All Publications of Austin Clyde

Journals and Magazines

[J9] "Scaffold-Induced Molecular Graph (SIMG): Effective Graph Sampling Methods for High-Throughput Computational Drug Discovery", Clyde, Austin and Shah, Ashka and Zvyagin, Max and Ramanathan, Arvind and Stevens, Rick, BMC Bioinformatics. 2022.

[J8] "Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action", Anda Trifan and Defne Gorgun and Michael Salim and Zongyi Li and Alexander Brace and Maxim Zvyagin and Heng Ma and Austin Clyde and David Clark and David J Hardy and Tom Burnley and Lei Huang and John McCalpin and Murali Emani and Hyenseung Yoo and Junqi Yin and Aristeidis Tsaris and Vishal Subbiah and Tanveer Raza and Jessica Liu and Noah Trebesch and Geoffrey Wells and Venkatesh Mysore and Thomas Gibbs and James Phillips and S Chakra Chennubhotla and Ian Foster and Rick Stevens and Anima Anandkumar and Venkatram Vishwanath and John E Stone and Emad Tajkhorshid and Sarah A Harris and Arvind Ramanathan, The International Journal of High Performance Computing Applications Vol. 0, Iss. 0, pp. 10943420221113513, DOI: 10.1177/10943420221113513, 2022. Finalist Gordan Bell Prize '21 '

[J7] "\# COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol", Dommer, Abigail and Casalino, Lorenzo and Kearns, Fiona and Rosenfeld, Mia and Wauer, Nicholas and Ahn, Surl-Hee and Russo, John and Oliveira, Sofia and Morris, Clare and Bogetti, Anthony and others, The International Journal of High Performance Computing Applications SAGE Publications Sage UK: London, England, pp. 10943420221128233, 2021. Finalist Gordan Bell Prize '21 '

[J6] "High-throughput virtual screening and validation of a sars-cov-2 main protease noncovalent inhibitor", Clyde, Austin and Galanie, Stephanie and Kneller, Daniel W and Ma, Heng and Babuji, Yadu and Blaiszik, Ben and Brace, Alexander and Brettin, Thomas and Chard, Kyle and Chard, Ryan and others, Journal of chemical information and modeling American Chemical Society, Vol. 62, Iss. 1, pp. 116--128, 2021.

[J5] "Structural, electronic, and electrostatic determinants for inhibitor binding to subsites S1 and S2 in SARS-CoV-2 main protease", Kneller, Daniel W and Li, Hui and Galanie, Stephanie and Phillips, Gwyndalyn and Labb\ 'e Aud, Journal of medicinal chemistry American Chemical Society, Vol. 64, Iss. 23, pp. 17366--17383, 2021.

[J4] "A cross-study analysis of drug response prediction in cancer cell lines", Xia, Fangfang and Allen, Jonathan and Balaprakash, Prasanna and Brettin, Thomas and Garcia-Cardona, Cristina and Clyde, Austin and Cohn, Judith and Doroshow, James and Duan, Xiaotian and Dubinkina, Veronika and others, Briefings in bioinformatics Oxford University Press, Vol. 23, Iss. 1, pp. bbab356, 2022.

[J3] "Pandemic drugs at pandemic speed: infrastructure for accelerating COVID-19 drug discovery with hybrid machine learning-and physics-based simulations on high-performance computers", Bhati, Agastya P and Wan, Shunzhou and Alf\ 'e Dar, Interface focus The Royal Society, Vol. 11, Iss. 6, pp. 20210018, 2021.

[J2] "AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics", Casalino, Lorenzo and Dommer, Abigail C and Gaieb, Zied and Barros, Emilia P and Sztain, Terra and Ahn, Surl-Hee and Trifan, Anda and Brace, Alexander and Bogetti, Anthony T and Clyde, Austin and others, The International Journal of High Performance Computing Applications SAGE Publications Sage UK: London, England, Vol. 35, Iss. 5, pp. 432--451, 2021. [ Gordan Bell Prize 2020]

[J1] "Learning curves for drug response prediction in cancer cell lines", Partin, Alexander and Brettin, Thomas and Evrard, Yvonne A and Zhu, Yitan and Yoo, Hyunseung and Xia, Fangfang and Jiang, Songhao and Clyde, Austin and Shukla, Maulik and Fonstein, Michael and others, BMC bioinformatics BioMed Central, Vol. 22, Iss. 1, pp. 1--18, 2021.

Conference Proceedings

[C12] "Spatial graph attention and curiosity-driven policy for antiviral drug discovery", Wu, Yulun and Choma, Nicholas and Chen, Andrew and Cashman, Mikaela and Prates, \ 'Erica T and Shah, Manesh and Vergara, Ver\ 'onica G Melesse and Clyde, Austin and Brettin, Thomas S and de Jong, Wibe A and others, The 10th International Conference on Learning Representations (ICLR) 2022 virtual 2021.

[C11] "Autodock on Enamine Hit Locator Library and Drugbank", Hubertus van Dam, Martin Purschke, Dean Hidas, Oleg Tchoubar, Maksim Rakitin, Xiaohui Qu, Austin Clyde, et al., IEEE Healthcare Summit Data Hackathon 2021. virtual 2021.

[C10] "IMPECCABLE: integrated modeling pipelinE for COVID cure by assessing better LEads", Saadi, Aymen Al and Alfe, Dario and Babuji, Yadu and Bhati, Agastya and Blaiszik, Ben and Brace, Alexander and Brettin, Thomas and Chard, Kyle and Chard, Ryan and Clyde, Austin and others, 50th International Conference on Parallel Processing virtual 2021.

[C9] "Stream-AI-MD: Streaming AI-driven adaptive molecular simulations for heterogeneous computing platforms", Brace, Alexander and Salim, Michael and Subbiah, Vishal and Ma, Heng and Emani, Murali and Trifa, Anda and Clyde, Austin R and Adams, Corey and Uram, Thomas and Yoo, Hyunseung and others, Proceedings of the Platform for Advanced Scientific Computing Conference virtual 2021.

[C8] "Scalable HPC \& AI infrastructure for COVID-19 therapeutics", Lee, Hyungro and Merzky, Andre and Tan, Li and Titov, Mikhail and Turilli, Matteo and Alfe, Dario and Bhati, Agastya and Brace, Alex and Clyde, Austin and Coveney, Peter and others, Proceedings of the Platform for Advanced Scientific Computing Conference virtual 2021.

[C7] "Targeting SARS-CoV-2 with AI-and HPC-enabled lead generation: a first data release", Babuji, Yadu and Blaiszik, Ben and Brettin, Tom and Chard, Kyle and Chard, Ryan and Clyde, Austin and Foster, Ian and Hong, Zhi and Jha, Shantenu and Li, Zhuozhao and others, virtual 2020.

[C6] "Created in our Likeness: Is Open-Source AI at Odds with animal Rights", Clyde, Austin, virtual 2020.

[C5] "Scaffold-Induced Molecular Graph (SIMG): Effective Graph Sampling Methods for High-Throughput Computational Drug Discovery", Clyde, Austin and Shah, Ashka and Zvyagin, Max and Ramanathan, Arvind and Stevens, Rick, virtual 2020.

[C4] "Integrating High-Performance Simulations and Learning toward Improved Cancer Therapy", Clyde, Austin and Wright, David and Jha, Shantenu, Fifth Computational Approaches for Cancer Workshop Boulder, CO 2019.

[C3] "Combining molecular simulation and machine learning to INSPIRE improved cancer therapy", Wright, DW and Devitt-Lee, A and Clyde, A and Palani, K and Xia, F and Turilli, M and Karanicolas, J and Jha, S and Stevens, R and Chodera, JD and others, CompBioMed Conference 2019 London, UK 2019.

[C2] "Benchmarking Machine Learning Workloads in Structural Bioinformatics Applications", Ma, Heng and Clyde, Austin and Trifan, Anda and Vishwanath, Venkatram and Ramanathan, Arvind and Bhowmik, Debsindhu and Jha, Shantenu, First International Workshop on Benchmarking Machine Learning Workloads on Emerging Hardware 2020.

[C1] "Virtual screening with deep learning using cancer cell line dose-response data", Clyde, Austin and Ramanathan, Arvind and Stevens, Rick, The American Association for Cancer Research, pp. Opinion Pieces, 2020.

Book Chapters

[B1] "Ultrahigh Throughput Protein--Ligand Docking with Deep Learning", Clyde, Austin, Artificial Intelligence in Drug Design Humana, New York, NY, pp. 301--319, DOI: https://doi.org/10.1016/j.patter.2022.100446, 2022.

Editorials

[E3] "AI for science and global citizens", Clyde, Austin, Elsevier, Vol. 3, pp. 100446, DOI: https://doi.org/10.1016/j.patter.2022.100446, 2022.

[E2] "Human-in-the-Loop Systems Are No Panacea for AI Accountability", Clyde, Austin, Tech Policy Press, 2021.

[E1] "Algorithmic Systems Designed to Reduce Polarization Could Hurt Democracy, Not Help It", Clyde, Austin, Tech Policy Press, 2022.

Preprints

[P4] "GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics.", Zvyagin, Max T and Brace, Alexander and Hippe, Kyle and Deng, Yuntian and Zhang, Bin and Bohorquez, Cindy Orozco and Clyde, Austin and Kale, Bharat and Perez-Rivera, Danilo and Ma, Heng and others, Cold Spring Harbor Laboratory, DOI: https://doi.org/10.1101/2022.10.10.511571, 2022.

[P3] "Open science discovery of oral non-covalent SARS-CoV-2 main protease inhibitor therapeutics", Achdout, Hagit and Aimon, Anthony and Bar-David, Elad and Barr, Haim and Ben-Shmuel, Amir and Bennett, James and Boby, Melissa L and Borden, Bruce and Bowman, Gregory R and Brun, Juliane and others, (), Cold Spring Harbor Laboratory, pp. 2020--10, DOI: https://doi.org/10.1101/2020.10.29.339317, 2021.

[P2] "Regression enrichment surfaces: a simple analysis technique for virtual drug screening models", Clyde, Austin and Duan, Xiaotian and Stevens, Rick, 2020.

[P1] "A systematic approach to featurization for cancer drug sensitivity predictions with deep learning", Clyde, Austin and Brettin, Tom and Partin, Alexander and Shaulik, Maulik and Yoo, Hyunseung and Evrard, Yvonne and Zhu, Yitan and Xia, Fangfang and Stevens, Rick, preprint, 2020.

Automatically generated from this bibtex using the Smartbib project

All Publications of Austin Clyde

Journals and Magazines

Conference Proceedings

Book Chapters

Editorials

Preprints