmutzler, Thomas Wolf, Erica Manesso, Djork-Arne Clevert. Standardizing the classification of herbicide phenotypes by transfer learning and ranking models

P30. Andrea Bizzego, Giulio Gabrieli, Marc H. Bornstein, Kirby Deater-Deckard, Diane L. Putnick, Jennifer E. Lansford, Robert H. Bradley, Megan Costa, Gianluca Esposito. Adapting the MAQC-DAP to the UNICEF MICS Dataset to Predict Child Mortality in Low- and Middle-Income Countries

P31. Yiran Tao, Dongsheng Yuan, Chengkai Lv, Tieliu Shi. X-CNV: predicting the pathogenicity of copy number variations with XGBoost

P32. Isotta Landi, Riccardo Miotto, Paola Venuti, Joel T. Dudley, Cesare Furlanello. Electronic Health Records encoding for neurodevelopmental disorders stratification

P33. Damiana Salvalai, Andrea Bizzego, Alessandro Fracchetti, Giuseppe Jurman, Francesco Ricci, Cesare Furlanello. Integrating Deep Learning and Radiomics for predictive models from CT/PET imaging

P34. Marco Chierici, Marco Giulini, Nicole Bussola, Giuseppe Jurman, Cesare Furlanello. ML4Tox - A Machine Learning Framework for Predictive Toxicology

P35. Gosia Golda, Lara Bossini-Castillo, Natalia Kunowska, Dafni Glinos, Paweł Łabaj, Gosia Trynka. The AIN: ATAC-seq integrity number for assessing pre-sequencing quality of the libraries

P36. Giovanni Guaraldi, Federica Mandreoli, Riccardo Martoglia. Intrinsic Capacity Index in Older Adults living with HIV: data analytics from a prospective clinical trial to standardise a healthy aging tool

P37. Ilaria Basadonne, Alessandro Zandonà, Stefano Levi Morter, Pamela Vernocchi, Marco Chierici, Andrea Quagliariello, Giuseppe Jurman, Cesare Furlanello, Lorenza Putignani, Paola Venuti. Metaproteomics in ASD Families: A New Approach for Gut Microbiota Profiling in Autism Spectrum Disorders

P38. Nicole Bussola, Andrea Bizzego, Marco Chierici, Valerio Maggio, Margherita Francescatto, Luca Cima, Marco Cristoforetti, Giuseppe Jurman, Cesare Furlanello. Evaluating reproducibility of Deep Learning models on Digital Pathology images

P39. Yuanting Zheng, Luyao Ren, Wanwan Hou, Jingcheng Yang, Yechao Huang, Ding Bao, Ying Yu, Leming Shi. Reproducible Integration of Real-World Sequencing Data to Benchmark Germline Variant Calls for Proficiency Test

P40. Chia-Jung Chang, Marcelo Fernandez-Viña, Wenzhong Xiao. Benchmarking NGS of HLA Genes – Current Status and Challenges

P41. Loai Abdallah and Malik Yousef. Grouping Classification Method based on Ensemble Clustering
What can we learn from histology about spatial gene expression?