Xiangjia (Jack) Min

Also known as: Xiang Jia Min

Professor in Bioinformatics and Plant Biology

Education: Ph.D. (1995) University of Hawaii; MSS (Master of Software Systems) (2002) University of British Columbia;

MS (1987) China Agricultural University; BS (1984) Qingdao Agricultural University

Postdoctoral Research: University of British Columbia (1996-1998); Institute of Physical and Chemical Research (RIKEN), Japan (1998-2000)

Work Experience: Research associate - University of British Columbia (2000-2002); Concordia University (2002-2008)

Contact Information
Department of Chemical and Biological Sciences College of Science, Technology, Engineering and Mathematics Youngstown State University One University Plaza Youngstown, Ohio 44555 USA Bioinformatics Tools and Databases

Current Research & Teaching at YSU (2008 - present)

Research projects: (1) Bioinformatics software and database development - software tools for DNA sequence analysis and identification of alternatively spliced genes; knowledge database development for secretomes and alternatively spliced genes; (2) Gene and genome annotation and evolutionary analysis.

Teaching: BIOL1505: Biology & the Modern World; BIOL2601: General Biology - Molecules and Cells; BIOL3721: Genetics; BIOL3745: Plant Physiology; BIOL4890L: Molecular Genetics Laboratory; BIOL6964: Advanced Molecluar Genetics; BIOL4800: Bioinformatics; BIOL6900: Advanced Bioinformatics; BIOL5858: Computational Bioinformatics

News on YSU Bioinformatics Research [more]

Dr. Min received a Long Service Award from PLOS ONE Editorial Board for serving as an academic editor.[link]
Pineapple genome sequence is published. Dr. Min participated in the annotation and analysis of the genome. The work is published in Nature Genetics.
Faculty receive distinguished professor awards. YSU News Center. 5/2/2013
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.

Publications (Full papers in journals, conference proceedings, and invited book chapters) [see Google Scholar for Citations]

2023
63. Ogungbayi A, Lee J, Vaghela V, Yu F, Min X (2023) Systematic collection and analysis of alternative splicing events in potato plants. Journal of Plant Sciences. 11: 98-106.[pdf]
62. Lee JA, Min X. (2023) Comparative analysis of alternative splicing events in foliar transcriptomes of potato plants inoculated with Phytophthora infestans. Computational Molecular Biology. 13(1):1-8. [pdf]
2022
61. Kafkas S, et al. (2022) The pistachio genomes provide insights into nut tree domestication and ZW sex chromosome evolution. Plant Communications.100497.
60. Min X, Kasamias T, Wagner M, Ogunbayi, Yu F (2022) 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, vol 83, pages 1-9.[link]
2021
59. 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.[pdf]
58. 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.[pdf]
2019
57. Clark S, Yu F, Gu L, Min XJ (2019) Expanding alternative splicing identification by integrating multiple sources of transcription data in tomato. Frontiers in Plant Sciences. 10:689. doi:10.3389/fpls.2019.00689.
2018
56. 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. Edited by R. Ming. Published by Springer International Publishing.
55. 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. Edited by R. Ming. Published by Springer International Publishing.
54. Min XJ (2018) A survey of alternative splicing in allotetraploid cotton (Gossypium hirsutum L.). Computational Molecular Biology. 8(1):1-13.[pdf]
2017
53. Min XJ (2017) Comprehensive Cataloging and Analysis of Alternative Splicing in Maize. Computational Molecular Biology 7(1):1-11.[pdf] [database] [data download]
52. 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.
2016
51. Khavari S, Min X, Munyon J, Chang G (2016) Prediction human and animal protein subcellular location. JSM Proceedings - Section on Statistics in Genomics and Genetics, 2982-2999.
50. 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).[data][database]
49. Wai CM, Powell B, Ming R, Min XJ (2016) Genome-wide identification and analysis of genes encoding proteolytic enzymes in pineapple. Tropical Plant Biology. 9(3):161-175. DOI: 10.1007/s12042-016-9172-5
48. Wai CM, Powell B, Ming R, Min XJ (2016) Analysis of alternative splicing landscape in pineapple (Ananas comosus). Tropical Plant Biology. 9(3):150-160. DOI: 10.1007/s12042-016-9168-1
2015
47. Munyon JD, Min X, Khavari S, Chang G-H (2015) Prediction of Subcellular Locations for Fungal Proteins. Proceeding of the Joint Statistics Meeting 2015 (JSM2015) - Section on Statistics in Genomics and Genetics. pp 2497-2508.[data and code]
46. Ming R, VanBuren R, Wai CM,...Min X, ..., et al. (2015) The pineapple genome and the evolution of CAM photosynthesis. Nat Genet 47(12):1435-1442. doi: 10.1038/ng.3435.
45. Min XJ, Powell B, Braessler J, Meinken J, Yu F, Sablok G. (2015) Genome-wide cataloging and analysis of alternatively spliced genes in cereal crops. BMC Genomics. 16:721.
44. Meinken J, Walker G, Cooper CR, Min XJ (2015) MetazSecKB: the human and animal secretome and subcellular proteome knowledgebase. Database, bav077.[database][[supp data]
43. 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). Honolulu, Hawaii, USA. pp 91-96.
42. Kalclits L, Min X, Guy R (2015) Interspecific variation in leaf-root differences in δ¹⁵N among three tree species grown with either nitrate or ammonium. Trees - Structure and Function. DOI 10.1007/s00468-015-1186-3
2014
41. Meinken J, Asch DK, Neizer-Ashun KA, Chang GH, Cooper JR CR, Min XJ. (2014) FunSecKB2: a fungal protein subcellular location knowledgebase. Computational Molecular Biology. 4(7): 1-17. [pdf] [database] [other data]
40. Lum G, Meinken J, Orr J, Frazier S, Min XJ. (2014) PlantSecKB: the plant secretome and subcellular proteome knowledgebase. Computational Molecular Biology. 4(1): 1-17 (doi:10.5376/cmb.2014.04.0001).[pdf] [other data]
2013
39. Sablok G, Harikrishna JA, Min XJ. (2013) Next generation sequencing for better understanding alternative splicing: way ahead for model and non-model plants. Transcriptomics 1:e103. doi:10.4172/toa.1000e103. [pdf]
38. VanBuren R, Walters B, Ming R, Min XJ. (2013) Analysis of expressed sequence tags and alternative splicing genes in sacred lotus (Nelumbo nucifera Gaertn.). Plant Omics J. 6:311-317.
37. Lum G, Vanburen R, Ming R, Min XJ. (2013) Secretome Prediction and Analysis in Sacred Lotus (Nelumbo nucifera Gaertn.). Tropical Plant Biol. 6:131-137. (doi: 10.1007/s12042-013-9121-5).
36. Ming R, Vanburen R, Liu Y, Yang M, Han Y, Li LT, Zhang Q, Kim MJ, Schatz MC,Campbell M, Li J, Bowers JE, Tang H, Lyons E, Ferguson AA, Narzisi G, Nelson DR, Blaby-Haas CE, Gschwend AR, Jiao Y, Der JP, Zeng F, Han J, Min XJ, Hudson KA,Singh R, Grennan AK, Karpowicz SJ, Watling JR, Ito K, Robinson SA, Hudson ME, Yu Q, Mockler TC, Carroll A, Zheng Y, Sunkar R, Jia R, Chen N, Arro J, Wai CM, Wafula E, Spence A, Han Y, Xu L, Zhang J, Peery R, Haus MJ, Xiong W, Walsh JA, Wu J, Wang ML, Zhu YJ, Paull RE, Britt AB, Du C, Downie SR, Schuler MA, Michael TP, Long SP, Ort DR, Schopf JW, Gang DR, Jiang N, Yandell M, Depamphilis CW, MerchantSS, Paterson AH, Buchanan BB, Li S, Shen-Miller J. (2013) Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biol. 14(5): R41. DOI: 10.1186/gb-2013-14-5-r41. Related news: U Illinoisi news release ; Science Daily ; UCLA news release
35. Melhem H, Min XJ, Butler G (2013) The impact of SignalP 4.0 on the prediction of secreted proteins. 2013 IEEE Symposium Series on Computational Intelligence (IIEEE SSCI 2013): The 10th annual IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). April 16-19, 2013. Singapore. pp.16-22. (doi: 10.1109/CIBCB.2013.6595383)
34. Walters B, Lum G, Sablok G and Min XJ. (2013) Genome-wide landscape of alternative splicing events in Brachypodium distachyon. DNA Res. 20:163-171. doi:10.1093/dnares/dss041. [download the data] [Link to Plant Alternative Splicing Database]
33. Lum G and Min XJ. (2013) Bioinformatic Protocols and the Knowledge-Base for Secretomes in Fungi. In: Laboratory Protocols in Fungal Biology: Current Methods in Fungal Biology. Gupta VK, Tuohy MG, Ayyachamy M, Turner KM, O'Donovan A. (Eds.). Springer. pp 545-557.
32. Min XJ. (2013) ASFinder: a tool for genome-wide identification of alternatively spliced transcripts from EST-derived sequences. International Journal of Bioinformatics Research and Applications. Vol. 9, No. 3, pp.221-226.
2012
31. Wang J, Na J-K, Yu Q, Gschwend AR, Han J, Zeng F, Aryal R, VanBuren R, Murray JE, Zhang W, Navajas-Perez R, Feltus FA, Lemke C, Tong EJ, Chen C, Wai CM, Singh R, Wang ML, Min XJ, Alam M, Charlesworth D, Moore PH, Jiang J, Paterson AH, Ming R. (2012) Sequencing papaya X and Yh chromosomes reveals molecular basis of incipient sex chromosome evolution. Proceedings of the National Academy of Sciences of the United States of America (PNAS) 109(34):13710-5. doi:10.1073/pnas.1207833109 (cover story)(news release).
30. Meinken J, Min XJ. (2012) Computational prediction of protein subcellular locations in eukaryotes: an experience report. Computational Molecular Biology. 2(1): 1-7 (doi: 10.5376/cmb.2012.02.0001).[pdf]
2011
29. Zhang Y, Min XJ. (2011) Computational Molecular Biology: an Integration of Experimental Molecular and Genome Biology with Computational Technology. Computational Molecular Biology. 1(1):1-3. (doi:10.5376/2011.cmb.01.0001).[pdf]
28. Lum G, Min XJ. (2011) Plant secretomes: current status and future perspectives. Plant Omics Journal. 4(2):114-119.
27. Lum G, Min XJ. (2011) FunSecKB: the Fungal Secretome KnowledgeBase. Database - the Journal of Biological Databases and Curation. Vol. 2011. doi: 10.1093/database/bar001. [link to FunSecKB]
26. Sablok* G, Gupta PK, Baek JM, Vazquez F, Min* XJ. (2011) Genome-wide survey of alternative splicing in the grass Brachypodium distachyon: an emerging model biosystem for plant functional genomics. Biotechnology Letters. 33(3):629-636. DOI: 10.1007/s10529-010-0475-6 (* contributed equally to the work).
2010
25. Min XJ. (2010) Evaluation of computational methods for secreted protein prediction in different eukaryotes. J. Proteomics Bioinform. 3:143-147.[pdf]
2009
24. Albu* M, Min* XJ, Golding B, Hickey D. (2009) Nucleotide substitution bias within the genus Drosophila affects the pattern of proteome evolution. Genome Biol. Evol. 1:288-293. (* contributed equally to the work)
23. Min XJ, Butler G, Storms R, Tsang A. (2009) Comparative assessment of DNA assemblers for assembling expressed sequence tags. 2009 Ohio Collaborative Conference on Bioinformatics. Cleveland, Ohio. The IEEE Computer Society. pp79-82.
2008
22. Albu M, Min XJ, Hickey D, Golding B. (2008) Uncorrected nucleotide bias in mtDNA can mimic the effects of positive Darwinian selection. Mol Biol Evol. 25:2521-2524.
21. Min XJ, Hickey DA. (2008) An evolutionary footprint of age-related natural selection in mitochondrial DNA. Journal of Molecular Evolution. 67:412-417.
2007
20. Butler G, Ding W, Longo J, Min XJ, Toole N, Pillai S, Shu R, Sun J, Yang Y, Xie Q, Benech R, Spermanis A, Ulycznyj P, Powlowski J, Storms R, Tsang A. (2007) Data management for fungal genomics: an experience report. Biological Database Modeling. J. Chen and A. S. Sidhu (eds). Artech House (Boston). pp103-118 (Book Chapter).
19. Min XJ, Hickey DA. (2007) DNA asymmetric strand bias affects the amino acid composition of mitochondrial proteins. DNA Research. 14:201-206.
18. Min XJ, Hickey DA. (2007) DNA barcodes provide a quick preview of mitochondrial genome composition. PLoS ONE. 2(3):e325.
17. Min, XJ, Hickey DA. (2007) Assessing the effect of varying sequence length on DNA barcoding of fungi. Molecular Ecology Notes. 7:365-373.
2006
16. O'Toole N, Min XJ, Storms R, Butler G, Tsang A. (2006) Sequence-based analysis of fungal secretomes. Applied Mycology and Biotechnology: Bioinformatics. Volume 6. pp277-296. (Book Chapter).
15. Semova N, Storms R, John T, Gaudet P, Ulycznyj P, Min XJ, Sun J, Butler G, Tsang A. (2006) Generation, analysis and annotation of an extensive Aspergillus niger EST collection. BMC Microbilogy 6:7.
2005
14. Zhang P, Min XJ. (2005) EST Data Mining and Applications in Fungal Genomics. Applied Mycology and Biotechnology: Gene and Genomics. Volume 5. pp.33-70. (Book Chapter).
13. Min XJ, Butler G, Storms R, Tsang A. (2005) TargetIdentifier: a web server for identifying full-length cDNAs from EST sequences. Nucleic Acids Res 33:W669-W672.
12. Min, XJ, Butler G, Storms R, Tsang A. (2005) OrfPredictor: predicting protein-coding regions in EST-derived sequences. Nucleic Acids Res. 33:W677-W680.
11. Min XJ, Bartholomew DP. (2005) Effects of flooding and drought on ethylene metabolism, titratable acidity and fruiting of pineapple. Acta Horticulturae 666:135-148.
2002
10. Siddiqi, MY, Malhotra B, Min X, Glass ADM. (2002) Effects of ammonium and inorganic carbon enrichment on growth and yield of a hydroponic tomato crop. J. Plant Nutr. Soil Sci. 165:191-197.
2000
9. Min X, Okada K, Brockmann B, Koshiba T, Kamiya Y. (2000) Molecular cloning and expression patterns of three functional aldehyde oxidase genes and isolation of two aldehyde oxidase pseudogenes in tomato. Biochimica et Biophysica Acta. 1493:337-341.
8. Min X, Siddiqi MY, Guy RD, Glass ADM, Kronzucker HJ. (2000) A comparative kinetic analysis of nitrate and ammonium influx in two early-successional tree species of temperate and boreal forest ecosystems. Plant, Cell and Environment. 23:321-328.
1999
7. Min X, Siddiqi MY, Guy RD, Glass ADM, Kronzucker HJ. (1999) A comparative study of fluxes and compartmentation of nitrate and ammonium in early-successional tree species. Plant, Cell and Environment. 22:821-830.
1998
6. Min X, Siddiqi MY, Guy RD, Glass ADM, Kronzucker HJ. (1998) Induction of nitrate uptake and nitrate reductase activity in trembling aspen and lodgepole pine. Plant, Cell and Environment. 21:1039-1046.
1997
5. Min X, Bartholomew DP. (1997) Temperature affects ethylene metabolism and fruit initiation and size of pineapple. Acta Horticulturae 425:329-338.
1996
4. Min X, Bartholomew DP. (1996) Effect of plant growth regulators on ethylene production, 1-aminocyclopropane-1-carboxylic acid oxidase activity, and initiation of inflorescence development of pineapple. J. Plant Growth Regulation 15:121-128.
1993
3. Min X, Bartholomew DP. (1993) Effects of growth regulators on ethylene production and floral initiation of pineapple. Acta Horticulturae 334:101-112.
1990
2. He Z, Min X, Li P, Xi H. (1990) Study on the effects of DPC on endogenous hormone levels and the development of cotton bolls. Acta Agronomica Sinica. 16:252-258.
1988
1. He Z, Min X, Li P, Xi H. (1988) The physiological effect of plant growth retardant DPC on the root activity of cotton plants. Journal of Beijing Agricultural Univ. (Acta Agriculturae Universitatis Pekinensis) 14:235-241.

Webserver and Database Links

Memebership in Prefessional Societies

1991 - 1995, Member, American Society of Plant Biologists
2009 - current, Member, International Society for Computational Biology
2011 - current, Member, International Plant Proteomics Organization
2016 - 2017, Member of AAAS.

Other Academic Activities

2009 - 2014, Member of the Excutive Committee, Ohio Plant Biotechnology Consortium
2009 - current, Member of editorial board, Journal of Proteomics & Bioinformatics
2010 - 2013, Associated Editor, Journal of Integrated Omics
2012 - 2017, Member of editorial board, Dataset Papers in Biology
2013 - current, Member of International Editorial Advisory Board, Computational Molecular Biology
2014 - current, Member of editorial board, Austin Journal of Computational Biology and Bioinformatics
2015 - 2023, Member of editorial board, PLOS ONE
2023 - current, Guest editor, MDPI Plants, Special issue: Emerging topics in plant bioinformatics and omics data analysis.
Reviewer for the following journals: Bioinformatics; Journal of Proteomics & Bioinformatics; Nucleic Acids Research; Molecular Biology and Evolution; Folia Microbiologica; FEMS Microbiology Letters ; BMC Genomics ; Tropical Plant Biology ; Journal of Data Mining in Genomics & Proteomics; Plant Omics Journal; Computational Molecular Biology; Journal of Phylogenetics & Evolutionary Biology ; Journal of Agricultural and Food Chemistry; BMC Plant Biology; BMC Bioinformatics; Scientific Reports; Scientific Data; PLOS ONE; Annal of Botany; Database (Oxford); etc.