Table of Contents

• Sequence model evaluation framework for STARR-seq peak callingChristopher R. Beal, John G. Peters, Ronald J. Nowling. [doi]
• Inferring interaction networks from microbial time series data: it's not just finding a statisticCaroline Cannistra, Alex Yuan, Wenying Shou. [doi]
• Novel genomic duplication models through integer linear programmingJaroslaw Paszek, Oliver Eulenstein, Pawel Górecki 0001. [doi]
• Deep neural network models to automate incident triage in the radiation oncology incident learning systemPriyankar Bose, William C. Sleeman IV, Khajamoinuddin Syed, Michael Hagan, Jatinder Palta, Rishabh Kapoor, Preetam Ghosh. [doi]
• Data mining for electroencephalogram signal processing and analysisRossana Mancuso, Marzia Settino, Mario Cannataro. [doi]
• A hybrid deep neural network for robust single-cell genome-wide DNA methylation detectionRussell A. Li, Zhandong Liu. [doi]
• Hybridized distance- and contact- based hierarchical protein structure modeling using DConStructRahmatullah Roche, Sutanu Bhattacharya, Debswapna Bhattacharya. [doi]
• A CNN-based cell tracking method for multi-slice intravital imaging dataKenji Fujimoto, Tsubasa Mizugaki, Utkrisht Rajkumar, Hironori Shigeta, Shigeto Seno, Yutaka Uchida, Masaru Ishii, Vineet Bafna, Hideo Matsuda. [doi]
• Segmenting thoracic cavities with neoplastic lesions: a head-to-head benchmark with fully convolutional neural networksZhao Li, Rongbin Li, Kendall J. Kiser, Luca Giancardo, W. Jim Zheng. [doi]
• k-mer query tool for assessing population diversity in pangenomesHang Su, Ziwei Chen, Maya L. Najarian, Martin T. Ferris, Fernando Pardo-Manuel de Villena, Leonard McMillan. [doi]
• Copy number variation detection using single cell sequencing dataFatima Zare, Jacob Stark, Sheida Nabavi. [doi]
• CNN models for eye state classification using EEG with temporal orderingFemi William, Feng Zhu. [doi]
• Modeling protein structures from predicted contacts with modern molecular dynamics potentials: accuracy, sensitivity, and refinementRussell B. Davidson, Mathialakan Thavappiragasam, T. Chad Effler, Jess Woods, Dwayne A. Elias, Jerry M. Parks, Ada Sedova. [doi]
• Improving the efficiency of de Bruijn graph construction using compact universal hitting setsYael Ben-Ari, Dan Flomin, Lianrong Pu, Yaron Orenstein, Ron Shamir. [doi]
• Signal quality detection towards practical non-touch vital sign monitoringZongxing Xie, Bing Zhou 0001, Fan Ye 0003. [doi]
• Transformer-based named entity recognition for parsing clinical trial eligibility criteriaShubo Tian, Arslan Erdengasileng, Xi Yang 0015, Yi Guo 0005, Yonghui Wu, Jinfeng Zhang, Jiang Bian 0001, Zhe He 0001. [doi]
• Application of natural language processing and machine learning to radiology reportsSeoungdeok Jeon, Zachary Colburn, Joshua Sakai, Ling-Hong Hung, Ka Yee Yeung. [doi]
• GNNfam: utilizing sparsity in protein family predictions using graph neural networksAnuj Godase, Md. Khaledur Rahman, Ariful Azad. [doi]
• DeepNote-GNN: predicting hospital readmission using clinical notes and patient networkSara Nouri Golmaei, Xiao Luo. [doi]
• M. tuberculosis using a long-term recurrent convolutional networkAmir Hosein Safari, Nafiseh Sedaghat, Hooman Zabeti, Alpha Forna, Leonid Chindelevitch, Maxwell W. Libbrecht. [doi]
• Privacy preserving neural networks for electronic health records de-identificationTanbir Ahmed, Md Momin Al Aziz, Noman Mohammed, Xiaoqian Jiang. [doi]
• LSHvec: a vector representation of DNA sequences using locality sensitive hashing and FastText word embeddingsLizhen Shi, Bo Chen. [doi]
• LDEncoder: reference deep learning-based feature detector for transfer learning in the field of epigenomicsGun Woo (Warren) Park, Kevin Bryson. [doi]
• Assigning ICD-O-3 codes to pathology reports using neural multi-task training with hierarchical regularizationAnthony Rios, Eric B. Durbin, Isaac Hands, Ramakanth Kavuluru. [doi]
• AW-Net: automatic muscle structure analysis on B-mode ultrasound images for injury preventionHugo Michard, Bertrand Luvison, Quoc-Cuong Pham, Antonio J. Morales-Artacho, Gaël Guilhem. [doi]
• Computational modeling of SARS-CoV-2 Nsp1 binding to human ribosomal 40S complexLinkel Boateng, Anita Nag, Homayoun Valafar. [doi]
• Designing novel antimicrobial peptides against multi-drug resistant bacteriaShravani Bobde, Fahad Alsaab, Guangshun Wang, Monique L. van Hoek. [doi]
• Low resource recognition and linking of biomedical concepts from a large ontologySunil Mohan, Rico Angell, Nicholas Monath, Andrew McCallum. [doi]
• SPEAR: self-supervised post-training enhancer for molecule optimizationTianfan Fu, Cao Xiao, Kexin Huang, Lucas M. Glass, Jimeng Sun. [doi]
• Real-time peptide identification from high-throughput mass-spectrometry dataSumesh Kumar, Fahad Saeed. [doi]
• Gene-disease-drug link prediction using tripartite graphsCheng Chen, Stephen K. Grady, Sally R. Ellingson, Michael A. Langston. [doi]
• Cancer molecular subtype classification by graph convolutional networks on multi-omics dataBingjun Li, Tianyu Wang, Sheida Nabavi. [doi]
• Formulating a gene signature for diagnosis of autoimmune and infectious diseasesRiya Gupta, Aditya M. Rao, Lara Murphy Jones, Purvesh Khatri. [doi]
• Gazelle: transcript abundance query against large-scale RNA-seq experimentsXiaofei Zhang, Ye Yu 0001, Chan Hee Mok, James N. MacLeod, Jinze Liu. [doi]
• Joint learning for biomedical NER and entity normalization: encoding schemes, counterfactual examples, and zero-shot evaluationJiho Noh, Ramakanth Kavuluru. [doi]
• Concurrent imputation and prediction on EHR data using bi-directional GANs: Bi-GANs for EHR imputation and predictionMehak Gupta, Thao-Ly T. Phan, H. Timothy Bunnell, Rahmatollah Beheshti. [doi]
• Towards an extensible ontology for streaming sensor data for clinical trialsRobert Lyons, Geoffrey Ross Low, Clare Bates Congdon, Melissa Ceruolo, Marissa Ballesteros, Steven Cambria, Paolo DePetrillo. [doi]
• CytoSet: predicting clinical outcomes via set-modeling of cytometry dataHaidong Yi, Natalie Stanley. [doi]
• Probing automated treatment of urinary tract infections for bias: a case-study where machine learning perpetuates structural differences and racial disparitiesGarrett Yoon, Vincent J. Major. [doi]
• Do microscopy imaging frequency and experiment duration impact the analysis of T cell movement?Viktor Zenkov, James O'Connor, Hayley McNamara, Ian A. Cockburn, Vitaly V. Ganusov. [doi]
• Search feasibility in distributed MS-proteomics big dataUmair Mohammad, Fahad Saeed. [doi]
• MultiRBP: multi-task neural network for protein-RNA binding predictionJonathan Karin, Hagai Michel, Yaron Orenstein. [doi]
• Transformer-based unsupervised patient representation learning based on medical claims for risk stratification and analysisXianlong Zeng, Simon M. Lin, Chang Liu 0028. [doi]
• COVID-19 classification using thermal images: thermal images capability for identifying COVID-19 using traditional machine learning classifiersMartha Rebeca Canales-Fiscal, Rocío Ortiz López, Regina Barzilay, Victor Treviño, Servando Cardona-Huerta, Luis Javier Ramírez-Treviño, Adam Yala, José G. Tamez-Peña. [doi]
• Synthesized difference in differencesEric V. Strobl, Thomas A. Lasko. [doi]
• Mechanistic model demonstrates importance of autocrine IL-8 secretion by neutrophilsWangui Mbuguiro, Feilim Mac Gabhann. [doi]
• Frontier: finding the boundaries of novel transposable element insertions in genomesAnwica Kashfeen, Leonard McMillan. [doi]
• ShareTrace: an iterative message passing algorithm for efficient and effective disease risk assessment on an interaction graphErman Ayday, Youngjin Yoo, Anisa Halimi. [doi]
• Predicting aneurysmal degeneration of type B aortic dissection with computational fluid dynamicsBradley Feiger, Erick Lorenzana, David Ranney, Muath Bishawi, Julie Doberne, Andrew Vekstein, Soraya Voigt, Chad Hughes, Amanda Randles. [doi]
• de novo primer discoveryMarie Hoffmann, Michael T. Monaghan, Knut Reinert. [doi]
• Towards dynamic simulation of a whole cell modelJae-Seung Yeom, Konstantia Georgouli, Robert Blake, Ali Navid. [doi]
• Pheno-mapper: an interactive toolbox for the visual exploration of phenomics dataYoujia Zhou, Methun Kamruzzaman, Patrick S. Schnable, Bala Krishnamoorthy, Ananth Kalyanaraman, Bei Wang 0001. [doi]
• A multi-resolution graph convolution network for contiguous epitope predictionLisa Oh, Bowen Dai, Chris Bailey-Kellogg. [doi]
• FARM: hierarchical association rule mining and visualization methodPetr Tsurinov, Oleg Shpynov, Nina Lukashina, Daria Likholetova, Maxim N. Artyomov. [doi]
• SPAN and JBR: analysis and visualization toolkit for peak callingOleg Shpynov, Roman Chernyatchik, Petr Tsurinov, Maxim N. Artyomov. [doi]
• The genetics of human aging: predicting age and age-related diseases by deep mining high dimensional biomarker dataHannah Guan. [doi]
• Match2: hybrid self-organizing map and deep learning strategies for treatment effect estimationXiao Shou, Tian Gao, Dharmashankar Subramanian, Kristin P. Bennett. [doi]
• Statistical analysis of GC-biased gene conversion and recombination hotspots in eukaryotic genomes: a phylogenetic hidden Markov model-based approachMeijun Gao, Kevin J. Liu. [doi]
• MVAR: a mouse variation registryBahá El Kassaby, Kunde Ramamoorthy Govindarajan, Francisco Castellanos, Carol Bult. [doi]
• Surveillance of COVID-19 pandemic using social media: a reddit study in North CarolinaChristopher Whitfield, Yang Liu, Mohd Anwar. [doi]
• PubTrends: a scientific literature explorerOleg Shpynov, Nikolai Kapralov. [doi]
• Explaining large-for-gestational-age births: a random forest classifier with a novel local interpretation methodYuhan Du, Anthony R. Rafferty, Fionnuala M. McAuliffe, Catherine Mooney. [doi]
• COVID-19 diagnosis using model agnostic meta-learning on limited chest X-ray imagesTarun Naren, Yuanda Zhu, May Dongmei Wang. [doi]
• Transfer learning for predicting virus-host protein interactions for novel virus sequencesJack Lanchantin, Tom Weingarten, Arshdeep Sekhon, Clint Miller, Yanjun Qi. [doi]
• Exploring target specificity of antimicrobial peptides through deep learning embeddingsLauren Losin, Daniel Veltri. [doi]
• Temporal analysis of social determinants associated with COVID-19 mortalityShayom Debopadhaya, John S. Erickson, Kristin P. Bennett. [doi]
• FastCount: a fast gene count software for single-cell RNA-seq dataJinpeng Liu, Xinan Liu, Ye Yu 0001, Chi Wang, Jinze Liu. [doi]
• k-means clustering with various distancesDaniel N. Baker, Nathan Dyjack, Vladimir Braverman, Stephanie C. Hicks, Ben Langmead. [doi]
• Supervised multi-specialist topic model with applications on large-scale electronic health record dataZiyang Song, Xavier Sumba Toral, Yixin Xu, Aihua Liu, Liming Guo, Guido Powell, Aman Verma, David L. Buckeridge, Ariane Marelli, Yue Li. [doi]
• SUPREME: a cancer subtype prediction methodology integrating multiple biological datatypes using graph convolutional neural networksZiynet Nesibe Kesimoglu, Serdar Bozdag. [doi]
• KGDAL: knowledge graph guided double attention LSTM for rolling mortality prediction for AKI-D patientsLucas Jing Liu, Victor Ortiz-Soriano, Javier A. Neyra, Jin Chen. [doi]
• Using electronic health records to accurately predict COVID-19 health outcomes through a novel machine learning pipelineAlice Feng. [doi]
• Developing a modified version of generative adversarial network to predict the potential anti-viral drug of COVID-19Md. Sadek Hossain Asif. [doi]
• A multi-instance support vector machine with incomplete data for clinical outcome prediction of COVID-19Lodewijk Brand, Lauren Zoe Baker, Hua Wang. [doi]
• Extracapsular extension identification for head and neck cancer using multi-scale 3D deep neural networkYibin Wang, William Neil Duggar, Toms V. Thomas, P. Russell Roberts, Linkan Bian, Haifeng Wang. [doi]
• A value-based approach for training of classifiers with high-throughput small molecule screening dataNatalia Khuri, Sarah Parsons. [doi]
• HYPON: embedding biomedical ontology with entity setsZhuoyan Li, Sheng Wang. [doi]
• ppIacerDC: a new scalable phylogenetic placement methodElizabeth R. Koning, Malachi Phillips, Tandy J. Warnow. [doi]
• Scalable non-invasive pediatric cerebral visual impairment screening with the higher visual function question inventory (HVFQI)Mike Wong 0001, Saeideh Ghahghaei, Arvind Chandna, Anagha Kulkarni 0001. [doi]
• COP-E-CAT: cleaning and organization pipeline for EHR computational and analytic tasksAishwarya Mandyam, Elizabeth C. Yoo, Jeff Soules, Krzysztof Laudanski, Barbara E. Engelhardt. [doi]
• DBNet: a novel deep learning framework for mechanical ventilation prediction using electronic health recordsKai Zhang, Xiaoqian Jiang, Mahboubeh Madadi, Luyao Chen, Sean Savitz, Shayan Shams. [doi]
• caulobacter crescentusChunrui Xu, Yang Cao. [doi]
• Browsing weighted interactome models using GeneDiveMike Wong 0001, Nayana Laxmeshwar, Rachit Joshi, Anagha Kulkarni 0001. [doi]
• Investigating statistical analysis for network motifsZican Li, WooYoung Kim. [doi]
• BioNumQA-BERT: answering biomedical questions using numerical facts with a deep language representation modelYe Wu 0007, Hing-Fung Ting, Tak Wah Lam, Ruibang Luo. [doi]
• GWAS analysis to compute genetic markers of progression to Alzheimer's diseaseYashu Vashishath, Serdar Bozdag. [doi]