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Items: 1 to 50 of 64

1.

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

González-Pech RA, Stephens TG, Chan CX.

Bioinformatics. 2018 Dec 12. doi: 10.1093/bioinformatics/bty1018. [Epub ahead of print] No abstract available.

PMID:
30541060
2.

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

Bernard G, Greenfield P, Ragan MA, Chan CX.

mSystems. 2018 Nov 20;3(6). pii: e00257-18. doi: 10.1128/mSystems.00257-18. eCollection 2018 Nov-Dec.

3.

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

Stephens TG, Ragan MA, Bhattacharya D, Chan CX.

Sci Rep. 2018 Nov 21;8(1):17175. doi: 10.1038/s41598-018-35620-z.

4.

Erratum: Publisher Correction: Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis.

Liu H, Stephens TG, González-Pech RA, Beltran VH, Lapeyre B, Bongaerts P, Cooke I, Aranda M, Bourne DG, Forêt S, Miller DJ, van Oppen MJH, Voolstra CR, Ragan MA, Chan CX.

Commun Biol. 2018 Aug 23;1:126. doi: 10.1038/s42003-018-0117-4. eCollection 2018.

5.

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

Liu H, Stephens TG, González-Pech RA, Beltran VH, Lapeyre B, Bongaerts P, Cooke I, Aranda M, Bourne DG, Forêt S, Miller DJ, van Oppen MJH, Voolstra CR, Ragan MA, Chan CX.

Commun Biol. 2018 Jul 17;1:95. doi: 10.1038/s42003-018-0098-3. eCollection 2018. Erratum in: Commun Biol. 2018 Aug 23;1:126.

6.

The presence of concomitant intra-articular injuries and bone bruise does not affect pre-operative knee pain and symptoms in patients undergoing anterior cruciate ligament reconstruction.

Panjwani T, Mok YR, Wong KL, Chan CX, Toh SJ, Krishna L.

Knee Surg Sports Traumatol Arthrosc. 2018 Sep 29. doi: 10.1007/s00167-018-5168-z. [Epub ahead of print]

PMID:
30267189
7.

The Effectiveness of Full-body EOS Compared With Conventional Chest X-ray in Preoperative Evaluation of the Chest for Patients Undergoing Spine Operations: A Preliminary Study.

Hey HWD, Chan CX, Wong YM, Sng JW, Ong HY, Tan CS, Liu GK, Wong HK, Quek ST.

Spine (Phila Pa 1976). 2018 Nov 1;43(21):1502-1511. doi: 10.1097/BRS.0000000000002845.

PMID:
30113535
8.

Gender Differences in Intra-articular and Extra-articular Injuries Associated with Acute Anterior Cruciate Ligament Ruptures.

Sharon Tan SH, Kripesh A, Chan CX, Krishna L.

J Knee Surg. 2018 Aug 1. doi: 10.1055/s-0038-1666828. [Epub ahead of print]

PMID:
30068011
9.

Epidemiology of patients with anterior cruciate ligament injuries undergoing reconstruction surgery in a multi-ethnic Asian population.

Chan CX, Wong KL, Toh SJ, Krishna L.

Res Sports Med. 2018 Jul 9:1-13. doi: 10.1080/15438627.2018.1492391. [Epub ahead of print]

PMID:
29985059
10.

Anterior cruciate ligament reconstruction performed within 12 months of the index injury is associated with a lower rate of medial meniscus tears.

Mok YR, Wong KL, Panjwani T, Chan CX, Toh SJ, Krishna L.

Knee Surg Sports Traumatol Arthrosc. 2018 Jul 5. doi: 10.1007/s00167-018-5027-y. [Epub ahead of print]

PMID:
29978305
11.

Association of Compartmental Bone Bruise Distribution With Concomitant Intra-articular and Extra-articular Injuries in Acute Anterior Cruciate Ligament Tears After Noncontact Sports Trauma.

Aravindh P, Wu T, Chan CX, Wong KL, Krishna L.

Orthop J Sports Med. 2018 Apr 24;6(4):2325967118767625. doi: 10.1177/2325967118767625. eCollection 2018 Apr.

12.

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

Lee J, Yang EC, Graf L, Yang JH, Qiu H, Zelzion U, Chan CX, Stephens TG, Weber APM, Boo GH, Boo SM, Kim KM, Shin Y, Jung M, Lee SJ, Yim HS, Lee JH, Bhattacharya D, Yoon HS.

Mol Biol Evol. 2018 Aug 1;35(8):1869-1886. doi: 10.1093/molbev/msy081.

PMID:
29688518
13.

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

Chan CX, Vaysberg P, Price DC, Pelletreau KN, Rumpho ME, Bhattacharya D.

Mol Biol Evol. 2018 Jul 1;35(7):1706-1711. doi: 10.1093/molbev/msy061.

PMID:
29659974
14.

Two year outcomes of minimally invasive hallux valgus surgery.

Chan CX, Gan JZ, Chong HC, Rikhraj Singh I, Ng SYC, Koo K.

Foot Ankle Surg. 2017 Oct 13. pii: S1268-7731(17)31295-X. doi: 10.1016/j.fas.2017.09.007. [Epub ahead of print]

PMID:
29409293
15.

Chinese Ethnicity Is Associated With Concomitant Cartilage Injuries in Anterior Cruciate Ligament Tears.

Chan CX, Wong KL, Toh SJ, Krishna L.

Orthop J Sports Med. 2018 Jan 18;6(1):2325967117750083. doi: 10.1177/2325967117750083. eCollection 2018 Jan.

16.

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

Jackson C, Knoll AH, Chan CX, Verbruggen H.

Sci Rep. 2018 Jan 24;8(1):1523. doi: 10.1038/s41598-017-18805-w.

17.

Elucidating the genomic architecture of Asian EGFR-mutant lung adenocarcinoma through multi-region exome sequencing.

Nahar R, Zhai W, Zhang T, Takano A, Khng AJ, Lee YY, Liu X, Lim CH, Koh TPT, Aung ZW, Lim TKH, Veeravalli L, Yuan J, Teo ASM, Chan CX, Poh HM, Chua IML, Liew AA, Lau DPX, Kwang XL, Toh CK, Lim WT, Lim B, Tam WL, Tan EH, Hillmer AM, Tan DSW.

Nat Commun. 2018 Jan 15;9(1):216. doi: 10.1038/s41467-017-02584-z.

18.

Deciphering the nature of the coral-Chromera association.

Mohamed AR, Cumbo VR, Harii S, Shinzato C, Chan CX, Ragan MA, Satoh N, Ball EE, Miller DJ.

ISME J. 2018 Mar;12(3):776-790. doi: 10.1038/s41396-017-0005-9. Epub 2018 Jan 10.

19.

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

González-Pech RA, Ragan MA, Chan CX.

Sci Rep. 2017 Nov 3;7(1):15021. doi: 10.1038/s41598-017-15029-w.

20.

Patella Height Changes Post High Tibial Osteotomy.

Gooi SG, Chan CXY, Tan MKL, Lim AKS, Satkunanantham K, Hui JHP.

Indian J Orthop. 2017 Sep-Oct;51(5):545-551. doi: 10.4103/ortho.IJOrtho_214_17.

21.

Biotic interactions as drivers of algal origin and evolution.

Brodie J, Ball SG, Bouget FY, Chan CX, De Clerck O, Cock JM, Gachon C, Grossman AR, Mock T, Raven JA, Saha M, Smith AG, Vardi A, Yoon HS, Bhattacharya D.

New Phytol. 2017 Nov;216(3):670-681. doi: 10.1111/nph.14760. Epub 2017 Aug 31. Review.

22.

Using spinopelvic parameters to estimate residual lumbar lordosis assuming previous lumbosacral fusion-a study of normative values.

Hey HWD, Tan KA, Kantharajanna SB, Teo AQA, Chan CX, Liu KG, Wong HK.

Spine J. 2018 Mar;18(3):422-429. doi: 10.1016/j.spinee.2017.08.232. Epub 2017 Aug 16.

PMID:
28822824
23.

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

Brawley SH, Blouin NA, Ficko-Blean E, Wheeler GL, Lohr M, Goodson HV, Jenkins JW, Blaby-Haas CE, Helliwell KE, Chan CX, Marriage TN, Bhattacharya D, Klein AS, Badis Y, Brodie J, Cao Y, Collén J, Dittami SM, Gachon CMM, Green BR, Karpowicz SJ, Kim JW, Kudahl UJ, Lin S, Michel G, Mittag M, Olson BJSC, Pangilinan JL, Peng Y, Qiu H, Shu S, Singer JT, Smith AG, Sprecher BN, Wagner V, Wang W, Wang ZY, Yan J, Yarish C, Zäuner-Riek S, Zhuang Y, Zou Y, Lindquist EA, Grimwood J, Barry KW, Rokhsar DS, Schmutz J, Stiller JW, Grossman AR, Prochnik SE.

Proc Natl Acad Sci U S A. 2017 Aug 1;114(31):E6361-E6370. doi: 10.1073/pnas.1703088114. Epub 2017 Jul 17.

24.

Alignment-free inference of hierarchical and reticulate phylogenomic relationships.

Bernard G, Chan CX, Chan YB, Chua XY, Cong Y, Hogan JM, Maetschke SR, Ragan MA.

Brief Bioinform. 2017 Jun 30. doi: 10.1093/bib/bbx067. [Epub ahead of print]

PMID:
28673025
25.

The Algal Revolution.

Brodie J, Chan CX, De Clerck O, Cock JM, Coelho SM, Gachon C, Grossman AR, Mock T, Raven JA, Smith AG, Yoon HS, Bhattacharya D.

Trends Plant Sci. 2017 Aug;22(8):726-738. doi: 10.1016/j.tplants.2017.05.005. Epub 2017 Jun 10. Review.

PMID:
28610890
26.

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

Bernard G, Ragan MA, Chan CX.

Version 2. F1000Res. 2016 Nov 29 [revised 2016 Jan 1];5:2789. doi: 10.12688/f1000research.10225.2. eCollection 2016.

27.

Reproducibility of sagittal radiographic parameters in adolescent idiopathic scoliosis-a guide to reference values using serial imaging.

Hey HWD, Wong GC, Chan CX, Lau LL, Kumar N, Thambiah JS, Ruiz JN, Liu KG, Wong HK.

Spine J. 2017 Jun;17(6):830-836. doi: 10.1016/j.spinee.2017.01.001. Epub 2017 Jan 5.

PMID:
28065817
28.

Scaling Up the Phylogenetic Detection of Lateral Gene Transfer Events.

Chan CX, Beiko RG, Ragan MA.

Methods Mol Biol. 2017;1525:421-432.

PMID:
27896730
29.

Force Sensitivity in Saccharomyces cerevisiae Flocculins.

Chan CX, El-Kirat-Chatel S, Joseph IG, Jackson DN, Ramsook CB, Dufrêne YF, Lipke PN.

mSphere. 2016 Aug 17;1(4). pii: e00128-16. doi: 10.1128/mSphere.00128-16. eCollection 2016 Jul-Aug.

30.
31.

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

Stephens TG, Bhattacharya D, Ragan MA, Chan CX.

PeerJ. 2016 May 12;4:e2038. doi: 10.7717/peerj.2038. eCollection 2016.

32.

The transcriptomic response of the coral Acropora digitifera to a competent Symbiodinium strain: the symbiosome as an arrested early phagosome.

Mohamed AR, Cumbo V, Harii S, Shinzato C, Chan CX, Ragan MA, Bourne DG, Willis BL, Ball EE, Satoh N, Miller DJ.

Mol Ecol. 2016 Jul;25(13):3127-41. doi: 10.1111/mec.13659. Epub 2016 May 18.

PMID:
27094992
33.

Quantitative Analyses of Force-Induced Amyloid Formation in Candida albicans Als5p: Activation by Standard Laboratory Procedures.

Chan CX, Joseph IG, Huang A, Jackson DN, Lipke PN.

PLoS One. 2015 Jun 5;10(6):e0129152. doi: 10.1371/journal.pone.0129152. eCollection 2015.

34.

High-depth sequencing of over 750 genes supports linear progression of primary tumors and metastases in most patients with liver-limited metastatic colorectal cancer.

Tan IB, Malik S, Ramnarayanan K, McPherson JR, Ho DL, Suzuki Y, Ng SB, Yan S, Lim KH, Koh D, Hoe CM, Chan CY, Ten R, Goh BK, Chung AY, Tan J, Chan CX, Tay ST, Alexander L, Nagarajan N, Hillmer AM, Tang CL, Chua C, Teh BT, Rozen S, Tan P.

Genome Biol. 2015 Feb 12;16:32. doi: 10.1186/s13059-015-0589-1.

35.

Inferring phylogenies of evolving sequences without multiple sequence alignment.

Chan CX, Bernard G, Poirion O, Hogan JM, Ragan MA.

Sci Rep. 2014 Sep 30;4:6504. doi: 10.1038/srep06504.

36.

Between Amyloids and Aggregation Lies a Connection with Strength and Adhesion.

Lipke PN, Ramsook C, Garcia-Sherman MC, Jackson DN, Chan CX, Bois M, Klotz SA.

New J Sci. 2014;2014:815102.

37.

Role of force-sensitive amyloid-like interactions in fungal catch bonding and biofilms.

Chan CX, Lipke PN.

Eukaryot Cell. 2014 Sep;13(9):1136-42. doi: 10.1128/EC.00068-14. Epub 2014 Mar 28.

38.

Molecular phylogenetics before sequences: oligonucleotide catalogs as k-mer spectra.

Ragan MA, Bernard G, Chan CX.

RNA Biol. 2014;11(3):176-85. doi: 10.4161/rna.27505. Epub 2014 Jan 14. Review.

39.

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

Chan CX, Bhattacharya D.

Mob Genet Elements. 2013 Nov 1;3(6):e27669. Epub 2014 Jan 2.

40.

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

Chan CX, Baglivi FL, Jenkins CE, Bhattacharya D.

Mob Genet Elements. 2013 Sep 1;3(5):e27313. Epub 2013 Dec 10.

41.

A new species of Burkholderia isolated from sugarcane roots promotes plant growth.

Paungfoo-Lonhienne C, Lonhienne TG, Yeoh YK, Webb RI, Lakshmanan P, Chan CX, Lim PE, Ragan MA, Schmidt S, Hugenholtz P.

Microb Biotechnol. 2014 Mar;7(2):142-54. doi: 10.1111/1751-7915.12105. Epub 2013 Dec 19.

42.

Biological intuition in alignment-free methods: response to Posada.

Ragan MA, Chan CX.

J Mol Evol. 2013 Aug;77(1-2):1-2. doi: 10.1007/s00239-013-9573-0. Epub 2013 Jul 23.

PMID:
23877343
43.

Evidence for widespread exonic small RNAs in the glaucophyte alga Cyanophora paradoxa.

Gross J, Wajid S, Price DC, Zelzion E, Li J, Chan CX, Bhattacharya D.

PLoS One. 2013 Jul 3;8(7):e67669. doi: 10.1371/journal.pone.0067669. Print 2013.

44.

Technology platform development for targeted plasma metabolites in human heart failure.

Chan CX, Khan AA, Choi JH, Ng CD, Cadeiras M, Deng M, Ping P.

Clin Proteomics. 2013 Jul 4;10(1):7. doi: 10.1186/1559-0275-10-7. eCollection 2013.

45.

Genome of the red alga Porphyridium purpureum.

Bhattacharya D, Price DC, Chan CX, Qiu H, Rose N, Ball S, Weber AP, Arias MC, Henrissat B, Coutinho PM, Krishnan A, Zäuner S, Morath S, Hilliou F, Egizi A, Perrineau MM, Yoon HS.

Nat Commun. 2013;4:1941. doi: 10.1038/ncomms2931.

46.

Clustering evolving proteins into homologous families.

Chan CX, Mahbob M, Ragan MA.

BMC Bioinformatics. 2013 Apr 8;14:120. doi: 10.1186/1471-2105-14-120.

47.

Next-generation phylogenomics.

Chan CX, Ragan MA.

Biol Direct. 2013 Jan 22;8:3. doi: 10.1186/1745-6150-8-3.

48.

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

Chan CX, Blouin NA, Zhuang Y, Zäuner S, Prochnik SE, Lindquist E, Lin S, Benning C, Lohr M, Yarish C, Gantt E, Grossman AR, Lu S, Müller K, W Stiller J, Brawley SH, Bhattacharya D.

J Phycol. 2012 Dec;48(6):1328-42. doi: 10.1111/j.1529-8817.2012.01229.x. Epub 2012 Oct 3.

PMID:
27009986
49.

ANALYSIS OF ALEXANDRIUM TAMARENSE (DINOPHYCEAE) GENES REVEALS THE COMPLEX EVOLUTIONARY HISTORY OF A MICROBIAL EUKARYOTE().

Chan CX, Soares MB, Bonaldo MF, Wisecaver JH, Hackett JD, Anderson DM, Erdner DL, Bhattacharya D.

J Phycol. 2012 Oct 1;48(5):1130-1142. Epub 2012 Jun 19.

50.

Endosymbiotic and horizontal gene transfer in microbial eukaryotes: Impacts on cell evolution and the tree of life.

Chan CX, Bhattacharya D, Reyes-Prieto A.

Mob Genet Elements. 2012 Mar 1;2(2):101-105.

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