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Paul Horton, Readings in Computational Biology 2023

Course Overview

Papers Presented

  • Genetic algorithm-based clustering technique
    U. Maulik & S. Bandyopadhyay
    Pattern recognition, 33(9):1455-1465, 2000.
  • A benchmark study of sequence alignment methods for protein clustering
    Yingying Wang, Hongyan Wu & Yunpeng Ca
    BMC Bioinformatics, 19(Suppl 19):529, 2018.
  • A Fast UPGMA Algorithm With Multiple Graphics Processing Units Using NCCL
    Guan-Jie Hua, Che-Lun Hung, Chun-Yuan Lin, Fu-Che Wu, Yu-Wei Chan & Chuan Yi Tang
    Evol Bioinform Online13:1176934317734220, 2017.
  • DeepTorrent: a deep learning-based approach for predicting DNA N(4)-methylcytosine sites
    Quanzhong Liu, Jinxiang Chen, Yanze Wang, Shuqin Li, Cangzhi Jia, Jiangning Song & Fuyi Li
    Briefings in Bioinformatics, 22(3):1-14, 2021.
  • Long non-coding RNA 2310069B03Rik functions as a suppressor of Ucp1 expression under prolonged cold exposure in murine beige adipocytes
    Mari Iwase et al.
    Bioscience, Biotechnology, and Biochemistry, 84(2), 2020.
  • Machine learning applications in cancer prognosis and prediction
    Konstantina Kourou, Themis P. Exarchos, Konstantinos P. Exarchos, Michalis V. Karamouzis, Dimitrios I. Fotiadis
    Computational and Structural Biotechnology Journal, 13,8-17, 2015.
  • Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion.
    Thomsen MC & Nielsen M.
    Nucleic Acids Res., 40(Web Server issue):W281-7, 2012.
  • MethylSeqLogo: DNA methylation smart sequence logos
    Fei-Man Hsu & Paul Horton BMC Bioinformatics, 2023
  • Predicting DNA methylation status using word composition
    Lingyi Lu, Kao Lin, Ziliang Qian, Haipeng Li, Yudong Cai, Yixue Li
    Journal of Biomedical Science and Engineering, 03:(07) 672-676, 2010.
  • DNA Methylation Biomarkers-Based Human Age Prediction Using Machine Learning
    Atef Zaguia,..., & Neelam Goel
    Computational Intelligence and Neuroscience, 2022.
  • BERT-GT: cross-sentence n-ary relation extraction with BERT and Graph Transformer
    Po-Ting Lai & Zhiyong Lu
    Bioinformatics, 36(24):5678-5685, 2020.
  • enoLOGOS: a versatile web tool for energy normalized sequence logos
    Christopher T. Workman, Yutong Yin, David L. Corcoran, Trey Ideker, Gary D. Stormo, Panayiotis V. Benos,
    Nucleic Acids Research, 33suppl_2:W389–W392, 2005.
  • Ice-cream used as cryotherapy during high-dose melphalan conditioning reduces oral mucositis after autologous hematopoietic stem cell transplantation
    Marcin Jasiński, Martyna Maciejewska, Anna Brodziak, Michał Górka, Kamila Skwierawska, Wiesław W. Jędrzejczak, Agnieszka Tomaszewska, Grzegorz W. Basak & Emilian Snarski
    Scientific Reports, 11(1):22507, 2021
  • Diagnostic classification of cancers using DNA methylation of paracancerous tissues
    Baoshan Ma et al.
    Scientific Reports, 12(1):10646, 2022.
  • CPEM: 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, 9(1):16927, 2019.
  • Performance Evaluation of Machine Learning Methods for Breast Cancer Prediction: A case study
    M. S., H. K-A, M. G. & A. O.
    Informatics in Medicine Unlocked, 31, 2022.
  • A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
    Guillaume Marçais & Carl Kingsford
    Bioinformatics, 276:764–770, 2011.
  • Validation of a Functional Pyelocalyceal Renal Model for the Evaluation of Renal Calculi Passage While Riding a Roller Coaster
    Marc A Mitchell & David D Wartinger J Am Osteopath Assoc, 116(10):647-52, 2016.
  • An innovative approach for testing bioinformatics programs using metamorphic testing
    Tsong Yueh Chen, Joshua W K Ho, Huai Liu & Xiaoyuan Xie
    BMC Bioinformatics, 10:24, 2009.
  • Bio-semantic relation extraction with attention-based external knowledge reinforcement
    Zhijing Li,,Yuchen Lian, Xiaoyong Ma, Xiangrong Zhang, Chen Li
    BMC Bioinformatics, 21:213, 2020.
  • Histopathology images predict multi-omics aberrations and prognoses in colorectal cancer patients.
    Pei-Chen Tsai et. al
    Nat Commun., 14(1):2102, 2023.
  • STAR: ultrafast universal RNA-seq aligner
    Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras
    Bioinformatics, 29(1):15-21, 2013.
  • Cancer type prediction base on copy number aberration and chromatin 3D structure
    Yuchen Yuan et al.
    BMC Genomics, 19(Suppl 6):565, 2018.
  • Itch Relief by Mirror Scratching. A Psychophysical Study
    Christoph Helmchen, Carina Palzer, Thomas F. Münte, Silke Anders, & Andreas Sprenger
    PLoS ONE, doi:10.1371, 2013
  • Learning Deep Features for DNA Methylation Data Analysis
    Zhongwei Si, Hong Yu, Zhanyu Ma
    IEEE Access, 4:2732–2737, 2016
  • Logarithmic gap costs decrease alignment accuracy
    Reed A Cartwright
    BMC Bioinformatics, 7527, 2006.
  • Multiple Sequence Alignment
    Robert C. Edgar & Serafim Batzoglou
    Current Opinion in Structural Biology, 163, 2006.
  • iDNA-ABF: multi-scale deep biological language learning model for the interpretable prediction of DNA methylations
    Junru Jin, Yingying Yu, Ruheng Wang, Xin Zeng, Chao Pang, Yi Jiang, Zhongshen Li, Yutong Dai, Ran Su, Quan Zou, Kenta Nakai & Leyi Wei
    Genome Biology, 23:219, 2022
  • COVID-19 Deep Learning Prediction Model Using Publicly Available Radiologist-Adjudicated Chest X-Ray Images as Training Data: Preliminary Findings
    Mohd Zulfaezal Che Azemin, Radhiana Hassan, Mohd Izzuddin Mohd Tamrin & Mohd Adli Md Ali
    Int J Biomed Imaging, 2020.
  • Auditory stimulation of opera music induced prolongation of murine cardiac allograft survival and maintained generation of regulatory CD4+CD25+ cells
    M. Uchiyama et al.
    Journal of Cardiothoracic Surgery, 7:26, 2012.
  • Unsupervised Learning Composite Network to Reduce Training Cost of Deep Learning Model for Colorectal Cancer Diagnosis
    Jirui Guo, Wuteng Cao, Bairun Nie & Qiyuan Qin
    IEEE J Transl Eng Health Med, 11:54, 2023.
  • The Heros of CRISPR
    Eric Lander
    Cell, 164:18–28 2016
  • The effects of unilateral forced nostril breathing on cognition
    S A Jella & D S Shannahoff-Khalsa
    Int J Neuroscience, 73(1-2):61-8 1993.
  • A DNA methylation age predictor for zebrafish
    Benjamin Mayne, Darren Korbie, Lisa Kenchington, Ben Ezzy, Oliver Berry & Simon Jarman
    Aging, 12(24):24817-24835, 2020.
  • Prediction of Alzheimer's disease based on deep neural network by integrating gene expression and DNA methylation dataset Park Chihyn, Ha Jihwan & Park Sanghyun
    Expert Systems with Applications, 140, 2020.
  • CheXNet: Radiologist-Level Pneumonia Detection on Chest X-Rays with Deep Learning
    Pranav Rajpurkar, Jeremy Irvin, Kaylie Zhu, Brandon Yang, Hershel Mehta, Tony Duan, Daisy Ding, Aarti Bagul, Curtis Langlotz, Katie Shpanskaya, Matthew P. Lungren & Andrew Y. Ng
    arXiv, 1711.05225, 2017.

    • Entry Format

    <li>TITLE<br> Author, Author, ...<br> <i>Journal</i>, <b>VOL</b>:NUM, YYYY.</li>