Bronze Contributor

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Bronze Contributor

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.

Adaptive & Self-Organizing Systems Artificial Intelligence Bioengineering Bioinformatics Computational Biology Data Mining & Machine Learning Data Science Drugs & Devices Genomics Network Science & Online Social Networks Oncology Pharmacology Synthetic Biology Translational Medicine

Editorial Board Member

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

Identities

@shawnmgomez

Websites

PeerJ Contributions

November 16, 2023

Integrated single-dose kinome profiling data is predictive of cancer cell line sensitivity to kinase inhibitors

Chinmaya U. Joisa, Kevin A. Chen, Matthew E. Berginski, Brian T. Golitz, Madison R. Jenner, Gabriela Herrera Loeza, Jen Jen Yeh, Shawn M. Gomez

https://doi.org/10.7717/peerj.16342

July 1, 2014

Automated analysis of invadopodia dynamics in live cells

Matthew E. Berginski, Sarah J. Creed, Shelly Cochran, David W. Roadcap, James E. Bear, Shawn M. Gomez

https://doi.org/10.7717/peerj.462 PubMed 25071988

March 28, 2014 - Version: 1

Automated analysis of invadopodia dynamics in live cells

Matthew E Berginski, Sarah J Creed, Shelly Cochran, David W Roadcap, James E Bear, Shawn M Gomez

https://doi.org/10.7287/peerj.preprints.320v1

Academic Editor on

November 8, 2023

Dex-Benchmark: datasets and code to evaluate algorithms for transcriptomics data analysis

Zhuorui Xie, Clara Chen, Avi Ma’ayan

https://doi.org/10.7717/peerj.16351 PubMed 37953774

October 6, 2023

KSFinder—a knowledge graph model for link prediction of novel phosphorylated substrates of kinases

Manju Anandakrishnan, Karen E. Ross, Chuming Chen, Vijay Shanker, Julie Cowart, Cathy H. Wu

https://doi.org/10.7717/peerj.16164 PubMed 37818330

March 14, 2023

Explainability of deep learning models in medical video analysis: a survey

Michal Kolarik, Martin Sarnovsky, Jan Paralic, Frantisek Babic

https://doi.org/10.7717/peerj-cs.1253

February 27, 2023

PrismEXP: gene annotation prediction from stratified gene-gene co-expression matrices

Alexander Lachmann, Kaeli A. Rizzo, Alon Bartal, Minji Jeon, Daniel J. B. Clarke, Avi Ma’ayan

https://doi.org/10.7717/peerj.14927 PubMed 36874981

June 15, 2022

Are all thermometers equal? A study of three infrared thermometers to detect fever in an African outpatient clinic

Nirmal Ravi, Mathura Vithyananthan, Aisha Saidu

https://doi.org/10.7717/peerj.13283 PubMed 35726256

June 10, 2022

The DNA methylation landscape of five pediatric-tumor types

Alyssa C. Parker, Badí I. Quinteros, Stephen R. Piccolo

https://doi.org/10.7717/peerj.13516 PubMed 35707123

May 3, 2022

Network subgraph-based approach for analyzing and comparing molecular networks

Chien-Hung Huang, Efendi Zaenudin, Jeffrey J.P. Tsai, Nilubon Kurubanjerdjit, Ka-Lok Ng

https://doi.org/10.7717/peerj.13137 PubMed 35529499

March 14, 2022

PhosVarDeep: deep-learning based prediction of phospho-variants using sequence information

Xia Liu, Minghui Wang, Ao Li

https://doi.org/10.7717/peerj.12847 PubMed 35310161

March 4, 2022

Machine-learning-based automated quantification machine for virus plaque assay counting

Gridsada Phanomchoeng, Chayatorn Kukiattikoon, Suphanut Plengkham, Siwaporn Boonyasuppayakorn, Saran Salakij, Suvit Poomrittigul, Lunchakorn Wuttisittikulkij

https://doi.org/10.7717/peerj-cs.878

September 15, 2021

Novel ACE2 protein interactions relevant to COVID-19 predicted by evolutionary rate correlations

Austin A. Varela, Sammy Cheng, John H. Werren

https://doi.org/10.7717/peerj.12159 PubMed 34616619

July 1, 2021

A synthetic defective interfering SARS-CoV-2

Shun Yao, Anoop Narayanan, Sydney A. Majowicz, Joyce Jose, Marco Archetti

https://doi.org/10.7717/peerj.11686 PubMed 34249513

May 25, 2021

Cuffless blood pressure estimation based on haemodynamic principles: progress towards mobile healthcare

Takehiro Yamakoshi, Peter Rolfe, Ken-ichi Yamakoshi

https://doi.org/10.7717/peerj.11479 PubMed 34141472

May 18, 2021

High glucose treatment promotes extracellular matrix proteome remodeling in Müller glial cells

Sandra Sagmeister, Juliane Merl-Pham, Agnese Petrera, Cornelia A. Deeg, Stefanie M. Hauck

https://doi.org/10.7717/peerj.11316 PubMed 34046254

April 5, 2021

Multi-schema computational prediction of the comprehensive SARS-CoV-2 vs. human interactome

Kevin Dick, Anand Chopra, Kyle K. Biggar, James R. Green

https://doi.org/10.7717/peerj.11117 PubMed 33868814

December 7, 2020

Developing a machine learning model to identify protein–protein interaction hotspots to facilitate drug discovery

Rohit Nandakumar, Valentin Dinu

https://doi.org/10.7717/peerj.10381 PubMed 33354416

November 27, 2020

A diverse global fungal library for drug discovery

Guodong Niu, Thirunavukkarasu Annamalai, Xiaohong Wang, Sheng Li, Stephen Munga, Guomin Niu, Yuk-Ching Tse-Dinh, Jun Li

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

Elly Poretsky, Alisa Huffaker

https://doi.org/10.7717/peerj.10264 PubMed 33240618

October 1, 2020

Differential effects of cisplatin on cybrid cells with varying mitochondrial DNA haplogroups

Sina Abedi, Gregory Yung, Shari R. Atilano, Kunal Thaker, Steven Chang, Marilyn Chwa, Kevin Schneider, Nitin Udar, Daniela Bota, M. Cristina Kenney

https://doi.org/10.7717/peerj.9908 PubMed 33062421

September 24, 2020

Characterization of a high-resolution breath acetone meter for ketosis monitoring

Donald J. Suntrup III, Timothy V. Ratto, Matt Ratto, James P. McCarter

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

Yuan Li, Zuhua Chen, Long Wu, Junjie Ye, Weiping Tao

https://doi.org/10.7717/peerj.9478 PubMed 32728493

July 7, 2020

Small molecule therapeutics for COVID-19: repurposing of inhaled furosemide

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

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

Mark Borthwick, Danny McAuley, John Warburton, Rohan Anand, Judy Bradley, Bronwen Connolly, Bronagh Blackwood, Brenda O’Neill, Marc Chikhani, Paul Dark, Murali Shyamsundar

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

Sivaramakrishnan Rajaraman, Incheol Kim, Sameer K. Antani

https://doi.org/10.7717/peerj.8693 PubMed 32211231

February 28, 2020

Correcting nuisance variation using Wasserstein distance

Gil Tabak, Minjie Fan, Samuel Yang, Stephan Hoyer, Geoffrey Davis

https://doi.org/10.7717/peerj.8594 PubMed 32161688

February 17, 2020

DISNET: a framework for extracting phenotypic disease information from public sources

Gerardo Lagunes-García, Alejandro Rodríguez-González, Lucía Prieto-Santamaría, Eduardo P. García del Valle, Massimiliano Zanin, Ernestina Menasalvas-Ruiz

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

Kagan J. Ducker, Robin L.J. Lines, Michael T. Chapman, Peter Peeling, Alannah K.A. McKay, Daniel F. Gucciardi

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

Zhenkai Zhao, Gen Li, Qing Xiao, Hui-Rong Jiang, Gabriel Mbuta Tchivelekete, Xinhua Shu, Hao Liu

https://doi.org/10.7717/peerj.8374 PubMed 31938582

January 6, 2020

The Rametrix^™ PRO Toolbox v1.0 for MATLAB^®

Ryan S. Senger, John L. Robertson

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

Øyvind P. Haugen, Evan M. Vallenari, Imen Belhaj, Milada Cvancarova Småstuen, Jon Storm-Mathisen, Linda H. Bergersen, Ingrid Åmellem

https://doi.org/10.7717/peerj.8328 PubMed 31934509

November 11, 2019

Blind normalization of public high-throughput databases

Sebastian Ohse, Melanie Boerries, Hauke Busch

https://doi.org/10.7717/peerj-cs.231

October 7, 2019

NIPS4Bplus: a richly annotated birdsong audio dataset

Veronica Morfi, Yves Bas, Hanna Pamuła, Hervé Glotin, Dan Stowell

https://doi.org/10.7717/peerj-cs.223

September 24, 2019

ViralPlaque: a Fiji macro for automated assessment of viral plaque statistics

Marco Cacciabue, Anabella Currá, Maria I. Gismondi

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

Kamela C. S. Ng, Jean Claude S. Ngabonziza, Pauline Lempens, Bouke C. de Jong, Frank van Leth, Conor J. Meehan

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

Yu Yao, Xiuquan Du, Yanyu Diao, Huaixu Zhu

https://doi.org/10.7717/peerj.7126 PubMed 31245182

March 28, 2019

Factors that influence response classifications in chemotherapy treated patient-derived xenografts (PDX)

Joan E. Malcolm, Timothy M. Stearns, Susan D. Airhart, Joel H. Graber, Carol J. Bult

https://doi.org/10.7717/peerj.6586 PubMed 30944774

March 1, 2019

An interpretable machine learning model for diagnosis of Alzheimer's disease

Diptesh Das, Junichi Ito, Tadashi Kadowaki, Koji Tsuda

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

Nguyen Quoc Khanh Le, Van-Nui Nguyen

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

Mikko J. Pyysalo, Pashupati P. Mishra, Kati Sundström, Terho Lehtimäki, Pekka J. Karhunen, Tanja Pessi

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

Mohammad Jafar Khatibipour, Furkan Kurtoğlu, Tunahan Çakır

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

Bhuvan Molparia, Brian N. Schrader, Eli Cohen, Jennifer L. Wagner, Sandeep R. Gupta, Sherrie Gould, Nelson Hwynn, Emily G. Spencer, Ali Torkamani

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

Vishwaratn Asthana, Yuqi Tang, Adam Ferguson, Pallavi Bugga, Anantratn Asthana, Emily R. Evans, Allen L. Chen, Brett S. Stern, Rebekah A. Drezek

https://doi.org/10.7717/peerj.4937 PubMed 29888136

May 30, 2018

Characterization of tumor heterogeneity by latent haplotypes: a sequential Monte Carlo approach

Oyetunji E. Ogundijo, Xiaodong Wang

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

Quan Liu, Li Ma, Shou-Zen Fan, Maysam F. Abbod, Jiann-Shing Shieh

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

Fatima Sinkala, Richard Parsons, Bruce Sunderland, Kreshnik Hoti, Petra Czarniak

https://doi.org/10.7717/peerj.4726 PubMed 29761047

May 4, 2018

Repurposing drugs to fast-track therapeutic agents for the treatment of cryptococcosis

Megan Truong, Leigh G. Monahan, Dee A. Carter, Ian G. Charles

https://doi.org/10.7717/peerj.4761 PubMed 29740519

January 31, 2018

Evidence for widespread dysregulation of circadian clock progression in human cancer

Jarrod Shilts, Guanhua Chen, Jacob J. Hughey

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

Minghui Wang, Tao Wang, Ao Li

https://doi.org/10.7717/peerj.4182 PubMed 29340231

September 7, 2017

MetaCRAST: reference-guided extraction of CRISPR spacers from unassembled metagenomes

Abraham G. Moller, Chun Liang

https://doi.org/10.7717/peerj.3788 PubMed 28894651

August 28, 2017

PrePhyloPro: phylogenetic profile-based prediction of whole proteome linkages

Yulong Niu, Chengcheng Liu, Shayan Moghimyfiroozabad, Yi Yang, Kambiz N. Alavian

https://doi.org/10.7717/peerj.3712 PubMed 28875072

June 12, 2017

AliTV—interactive visualization of whole genome comparisons

Markus J. Ankenbrand, Sonja Hohlfeld, Thomas Hackl, Frank Förster

https://doi.org/10.7717/peerj-cs.116

December 14, 2016

Probabilistic adaptation in changing microbial environments

Yarden Katz, Michael Springer

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

Kam D. Dahlquist, John David N. Dionisio, Ben G. Fitzpatrick, Nicole A. Anguiano, Anindita Varshneya, Britain J. Southwick, Mihir Samdarshi

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

Yanika Borg, Aurelija Marija Grigonyte, Philipp Boeing, Bethan Wolfenden, Patrick Smith, William Beaufoy, Simon Rose, Tonderai Ratisai, Alexey Zaikin, Darren N. Nesbeth

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

Jeffrey A. Thompson, Jie Tan, Casey S. Greene

https://doi.org/10.7717/peerj.1621 PubMed 26844019

December 22, 2015

Identifying communities from multiplex biological networks

Gilles Didier, Christine Brun, Anaïs Baudot

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

Michael W. Henson, Jorge W. Santo Domingo, Peter S. Kourtev, Roderick V. Jensen, James A. Dunn, Deric R. Learman