- Decision tree‐based classifiers for lung cancer diagnosis and subtyping using TCGA miRNA expression data.
Masih Sherafatian & Fateme Arjmand
Oncology Letters, 18:2125–2131, 2019.
- Deep learning: a new computational modelling techniques for genomics
Gökcen Eraslan, Žiga Avsec Julien Gagneur, & Fabian J. Theis
Nature Reviews Genetics, 2019.
- VEF: a variant filtering tool based on ensemble methods
Chuanyi Zhang & Idoia Ochoa
Bioinformatics, 30(8), 2020.
- Continuous blood glucose level prediction of Type 1 Diabetes based on Artificial Neural Network
Jaouher Ben Ali, Takoua Hamdi, Nader Fnaiech, Véronique Di Costanzo, Farhat Fnaiech & Jean-Marc Ginoux
Biocybernetics and Biomedical Engineering, 2019.
- Improved indel detection in DNA and RNA via realignment with ABRA2
Lisle E Mose, Charles M Perou & Joel S Parker
Bioinformatics, 35(17):2966–2973, 2019.
- A framework for variation discovery and genotyping using next-generation DNA sequencing data
DePristo, M. A., Banks, E., Poplin, R., Garimella, K. V., Maguire, J. R., Hartl, C., ... & McKenna, A.
Nature genetics, 43:(5), 4912011.
- LOTUS: A single- and multitask machine learning algorithm for the prediction of cancer driver genes
Olivier Collier, Véronique Stoven & Jean-Philippe Vert
PLoS Computational Biology, 2019.
- Pan-cancer machine learning predictors of primary site of origin and molecular subtype
William F. Flynn, Sandeep Namburi, Carolyn A. Paisie, Honey V. Reddi, Sheng Li, R. Krishna Murthy Karuturi, Joshy George
bioRxiv, July 05, 2018.
- U-Net: Convolutional Networks for Biomedical Image Segmentation
Olaf Ronneberger, Philipp Fischer & Thomas Brox
Part of the Lecture Notes in Computer Science book series (LNCS 9351), 2015.
- Logarithmic gap costs decrease alignment accuracy
Reed A Cartwright
BMC Bioinformatics, 7527, 2006.
- Discriminating stress from cognitive load using a wearable EDA device
Cornelia Setz, Bert Arnrich, Johannes Schumm, Roberto La Marca, Gerhard Tröster, & Ulrike Ehlert
IEEE Transactions on Information Technology in Biomedicine, 2010.
- The kipoi repository accelerates community exchange and reuse of predictive models for genomics
Žiga Avsec, Roman Kreuzhuber, Johnny Israeli, ... & Julien Gagneur
Nature Biotechnology, 37 589--600, 2019.
- Systematic comparison of variant calling pipelines using gold standard personal exome variant
Sohyun Hwang, Eiru Kim, Insuk Lee & Edward M. Marcotte
Scientific Reports, 5:17875, 2015.
- A machine learning-based model for survival prediction in patients with severe COVID-19 infection
Li Yan, Hai-Tao Zhang, ..., et al.
medRxiv, 2020.
- Assembly algorithms for next-generation sequencing data
Jason R. Miller, Sergey Koren & Granger Sutton
Genomics, 95(6):315–327, 2010.
- How to apply de Bruijn graphs to genome assembly
Phillip E C Compeau, Pavel Pezner, & Glenn Tesler
Nature Biotechnology, 29:987–991, 2011.
- On genomic repeats and reproducibility
Can Firtina, Can Alkan
Bioinformatics, 32(15), 2243-2247, 2016.
- Predicting Meridian in Chinese traditional medicine using machine learning approaches
Yinyin Wang, Mohieddin Jafari, Yun Tang & Jing Tang
PLoS Computational Biology, November 25, 2019.
- Development of Genome-Derived Tumor Type Prediction to Inform Clinical Cancer Care
Alexander Penson, Niedzica Camacho, Youyun Zheng, et al.
JAMA Oncology, 14 Nov 2019.
- Local Binary Convolutional Neural Networks
F. Jeufei-Xu, V. Boddeti, M. Savvides
CVPR, 2017.
- The Heros of CRISPR
Eric Lander
Cell, 164:18–28 2016
- TooT-T: discrimination of transport proteins from non-transport proteins
Munira Alballa & Gregory Butler
BMC Bioinformatics, 21:25, 2020.
- Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomes
Ehsaneddin Asgari, Mohammad R. K. Mofrad
PLoS ONE, November, 2015.
- EAGLE: Multi-locus Association Mapping on a Genome-wide scale made routine
Andrew W. George, Arunas Verbyla & Joshua Bowden
Bioinformatics, 36 1509–1516, 2020.
- The Precision-Recall Plot is more Informative than the ROC when evaluating binary classifiers on Imbalanced Datasets
Takaya Saito & Marc Rehmsmeier
PLoS ONE, 10:(3), e0118432, 2015.
- Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs
Antoine Limasset, Jean-François Flot & Pierre Peterlongo
Bioinformatics, 36:5, 1374–1381, 2020.
- A universal SNP and small-indel variant caller using deep neural networks
Poplin, R., Chang, P. C., Alexander, D., Schwartz, S., Colthurst, T., Ku, A., & Gross, S. S.
Nature Biotechnology, 36(10), 983–987, 2018.
- Google Goes Cancer Prediction: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes
Christof Winter, Glen Kristiansen, ..., & Robert Grüztmann
PLoS Computational Biology, 8(5): e1002511 2012
- Identification of 12 cancer types through genome deep learning
Yingshuai Sun, Sitao Zhu, ..., & Wenbin Chen
Scientific Reports, 9:17256, 2019.
- DNA Cryptography and Deep Learning using Genetic Algorithm with NW algorithm for Key Generation
Shruti Kalsi, Harleen Kaur & Victor Chang
Journal of Medical Systems, 42:17, 2018.
- Hybrid Retrieval-Generation Reinforced Agent (HRGR-Agent) for Medical Image Report Generation
Christy Y. Li, Xiaodan Liang, Zhiting Hu & Eric P. Xing
Proceedings 32th NeuiIPS, Montréal, Canada 2018.
- The proximal origin of SARS-CoV-2
Kristian G. Andersen, Andrew Rambaut, W. Ian Lipkin, Edward C. Holmes & Robert F. Garry
Nature Medicine, 26 450–455, 2020.
- DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning
Christof Angermueller, Heather Lee, Wolk Reik & Oliver Stegle
Genome Biology, 18:6, 2017.
- DeepGo: predicting protein functions from sequence and interactions using a deep ontology-aware classifier
Kulmanov M1, Khan MA1, Hoehndorf R1 & Wren J.
Bioinformatics, 34, 660-668, 2018.
- Lean and deep models for more accurate filtering of SNP and INDEL variant calls
Sam Friedman, Gauthier L, Farjoun Y & Eric Banks
Bioinformatics, 36, 2060-2067, 2020.
- The Impact of DNA Methylation on the cancer proteome
Majed Mohamed Magzoub, Marcos Prunello, Kevin Brennan & Olivier Gevaert
PLoS Computational Biology, 2019.
- Accurate cancer type classification based on somatic alterations using an ensemble of a random forest and a deep neural network
Kanggeun Lee, Hyoung-oh Jeong, Semin Lee & Won-Ki Jeong
Scientific Reports, 209(1):16927 2019.
- Alcoholism Detetection by Data Augmentation and Convolutional Neural Network with Stochastic Pooling
Shui-Hua Wang, Yi-Ding Lv, Yuxiu Sui, Shuai Liu, Su-Jing Wang & Yu-Dong Zhang
J Med Syst., 42:2, 2018.
- Standing Genetic Variation and the Evolution of Drug Resistance in HIV
Pleuni Simone Pennings
PLoS Computational Biology, 2012.
- Lost in translation: bioinformatics analysis of variations affecting the translation initiation codon in the human genome
Francisco Abad-Navarro, María Eugenia de la Morena-Barrio, Jesualdo Tomás Fernández-Breis & Javier Corral
Bioinformatics, 34(22):3788–3794, 2018.
- Hybridization Kinetics Explains CRISPR-Cas Off-Targeting Rules
Misha Klein, Behrouz Eslami-Mossallam, Dylan Gonzalez Arroyo & Martin Depken
Cell Reports, 22(6):1413-1423, 2018.
- Is artificial data useful for biomedical natural language processsing algorithms?
Zixu Wang, Julia Ive, Sumithra Velupillai, Lucia Specia
arXiv:1907.01055, BioNLP 2019
- Gene2vec: gene subsequence embedding for prediction of mammalian N6-methyladenosine sites from mRNA
Quan Zou, Pendgwei Xing, Leyi Wei & Bin Liu
RNA, 25(2):205-218, 2019.
- Predicting protein-protein interactions via multivariate mutual information of protein sequencing
Yijie Ding, Jijun Tang & Fei Guo
BMC Bioinformatics, 17:398, 2016.
- Comparing a few SNP calling algorithms using low-coverage sequencing data
X. Yu & S. Sun
BMC Bioinformatics, 14(1):274, 2013.
- PPCD: Privacy-preserving clinical decision with cloud support
Hui Ma, Xuyang Guo, Yuan Ping, Baocang Wang, Yuehua Yang, Zhili Zhang & Jingxian Zhou
PLoS ONE, 14(5):e0217349, 2019.
- Meta-Analysis of age-related gene expression profiles identifies common signatures of aging
João Pedro de Magalhães, João Curado & George M. Church
Bioinformatics, 25(7):875–881, 2009
- Gene2vec: distributed representation of genes based on co-expression
Jingcheng Du, Peilin Jia, Yulin Dai, Cui Tao, Zhongming Zhao & Degui Zhi
BMC Genomics, 20(Supl 1):82, 2019