Ye Bi 毕晔

Address: Litton-Reaves Hall, Blacksburg, Virginia 24061

I am a Ph.D. student from Dr. Gota Morota ‘s group in the School of Animal Sciences at Virginia Polytechnic Institute and State University.

My research interests focus on incorporating statistics, machine learning, and bioinformatics into the study of animal and plant genetics in the omics era.

I am also interested in the application of computer vision systems for high-throughput phenotyping in precision agriculture.

News

May 16, 2023	Oral Presentation. Depth video data-enabled predictions of longitudinal dairy cow body weight using thresholding and Mask R-CNN algorithms. School of Animal Sciences Research Day. Slides.
May 3, 2023	Oral Presentation. Diversity for Global Society Presentation. Engaging in Anti-Asian-Hate on Virginia Tech Campus. Slides. Interesting class.
Mar 16, 2023	Poster Presentation. Depth video data enabled prediction of dairy cow body weight. Virginia Tech Center for Advanced Innovation in Agriculture (CAIA) Big Event.
Feb 28, 2023	Guest Lecture ALS 3104 Animal Breeding and Genetics – Statistical Concepts in Quantitative Genetics

Selected Publications

Paper

An atlas of regulatory elements in chicken: A resource for chicken genetics and genomics

Zhangyuan Pan, Ying Wang, Mingshan Wang, Yuzhe Wang, Xiaoning Zhu, Shenwen Gu, Conghao Zhong, Liqi An, Mingzhu Shan, Joana Damas, and 15 more authors

Science Advances 2023

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A comprehensive characterization of regulatory elements in the chicken genome across tissues will have substantial impacts on both fundamental and applied research. Here, we systematically identified and characterized regulatory elements in the chicken genome by integrating 377 genome-wide sequencing datasets from 23 adult tissues. In total, we annotated 1.57 million regulatory elements, representing 15 distinct chromatin states, and predicted about 1.2 million enhancer-gene pairs and 7662 super-enhancers. This functional annotation of the chicken genome should have wide utility on identifying regulatory elements accounting for gene regulation underlying domestication, selection, and complex trait regulation, which we explored. In short, this comprehensive atlas of regulatory elements provides the scientific community with a valuable resource for chicken genetics and genomics. Decoding the chicken regulatory machinery helps to inform selection for simple and complex traits.
Paper

Automated acquisition of top-view dairy cow depth image data using an RGB-D sensor camera

Robert Kadlec, Sam Indest, Kayla Castro, Shayan Waqar, Leticia M Campos, Sabrina T Amorim, Ye Bi, Mark D Hanigan, and Gota Morota

Translational Animal Science 2023

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Paper

Multi-environment analysis enhances genomic prediction accuracy of agronomic traits in sesame

Idan Sabag, Ye Bi, Zvi Peleg, and Gota Morota

Frontiers in Genetics 2023

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Paper

Evaluating metabolic and genomic data for predicting grain traits under high night temperature stress in rice

Ye Bi, Rafael Massahiro Yassue, Puneet Paul, Balpreet Kaur Dhatt, Jaspreet Sandhu, Thi Phuc Do, Harkamal Walia, Toshihiro Obata, and Gota Morota

G3: Genes, Genomes, Genetics 2023

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