This page contains the tools and software packages we have developed here at WangLab or previously at other institutions.

Please visit our GitHub page for our latest releases.

One Cell At a Time (OCAT)

OCAT: a unified framework to integrate and analyze single-cell RNA-seq data.

Related publications:

Chloe X. Wang, Lin Zhang Bo Wang. Genome Biology, 2022. Long-term mortality risk stratification of liver transplant recipients.

Real-time application of deep learning algorithms on longitudinal data.

Related publications:

Osvald Nitski, Amirhossein Azhie, Fakhar Ali Qazi-Arisar, Xueqi Wang, Shihao Ma, Leslie Lilly, Kymberly D Watt, Josh Levitsky, Sumeet K Asrani, Douglas S Lee, Barry B Rubin, Mamatha Bhat, Bo Wang. The Lancet Digital Health, 2021. simATAC: a single-cell ATAC-seq simulation framework.

simATAC provides a robust and systematic approach to generate in silico scATAC-seq samples with known cell labels for assessing analytical pipelines.

Related publications:

Zeinab Navidi, Lin Zhang Bo Wang. Genome Biology, 2021. COVID Genotyper: Genotyping SARS-CoV-2 through an interactive web application

An online, user-friendly platform where researchers can compare the genome sequence of the SARS-CoV-2 virus in their hospital against the global picture.

Related publications:

Hassaan Maan, Hamza Mbareche, Amogelang R Raphenya, Arinjay Banerjee, Jalees A Nasir, Robert A Kozak, Natalie Knox, Samira Mubareka, Andrew G McArthur, Bo Wang. The Lancet Digital Health, 2020. SAUNet: Shape Attentive U-Net for Interpretable Medical Image Segmentation

A new medical image segmentation architecture which focuses on model interpretability and robustness.

Related publications:

Jesse Sun, Fatemeh Darbeha, Mark Zaidi, Bo Wang. MICCAI, 2020. M3SDA: Moment Matching for Multi-Source Domain Adaptation

Transfer knowledge learned from multiple labeled source domains to an unlabeled target domain by dynamically aligning moments of their feature distributions.

Related publications:

Xingchao Peng, Qinxun Bai, Xide Xia, Zijun Huang, Kate Saenko, Bo Wang. ICCV, 2019. SNF: Computational method for data integration

A new computational method for data integration.

Related publications:

Bo Wang, Aziz M Mezlini, Feyyaz Demir, Marc Fiume, Zhuowen Tu, Michael Brudno, Benjamin Haibe-Kains, Anna Goldenberg. Similarity network fusion for aggregating data types on a genomic scale. Nature Methods, 2014. SIMLR: Single-cell interpretation via multi-kernel learning

A novel similarity-learning framework for dimension reduction, clustering and visualization.

Related publications:

Bo Wang, Junjie Zhu, Emma Pierson, Serafim Batzoglou. Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning. Nature Methods, 2017.
Bo Wang, Daniele Ramazzotti, Luca De Sano, Junjie Zhu, Emma Pierson, Serafim Batzoglou. SIMLR: A Tool for Large‐Scale Genomic Analyses by Multi‐Kernel Learning. Proteomics, 2018. Vicus: Capturing neighborhood structures of the network

Exploiting local structures to improve network-based analysis of biological data.

Related publications:

Bo Wang, Lin Huang, Yuke Zhu, Anshul Kundaje, Serafim Batzoglou, Anna Goldenberg. Vicus: Exploiting local structures to improve network-based analysis of biological data. PLoS Computational Biology, 2017. Network Enhancement: Denoising weighted biological networks

A general method to denoise weighted biological networks.

Related publications:

Bo Wang, Armin Pourshafeie, Marinka Zitnik, Junjie Zhu, Carlos D Bustamante, Serafim Batzoglou, Jure Leskovec. Network Enhancement: a general method to denoise weighted biological networks. Nature Communications, 2018.

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