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Anand Singh Rathore, Saloni Jain, Shubham Choudhury, Gajendra P. S. Raghava

Lin Zhu, Yi Fang, Shuting Liu, Hong-Bin Shen, Wesley De Neve, Xiaoyong Pan

Tanja Krueger, Damla A. Durmaz, Luisa F. Jimenez-Soto

Helen C Mendel, Gene Hopping, Eivind A B Undheim, Johannes Zuegg, Richard J Lewis, Briony E Forbes, Quentin Kaas, Markus Muttenthaler

Raghvendra Mall, Ankita Singh, Chirag N Patel, Gregory Guirimand, Filippo Castiglione

Jorge F. Beltrán, Lisandra Herrera-Belén, Fernanda Parraguez-Contreras, Jorge G. Farías, Jorge Machuca-Sepúlveda, Stefania Short

L. Palazzolo, T. Laurenzi, O. Ben Mariem, A. Bassan, U. Guerrini, I. Eberini

Giulia Zancolli, Björn Marcus von Reumont, Gregor Anderluh, Figen Caliskan, Maria Luisa Chiusano, Jacob Fröhlich, Evroula Hapeshi, Benjamin-Florian Hempel, Maria P Ikonomopoulou, Florence Jungo, Pascale Marchot, Tarcisio Mendes de Farias, Maria Vittoria Modica, Yehu Moran, Ayse Nalbantsoy, Jan Procházka, Andrea Tarallo, Fiorella Tonello, Rui Vitorino, Mark Lawrence Zammit, Agostinho Antunes

Vladimir Morozov, Carlos H. M. Rodrigues, David B. Ascher

Khin Than Yee, Jason Macrander, Olga Vasieva, Ponlapat Rojnuckarin

Rebecca Kusko, Huixiao Hong

Elena Efremenko, Aysel Aslanli, Ilya Lyagin

Qingxiang Guo, Christopher M. Whipps, Yanhua Zhai, Dan Li, Zemao Gu

Guillermin Agüero-Chapin, Deborah Galpert-Cañizares, Dany Domínguez-Pérez, Yovani Marrero-Ponce, Gisselle Pérez-Machado, Marta Teijeira, Agostinho Antunes

Hua Shi, Yan Li, Yi Chen, Yuming Qin, Yifan Tang, Xun Zhou, Ying Zhang, Yun Wu

Lesong Wei, Xiucai Ye, Tetsuya Sakurai

Neelam Sharma, Leimarembi Devi Naorem, Shipra Jain, Gajendra P S Raghava

Débora Andrade-Silva, André Zelanis, Silvia R. Travaglia-Cardoso, Milton Y. Nishiyama, Solange M. T. Serrano

Woochang Hwang, Winnie Lei, Nicholas M Katritsis, Méabh MacMahon, Kathryn Chapman, Namshik Han

Sajjad Shumaly, Mohsen Yazdinejad, Yanhui Guo

Benjamin Americus, Nicole Hams, Anna M. L. Klompen, Gema Alama-Bermejo, Tamar Lotan, Jerri L. Bartholomew, Stephen D. Atkinson

Damianos P. Melidis, Wolfgang Nejdl

Yi Wang, Yanni Li, Xiaoyi Wang, Ranko Gacesa, Jie Zhang, Lu Zhou, Bangmao Wang

Thomas C. N. Leung, Zhe Qu, Wenyan Nong, Jerome H. L. Hui, Sai Ming Ngai

Marcelo V. Kitahara, Adrian Jaimes‐Becerra, Edgar Gamero‐Mora, Gabriel Padilla, Liam B. Doonan, Malcolm Ward, Antonio C. Marques, André C. Morandini, Paul F. Long

Dhananjay Kimothi, Pravesh Biyani, James M. Hogan, Akshay Soni, Wayne Kelly

Cassandra M. Modahl, Stephen P. Mackessy

Ehsaneddin Asgari, Alice C. McHardy, Mohammad R. K. Mofrad

Jyotsna T. Wassan, Haiying Wang, Huiru Zheng

Adrian Jaimes-Becerra, Ranko Gacesa, Liam B Doonan, Ashlie Hartigan, Antonio C Marques, Beth Okamura, Paul F Long

Beth Okamura, Paul F Long, Laura D Mydlarz

Liam B. Doonan, Steven Lynham, Catherine Quinlan, Spike C. Ibiji, Carlos E. Winter, Gabriel Padilla, Adrian Jaimes-Becerra, André C. Morandini, Antonio C. Marques, Paul F. Long

T. Jeffrey Cole, Michael S. Brewer

Jason Macrander, Jyothirmayi Panda, Daniel Janies, Marymegan Daly, Adam M. Reitzel

Björn Marcus Von Reumont

Jutty Rajan Prashanth, Nojod Hasaballah, Irina Vetter

Samuel D. Robinson, Eivind A. B. Undheim, Beatrix Ueberheide, Glenn F. King

Paola Ojeda, David Ramírez, Jans Alzate-Morales, Julio Caballero, Quentin Kaas, Wendy González

Jason Macrander, Marymegan Daly

2025	A large language model for predicting neurotoxic peptides and neurotoxins Protein Science Anand Singh Rathore, Saloni Jain, Shubham Choudhury, Gajendra P. S. Raghava
2025	ToxDL 2.0: Protein toxicity prediction using a pretrained language model and graph neural networks Computational and Structural Biotechnology Journal Lin Zhu, Yi Fang, Shuting Liu, Hong-Bin Shen, Wesley De Neve, Xiaoyong Pan
2025	Exo-Tox: Identifying Exotoxins from secreted bacterial proteins BioData Mining Tanja Krueger, Damla A. Durmaz, Luisa F. Jimenez-Soto
2025	PeptideMiner—neuropeptide discovery across the animal kingdom GigaScience Helen C Mendel, Gene Hopping, Eivind A B Undheim, Johannes Zuegg, Richard J Lewis, Briony E Forbes, Quentin Kaas, Markus Muttenthaler
2024	VISH-Pred: an ensemble of fine-tuned ESM models for protein toxicity prediction Briefings in Bioinformatics Raghvendra Mall, Ankita Singh, Chirag N Patel, Gregory Guirimand, Filippo Castiglione
2024	MultiToxPred 1.0: a novel comprehensive tool for predicting 27 classes of protein toxins using an ensemble machine learning approach BMC Bioinformatics Jorge F. Beltrán, Lisandra Herrera-Belén, Fernanda Parraguez-Contreras, Jorge G. Farías, Jorge Machuca-Sepúlveda, Stefania Short
2024	Development of in silico methodologies to predict the toxicity of novel proteins in the context of food and feed risk assessment EFSA Supporting Publications L. Palazzolo, T. Laurenzi, O. Ben Mariem, A. Bassan, U. Guerrini, I. Eberini
2024	Web of venom: exploration of big data resources in animal toxin research GigaScience Giulia Zancolli, Björn Marcus von Reumont, Gregor Anderluh, Figen Caliskan, Maria Luisa Chiusano, Jacob Fröhlich, Evroula Hapeshi, Benjamin-Florian Hempel, Maria P Ikonomopoulou, Florence Jungo, Pascale Marchot, Tarcisio Mendes de Farias, Maria Vittoria Modica, Yehu Moran, Ayse Nalbantsoy, Jan Procházka, Andrea Tarallo, Fiorella Tonello, Rui Vitorino, Mark Lawrence Zammit, Agostinho Antunes
2023	CSM-Toxin: A Web-Server for Predicting Protein Toxicity Pharmaceutics Vladimir Morozov, Carlos H. M. Rodrigues, David B. Ascher
2023	Exploring Toxin Genes of Myanmar Russell’s Viper, Daboia siamensis, through De Novo Venom Gland Transcriptomics Toxins Khin Than Yee, Jason Macrander, Olga Vasieva, Ponlapat Rojnuckarin
2023	Computational Methods in Engineering & the Sciences Rebecca Kusko, Huixiao Hong
2023	Advanced Situation with Recombinant Toxins: Diversity, Production and Application Purposes International Journal of Molecular Sciences Elena Efremenko, Aysel Aslanli, Ilya Lyagin
2022	Quantitative Insights into the Contribution of Nematocysts to the Adaptive Success of Cnidarians Based on Proteomic Analysis Biology Qingxiang Guo, Christopher M. Whipps, Yanhua Zhai, Dan Li, Zemao Gu
2022	Emerging Computational Approaches for Antimicrobial Peptide Discovery Antibiotics Guillermin Agüero-Chapin, Deborah Galpert-Cañizares, Dany Domínguez-Pérez, Yovani Marrero-Ponce, Gisselle Pérez-Machado, Marta Teijeira, Agostinho Antunes
2022	ToxMVA: An end-to-end multi-view deep autoencoder method for protein toxicity prediction Computers in Biology and Medicine Hua Shi, Yan Li, Yi Chen, Yuming Qin, Yifan Tang, Xun Zhou, Ying Zhang, Yun Wu
2022	Proceedings of the Conference on Research in Adaptive and Convergent Systems Lesong Wei, Xiucai Ye, Tetsuya Sakurai
2022	ToxinPred2: an improved method for predicting toxicity of proteins Briefings in Bioinformatics Neelam Sharma, Leimarembi Devi Naorem, Shipra Jain, Gajendra P S Raghava
2021	Venom Profiling of the Insular Species Bothrops alcatraz: Characterization of Proteome, Glycoproteome, and N-Terminome Using Terminal Amine Isotopic Labeling of Substrates Journal of Proteome Research Débora Andrade-Silva, André Zelanis, Silvia R. Travaglia-Cardoso, Milton Y. Nishiyama, Solange M. T. Serrano
2021	Current and prospective computational approaches and challenges for developing COVID-19 vaccines Advanced Drug Delivery Reviews Woochang Hwang, Winnie Lei, Nicholas M Katritsis, Méabh MacMahon, Kathryn Chapman, Namshik Han
2021	Persian sentiment analysis of an online store independent of pre-processing using convolutional neural network with fastText embeddings PeerJ Computer Science Sajjad Shumaly, Mohsen Yazdinejad, Yanhui Guo
2021	The cnidarian parasite Ceratonova shasta utilizes inherited and recruited venom-like compounds during infection PeerJ Benjamin Americus, Nicole Hams, Anna M. L. Klompen, Gema Alama-Bermejo, Tamar Lotan, Jerri L. Bartholomew, Stephen D. Atkinson
2021	Capturing Protein Domain Structure and Function Using Self-Supervision on Domain Architectures Algorithms Damianos P. Melidis, Wolfgang Nejdl
2020	Predicting Liver Disease Risk Using a Combination of Common Clinical Markers: A Screening Model from Routine Health Check-Up Disease Markers Yi Wang, Yanni Li, Xiaoyi Wang, Ranko Gacesa, Jie Zhang, Lu Zhou, Bangmao Wang
2020	Proteomic Analysis of the Venom of Jellyfishes Rhopilema esculentum and Sanderia malayensis Marine Drugs Thomas C. N. Leung, Zhe Qu, Wenyan Nong, Jerome H. L. Hui, Sai Ming Ngai
2020	Reciprocal transplantation of the heterotrophic coral Tubastraea coccinea (Scleractinia: Dendrophylliidae) between distinct habitats did not alter its venom toxin composition Ecology and Evolution Marcelo V. Kitahara, Adrian Jaimes‐Becerra, Edgar Gamero‐Mora, Gabriel Padilla, Liam B. Doonan, Malcolm Ward, Antonio C. Marques, André C. Morandini, Paul F. Long
2020	Learning supervised embeddings for large scale sequence comparisons PLOS ONE Dhananjay Kimothi, Pravesh Biyani, James M. Hogan, Akshay Soni, Wayne Kelly
2019	Venoms of Rear-Fanged Snakes: New Proteins and Novel Activities Frontiers in Ecology and Evolution Cassandra M. Modahl, Stephen P. Mackessy
2019	Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX) Scientific Reports Ehsaneddin Asgari, Alice C. McHardy, Mohammad R. K. Mofrad
2019	Encyclopedia of Bioinformatics and Computational Biology Jyotsna T. Wassan, Haiying Wang, Huiru Zheng
2019	“Beyond Primary Sequence”—Proteomic Data Reveal Complex Toxins in Cnidarian Venoms Integrative and Comparative Biology Adrian Jaimes-Becerra, Ranko Gacesa, Liam B Doonan, Ashlie Hartigan, Antonio C Marques, Beth Okamura, Paul F Long
2019	Chemical Responses to the Biotic and Abiotic Environment by Early Diverging Metazoans Revealed in the Post-Genomic Age Integrative and Comparative Biology Beth Okamura, Paul F Long, Laura D Mydlarz
2019	Venom Composition Does Not Vary Greatly Between Different Nematocyst Types Isolated from the Primary Tentacles of Olindias sambaquiensis (Cnidaria: Hydrozoa) The Biological Bulletin Liam B. Doonan, Steven Lynham, Catherine Quinlan, Spike C. Ibiji, Carlos E. Winter, Gabriel Padilla, Adrian Jaimes-Becerra, André C. Morandini, Antonio C. Marques, Paul F. Long
2019	TOXIFY: a deep learning approach to classify animal venom proteins PeerJ T. Jeffrey Cole, Michael S. Brewer
2018	Venomix: a simple bioinformatic pipeline for identifying and characterizing toxin gene candidates from transcriptomic data PeerJ Jason Macrander, Jyothirmayi Panda, Daniel Janies, Marymegan Daly, Adam M. Reitzel
2018	Studying Smaller and Neglected Organisms in Modern Evolutionary Venomics Implementing RNASeq (Transcriptomics)—A Critical Guide Toxins Björn Marcus Von Reumont
2017	Pharmacological screening technologies for venom peptide discovery Neuropharmacology Jutty Rajan Prashanth, Nojod Hasaballah, Irina Vetter
2017	Venom peptides as therapeutics: advances, challenges and the future of venom-peptide discovery Expert Review of Proteomics Samuel D. Robinson, Eivind A. B. Undheim, Beatrix Ueberheide, Glenn F. King
2017	Computational Studies of Snake Venom Toxins Toxins Paola Ojeda, David Ramírez, Jans Alzate-Morales, Julio Caballero, Quentin Kaas, Wendy González
2016	Evolution of the Cytolytic Pore-Forming Proteins (Actinoporins) in Sea Anemones Toxins Jason Macrander, Marymegan Daly
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