Bioinformatics Laboratory at YSU

News on YSU Bioinformatics Research

• Dr. Min, Dr. Yu (CSIS), Theoni Kasamias (undergraduate), Mykaela Wagner (MS graduate), Atinuke Ogunbayi (MS graduate) pulished a paper titled "Identification and analysis of alternative splicing in soybean plants". In: Hisham Al-Mubaid, Tamer Aldwairi and Oliver Eulenstein (editors). Proceedings of 14th International Conference on Bioinformatics and Computational Biology, 2022, vol 83, pages 1-9.[link to abstract]
• Drs. Asch and Min with Jannet Ziegle (undergraduate in Biological Sciences) published a paper in CMB. Asch DK, Ziegler J, Min XJ (2021) Molecular evolution of genes involved in quinic acid utilization in fungi. Computational Molecular Biology. 11(5):1-15.
• We just got the soybean RNA-seq review paper published in CMB. Min XJ, Wagner M, Kasamias T (2021) Advances in transcriptome analyses using RNA sequencing technology in soybean plants [Glycine max]. Computational Molecular Biology. 11(1):1-14.
• Recent publication (2019) on tomato alternative splicing: Expanding alternative splicing identification by intergrating multiple sources of transcription data in tomato. Frontiers in Plant Sciences. 10:689.
• The book "Genetics and Genomics of Pineapple" edited by R. Ming is published by Springer Internationl Publishing in 2018. Dr. Min's group in collaboration with Dr. Ming's group contributed two chapters in the book. (1) Min XJ, Wai CM, Powell B, Ming R (2018) Genome-Wide Identification and Analysis of Protease-Coding Genes in Pineapple. Genetics and Genomics of Pineapple. pp. 215-229.(2) Wai CM, Powell B, Ming R, Min XJ (2018) Analysis of Transcriptome and Alternative Splicing Landscape in Pineapple. Genetics and Genomics of Pineapple. pp. 195-213. Link to the book.
• The cotton (Gossipium hirsutum L.) alternatively spliced genes are collected and analyzed. The work is published as: Min XJ (2018) A survey of alternative splicing in allotetraploid cotton (Gossypium hirsutum L.). Computational Molecular Biology. 8(1):1-13.
• The maize alternative splicing events and associated genes are comprehensively cataloged and analyzed.The work is published as: Min XJ (2017) Comprehensive Cataloging and Analysis of Alternative Splicing in Maize. Computational Molecular Biology 7(1):1-11.[database] [data download]
• The fruit alternative splicing work is published in Current Plant Biology. Sablok G, Powell B, Braessler J, Yu F, Min XJ (2017) Comparative landscape of alternative splicing in fruit plants. Current Plant Biology. DOI: 10.1016/j.cpb.2017.06.001. The data and database can be found at Plant Alternative Splicing Database.
• The paper on Protist Secretome Database is published in Computational Molecular Bioloy. Powell B, Amerishetty V, Meinken J, Knott G, Yu F, Cooper C, Min XJ (2016) ProtSecKB: The Protist Secretome and Subcellular Proteome Knowledgebase. Computational Molecular Biology 6(4):1-12. (Doi:10.5376/cmb.2016.06.0004).
• Two new papers on pineapple genomics were published online in Tropical Plant Biology. The papers are (1) Genome-wide identification and analysis of genes encoding proteolytic enzymes in pineapple; and (2) Analysis of alternative splicing landscape in pineapple (Ananas comosus). These works are collaborated with Dr. Ming's group.
• Pineapple genome sequence is published. Dr. Min participated in the annotation and analysis of the genome. The work is published in Nature Genetics.
• The cereal crop alternative splicing work was published in BMC Genomics - Link to the paper.
• The paper on MetazSecKB is published online: Meinken J, Walker G, Cooper CR, Min XJ (2015) MetazSecKB: the human and animal secretome and subcellular proteome knowledgebase. Database, bav077. Also see the YSU News
• Neizer-Ashun K, Yu F, Meinken J, Min X, Chang G-H. (2015) Prediction of plant protein subcellular locations. In: Saeed F. and Haspel N. (ed), Proceedings of the 7th International Conference on Bioinformatics and Computational Biology (BICOB-2015). March 9 - 11, 2015, Honolulu, Hawaii, USA. pp 91-96. (The work was presended by Neizer-Ashun and Dr. Chang at the meeting).
• The Protist Secretome and Subcellular Proteome KnowledgeBase (ProtSecKB) is released. 11/14/2014.
• Human/animal secretome and subcellular proteome knowledgebase (MetazSecKB) is released. 5/9/2014.
• Fungal secretome and subcellular proteome knowledgeBase 2.1 (FunSecKB2) is released. 3/1/2014.
• "PlantSecKB: the Plant Secretome and Subcellular Proteome KnowledgeBase" is published in Computational Molecular Biology. 4(1): 1-17 (doi:10.5376/cmb.2014.04.0001). [database] [pdf].
• Recent Publications. Faculty/staff achievements. YSU News Center.2/22/2013
• Revealing the secrets behind secretomes. theJambar.com. 10/24/2012
• Prof research peeks into early evolution. YSU News Center. 9/17/2012
• Researchers Peek at the Early Evolution of Sex Chromosomes. ScienceDaily 8/16/2012
• Cutting-edge research with bioinformatics. Frontiers. School of Graduate Studies and Research. Youngstown State University. Winter 2012.
• Other recent publications

Other Related News (Participated Project News)

• Sacred lotus genome sequence enlightens scientists: Sacred lotus genome news release by U Illinois and Science Daily
• Scientists sequence genome of 'sacred lotus,' which likely holds anti-aging secrets: Sacred lotus genome news release by UCLA
• Scientists discover clues about plant evolution: Sacred lotus genome news release by U Hawaii

Bioinformatics Research Projects

• Bioinformatics software tool development.
• Bioinformatics database development: we focus on secretome and alternative splicing.
• Comparative genomics.

Personnel

• Dr. Xiangjia "Jack" Min (Professor in Bioinformatics)
• Biology Undergraduate Students (Spring 2024 -): Bilal Wekhyan
• MS Graduate: Pasan Thilakarathan Mudiyanselage (MS, CSIS)

*********** Note ************

• Dr. Min is continuously recruiting undergraduate and graduate students who have interests in both biological sciences and computer informatics to work on his research projects. Please contact him by email or visit him in office.

Lab Alumni

• Gengkon Lum (MS graduate, CSIS)
• John Meinken (MS graduate, CSIS)
• Atinuke Ogungbayi (MS. Graduate, BIOL)
• Courtney Jones, Jessica Lee, Logan Burrowns, Maria Campean, Chetan Dadana, Aaryan Patel (Bio Major, Undergraduates)
• Theoni Kasamias (Bio Major, Undergraduate)
• Benjamin Annan (MS Graduate, Math & Statistics - co-supervised by Dr. A. G-H. Chang)
• Brian Powell (M. S. graduate, CSIS)
• Geneva Knott (Undergraduate, BIOL)
• Sepideh Khavari (M. S. graduate, Math & Statistics, co-supervised by Dr. Chang)
• Vamshi Amerishetty (MS graduate, CSIS)
• Kofi A. Neizer-Ashun (MS graduate, Math & Statistics, co-supervised with Drs. G. Chang and F. Yu)
• David Arthur (MS graduate, Math & Statistics, co-supervised with Dr. Chang)
• Braden Walters (Undergraduate, CSIS)
• Jessica Orr (Undergraduate, BIOL)
• Stephanie Frazier (Undergraduate, BIOL)
• Jonathan Braessler (Undergraduae, CSIS)
• James Munyon (Undergraduate, Math & Statistics, co-supervised by Dr. Chang)
• Sarah Clark (Undergraduate, BIOL)
• Vishwa Vaghela (Biol. Major, Undergraduate)
• Janett Ziegler (Undergraduate, BIOL)

Collaborators

• Ray Ming
• Gaurav Sablok
• Andy Chang
• Feng Yu