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Yimeng Dou

dblp:02/6635 · DBLP profile ↗
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3ranked-venue papers
1as first author
1since 2021 · last 2025
0000-0003-2202-6263ORCID · corroborated

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 2 · 1 first-authorComputer networks · 1 · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
2 papers
Bioinformatics and computational biology · 100%

Topics — the 4 heaviest of 5, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › molecular informatics
cheminformatics
0.112005
ChemDB: a public database of small molecules and related chemoinformatics resources · Bioinform. 2005
Bioinformatics and computational biology › protein analysis
protein-protein interaction
0.012004
ICBS: a database of interactions between protein chains mediated by ?-sheet formation · Bioinform. 2004
Bioinformatics and computational biology
molecular property prediction
0.012005
ChemDB: a public database of small molecules and related chemoinformatics resources · Bioinform. 2005
Bioinformatics and computational biology › protein structure analysis
quaternary structure
0.012004
ICBS: a database of interactions between protein chains mediated by ?-sheet formation · Bioinform. 2004

Methods — techniques the papers use, named apart from their topics

computational annotation · 0.1statistical analysis · 0.0
YearPublicationVenuePosition
2025 Adaptive Hash Ring-Based Efficient Fuzzy and Over-Threshold Multi-Party PSI
abstract
Private Set Intersection (PSI) enables participants to compute the intersection of private data without revealing other information. Over-Threshold Multi-Party PSI (OT-MPPSI) extends this capability by revealing elements shared by at least t participants, but existing schemes only support exact matches. Fuzzy PSI (FPSI) allows approximate matching, yet lacks scalability in multi-party settings. To address this gap, we propose AH-FTM-PSI, the first protocol that integrates fuzzy matching with over-threshold multi-party PSI. The protocol combines character padding, chunk processing, and slidingwindow extraction to enhance fuzzy fault tolerance, and introduces an adaptive hash ring that employs consistent hashing with dynamic virtual nodes to achieve load balancing, reduce collisions, and improve efficiency without pre-allocated space. Experiments on datasets of up to one million records show that AH-FTM-PSI achieves over 99.9% fuzzy matching accuracy, reduces communication overhead by 99.9% compared to mainstream PSI protocols, and improves operational efficiency by 50%. Moreover, the protocol maintains high completion rates and low latency under unstable environments such as satellite and mobile networks, offering an efficient solution for large-scale privacy-preserving computation.
Ruoyun Zhao, Yimeng Dou
IPCCC4
2005 ChemDB: a public database of small molecules and related chemoinformatics resources
abstract
MOTIVATION: The development of chemoinformatics has been hampered by the lack of large, publicly available, comprehensive repositories of molecules, in particular of small molecules. Small molecules play a fundamental role in organic chemistry and biology. They can be used as combinatorial building blocks for chemical synthesis, as molecular probes in chemical genomics and systems biology, and for the screening and discovery of new drugs and other useful compounds. RESULTS: We describe ChemDB, a public database of small molecules available on the Web. ChemDB is built using the digital catalogs of over a hundred vendors and other public sources and is annotated with information derived from these sources as well as from computational methods, such as predicted solubility and three-dimensional structure. It supports multiple molecular formats and is periodically updated, automatically whenever possible. The current version of the database contains approximately 4.1 million commercially available compounds and 8.2 million counting isomers. The database includes a user-friendly graphical interface, chemical reactions capabilities, as well as unique search capabilities. AVAILABILITY: Database and datasets are available on http://cdb.ics.uci.edu.
Jonathan H. Chen, Sanjay Joshua Swamidass, Yimeng Dou, Jocelyne Bruand, Pierre Baldi
Bioinform.3
2004 ICBS: a database of interactions between protein chains mediated by ?-sheet formation
abstract
MOTIVATION: Interchain beta-sheet (ICBS) interactions occur widely in protein quaternary structures, interactions between proteins and protein aggregation. These interactions play a central role in many biological processes and in diseases ranging from AIDS and cancer to anthrax and Alzheimer's. RESULTS: We have created a comprehensive database of ICBS interactions that is updated on a weekly basis and allows entries to be sorted and searched by relevance and other criteria through a simple Web interface. We derive a simple ICBS index to quantify the relative contributions of the beta-ladders in the overall interchain interaction and compute first- and second-order statistics regarding amino acid composition and pairing at different relative positions in the beta-strands. Analysis of the database reveals a 15.8% prevalence of significant ICBS interactions, the majority of which involve the formation of antiparallel beta-sheets and many of which involve the formation of dimers and oligomers. The frequencies of amino acids in ICBS interfaces are similar to those in intrachain beta-sheet interfaces. A full range of non-covalent interactions between side chains complement the hydrogen-bonding interactions between the main chains. Polar amino acids pair preferentially with polar amino acids and non-polar amino acids pair preferentially with non-polar amino acids among antiparallel (i, j) pairs. We anticipate that the statistics and insights gained from the database will guide the development of agents that control interchain beta-sheet interactions and that the database will help identify new protein interactions and targets for these agents. AVAILABILITY: The database is available at: http://www.igb.uci.edu/servers/icbs/
Yimeng Dou, Pierre-François Baisnée, Gianluca Pollastri, Yann Pécout, James Nowick, Pierre Baldi
Bioinform.1