Table of Contents

• HMSC: a Hybrid Metagenomic Sequence Classification AlgorithmSubrata Saha, Zigeng Wang, Sanguthevar Rajasekaran. [doi]
• Deep Ranking in Template-free Protein Structure PredictionXiao Chen, Nasrin Akhter, Zhiye Guo, Tianqi Wu, Jie Hou, Amarda Shehu, Jianlin Cheng. [doi]
• Three Co-expression Pattern Types across Microbial Transcriptional Networks of Plankton in Two Oceanic WatersRuby Sharma, Xuye Luo, Sajal Kumar, Mingzhou Song 0001. [doi]
• Multi-Site Assessment of Pediatric Bone Age Using Deep LearningAly A. Valliani, John T. Schwartz, Varun Arvind, Amir Taree, Jun S. Kim, Samuel K. Cho. [doi]
• How to build regulatory networks from single-cell gene expression dataAditya Pratapa, Amogh P. Jalihal, Jeffrey N. Law, Aditya Bharadwaj, T. M. Murali 0001. [doi]
• Avocado: Deep tensor factorization characterizes the human epigenome via imputation of tens of thousands of functional experimentsJacob M. Schreiber, Timothy Durham, William S. Noble, Jeffrey A. Bilmes. [doi]
• EXAM: An Explainable Attention-based Model for COVID-19 Automatic DiagnosisWenqi Shi, Li Tong, Yuchen Zhuang, Yuanda Zhu, May D. Wang. [doi]
• Staging Epileptogenesis with Deep Neural NetworksDiyuan Lu, Sebastian Bauer, Valentin Neubert, Lara Sophie Costard, Felix Rosenow, Jochen Triesch. [doi]
• A Supervised Machine Learning Approach for Distinguishing Between Additive and Replacing Horizontal Gene TransfersAbhijit Mondal, Misagh Kordi, Mukul S. Bansal. [doi]
• Smart Computational Approaches with Advanced Feature Selection Algorithms for Optimizing the Classification of Mobility Data in Health InformaticsElham Rastegari, Donovan Orn, Hesham H. Ali. [doi]
• Identifying Evolutionary Origins of Repeat Domains in Protein FamiliesChaitanya Aluru, Mona Singh 0001. [doi]
• Transforming the Language of Life: Transformer Neural Networks for Protein Prediction TasksAnanthan Nambiar, Maeve Heflin, Simon Liu, Sergei Maslov, Mark Hopkins, Anna M. Ritz. [doi]
• Prefix/Suffix Variation in Retinoic Acid Response ElementsYuan Zhuang, Kara L. Cerveny, Anna M. Ritz. [doi]
• Novel Generated Peptides for COVID-19 TargetsAllison M. Rossetto, Wenjin Zhou. [doi]
• Global Surveillance of COVID-19 by mining news media using a multi-source dynamic embedded topic modelYue Li, Pratheeksha Nair, Zhi-Wen, Imane Chafi, Anya Okhmatovskaia, Guido Powell, Yannan Shen, David L. Buckeridge. [doi]
• Functional Enrichment Analysis of Deregulated Long Non-Coding RNAs in Cancer Based on their Genomic NeighborsGulden Olgun, Oznur Tastan. [doi]
• CTDPathSim: Cell line-tumor deconvoluted pathway-based similarity in the context of precision medicine in cancerBanabithi Bose, Serdar Bozdag. [doi]
• Joint Grid Discretization for Biological Pattern DiscoveryJiandong Wang, Sajal Kumar, Mingzhou Song 0001. [doi]
• Bio-JOIE: Joint Representation Learning of Biological Knowledge BasesJunheng Hao, Chelsea J.-T. Ju, Muhao Chen, Yizhou Sun, Carlo Zaniolo, Wei Wang 0010. [doi]
• A multi-context feature learning approach to identify disease-specific gene neighborhoodsSudhir Ghandikota, Anil G. Jegga. [doi]
• Beyond B-Cell Epitopes: Curating Positive Data on Antipeptide Paratope Binding to Support Development of Computational Tools for Vaccine Design and Other Translational ApplicationsSalvador Eugenio C. Caoili. [doi]
• RA2Vec: Distributed Representation of Protein Sequences with Reduced Alphabet Embeddings: RA2Vec: Distributed RepresentationRajitha Yasas Wijesekara, Ashwin Lahorkar, Kunal Rathore, Jayaraman Valadi. [doi]
• Deep Neural Network Modeling for Phenotypic Prediction of Metagenomic SamplesYassin Mreyoud, Tae-Hyuk Ahn. [doi]
• A Unified Cloud-Native Architecture For Heterogeneous Data Aggregation And ComputationFatemeh Rouzbeh, Ananth Grama, Paul M. Griffin, Mohammad Adibuzzaman. [doi]
• Characterization of S. cerevisiae Protein Complexes by Representative DDI Graph PlanarityWilliam Gasper, Kathryn Cooper, Nathan Cornelius, Hesham Ali 0001, Sanjukta Bhowmick. [doi]
• Collaborative Cloud Computing Framework for Health Data with Open Source TechnologiesFatemeh Rouzbeh, Ananth Grama, Paul M. Griffin, Mohammad Adibuzzaman. [doi]
• Re-balancing Variational Autoencoder Loss for Molecule Sequence GenerationChaochao Yan, Sheng Wang, Jinyu Yang, Tingyang Xu, JunZhou Huang. [doi]
• Refinement of G protein-coupled receptor structure models: Improving the prediction of loop conformations and the virtual ligand screening performancesBhumika Arora. [doi]
• NeTFactor, a framework for identifying transcriptional regulators of gene expression-based biomarkersMehmet Eren Ahsen, Yoojin Chun, Alexander Grishin, Galina Grishina, Gustavo Stolovitzky, Gaurav Pandey, Supinda Bunyavanich. [doi]
• Multi-omics characterization of Microtubule-actin cross linking factor 1 (MACF1) using the ISB-Cancer Genomics CloudDondra Bailey, Kawther Abdilleh, Boris Aguilar, Alexis McClary. [doi]
• Modularity Analysis of Bipartite Networks and Multivariate ANOVA for Identification of Differentially Expressed Proteins in a Mouse Model of Down SyndromeAli Jazayeri, Sara Pajouhanfar, Sadaf Saba, Christopher C. Yang. [doi]
• Ir-Man: An Information Retrieval Framework for Marine Animal Necropsy AnalysisAlexander F. B. Carmichael, Deepayan Bhowmik, Johanna Baily, Andrew Brownlow, George J. Gunn, Aaron Reeves. [doi]
• A Novel Pupillometric-Based Application for the Automated Detection of ADHD Using Machine LearningWilliam Das, Shubh Khanna. [doi]
• MinIsoClust: Isoform clustering using minhash and locality sensitive hashingSairam Behera, Jitender S. Deogun, Etsuko N. Moriyama. [doi]
• iSOM-GSN: An Integrative Approach for Transforming Multi-omic Data into Gene Similarity Networks via Self-organizing MapsLuis Rueda, Nazia Fatima. [doi]
• CNN Based Segmentation of Infarcted Regions in Acute Cerebral Stroke Patients From Computed Tomography Perfusion ImagingLuca Tomasetti, Kjersti Engan, Mahdieh Khanmohammadi, Kathinka Dæhli Kurz. [doi]
• An Integer Linear Programming Solution for the Most Parsimonious Reconciliation Problem under the Duplication-Loss-Coalescence ModelMorgan Carothers, Joseph Gardi, Gianluca Gross, Tatsuki Kuze, Nuo Liu, Fiona Plunkett, Julia Qian, Yi-Chieh Wu. [doi]
• SMART: SuperMaximal approximate repeats toolLorraine A. K. Ayad, Panagiotis Charalampopoulos, Solon P. Pissis. [doi]
• Structural representations of DNA regulatory substrates can enhance sequence-based algorithms by associating functional sequence variantsJan Zrimec. [doi]
• Rhabdomyosarcoma Histology Classification using Ensemble of Deep Learning NetworksSaloni Agarwal, Mohamedelfatih Eltigani, Osman Abaker, Xinyi Zhang, Ovidiu Daescu, Donald A. Barkauskas, Erin R. Rudzinski, Patrick Leavey. [doi]
• ELMV: an Ensemble-Learning Approach for Analyzing Electrical Health Records with Significant Missing ValuesLucas Jing Liu, Hongwei Zhang, Jianzhong Di, Jin Chen. [doi]
• Submodular sketches of single-cell RNA-seq measurementsWei Yang, Jeffrey A. Bilmes, William Stafford Noble. [doi]
• Cross-Global Attention Graph Kernel Network Prediction of Drug PrescriptionHao-Ren Yao, Der-Chen Chang, Ophir Frieder, Wendy Huang, I-Chia Liang, Chi-Feng Hung. [doi]
• Comparing Type 2 Diabetes Self-Management Apps Against the Needs of Low-Income Minority Patients: Is There An Implicit Functionality Bias?Wayne Zachary, Hita Gupta. [doi]
• GANDALF: Peptide Generation for Drug Design using Sequential and Structural Generative Adversarial NetworksAllison M. Rossetto, Wenjin Zhou. [doi]
• Multi-omics data integration in the Cloud: Analysis of Statistically Significant Associations Between Clinical and Molecular Features in Breast CancerKawther Abdilleh, Boris Aguilar, J. Ross Thomson. [doi]
• Filtering STARR-Seq Peaks for Enhancers with Sequence ModelsRonald J. Nowling, Rafael Reple Geromel, Benjamin Halligan. [doi]
• A data-centric pipeline using convolutional neural network to select better multiple sequence alignment methodMengmeng Kuang, Hing-Fung Ting. [doi]
• DeCoDe: degenerate codon design for complete protein-coding DNA librariesTyler C. Shimko, Polly M. Fordyce, Yaron Orenstein. [doi]
• Benchmarking of computational error-correction methods for next-generation sequencing dataKeith Mitchell, Jaqueline J. Brito, Igor Mandric, Qiaozhen Wu, Sergey Knyazev, Sei Chang, Lana S. Martin, Aaron Karlsberg, Ekaterina Gerasimov, Russell Littman, Brian L. Hill, Nicholas C. Wu, Harry (Taegyun) Yang, Kevin Hsieh, Linus Chen, Eli Littman, Taylor Shabani, German Enik, Douglas Yao, Ren Sun, Jan Schroeder, Eleazar Eskin, Alex Zelikovsky, Pavel Skums, Mihai Pop, Serghei Mangul. [doi]
• Translocator: local realignment and global remapping enabling accurate translocation detection using single-molecule sequencing long readsYe Wu, Ruibang Luo, Tak Wah Lam, Hing-Fung Ting, Junwen Wang. [doi]
• Integrative Deep Learning for PanCancer Molecular Subtype Classification Using Histopathological Images and RNAseq DataFatima Zare, Javad Noorbakhsh, Tianyu Wang, Jeffrey H. Chuang, Sheida Nabavi. [doi]
• Linearization of Ancestral Genomes with Duplicated GenesPavel Avdeyev, Max A. Alekseyev. [doi]
• Graphery: a Biological Network Algorithm Tutorial WebserviceHeyuan Zeng, Anna M. Ritz. [doi]
• Using Patient Information for the Prediction of Caregiver Burden in Amyotrophic Lateral SclerosisAnna Antoniadi, Miriam Galvin, Mark Heverin, Orla Hardiman, Catherine Mooney. [doi]
• Zero-shot imputations across species are enabled through joint modeling of human and mouse epigenomicsJacob M. Schreiber, Deepthi Hegde, William S. Noble. [doi]
• Automated Classification of Acute Rejection from Endomyocardial BiopsiesFelipe Giuste, Mythreye Venkatesan, Conan Zhao, Li Tong, Yuanda Zhu, Shriprasad R. Deshpande, May D. Wang. [doi]
• A Qualitative Evaluation of Language Models on Automatic Question-Answering for COVID-19David Oniani, Yanshan Wang. [doi]
• FINDER: A fully automated pipeline to FIND accurate gene structures from proteins and RNA-Seq expression dataSagnik Banerjee, Margaret Woodhouse, Roger P. Wise, Priyanka Bhandary, Taner Z. Sen, Carson M. Andorf. [doi]
• Predicting protein secondary structure by an ensemble through feature-based accuracy estimationSpencer Krieger, John D. Kececioglu. [doi]
• Boosting the accuracy of protein secondary structure prediction through nearest neighbor search and method hybridizationSpencer Krieger, John D. Kececioglu. [doi]
• Pairwise Versus Multiple Global Network AlignmentVipin Vijayan, Shawn Gu, Eric T. Krebs, Lei Meng, Tijana Milenkovic. [doi]
• A deep learning fusion model for brain disorder classification: Application to distinguishing schizophrenia and autism spectrum disorderYuhui Du, Bang Li, Yuliang Hou, Vince D. Calhoun. [doi]
• Representing Cellular Lines with SVM and Text ProcessingIván Carrera, Inês Dutra, Eduardo Tejera. [doi]
• Augmenting Signaling Pathway ReconstructionsTobias Rubel, Anna M. Ritz. [doi]
• Abstract MiningEllie Small, Javier Cabrera, John B. Kostis. [doi]
• Prediction of Large for Gestational Age Infants in Overweight and Obese Women at Approximately 20 Gestational WeeksYuhan Du, John Mehegan, Fionnuala M. McAuliffe, Catherine Mooney. [doi]
• GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 ResearchScott Legrand, Aaron Scheinberg, Andreas F. Tillack, Mathialakan Thavappiragasam, Josh V. Vermaas, Rupesh Agarwal, Jeff Larkin, Duncan Poole, Diogo Santos-Martins, Leonardo Solis-Vasquez, Andreas Koch 0001, Stefano Forli, Oscar R. Hernandez, Jeremy C. Smith, Ada Sedova. [doi]
• PeakMatcher: Matching Peaks Across Genome AssembliesRonald J. Nowling, Christopher R. Beal, Scott J. Emrich, Susanta K. Behura, Marc S. Halfon, Molly Duman-Scheel. [doi]
• Efficiently mining rich subgraphs from vertex-attributed graphsRiyad Hakim, Saeed Salem. [doi]
• Performance Evaluation of Viral Infection Diagnosis using T-Cell Receptor Sequence and Artificial IntelligenceTim Kosfeld, Jonathan McMillan, Richard J. DiPaolo, Jie Hou, Tae-Hyuk Ahn. [doi]
• MeSH Indexing Using the Biomedical Citation NetworkWilliam Gasper, Parvathi Chundi, Dario Ghersi. [doi]
• Predicting Criticality in COVID-19 PatientsRoger A. Hallman, Anjali Chikkula, Temiloluwa Prioleau. [doi]
• A Generalized Robinson-Foulds Distance for Clonal Trees, Mutation Trees, and Phylogenetic Trees and NetworksMercè Llabrés, Francesc Rosselló, Gabriel Valiente. [doi]
• Correlation Imputation in Single cell RNA-seq using Auxiliary Information and Ensemble LearningLuqin Gan, Giuseppe Vinci, Genevera I. Allen. [doi]
• Variational Autoencoders for Protein Structure PredictionFardina Fathmiul Alam, Amarda Shehu. [doi]
• Protein evolution is structure dependent and non-homogeneous across the tree of lifeAkanksha Pandey, Edward L. Braun. [doi]
• The impact of sample size and tissue type on the reproducibility of gene co-expression networksKatie Ovens, B. Frank Eames, Ian McQuillan. [doi]
• Multimodal Learning for Cardiovascular Risk Prediction using EHR DataAyoub Bagheri, T. Katrien J. Groenhof, Wouter B. Veldhuis, Pim A. de Jong, Folkert W. Asselbergs, Daniel L. Oberski. [doi]
• A Dynamics-based Approach for the Target Control of Boolean NetworksCui Su, Jun Pang 0001. [doi]
• Fusion Lasso and Its Applications to Cancer Subtype and Stage PredictionZhong Chen 0003, Andrea Edwards, Kun Zhang 0012. [doi]
• Processing Millions of Single Cells by SHARPShibiao Wan, Junil Kim, Yiping Fan, Kyoung-Jae Won. [doi]
• Unsupervised manifold alignment for single-cell multi-omics dataRitambhara Singh, Pinar Demetci, Giancarlo Bonora, Vijay Ramani, Choli Lee, He Fang, Zhi-jun Duan, Xinxian Deng, Jay Shendure, Christine Disteche, William Stafford Noble. [doi]
• Learning the regulatory grammar of DNA for gene expression engineeringJan Zrimec, Aleksej Zelezniak. [doi]
• A Protein-Protein Interactome for an African CichlidGabriel A. Preising, Joshua J. Faber-Hammond, Suzy C. P. Renn, Anna M. Ritz. [doi]
• TLSurv: Integrating Multi-Omics Data by Multi-Stage Transfer Learning for Cancer Survival PredictionYixing Jiang, Kristen Alford, Frank Ketchum, Li Tong, May D. Wang. [doi]
• Population-scale Genomic Data Augmentation Based on Conditional Generative Adversarial NetworksJunjie Chen, Mohammad Erfan Mowlaei, Xinghua Shi. [doi]
• Objective risk stratification of prostate cancer using machine learning and radiomics applied to multiparametric magnetic resonance imagesBino A. Varghese, Frank Chen, Darryl Hwang, Suzanne L. Palmer, Andre Luis De Castro Abreu, Osamu Ukimura, Monish Aron, Manju Aron, Inderbir Gill, Vinay A. Duddalwar, Gaurav Pandey. [doi]
• A Preliminary Investigation in the Molecular Basis of Host Shutoff Mechanism in SARS-CoVNiharika Pandala, Casey A. Cole, Devaun McFarland, Anita Nag, Homayoun Valafar. [doi]