All Stories

  1. deepTFBS: Improving within‐ and Cross‐Species Prediction of Transcription Factor Binding Using Deep Multi‐Task and Transfer Learning

    Article • Advanced Science, May 2025, Wiley

    Chuang Ma

  2. The N6-methyladenosine reader ECT1 regulates seed germination via gibberellic acid- and phytochrome B-mediated signaling

    Article • PLANT PHYSIOLOGY, April 2025, Oxford University Press (OUP)

    Chuang Ma

  3. Editorial: Applications of artificial intelligence, machine learning, and deep learning in plant breeding

    Article • Frontiers in Plant Science, May 2024, Frontiers

    Chuang Ma

  4. PEA-m6A: an ensemble learning framework for accurately predicting N6-methyladenosine modifications in plants

    Article • PLANT PHYSIOLOGY, March 2024, Oxford University Press (OUP)

    Chuang Ma

  5. Genome assembly of KA105, a new resource for maize molecular breeding and genomic research

    Article • The Crop Journal, December 2023, Tsinghua University Press

    Chuang Ma

  6. IPOP: An Integrative Plant Multi-omics Platform for Cross-species Comparison and Evolutionary Study

    Article • Molecular Biology and Evolution, November 2023, Oxford University Press (OUP)

    Chuang Ma

  7. Changes in m6A RNA methylation are associated with male sterility in wolfberry

    Article • BMC Plant Biology, September 2023, Springer Science + Business Media

    Chuang Ma

  8. Global hypermethylation of the N6-methyladenosine RNA modification associated with apple heterografting

    Article • PLANT PHYSIOLOGY, August 2023, Oxford University Press (OUP)

    Chuang Ma

  9. G2P Provides an Integrative Environment for Multi-model genomic selection analysis to improve genotype-to-phenotype prediction

    Article • Frontiers in Plant Science, August 2023, Frontiers

    Chuang Ma

  10. Time-resolved multiomics analysis of the genetic regulation of maize kernel moisture

    Article • The Crop Journal, February 2023, Elsevier

    Chuang Ma

  11. easyMF: A Web Platform for Matrix Factorization-Based Gene Discovery from Large-scale Transcriptome Data

    Article • Interdisciplinary Sciences Computational Life Sciences, May 2022, Springer Science + Business Media

    Chuang Ma

  12. Genome optimization via virtual simulation to accelerate maize hybrid breeding

    Article • Briefings in Bioinformatics, October 2021, Oxford University Press (OUP)

    Chuang Ma

  13. SMART v1.0: A Database for Small Molecules with Functional Implications in Plants

    Article • Interdisciplinary Sciences Computational Life Sciences, October 2021, Springer Science + Business Media

    Chuang Ma

  14. Evolutionary Implications of the RNA N6-Methyladenosine Methylome in Plants

    Article • Molecular Biology and Evolution, October 2021, Oxford University Press (OUP)

    Chuang Ma

  15. LightGBM: accelerated genomically designed crop breeding through ensemble learning

    Article • Genome Biology, September 2021, Springer Science + Business Media

    Chuang Ma

  16. Interactive Web-Based Annotation of Plant MicroRNAs with iwa-miRNA

    Article • Genomics Proteomics & Bioinformatics, July 2021, Oxford University Press (OUP)

    Chuang Ma

  17. The genetic mechanism of heterosis utilization in maize improvement

    Article • Genome Biology, May 2021, Springer Science + Business Media

    Chuang Ma

  18. Editorial: Genomics-Enabled Crop Genetics

    Article • Frontiers in Genetics, May 2021, Frontiers

    Chuang Ma

  19. easyMF: A Web Platform for Matrix Factorization-based Biological Discovery from Large-scale Transcriptome Data

    Article • December 2020, Cold Spring Harbor Laboratory Press

    Chuang Ma

  20. Interactive Web-based Annotation of Plant MicroRNAs with iwa-miRNA

    Article • December 2020, Cold Spring Harbor Laboratory Press

    Chuang Ma

  21. deepEA: a containerized web server for interactive analysis of epitranscriptome sequencing data

    Article • PLANT PHYSIOLOGY, November 2020, Oxford University Press (OUP)

    Chuang Ma

  22. Exploring transcriptional switches from pairwise, temporal and population RNA-Seq data using deepTS

    Article • Briefings in Bioinformatics, July 2020, Oxford University Press (OUP)

    Chuang Ma

  23. Author Correction: Integration of metabolome and transcriptome reveals flavonoid accumulation in the intergeneric hybrid between Brassica rapa and Raphanus sativus

    Article • Scientific Reports, July 2020, Springer Science + Business Media

    Chuang Ma

  24. Integration of metabolome and transcriptome reveals flavonoid accumulation in the intergeneric hybrid between Brassica rapa and Raphanus sativus

    Article • Scientific Reports, December 2019, Springer Science + Business Media

    Chuang Ma

  25. Evolution of the RNA N6-Methyladenosine Methylome Mediated by Genomic Duplication

    Article • PLANT PHYSIOLOGY, August 2019, American Society of Plant Biologists (ASPB)

    Chuang Ma

  26. Hybrid sequencing reveals insight into heat sensing and signaling of bread wheat

    Article • The Plant Journal, April 2019, Wiley

    Chuang Ma

  27. CAFU: a Galaxy framework for exploring unmapped RNA-Seq data

    Article • Briefings in Bioinformatics, February 2019, Oxford University Press (OUP)

    Chuang Ma

  28. Large expert-curated database for benchmarking document

    Article • Database, January 2019, Oxford University Press (OUP)

    Dr Daniel Prieto, Associate Professor James A.L. Brown, Professor Amanda G Thrift, Docent Kutty Selva Nandakumar, Professor Miguel Viveiros, MD Diego A. Valera-Cornejo, Dr Soroush Safaei, Dr Carmen San Martín, Piero Carninci, Dr Florian Rehfeldt, Dr Yoichi Watanabe, Kazuki Ide, Mr Alvin Wong, PD Dr. Adrian Meule, Dr Maurizio Petrelli, Dr Christine McGarrigle, Dr Tristan Reddan, Dr Nicola Roberts, Professor Stefan Lorkowski, Dr Cyrille Goarant, Dr Emma C Hobbs, Dr. Saurab Sharma, Ph.D., Dr Farid Rahimi, Prof. Iseult Lynch, Mirella Walker, Dr Luca Galluzzi, Sophie Ohlsson, Professor Tullio Florio, Dr Rabea A Gadelkareem, Dr Azubuike Christian Ukubuiwe, Prof Gajendra PS Raghava, Prof Jun Shen, Lubna Razak, ABHISHEKA BANSAL, Craig Billington, Dr Alejandro Lazo-Langner, Joan Albiol, MOURAD TAYEBI, Chuang Ma, Christine Toelzer , Dr. Kathrin Karsay, Professor Andrew M Beale, Professor Hugh James Byrne, Dr Ugo Marzocchi, Ana Nordberg, Martin Bartas, Natalia Echeverría, Dr Patricia M Graves

  29. miRLocator: A Python Implementation and Web Server for Predicting miRNAs from Pre-miRNA Sequences

    Article • January 2019, Springer Science + Business Media

    Chuang Ma

  30. Corrigendum: Transcriptome-Wide Annotation of m5C RNA Modifications Using Machine Learning

    Article • Frontiers in Plant Science, November 2018, Frontiers

    Chuang Ma

  31. Opaque-2 Regulates a Complex Gene Network Associated with Cell Differentiation and Storage Functions of Maize Endosperm

    Article • The Plant Cell, September 2018, American Society of Plant Biologists (ASPB)

    Chuang Ma

  32. A deep convolutional neural network approach for predicting phenotypes from genotypes

    Article • Planta, August 2018, Springer Science + Business Media

    Chuang Ma

  33. PEA: an integrated R toolkit for plant epitranscriptome analysis

    Article • Bioinformatics, May 2018, Oxford University Press (OUP)

    Chuang Ma

  34. Transcriptome-Wide Annotation of m5C RNA Modifications Using Machine Learning

    Article • Frontiers in Plant Science, April 2018, Frontiers

    Chuang Ma

  35. Evolutionary Origin, Gradual Accumulation and Functional Divergence of Heat Shock Factor Gene Family with Plant Evolution

    Article • Frontiers in Plant Science, February 2018, Frontiers

    Chuang Ma

  36. DeepGS: Predicting phenotypes from genotypes using Deep Learning

    Article • December 2017, Cold Spring Harbor Laboratory Press

    Chuang Ma

  37. PEA: an integrated R toolkit for plant epitranscriptome analysis

    Article • December 2017, Cold Spring Harbor Laboratory Press

    Chuang Ma

  38. Evolution of intron-poor clades and expression patterns of the glycosyltransferase family 47

    Article • Planta, December 2017, Springer Science + Business Media

    Chuang Ma

  39. A systems approach to a spatio-temporal understanding of the drought stress response in maize

    Article • Scientific Reports, July 2017, Springer Science + Business Media

    Chuang Ma

  40. Massive expansion and differential evolution of small heat shock proteins with wheat (Triticum aestivum L.) polyploidization

    Article • Scientific Reports, May 2017, Springer Science + Business Media

    Chuang Ma

  41. An Effective Strategy for Trait Combinations in Multiple-Trait Genomic Selection

    Article • January 2017, Springer Science + Business Media

    Chuang Ma

  42. A Meta-Analysis Based Method for Prioritizing Candidate Genes Involved in a Pre-specific Function

    Article • Frontiers in Plant Science, December 2016, Frontiers

    Chuang Ma

  43. Transcriptome Dynamics during Maize Endosperm Development

    Article • PLOS One, October 2016, PLOS

    Chuang Ma

  44. Coexpression Network Analysis of Benign and Malignant Phenotypes of SIV-Infected Sooty Mangabey and Rhesus Macaque

    Article • PLOS One, June 2016, PLOS

    Chuang Ma

  45. Application of Machine Learning-Based Classification to Genomic Selection and Performance Improvement

    Article • January 2016, Springer Science + Business Media

    Chuang Ma

  46. miRLocator: Machine Learning-Based Prediction of Mature MicroRNAs within Plant Pre-miRNA Sequences

    Article • PLOS One, November 2015, PLOS

    Chuang Ma

  47. A Census of Nuclear Cyanobacterial Recruits in the Plant Kingdom

    Article • PLOS One, March 2015, PLOS

    Dr Javeed Hussain, Chuang Ma

  48. RNA Sequencing of Laser-Capture Microdissected Compartments of the Maize Kernel Identifies Regulatory Modules Associated with Endosperm Cell Differentiation

    Article • The Plant Cell, March 2015, Oxford University Press (OUP)

    Chuang Ma

  49. DNA sequence and structure properties analysis reveals similarities and differences to promoters of stress responsive genes in Arabidopsis thaliana

    Article • International Journal of Data Mining and Bioinformatics, January 2015, Inderscience Publishers

    Chuang Ma

  50. Machine learning for Big Data analytics in plants

    Article • Trends in Plant Science, December 2014, Elsevier

    Chuang Ma

  51. Relative importance of various regeneration mechanisms in different restoration stages of Quercus variabilis forest after selective logging

    Article • Forest Systems, August 2014, Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA)

    Chuang Ma

  52. Dynamic parent-of-origin effects on small interfering RNA expression in the developing maize endosperm

    Article • BMC Plant Biology, July 2014, Springer Science + Business Media

    Chuang Ma

  53. Machine Learning–Based Differential Network Analysis: A Study of Stress-Responsive Transcriptomes in Arabidopsis

    Article • The Plant Cell, February 2014, American Society of Plant Biologists (ASPB)

    Chuang Ma

  54. Effects of drought stress on growth, physiological and biochemical parameters in fine roots of Quercus variabilis Bl. seedlings

    Article • Acta Ecologica Sinica, January 2014, Acta Ecologica Sinica

    Chuang Ma

  55. Fine root architecture, morphology, and biomass response to cutting in a Chinese cork oak (Quercus variabilis Blume) forest

    Article • TURKISH JOURNAL OF AGRICULTURE AND FORESTRY, January 2014, The Scientific and Technological Research Council of Turkey (TUBITAK-ULAKBIM) - DIGITAL COMMONS JOURNALS

    Chuang Ma

  56. A novel two-layer SVM model in miRNA Drosha processing site detection

    Article • BMC Systems Biology, October 2013, Springer Science + Business Media

    Chuang Ma

  57. Dynamic Expression of Imprinted Genes Associates with Maternally Controlled Nutrient Allocation during Maize Endosperm Development

    Article • The Plant Cell, September 2013, Oxford University Press (OUP)

    Chuang Ma

  58. Changes in morphological, physiological, and biochemical responses to different levels of drought stress in chinese cork oak (Quercus variabilis Bl.) seedlings

    Article • Russian Journal of Plant Physiology, August 2013, Pleiades Publishing Ltd

    Chuang Ma

  59. Using Amino Acid Factor Scores to Predict Avian-to-Human Transmission of Avian Influenza Viruses: A Machine Learning Study

    Article • Protein and Peptide Letters, August 2013, Bentham Science Publishers

    Chuang Ma

  60. Effects of stump diameter, stump height, and cutting season onQuercus variabilisstump sprouting

    Article • Scandinavian Journal of Forest Research, April 2013, Taylor & Francis

    Chuang Ma

  61. Predicting transmission of avian influenza A viruses from avian to human by using informative physicochemical properties

    Article • International Journal of Data Mining and Bioinformatics, January 2013, Inderscience Publishers

    Chuang Ma

  62. The Reference Genome of the Halophytic Plant Eutrema salsugineum

    Article • Frontiers in Plant Science, January 2013, Frontiers

    Chuang Ma

  63. Effect of aboveground intervention on fine root mass, production, and turnover rate in a Chinese cork oak (Quercus variabilis Blume) forest

    Article • Plant and Soil, November 2012, Springer Science + Business Media

    Chuang Ma

  64. KGBassembler: a karyotype-based genome assembler for Brassicaceae species

    Article • Bioinformatics, October 2012, Oxford University Press (OUP)

    Chuang Ma

  65. Recognizing drosha processing sites by a two-step prediction model with structure and sequence information

    Article • October 2012, Institute of Electrical & Electronics Engineers (IEEE)

    Chuang Ma

  66. Application of the Gini Correlation Coefficient to Infer Regulatory Relationships in Transcriptome Analysis

    Article • PLANT PHYSIOLOGY, July 2012, American Society of Plant Biologists (ASPB)

    Chuang Ma

  67. GPS-MBA: Computational Analysis of MHC Class II Epitopes in Type 1 Diabetes

    Article • PLOS One, March 2012, PLOS

    Chuang Ma

  68. Accurately Predicting Transcription Start Sites Using Logitlinear Model and Local Oligonucleotide Frequencies

    Article • January 2012, Springer Science + Business Media

    Chuang Ma

  69. Sequence similarity analysis of non-self CTL epitopes and mouse proteins using sequence alignment

    Article • Wuhan University Journal of Natural Sciences, February 2011, EDP Sciences

    Chuang Ma

  70. Inequalities and Duality in Gene Coexpression Networks of HIV-1 Infection Revealed by the Combination of the Double-Connectivity Approach and the Gini's Method

    Article • Journal of Biomedicine and Biotechnology, January 2011, Hindawi Publishing Corporation

    Chuang Ma

  71. Identification of true EST alignments for recognising transcribed regions

    Article • International Journal of Data Mining and Bioinformatics, January 2011, Inderscience Publishers

    Chuang Ma

  72. Accurate Prediction of Alternatively Spliced Cassette Exons Using Evolutionary Conservation Information and Logitlinear Model

    Article • January 2009, Institute of Electrical & Electronics Engineers (IEEE)

    Chuang Ma

  73. Position-specific residue preference features around the ends of helices and strands and a novel strategy for the prediction of secondary structures

    Article • Protein Science, September 2008, Wiley

    Chuang Ma

  74. Feature Mining and Integration for Improving the Prediction Accuracy of Translation Initiation Sites in Eukaryotic mRNAs

    Article • January 2006, Institute of Electrical & Electronics Engineers (IEEE)

    Chuang Ma