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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
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Posts
Looking for students
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In March of 2019 I’ll be joining the Department of Earth Sciences at Dartmouth as an assistant professor, so will be looking for future grad students!
Which came first: complex life or high atmospheric oxygen?
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UC Berkeley press release for the new paper out this week in Nature “A record of deep-ocean dissolved O2 from the oxidation state of iron in submarine basalts” by Stolper and Keller.
The Igneous Architecture of Arcs throughout the Crustal Column
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Barbara Ratschbacher, Kyle Samperton, Katie Ardill and I will be convening a session on arc magmatism at the 2018 Goldschmidt Conference in Boston (August 12-18th). Abstract submission will begin in early 2018 - read more here
Plate tectonics and basalt geochemistry
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New paper on basalt geochemistry with implications for the prevalence of plate tectonics and arc-style magmatism (hydrous flux melting) throughout the preserved continental rock record. Read all about it here!
fieldwork
Hell Creek, Montana
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The K-Pg boundary claystone (lower pencil) just below the IrZ tonstein (upper pencil) within the IrZ coal at Herpejunk, Hell Creek, Montana
Needle Mountains, Colorado
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Talkeetna Arc, Alaska
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Bergell Pluton, Central Alps
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Flinders Range, South Australia
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Los Frailes Volcanic Complex, Bolivia
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Other field trips
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notes
Weekly notes for Kaizhong’s lab. Topics including CNN, LSTM, peptide binding prediction (MHC).
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Data structures and algorithm
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CSC2515: Machine Learning
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Data Analysis Tools - PCA
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publications
MHCherryPan. a novel model to predict the binding affinity of pan-specific class I HLA-peptide
Xuezhi Xie, Yuanyuan Han, Kaizhong ZhangIEEE International Conference on Bioinformatics and Biomedicine (IEEE - BIBM), 2019: https://ieeexplore.ieee.org/document/8982962
MHCherryPan, a novel pan-specific model for binding affinity prediction of class I HLA-peptide
Xuezhi Xie, Yuanyuan Han, Kaizhong ZhangInt. J. Data Mining and Bioinformatics, 2020: https://www.inderscienceonline.com/doi/abs/10.1504/IJDMB.2020.112850?mobileUi=0
HelixGAN: A bidirectional Generative Adversarial Network with search in latent space for generation under constraints
Xuezhi Xie and Philip M. Kim.Machine Learning for Structural Biology (MLSB) Workshop at NeurIPS, 2021: https://doi.org/10.1016/j.chemgeo.2015.10.024
HelixGAN a deep learning methodology for conditional de novo design of α-helix structures
Xuezhi Xie, Pedro A Valiente, Philip M KimBioinformatics, 2023: https://academic.oup.com/bioinformatics/article/39/1/btad036/6991169
Antibody-SGM: Antigen-Specific Joint Design of Antibody Sequence and Structure using Diffusion Models
Xuezhi Xie, Jin Sub Lee, Dongki Kim, Jaehyeong Jo, Jisun Kim, Philip M. KimICML - Computational Biology, 2023: https://icml-compbio.github.io/2023/papers/WCBICML2023_paper143.pdf