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    Shawn Gomez
    PeerJ Editor & Author
    6,370 Points

    Contributions by role

    Editor 6200
    PeerJ author 135
    PeerJ PrePrints author 35

    Contributions by subject area

    Bioinformatics 3570
    Computational-Biology 2870
    Computational-Science 1270
    Drugs-and-Devices 1100
    Data-Mining-and-Machine-Learning 1000
    Genomics 1000
    Bioengineering 970
    Microbiology 700
    Infectious-Diseases 600
    Pharmacology 600
    Oncology 600
    Molecular-Biology 500
    Cell-Biology 470
    Immunology 400
    Statistics 300
    Respiratory-Medicine 300
    Diabetes-and-Endocrinology 300
    Genetics 300
    Metabolic-Sciences 300
    Neuroscience 300
    Biotechnology 200
    Mycology 200
    Ecology 200
    Synthetic-Biology 200
    Data-Science 200
    Multimedia 200
    Translational-Medicine 200
    Emergency-and-Critical-Care 200
    Gynecology-and-Obstetrics 200
    Anesthesiology-and-Pain-Management 200
    Marine-Biology 100
    Science-Policy 100
    Graphics 100
    Software-Engineering 100
    Mathematical-Biology 100
    Computational-biology 100
    Environmental-Sciences 100
    Health-Policy 100
    Science-and-Medical-Education 100
    Human–Computer-Interaction 100
    Pediatrics 100
    Psychiatry-and-Psychology 100
    Urology 100
    Computer-Vision 100
    Artificial-Intelligence 100
    Plant-Science 100
    Womens-Health 100
    Ophthalmology 100
    Nutrition 100
    Radiology-and-Medical-Imaging 100
    Kinesiology 100
    Anatomy-and-Physiology 100
    Animal-Behavior 100
    Nephrology 100
    Dentistry 100
    Data-mining-and-Machine-learning 100
    Algorithms-and-Analysis-of-Algorithms 100
    Databases 100
    Virology 100
    Epidemiology 100
    Global-Health 100
    Public-Health 100
    Cognitive-Disorders 100
    Hematology 100
    Gastroenterology-and-Hepatology 100
    Natural-Language-and-Speech 100

    Shawn M Gomez

    PeerJ Editor & Author

    Summary

    Professor, Joint Department of Biomedical Engineering at UNC-CH and NCSU and Department of Pharmacology at UNC-CH. Previous Florence Gould Scholar and Pasteur Foundation Fellow. Current research interests in systems and synthetic biology, bioimage informatics, and network science applied to biology. Broader interests in translational medicine and the fostering of innovative solutions to problems in healthcare.

    Bioengineering Bioinformatics Computational Biology Data Mining & Machine Learning Drugs & Devices Genomics Network Science & Online Social Networks Pharmacology Synthetic Biology Translational Medicine

    Editing Journals

    PeerJ - the Journal of Life & Environmental Sciences
    PeerJ Computer Science

    Past or current institution affiliations

    University of North Carolina at Chapel Hill

    Work details

    Professor

    University of North Carolina at Chapel Hill
    Joint Dept. of Biomedical Engineering at UNC and NC State University

    Websites

    • LinkedIn
    • Gomez Lab

    PeerJ Contributions

    • Articles 1
    • Preprints 1
    • Edited 46
    July 1, 2014
    Automated analysis of invadopodia dynamics in live cells
    5 citations
    696 downloads
    2,730 views
    Matthew E. Berginski, Sarah J. Creed, Shelly Cochran, David W. Roadcap, James E. Bear, Shawn M. Gomez
    bioengineering
    bioinformatics
    cell-biology
    computational-biology
    computational-science
    https://doi.org/10.7717/peerj.462 PubMed 25071988
    March 28, 2014 - Version: 1
    Automated analysis of invadopodia dynamics in live cells
    317 downloads
    775 views
    Matthew E Berginski, Sarah J Creed, Shelly Cochran, David W Roadcap, James E Bear, Shawn M Gomez
    bioengineering
    bioinformatics
    cell-biology
    computational-biology
    computational-science
    https://doi.org/10.7287/peerj.preprints.320v1

    Academic Editor on

    December 7, 2020
    Developing a machine learning model to identify protein–protein interaction hotspots to facilitate drug discovery
    133 downloads
    1,328 views
    Rohit Nandakumar, Valentin Dinu
    bioinformatics
    computational-biology
    drugs-and-devices
    data-mining-and-machine-learning
    https://doi.org/10.7717/peerj.10381 PubMed 33354416
    November 27, 2020
    A diverse global fungal library for drug discovery
    153 downloads
    633 views
    Guodong Niu, Thirunavukkarasu Annamalai, Xiaohong Wang, Sheng Li, Stephen Munga, Guomin Niu, Yuk-Ching Tse-Dinh, Jun Li
    molecular-biology
    mycology
    drugs-and-devices
    infectious-diseases
    https://doi.org/10.7717/peerj.10392 PubMed 33312768
    November 9, 2020
    MutRank: an R shiny web-application for exploratory targeted mutual rank-based coexpression analyses integrated with user-provided supporting information
    91 downloads
    474 views
    Elly Poretsky, Alisa Huffaker
    bioinformatics
    genetics
    genomics
    molecular-biology
    plant-science
    https://doi.org/10.7717/peerj.10264 PubMed 33240618
    October 1, 2020
    Differential effects of cisplatin on cybrid cells with varying mitochondrial DNA haplogroups
    182 downloads
    824 views
    Sina Abedi, Gregory Yung, Shari R. Atilano, Kunal Thaker, Steven Chang, Marilyn Chwa, Kevin Schneider, Nitin Udar, Daniela Bota, M. Cristina Kenney
    cell-biology
    genomics
    oncology
    ophthalmology
    pharmacology
    https://doi.org/10.7717/peerj.9908 PubMed 33062421
    September 24, 2020
    Characterization of a high-resolution breath acetone meter for ketosis monitoring
    1 citation
    199 downloads
    1,879 views
    Donald J. Suntrup III, Timothy V. Ratto, Matt Ratto, James P. McCarter
    diabetes-and-endocrinology
    drugs-and-devices
    nutrition
    respiratory-medicine
    metabolic-sciences
    https://doi.org/10.7717/peerj.9969 PubMed 33024634
    July 10, 2020
    Cellular heterogeneity map of diverse immune and stromal phenotypes within breast tumor microenvironment
    159 downloads
    546 views
    Yuan Li, Zuhua Chen, Long Wu, Junjie Ye, Weiping Tao
    bioinformatics
    immunology
    oncology
    https://doi.org/10.7717/peerj.9478 PubMed 32728493
    July 7, 2020
    Small molecule therapeutics for COVID-19: repurposing of inhaled furosemide
    2 citations
    450 downloads
    1,890 views
    Zhiyu Wang, Yanfei Wang, Prachi Vilekar, Seung-Pil Yang, Mayuri Gupta, Myong In Oh, Autumn Meek, Lisa Doyle, Laura Villar, Anja Brennecke, Imindu Liyanage, Mark Reed, Christopher Barden, Donald F. Weaver
    cell-biology
    immunology
    infectious-diseases
    pharmacology
    respiratory-medicine
    https://doi.org/10.7717/peerj.9533 PubMed 32704455
    May 4, 2020
    Mucoactive agent use in adult UK Critical Care Units: a survey of health care professionals’ perception, pharmacists’ description of practice, and point prevalence of mucoactive use in invasively mechanically ventilated patients
    2 citations
    235 downloads
    957 views
    Mark Borthwick, Danny McAuley, John Warburton, Rohan Anand, Judy Bradley, Bronwen Connolly, Bronagh Blackwood, Brenda O’Neill, Marc Chikhani, Paul Dark, Murali Shyamsundar
    drugs-and-devices
    emergency-and-critical-care
    pharmacology
    respiratory-medicine
    https://doi.org/10.7717/peerj.8828 PubMed 32411506
    March 17, 2020
    Detection and visualization of abnormality in chest radiographs using modality-specific convolutional neural network ensembles
    2 citations
    319 downloads
    1,454 views
    Sivaramakrishnan Rajaraman, Incheol Kim, Sameer K. Antani
    bioengineering
    infectious-diseases
    radiology-and-medical-imaging
    computational-science
    data-mining-and-machine-learning
    https://doi.org/10.7717/peerj.8693 PubMed 32211231
    February 28, 2020
    Correcting nuisance variation using Wasserstein distance
    277 downloads
    1,083 views
    Gil Tabak, Minjie Fan, Samuel Yang, Stephan Hoyer, Geoffrey Davis
    bioinformatics
    computational-biology
    data-mining-and-machine-learning
    https://doi.org/10.7717/peerj.8594 PubMed 32161688
    February 17, 2020
    DISNET: a framework for extracting phenotypic disease information from public sources
    2 citations
    243 downloads
    1,727 views
    Gerardo Lagunes-García, Alejandro Rodríguez-González, Lucía Prieto-Santamaría, Eduardo P. García del Valle, Massimiliano Zanin, Ernestina Menasalvas-Ruiz
    bioinformatics
    statistics
    computational-science
    data-mining-and-machine-learning
    data-science
    https://doi.org/10.7717/peerj.8580 PubMed 32110491
    January 8, 2020
    Validity and reliability evidence of a point of care assessment of salivary cortisol and α-amylase: a pre-registered study
    229 downloads
    957 views
    Kagan J. Ducker, Robin L.J. Lines, Michael T. Chapman, Peter Peeling, Alannah K.A. McKay, Daniel F. Gucciardi
    anatomy-and-physiology
    diabetes-and-endocrinology
    drugs-and-devices
    kinesiology
    https://doi.org/10.7717/peerj.8366 PubMed 31938581
    January 8, 2020
    Quantification of the influence of drugs on zebrafish larvae swimming kinematics and energetics
    2 citations
    394 downloads
    944 views
    Zhenkai Zhao, Gen Li, Qing Xiao, Hui-Rong Jiang, Gabriel Mbuta Tchivelekete, Xinhua Shu, Hao Liu
    animal-behavior
    bioengineering
    computational-biology
    computational-science
    https://doi.org/10.7717/peerj.8374 PubMed 31938582
    January 6, 2020
    The Rametrix™ PRO Toolbox v1.0 for MATLAB®
    8 citations
    153 downloads
    553 views
    Ryan S. Senger, John L. Robertson
    bioengineering
    computational-biology
    nephrology
    urology
    statistics
    https://doi.org/10.7717/peerj.8179 PubMed 31934499
    January 6, 2020
    Blood lactate dynamics in awake and anaesthetized mice after intraperitoneal and subcutaneous injections of lactate—sex matters
    372 downloads
    1,614 views
    Øyvind P. Haugen, Evan M. Vallenari, Imen Belhaj, Milada Cvancarova Småstuen, Jon Storm-Mathisen, Linda H. Bergersen, Ingrid Åmellem
    neuroscience
    pharmacology
    metabolic-sciences
    https://doi.org/10.7717/peerj.8328 PubMed 31934509
    November 11, 2019
    Blind normalization of public high-throughput databases
    185 downloads
    650 views
    Sebastian Ohse, Melanie Boerries, Hauke Busch
    bioinformatics
    data-mining-and-machine-learning
    https://doi.org/10.7717/peerj-cs.231
    October 7, 2019
    NIPS4Bplus: a richly annotated birdsong audio dataset
    1 citation
    979 downloads
    1,520 views
    Veronica Morfi, Yves Bas, Hanna Pamuła, Hervé Glotin, Dan Stowell
    bioinformatics
    computational-biology
    data-mining-and-machine-learning
    databases
    multimedia
    https://doi.org/10.7717/peerj-cs.223
    September 24, 2019
    ViralPlaque: a Fiji macro for automated assessment of viral plaque statistics
    497 downloads
    744 views
    Marco Cacciabue, Anabella Currá, Maria I. Gismondi
    bioinformatics
    virology
    https://doi.org/10.7717/peerj.7729 PubMed 31579606
    August 26, 2019
    Bridging the TB data gap: in silico extraction of rifampicin-resistant tuberculosis diagnostic test results from whole genome sequence data
    321 downloads
    1,030 views
    Kamela C. S. Ng, Jean Claude S. Ngabonziza, Pauline Lempens, Bouke C. de Jong, Frank van Leth, Conor J. Meehan
    bioinformatics
    genomics
    microbiology
    epidemiology
    infectious-diseases
    https://doi.org/10.7717/peerj.7564 PubMed 31523514
    June 17, 2019
    An integration of deep learning with feature embedding for protein–protein interaction prediction
    8 citations
    1,257 downloads
    3,381 views
    Yu Yao, Xiuquan Du, Yanyu Diao, Huaixu Zhu
    bioinformatics
    computational-biology
    data-mining-and-machine-learning
    https://doi.org/10.7717/peerj.7126 PubMed 31245182
    March 28, 2019
    Factors that influence response classifications in chemotherapy treated patient-derived xenografts (PDX)
    2 citations
    604 downloads
    893 views
    Joan E. Malcolm, Timothy M. Stearns, Susan D. Airhart, Joel H. Graber, Carol J. Bult
    bioengineering
    drugs-and-devices
    oncology
    translational-medicine
    https://doi.org/10.7717/peerj.6586 PubMed 30944774
    March 1, 2019
    An interpretable machine learning model for diagnosis of Alzheimer's disease
    5 citations
    1,140 downloads
    3,363 views
    Diptesh Das, Junichi Ito, Tadashi Kadowaki, Koji Tsuda
    bioinformatics
    computational-biology
    neuroscience
    cognitive-disorders
    data-mining-and-machine-learning
    https://doi.org/10.7717/peerj.6543 PubMed 30842909
    February 25, 2019
    SNARE-CNN: a 2D convolutional neural network architecture to identify SNARE proteins from high-throughput sequencing data
    13 citations
    554 downloads
    2,627 views
    Nguyen Quoc Khanh Le, Van-Nui Nguyen
    bioinformatics
    computational-biology
    data-mining-and-machine-learning
    https://doi.org/10.7717/peerj-cs.177
    January 25, 2019
    Increased tooth brushing frequency is associated with reduced gingival pocket bacterial diversity in patients with intracranial aneurysms
    4 citations
    350 downloads
    1,701 views
    Mikko J. Pyysalo, Pashupati P. Mishra, Kati Sundström, Terho Lehtimäki, Pekka J. Karhunen, Tanja Pessi
    bioinformatics
    microbiology
    dentistry
    https://doi.org/10.7717/peerj.6316 PubMed 30701137
    December 6, 2018
    JacLy: a Jacobian-based method for the inference of metabolic interactions from the covariance of steady-state metabolome data
    285 downloads
    1,157 views
    Mohammad Jafar Khatibipour, Furkan Kurtoğlu, Tunahan Çakır
    bioengineering
    bioinformatics
    biotechnology
    computational-biology
    computational-science
    https://doi.org/10.7717/peerj.6034 PubMed 30564518
    July 20, 2018
    Combined accelerometer and genetic analysis to differentiate essential tremor from Parkinson’s disease
    6 citations
    420 downloads
    1,360 views
    Bhuvan Molparia, Brian N. Schrader, Eli Cohen, Jennifer L. Wagner, Sandeep R. Gupta, Sherrie Gould, Nelson Hwynn, Emily G. Spencer, Ali Torkamani
    computational-biology
    genetics
    https://doi.org/10.7717/peerj.5308 PubMed 30042899
    June 5, 2018
    An inexpensive, customizable microscopy system for the automated quantification and characterization of multiple adherent cell types
    3 citations
    356 downloads
    1,173 views
    Vishwaratn Asthana, Yuqi Tang, Adam Ferguson, Pallavi Bugga, Anantratn Asthana, Emily R. Evans, Allen L. Chen, Brett S. Stern, Rebekah A. Drezek
    bioengineering
    biotechnology
    https://doi.org/10.7717/peerj.4937 PubMed 29888136
    May 30, 2018
    Characterization of tumor heterogeneity by latent haplotypes: a sequential Monte Carlo approach
    2 citations
    278 downloads
    1,687 views
    Oyetunji E. Ogundijo, Xiaodong Wang
    bioinformatics
    computational-biology
    https://doi.org/10.7717/peerj.4838 PubMed 29868266
    May 23, 2018
    Sample entropy analysis for the estimating depth of anaesthesia through human EEG signal at different levels of unconsciousness during surgeries
    17 citations
    950 downloads
    1,899 views
    Quan Liu, Li Ma, Shou-Zen Fan, Maysam F. Abbod, Jiann-Shing Shieh
    anesthesiology-and-pain-management
    statistics
    computational-science
    https://doi.org/10.7717/peerj.4817 PubMed 29844970
    May 7, 2018
    A survey of the views and capabilities of community pharmacists in Western Australia regarding the rescheduling of selected oral antibiotics in a framework of pharmacist prescribing
    1 citation
    447 downloads
    1,435 views
    Fatima Sinkala, Richard Parsons, Bruce Sunderland, Kreshnik Hoti, Petra Czarniak
    health-policy
    translational-medicine
    https://doi.org/10.7717/peerj.4726 PubMed 29761047
    May 4, 2018
    Repurposing drugs to fast-track therapeutic agents for the treatment of cryptococcosis
    20 citations
    514 downloads
    1,972 views
    Megan Truong, Leigh G. Monahan, Dee A. Carter, Ian G. Charles
    microbiology
    mycology
    drugs-and-devices
    infectious-diseases
    https://doi.org/10.7717/peerj.4761 PubMed 29740519
    January 31, 2018
    Evidence for widespread dysregulation of circadian clock progression in human cancer
    20 citations
    690 downloads
    3,157 views
    Jarrod Shilts, Guanhua Chen, Jacob J. Hughey
    bioinformatics
    computational-biology
    genomics
    oncology
    https://doi.org/10.7717/peerj.4327 PubMed 29404219
    December 20, 2017
    ksrMKL: a novel method for identification of kinase–substrate relationships using multiple kernel learning
    1 citation
    329 downloads
    1,327 views
    Minghui Wang, Tao Wang, Ao Li
    bioinformatics
    computational-biology
    https://doi.org/10.7717/peerj.4182 PubMed 29340231
    September 7, 2017
    MetaCRAST: reference-guided extraction of CRISPR spacers from unassembled metagenomes
    7 citations
    490 downloads
    3,193 views
    Abraham G. Moller, Chun Liang
    bioinformatics
    computational-biology
    ecology
    genomics
    microbiology
    https://doi.org/10.7717/peerj.3788 PubMed 28894651
    August 28, 2017
    PrePhyloPro: phylogenetic profile-based prediction of whole proteome linkages
    8 citations
    588 downloads
    2,909 views
    Yulong Niu, Chengcheng Liu, Shayan Moghimyfiroozabad, Yi Yang, Kambiz N. Alavian
    bioinformatics
    genomics
    https://doi.org/10.7717/peerj.3712 PubMed 28875072
    June 12, 2017
    AliTV—interactive visualization of whole genome comparisons
    25 citations
    746 downloads
    5,797 views
    Markus J. Ankenbrand, Sonja Hohlfeld, Thomas Hackl, Frank Förster
    bioinformatics
    computational-biology
    https://doi.org/10.7717/peerj-cs.116
    December 14, 2016
    Probabilistic adaptation in changing microbial environments
    7 citations
    779 downloads
    2,666 views
    Yarden Katz, Michael Springer
    computational-biology
    ecology
    mathematical-biology
    microbiology
    synthetic-biology
    https://doi.org/10.7717/peerj.2716 PubMed 27994963
    September 12, 2016
    GRNsight: a web application and service for visualizing models of small- to medium-scale gene regulatory networks
    1 citation
    535 downloads
    3,349 views
    Kam D. Dahlquist, John David N. Dionisio, Ben G. Fitzpatrick, Nicole A. Anguiano, Anindita Varshneya, Britain J. Southwick, Mihir Samdarshi
    bioinformatics
    graphics
    software-engineering
    https://doi.org/10.7717/peerj-cs.85
    July 7, 2016
    Open source approaches to establishing Roseobacter clade bacteria as synthetic biology chassis for biogeoengineering
    3 citations
    610 downloads
    3,515 views
    Yanika Borg, Aurelija Marija Grigonyte, Philipp Boeing, Bethan Wolfenden, Patrick Smith, William Beaufoy, Simon Rose, Tonderai Ratisai, Alexey Zaikin, Darren N. Nesbeth
    bioengineering
    marine-biology
    molecular-biology
    science-policy
    synthetic-biology
    https://doi.org/10.7717/peerj.2031 PubMed 27441104
    January 21, 2016
    Cross-platform normalization of microarray and RNA-seq data for machine learning applications
    44 citations
    2,135 downloads
    12,619 views
    Jeffrey A. Thompson, Jie Tan, Casey S. Greene
    bioinformatics
    computational-biology
    genomics
    https://doi.org/10.7717/peerj.1621 PubMed 26844019
    December 22, 2015
    Identifying communities from multiplex biological networks
    28 citations
    1,096 downloads
    3,783 views
    Gilles Didier, Christine Brun, Anaïs Baudot
    bioinformatics
    computational-biology
    molecular-biology
    https://doi.org/10.7717/peerj.1525 PubMed 26713261
    November 10, 2015
    Metabolic and genomic analysis elucidates strain-level variation in Microbacterium spp. isolated from chromate contaminated sediment
    12 citations
    666 downloads
    2,613 views
    Michael W. Henson, Jorge W. Santo Domingo, Peter S. Kourtev, Roderick V. Jensen, James A. Dunn, Deric R. Learman
    environmental-contamination-and-remediation
    environmental-sciences
    genomics
    microbiology
    https://doi.org/10.7717/peerj.1395 PubMed 26587353
    May 19, 2015
    PANDA: pathway and annotation explorer for visualizing and interpreting gene-centric data
    3 citations
    588 downloads
    3,935 views
    Steven N. Hart, Raymond M. Moore, Michael T. Zimmermann, Gavin R. Oliver, Jan B. Egan, Alan H. Bryce, Jean-Pierre A. Kocher
    computational-biology
    genetics
    genomics
    computational-science
    https://doi.org/10.7717/peerj.970 PubMed 26038725
    June 24, 2014
    Single cell transcriptional analysis reveals novel innate immune cell types
    8 citations
    1,143 downloads
    3,460 views
    Linda E. Kippner, Jinhee Kim, Greg Gibson, Melissa L. Kemp
    bioinformatics
    immunology
    https://doi.org/10.7717/peerj.452 PubMed 25024920
    June 19, 2014
    scikit-image: image processing in Python
    1,215 citations
    24,900 downloads
    93,553 views
    Stéfan van der Walt, Johannes L. Schönberger, Juan Nunez-Iglesias, François Boulogne, Joshua D. Warner, Neil Yager, Emmanuelle Gouillart, Tony Yu
    bioinformatics
    computational-biology
    computational-science
    human-computer-interaction
    science-and-medical-education
    https://doi.org/10.7717/peerj.453 PubMed 25024921
    December 19, 2013
    Pathway-GPS and SIGORA: identifying relevant pathways based on the over-representation of their gene-pair signatures
    27 citations
    655 downloads
    3,390 views
    Amir B.K. Foroushani, Fiona S.L. Brinkman, David J. Lynn
    bioinformatics
    computational-biology
    molecular-biology
    immunology
    infectious-diseases
    https://doi.org/10.7717/peerj.229 PubMed 24432194
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