Sitemap
A list of all the posts and pages found on the site. For you robots out there, there is an XML version available for digesting as well.
Pages
Posts
MoE All-to-All Dispatch and Ragged Routing
Published:
Global L2 Grad Norm and Gradient U-Shape
Published:
MoE 3D Architecture Visualizer: Interactive 3D Visualization of Modern MoE LLM Architectures
Published:
Adding Comments to My Static Website: Understanding Vercel, Neon Database, and Serverless Functions
Published:
Gemini CLI Silent Failure: How an Invalid package.json Version Breaks Slash Commands in VS Code
Published:
How to Set Up Claude Code on Your Mac
Published:
Virtual Cell Challenge 2025, Lesson 1
Published:
Reflection on the Boltz-2 Paper
Published:
Reflection on Eric Schmidt’s TED Interview
Published:
certificates
Introduction to Molecular Modeling in Drug Discovery
Completed on:
Schrödinger course on the fundamentals of small molecule drug discovery with Maestro and LiveDesign, covering protein preparation, ligand docking, and collaborative design.
Bioinformatics for Protein Identification
Completed on:
ASMS course on the fundamentals of protein identification from LC-MS/MS data, covering database searching, error rate estimation, and protein assembly.
LC-MS Practical Maintenance and Troubleshooting
Completed on:
ASMS course on the essential skills for maintaining LC-MS instrument performance, covering best practices, system suitability, tuning, calibration, and troubleshooting across various platforms.
Quantitative Proteomics: Case Studies
Completed on:
ASMS course on quantitative proteomics using case studies, focusing on SRM and DIA data analysis with Skyline and MSstats.
Machine Learning
Completed on:
Machine Learning Certificate.
Deep Learning Specialization
Completed on:
Deep Learning Specialization Certificate.
Associate Python Developer
Completed on:
DataCamp Associate Python Developer Certificate.
AI Agents Course
Completed on:
Hugging Face AI Agents Course Certificate.
Mentor Impact Award - CABS 2026 Data Science Summer Internship
Completed on:
Mentor Impact Award by Chinese American Biopharmaceutical Society (CABS).
notes
Claude macOS App Voice Mode Limitations
Published:
portfolio
AI-Enhanced Intact Mass Data Communication: Expert-Level Comment and Automated Visualization
Published:
Automated tool for LC-MS data: AI-driven expert comments and interactive 96-well plate heatmap visualization. 
Automated Sequence Generation and Data Prep Toolkit for LC-MS Intact Mass Analysis of Antibody Biologics
Published:
Toolkit to automate LC-MS sequence generation and data prep for antibody biologics. 
MoE 3D Architecture Visualizer: Interactive 3D Visualization of Modern MoE LLM Architectures Permalink
Published:
Interactive WebGL/Three.js 3D visualizer for modern 500B+ sparse MoE architectures, featuring LatentMoE communication compression, Quantile-Balanced routing, and real-time dynamic sampling pipelines.
publications
Synthesis and Mass Spectrometry Analysis of Oligo-peptoids
Published in Journal of Visualized Experiments, (132):56652, 2018, 2018
This article presents a method for manual synthesis of oligo-peptoids and sequence analysis using tandem mass spectrometry (MS/MS) techniques.
Recommended citation: Jianhua Ren, Yadwinder S Mann, Yuntao Zhang, Michael D Browne. (2018). "Synthesis and Mass Spectrometry Analysis of Oligo-peptoids." J Vis Exp, (132):56652. https://doi.org/10.3791/56652
Download Paper | Download Slides
Characterization of protonated AcAlaDab and AcDabAla by IRMPD spectroscopy and molecular modeling
Published in International Journal of Mass Spectrometry, Volume 444, October 2019, 116178, 2019
This paper characterizes protonated AcAlaDab and AcDabAla using IRMPD spectroscopy and molecular modeling, revealing structural insights into these isomeric dipeptides.
Recommended citation: Patrick Batoon, Yuntao Zhang, Giel Berden, Jos Oomens, Jianhua Ren. (2019). "Characterization of protonated AcAlaDab and AcDabAla by IRMPD spectroscopy and molecular modeling." International Journal of Mass Spectrometry, 444, 116178. https://doi.org/10.1016/j.ijms.2019.116178
Download Paper | Download Slides
Mass spectrometry studies of the fragmentation patterns and mechanisms of protonated peptoids
Published in Biopolymers, 111(7):e23358, 2020, 2020
This study uses tandem mass spectrometry to characterize the fragmentation patterns and mechanisms of singly and doubly protonated peptoids with basic residues at different positions.
Recommended citation: Jianhua Ren, Yuan Tian, Ekram Hossain, Joshua S Ho, Yadwinder S Mann, Yuntao Zhang, Michael D Browne, Michael D Connolly, Ronald N Zuckermann. (2020). "Mass spectrometry studies of the fragmentation patterns and mechanisms of protonated peptoids." Biopolymers, 111(7):e23358. https://doi.org/10.1002/bip.23358
Download Paper | Download Slides
Subtle chirality effects of a D/l-Cysteine on the intrinsic acidity and conformation of isomeric tripeptides ACA and AdCA
Published in International Journal of Mass Spectrometry, Volume 469, November 2021, 116685, 2021
This paper investigates the subtle chirality effects of a D/l-Cysteine on the intrinsic acidity and conformation of isomeric tripeptides ACA and AdCA.
Recommended citation: Yuntao Zhang, Zachary Buen, Michael D. Browne, Yadwinder S. Mann, Jianhua Ren. (2021). "Subtle chirality effects of a D/l-Cysteine on the intrinsic acidity and conformation of isomeric tripeptides ACA and AdCA." International Journal of Mass Spectrometry, 469, 116685. https://doi.org/10.1016/j.ijms.2021.116685
Download Paper | Download Slides
Chirality Effects on the Intrinsic Acidity of Isomeric Tripeptides Containing a D/L-Cysteine on the N-terminus: CAA and dCAA
Published in International Journal of Mass Spectrometry, Volume 514, August 2025, 117472, 2025
This paper investigates the chirality effects on the intrinsic acidity of isomeric tripeptides containing a D/L-Cysteine on the N-terminus.
Recommended citation: Shiyuan Wang, Zachary Buen, Kimberlyann R. Harvey, Yuntao Zhang, Jianhua Ren. (2025). "Chirality effects on the intrinsic acidity of isomeric tripeptides containing a D/L-Cysteine on the N-terminus: CAA and dCAA." International Journal of Mass Spectrometry, 514, 117472. https://doi.org/10.1016/j.ijms.2025.117472
Download Paper | Download Slides | Download Bibtex
Anti-LRRC15 Antibodies and Uses Thereof
Published in World Intellectual Property Organization (WIPO) & USPTO, 2026
Patent publication disclosing isolated anti-LRRC15 antibodies, antigen-binding fragments, bispecific antibodies, and conjugates for therapeutic and diagnostic oncology applications.
Recommended citation: Bristol-Myers Squibb Company (Co-inventor: Yuntao Zhang). (2026). "Anti-LRRC15 Antibodies and Uses Thereof." WIPO Patent Publication No. WO/2026/112469 A1 (U.S. Patent Application No. US 2026/0144885 A1).
Download Paper
Anti-LRRC15 Antibody Drug Conjugates
Published in World Intellectual Property Organization (WIPO) & USPTO, 2026
U.S. Patent Application Allowed. Discloses antibody-drug conjugates (ADCs) comprising anti-LRRC15 antibodies conjugated to exatecan (tubutecan platform) via a chemical linker for targeted cancer therapy.
Recommended citation: Sayumi Yamazoe, Sonia G. Tanlimco, Lore Florin, Philip M. Vitorino, Qinqin Cheng, Christine H. Tan, Yuntao Zhang, Sunitha Bachawal, Hok Yee Chan, Winse Hong Morishige, Andrew W. Drake, Deanne M. Lathers, Jaimee C. Wong. (2026). "Anti-LRRC15 Antibody Drug Conjugates." WIPO Patent Publication No. WO/2026/112472 A1 (U.S. Patent Application No. US 2026/0144884 A1; U.S. Notice of Allowance Issued).
Download Paper
talks
Chirality Induced Conformational and Thermochemical Changes in Cysteine Polyalanine Peptides
Published:
teaching
General Chemistry (CHEM23) Lab
Undergraduate course (Lab Instructor), University of the Pacific, Chemistry Department, 2017
Served as the Laboratory Instructor for General Chemistry (CHEM23) at the University of the Pacific. Guided undergraduate students through foundational chemical principles, laboratory safety protocols, volumetric analysis, and stoichiometry. This course is designed for general interest in physical science and for preparation for further study in chemistry.
General Chemistry (CHEM25) Lab
Undergraduate course (Lab Instructor), University of the Pacific, Chemistry Department, 2018
Served as the Laboratory Instructor for General Chemistry (CHEM25) at the University of the Pacific. Directed hands-on laboratory experiments, instructed students in data collection and analytical techniques, and reinforced core concepts in thermochemistry, atomic structure, and chemical equilibrium.
General Chemistry (CHEM27) Lab
Undergraduate course (Lab Instructor), University of the Pacific, Chemistry Department, 2019
Served as the Laboratory Instructor for General Chemistry (CHEM27) at the University of the Pacific. Led advanced undergraduate laboratories focusing on chemical kinetics, solution equilibria, electrochemistry, coordination compounds, organic chemistry, and biochemistry.