All Stories

  1. Developing model systems for dinoflagellates in the post‐genomic era

    Article • Journal of Phycology, September 2023, Wiley

    Dr Cheong Xin Chan

  2. Gene duplication is the primary driver of intraspecific genomic divergence in coral algal symbionts

    Article • Open Biology, September 2023, Royal Society Publishing

    Dr Cheong Xin Chan

  3. In vivo structure probing of RNA inArchaea: novel insights into the ribosome structure ofMethanosarcina acetivorans

    Article • RNA, July 2023, Cold Spring Harbor Laboratory Press

    Dr Cheong Xin Chan

  4. Evolutionary Responses of a Reef-building Coral to Climate Change at the End of the Last Glacial Maximum

    Article • Molecular Biology and Evolution, October 2022, Oxford University Press (OUP)

    Dr Cheong Xin Chan

  5. Genome-powered classification of microbial eukaryotes: focus on coral algal symbionts

    Article • Trends in Microbiology, September 2022, Elsevier

    Dr Cheong Xin Chan

  6. Improved Cladocopium goreaui Genome Assembly Reveals Features of a Facultative Coral Symbiont and the Complex Evolutionary History of Dinoflagellate Genes

    Article • Microorganisms, August 2022, MDPI AG

    Dr Cheong Xin Chan

  7. Transcriptome of the coralline alga Calliarthron tuberculosum (Corallinales, Rhodophyta) reveals convergent evolution of a partial lignin biosynthesis pathway

    Article • PLOS One, July 2022, PLOS

    Dr Cheong Xin Chan

  8. Building Consensus around the Assessment and Interpretation of Symbiodiniaceae Diversity

    Article • June 2022, MDPI AG

    Dr Senjie Lin, Dr Cheong Xin Chan

  9. Evolutionary responses of a reef-building coral to climate change at the end of the last glacial maximum

    Article • April 2022, Cold Spring Harbor Laboratory Press

    Dr Cheong Xin Chan

  10. Transcriptome of the coralline alga Calliarthron tuberculosum (Corallinales, Rhodophyta) reveals convergent evolution of a partial lignin biosynthesis pathway

    Article • March 2022, Cold Spring Harbor Laboratory Press

    Dr Cheong Xin Chan

  11. Nuclear genome of a pedinophyte pinpoints genomic innovation and streamlining in the green algae

    Article • New Phytologist, January 2022, Wiley

    Dr Cheong Xin Chan

  12. Tightly Constrained Genome Reduction and Relaxation of Purifying Selection during Secondary Plastid Endosymbiosis

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

    Dr Cheong Xin Chan

  13. Nuclear genome of a pedinophyte pinpoints genomic innovation and streamlining in the green algae

    Article • October 2021, Cold Spring Harbor Laboratory Press

    Dr Cheong Xin Chan

  14. Tightly constrained genome reduction and relaxation of purifying selection during secondary plastid endosymbiosis

    Article • May 2021, Cold Spring Harbor Laboratory Press

    Dr Cheong Xin Chan

  15. “Relationship Status” Changes Gene Expression in Corals & Symbiotic Algae

    Article • Molecular Ecology, August 2020, Wiley

    Dr Amin Mohamed, Dr Cheong Xin Chan

  16. Sex in Symbiodiniaceae dinoflagellates: genomic evidence for independent loss of the canonical synaptonemal complex

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

    Dr Cheong Xin Chan

  17. Comparative transcriptomic analyses of Chromera and Symbiodiniaceae

    Article • Environmental Microbiology Reports, May 2020, Wiley

    Dr Amin Mohamed, Dr Cheong Xin Chan

  18. Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions

    Article • BMC Biology, May 2020, Springer Science + Business Media

    Dr Amin Mohamed, Dr Cheong Xin Chan

  19. Evidence That Inconsistent Gene Prediction Can Mislead Analysis of Dinoflagellate Genomes

    Article • Journal of Phycology, February 2020, Wiley

    Dr Cheong Xin Chan

  20. Close relationship between coral-associated Chromera strains despite major differences within the Symbiodiniaceae

    Article • November 2019, Cold Spring Harbor Laboratory Press

    Dr Amin Mohamed, Dr Cheong Xin Chan

  21. Genomes of Symbiodiniaceae reveal extensive sequence divergence but conserved functions at family and genus levels

    Article • October 2019, Cold Spring Harbor Laboratory Press

    Dr Amin Mohamed, Dr Cheong Xin Chan

  22. Structural rearrangements drive extensive genome divergence between symbiotic and free-living Symbiodinium

    Article • September 2019, Cold Spring Harbor Laboratory Press

    Dr Amin Mohamed, Dr Cheong Xin Chan

  23. A genomic view of the reef-building coral Porites lutea and its microbial symbionts

    Article • Nature Microbiology, September 2019, Springer Science + Business Media

    Dr Cheong Xin Chan

  24. Genome Evolution of Coral Reef Symbionts as Intracellular Residents

    Article • Trends in Ecology & Evolution, September 2019, Elsevier

    Dr Cheong Xin Chan

  25. Polarella glacialis genomes encode tandem repeats of single-exon genes with functions critical to adaptation of dinoflagellates

    Article • July 2019, Cold Spring Harbor Laboratory Press

    Dr Amin Mohamed, Dr Cheong Xin Chan

  26. Evidence that inconsistent gene prediction can mislead analysis of algal genomes

    Article • July 2019, Cold Spring Harbor Laboratory Press

    Dr Cheong Xin Chan

  27. Commonly misunderstood parameters of NCBI BLAST and important considerations for users

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

    Dr Cheong Xin Chan

  28. Core genes in diverse dinoflagellate lineages include a wealth of conserved dark genes with unknown functions

    Article • Scientific Reports, November 2018, Springer Science + Business Media

    Dr Cheong Xin Chan

  29. k-mer Similarity, Networks of Microbial Genomes, and Taxonomic Rank

    Article • mSystems, November 2018, ASM Journals

    Dr Cheong Xin Chan

  30. Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis

    Article • Communications Biology, July 2018, Springer Science + Business Media

    Dr Cheong Xin Chan

  31. Selection of reference genes for transcript profiling of Sargassum polycystum by quantitative real-time polymerase chain reaction

    Article • Phycological Research, June 2018, Wiley

    Dr Cheong Xin Chan

  32. Analysis of the Draft Genome of the Red Seaweed Gracilariopsis chorda Provides Insights into Genome Size Evolution in Rhodophyta

    Article • Molecular Biology and Evolution, April 2018, Oxford University Press (OUP)

    Dr Cheong Xin Chan, Professor Seungjae Lee

  33. Active Host Response to Algal Symbionts in the Sea Slug Elysia chlorotica

    Article • Molecular Biology and Evolution, April 2018, Oxford University Press (OUP)

    Dr Cheong Xin Chan

  34. Plastid phylogenomics with broad taxon sampling further elucidates the distinct evolutionary origins and timing of secondary green plastids

    Article • Scientific Reports, January 2018, Springer Science + Business Media

    Dr Cheong Xin Chan

  35. Deciphering the nature of the coral–Chromera association

    Article • The ISME Journal, January 2018, Springer Science + Business Media

    Dr Cheong Xin Chan, Dr Amin Mohamed

  36. Signatures of adaptation and symbiosis in genomes and transcriptomes of Symbiodinium

    Article • Scientific Reports, November 2017, Nature

    Dr Cheong Xin Chan

  37. Symbiodinium genomes reveal adaptive evolution of functions related to symbiosis

    Article • October 2017, Cold Spring Harbor Laboratory Press

    Dr Cheong Xin Chan

  38. Biotic interactions as drivers of algal origin and evolution

    Article • New Phytologist, August 2017, Wiley

    Dr Cheong Xin Chan

  39. The Algal Revolution

    Article • Trends in Plant Science, August 2017, Elsevier

    Dr Cheong Xin Chan

  40. Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta)

    Article • Proceedings of the National Academy of Sciences, July 2017, Proceedings of the National Academy of Sciences

    Dr Cheong Xin Chan, Dr Senjie Lin

  41. Alignment-free inference of hierarchical and reticulate phylogenomic relationships

    Article • Briefings in Bioinformatics, June 2017, Oxford University Press (OUP)

    Dr Cheong Xin Chan

  42. K-mer Similarity, Networks Of Microbial Genomes And Taxonomic Rank

    Article • April 2017, Cold Spring Harbor Laboratory Press

    Dr Cheong Xin Chan

  43. Recapitulating phylogenies using k-mers: from trees to networks

    Article • F1000Research, December 2016, Faculty of 1000, Ltd.

    Dr Cheong Xin Chan

  44. Recapitulating phylogenies using k-mers: from trees to networks

    Article • F1000Research, November 2016, Faculty of 1000, Ltd.

    Dr Cheong Xin Chan

  45. Scaling Up the Phylogenetic Detection of Lateral Gene Transfer Events

    Article • November 2016, Springer Science + Business Media

    Dr Cheong Xin Chan

  46. Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer

    Article • Scientific Reports, July 2016, Nature

    Dr Cheong Xin Chan

  47. The transcriptomic response of the coralAcropora digitiferato a competentSymbiodiniumstrain: the symbiosome as an arrested early phagosome

    Article • Molecular Ecology, May 2016, Wiley

    Dr Cheong Xin Chan, Dr Amin Mohamed

  48. PhySortR: a fast, flexible tool for sorting phylogenetic trees in R

    Article • PeerJ, May 2016, PeerJ

    Dr Cheong Xin Chan

  49. Inferring phylogenies of evolving sequences without multiple sequence alignment

    Article • Scientific Reports, September 2014, Nature

    Dr Cheong Xin Chan

  50. Molecular phylogenetics before sequences

    Article • RNA Biology, January 2014, Taylor & Francis

    Dr Cheong Xin Chan

  51. A new species of B urkholderia isolated from sugarcane roots promotes plant growth

    Article • Microbial Biotechnology, December 2013, Wiley

    Dr Cheong Xin Chan

  52. Analysis of horizontal genetic transfer in red algae in the post-genomics age

    Article • Mobile Genetic Elements, November 2013, Taylor & Francis

    Dr Cheong Xin Chan

  53. Analysis of the Genome of Cyanophora paradoxa: An Algal Model for Understanding Primary Endosymbiosis

    Article • October 2013, Springer Science + Business Media

    Dr Cheong Xin Chan

  54. Foreign gene recruitment to the fatty acid biosynthesis pathway in diatoms

    Article • Mobile Genetic Elements, September 2013, Taylor & Francis

    Dr Cheong Xin Chan

  55. Biological Intuition in Alignment-Free Methods: Response to Posada

    Article • Journal of Molecular Evolution, July 2013, Springer Science + Business Media

    Dr Cheong Xin Chan

  56. Evidence for Widespread Exonic Small RNAs in the Glaucophyte Alga Cyanophora paradoxa

    Article • PLOS One, July 2013, PLOS

    Dr Cheong Xin Chan

  57. Genome of the red alga Porphyridium purpureum

    Article • Nature Communications, June 2013, Nature

    Dr Cheong Xin Chan

  58. Next-generation phylogenomics

    Article • Biology Direct, January 2013, Springer Science + Business Media

    Dr Cheong Xin Chan

  59. Clustering evolving proteins into homologous families

    Article • BMC Bioinformatics, January 2013, Springer Science + Business Media

    Dr Cheong Xin Chan

  60. Porphyra(Bangiophyceae) Transcriptomes Provide Insights Into Red Algal Development And Metabolism

    Article • Journal of Phycology, October 2012, Wiley

    Dr Cheong Xin Chan, Dr Senjie Lin

  61. ANALYSIS OFALEXANDRIUM TAMARENSE(DINOPHYCEAE) GENES REVEALS THE COMPLEX EVOLUTIONARY HISTORY OF A MICROBIAL EUKARYOTE1

    Article • Journal of Phycology, June 2012, Wiley

    Dr Cheong Xin Chan

  62. MAJOR DEVELOPMENTAL REGULATORS AND THEIR EXPRESSION IN TWO CLOSELY RELATED SPECIES OF PORPHYRA (RHODOPHYTA)1

    Article • Journal of Phycology, April 2012, Wiley

    Dr Cheong Xin Chan, Dr Senjie Lin

  63. Endosymbiotic and horizontal gene transfer in microbial eukaryotes

    Article • Mobile Genetic Elements, March 2012, Taylor & Francis

    Dr Cheong Xin Chan

  64. Cyanophora paradoxa Genome Elucidates Origin of Photosynthesis in Algae and Plants

    Article • Science, February 2012, American Association for the Advancement of Science

    Dr Cheong Xin Chan

  65. Analysis of Porphyra Membrane Transporters Demonstrates Gene Transfer among Photosynthetic Eukaryotes and Numerous Sodium-Coupled Transport Systems

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

    Dr Cheong Xin Chan, Dr Senjie Lin

  66. Red and Green Algal Origin of Diatom Membrane Transporters: Insights into Environmental Adaptation and Cell Evolution

    Article • PLOS One, December 2011, PLOS

    Dr Cheong Xin Chan

  67. Plastid Origin and Evolution

    Article • November 2011, Wiley

    Dr Cheong Xin Chan

  68. Lateral Transfer of Genes and Gene Fragments in Staphylococcus Extends beyond Mobile Elements

    Article • Journal of Bacteriology, May 2011, ASM Journals

    Dr Cheong Xin Chan

  69. Non-random sharing of Plantae genes

    Article • Communicative & Integrative Biology, May 2011, Taylor & Francis

    Dr Cheong Xin Chan

  70. Plastid Origin and Evolution: New Models Provide Insights into Old Problems

    Article • PLANT PHYSIOLOGY, February 2011, American Society of Plant Biologists (ASPB)

    Dr Cheong Xin Chan

  71. Red and Green Algal Monophyly and Extensive Gene Sharing Found in a Rich Repertoire of Red Algal Genes

    Article • Current Biology, February 2011, Elsevier

    Dr Cheong Xin Chan

  72. Porphyra: Complex Life Histories in a Harsh Environment: P. umbilicalis, an Intertidal Red Alga for Genomic Analysis

    Article • January 2010, Springer Science + Business Media

    Dr Cheong Xin Chan

  73. Lateral Transfer of Genes and Gene Fragments in Prokaryotes

    Article • Genome Biology and Evolution, November 2009, Oxford University Press (OUP)

    Dr Cheong Xin Chan

  74. Are Protein Domains Modules of Lateral Genetic Transfer?

    Article • PLOS One, February 2009, PLOS

    Dr Cheong Xin Chan

  75. Large-scale detection of recombination in nucleotide sequences

    Article • January 2008, American Institute of Physics

    Dr Cheong Xin Chan

  76. Trends in seaweed research

    Article • Trends in Plant Science, April 2006, Elsevier

    Dr Cheong Xin Chan

  77. Article • BMC Bioinformatics, January 2006, Springer Science + Business Media

    Dr Cheong Xin Chan

  78. A word-oriented approach to alignment validation

    Article • Bioinformatics, February 2005, Oxford University Press (OUP)

    Dr Cheong Xin Chan

  79. Optimisation of RNA extraction from Gracilaria changii (Gracilariales, Rhodophyta)

    Article • Environmental Biology of Fishes, August 2004, Springer Science + Business Media

    Dr Cheong Xin Chan

  80. Faculty of 1000 evaluation for Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes.

    Article • Faculty of 1000, Ltd.

    Dr Cheong Xin Chan

  81. Faculty of 1000 evaluation for Tracking a Hospital Outbreak of Carbapenem-Resistant Klebsiella pneumoniae with Whole-Genome Sequencing.

    Article • Faculty of 1000, Ltd.

    Dr Cheong Xin Chan

  82. Faculty of 1000 evaluation for MRSA epidemic linked to a quickly spreading colonization and virulence determinant.

    Article • Faculty of 1000, Ltd.

    Dr Cheong Xin Chan

  83. Faculty of 1000 evaluation for Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease.

    Article • Faculty of 1000, Ltd.

    Dr Cheong Xin Chan

  84. Faculty of 1000 evaluation for Conjugative DNA transfer into human cells by the VirB/VirD4 type IV secretion system of the bacterial pathogen Bartonella henselae.

    Article • Faculty of 1000, Ltd.

    Dr Cheong Xin Chan

  85. Faculty of 1000 evaluation for Evidence of intra-segmental homologous recombination in influenza A virus.

    Article • Faculty of 1000, Ltd.

    Dr Cheong Xin Chan

  86. Faculty of 1000 evaluation for Lateral genetic transfer and the construction of genetic exchange communities.

    Article • Faculty of 1000, Ltd.

    Dr Cheong Xin Chan

  87. Faculty of 1000 evaluation for Trees and networks before and after Darwin.

    Article • Faculty of 1000, Ltd.

    Dr Cheong Xin Chan

  88. Faculty of 1000 evaluation for A new strategy for genome assembly using short sequence reads and reduced representation libraries.

    Article • Faculty of 1000, Ltd.

    Dr Cheong Xin Chan

  89. Faculty of 1000 evaluation for Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods.

    Article • Faculty of 1000, Ltd.

    Dr Cheong Xin Chan