Microbiol Spectr. February 03, 2026. DOI: 10.1128/spectrum.03033-25.
High-throughput single-cell isolation of Bifidobacterium strains from the human gut microbiome
Ha LH, On YY, Pohan C, Lee J, How SHC, Teo Y-Y, Seedorf H, Gounot J-S, Nagarajan N
Publications
2026
Return to top2025
Return to topiScience. October 21, 2025. DOI: 10.1016/j.isci.2025.113791.
Efficient trace reconstruction in DNA storage systems using bidirectional beam search
Gu Z, Xin H, Sharma P, Goh GY, Wong L, Nagarajan N
Antibiotics (Basel). August 26, 2025. DOI: 10.3390/antibiotics14090860.
Comparative Genomics of DH5α-Inhibiting Escherichia coli Isolates from Feces of Healthy Individuals Reveals Common Co-Occurrence of Bacteriocin Genes with Virulence Factors and Antibiotic Resistance Genes
Er S, Ding Y, Tan LWL, Teo YY, Nagarajan N, Seedorf H
Pathogens. August 05, 2025. DOI: 10.3390/pathogens14080773.
Assessing Zoonotic Risks of Blastocystis Infection in Singapore
Aung TT, How CKQ, Chavatte JM, Nazir NB, Pena EM, Ogden B, Lim GR, Paramastri YA, Zitzow LA, Chen H, Nagarajan N, Tan KSW, Malleret B
Nat Biotechnol. August 28, 2025. DOI: 10.1038/s41587-025-02797-4.
Skin metatranscriptomics reveals a landscape of variation in microbial activity and gene expression across the human body
Chia M, Ng AHQ, Ravikrishnan A, Mohamed Naim AN, Wearne S, Common J, Nagarajan N
Cancer Res. October 01, 2025. DOI: 10.1158/0008-5472.CAN-24-3629.
Challenges and Opportunities in Analyzing Cancer-Associated Microbiomes
Chia M, Pop M, Salzberg SL, Nagarajan N
Nat Commun. July 30, 2025. DOI: 10.1038/s41467-025-62347-z.
Direct high-throughput deconvolution of non-canonical bases via nanopore sequencing and bootstrapped learning
Perez M, Kimoto M, Rajakumar P, Suphavilai C, Peres da Silva R, Tan HP, Ong NTX, Nicholas H, Hirao I, Chew WL, Nagarajan N
NPJ Antimicrob Resist. July 08, 2025. DOI: 10.1038/s44259-025-00132-0.
Citywide metagenomic surveillance of food centres reveals local microbial signatures and antibiotic resistance gene enrichment
Teo JJY, Ho EXP, Ng AHQ, How SHC, Chng KR, Ateş YC, Fau'di MT, Aung KT, Nagarajan N
Nat Microbiol. 2025-07. DOI: 10.1038/s41564-025-02035-2.
Guidelines for preventing and reporting contamination in low-biomass microbiome studies
Fierer N, Leung PM, Lappan R, Eisenhofer R, Ricci F, Holland SI, Dragone N, Blackall LL, Dong X, Dorador C, Ferrari BC, Goordial J, Holmes SP, Inagaki F, Korem T, Li SS, Makhalanyane TP, Metcalf JL, Nagarajan N, Orsi WD, Shanahan ER, Walker AW, Weyrich LS, Gilbert JA, Willis AD, Callahan BJ, Shade A, Parkhill J, Banfield JF, Greening C
Cell Rep Med. April 15, 2025. DOI: 10.1016/j.xcrm.2025.102053.
CAN-Scan: A multi-omic phenotype-driven precision oncology platform identifies prognostic biomarkers of therapy response for colorectal cancer
Chia S, Wen Seow JJ, Peres da Silva R, Suphavilai C, Shirgaonkar N, Murata-Hori M, Zhang X, Yong EY, Pan J, Thangavelu MT, Periyasamy G, Yap A, Anand P, Muliaditan D, Chan YS, Siyu W, Yong CW, Hong N, Ran G, Sim NL, Guo YA, Yi Teh AX, Wei Ling CC, Wei Tan EK, Pei Cherylin FW, Chang M, Han S, Seow-En I, Chen Hui LR, Hsia Gan AH, Yap CK, Ng HH, Skanderup AJ, Chinswangwatanakul V, Riansuwan W, Trakarnsanga A, Pithukpakorn M, Tanjak P, Chaiboonchoe A, Park D, Kim DK, Iyer NG, Tsantoulis P, Tejpar S, Kim JE, Kim TI, Sampattavanich S, Tan IB, Nagarajan N, DasGupta R
BMC Glob Public Health. March 21, 2025. DOI: 10.1186/s44263-025-00138-w.
Leveraging wastewater sequencing to strengthen global public health surveillance
Gordeev V, Hölzer M, Desirò D, Goraichuk IV, Knyazev S, Solo-Gabriele H, Skums P, Karthikeyan S, Evans A, Agrawal S, Lucaci AG, Mason CE, Su JM, Gibas C, Nagarajan N, Peres da Silva R, Drabcinski N, Munteanu V, Zhan L, Rubin J, Wu NC, Trister A, Ciorba D, Bostan V, Lobiuc A, Covasa M, Ophoff RA, Zelikovsky A, Dimian M, Mangul S
NPJ Biofilms Microbiomes. January 13, 2025. DOI: 10.1038/s41522-025-00652-7.
Life stage impact on the human skin ecosystem: lipids and the microbial community
Pagac MP, Davient B, Plado LA, Lam HYI, Lee SM, Ravikrishnan A, Chua WLE, Muralidharan S, Sridharan A, Irudayaswamy AS, Srinivas R, Wearne S, Mohamed Naim AN, Ho EXP, Ng HQA, Kwah JS, Png E, Bendt AK, Wenk MR, Torta F, Nagarajan N, Common J, Chong YS, Tham EH, Shek LP, Loo EXL, Chambers J, Yew YW, Loh M, Dawson TL Jr
2024
Return to topNat Commun. September 05, 2024. DOI: 10.1038/s41467-024-52097-9.
Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes
Ravikrishnan A, Wijaya I, Png E, Chng KR, Ho EXP, Ng AHQ, Mohamed Naim AN, Gounot JS, Guan SP, Hanqing JL, Guan L, Li C, Koh JY, de Sessions PF, Koh WP, Feng L, Ng TP, Larbi A, Maier AB, Kennedy BK, Nagarajan N
Lancet Microbe. 2024-09. DOI: 10.1016/S2666-5247(24)00101-0.
Detection and characterisation of a sixth Candida auris clade in Singapore: a genomic and phenotypic study
Suphavilai C, Ko KKK, Lim KM, Tan MG, Boonsimma P, Chu JJK, Goh SS, Rajandran P, Lee LC, Tan KY, Shaik Ismail BB, Aung MK, Yang Y, Sim JXY, Venkatachalam I, Cherng BPZ, Spruijtenburg B, Chan KS, Oon LLE, Tan AL, Tan YE, Wijaya L, Tan BH, Ling ML, Koh TH, Meis JF, Tsui CKM, Nagarajan N
Bioinformatics. June 28, 2024. DOI: 10.1093/bioinformatics/btae252.
Floria: fast and accurate strain haplotyping in metagenomes
Shaw J, Gounot JS, Chen H, Nagarajan N, Yu YW
Clin Transl Med. 2024-06. DOI: 10.1002/ctm2.1723.
Integrative genomic analyses of European intrahepatic cholangiocarcinoma: Novel ROS1 fusion gene and PBX1 as prognostic marker
Plum PS, Hess T, Bertrand D, Morgenstern I, Velazquez Camacho O, Jonas C, Alidousty C, Wagner B, Roessler S, Albrecht T, Becker J, Richartz V, Holz B, Hoppe S, Poh HM, Chia BKH, Chan CX, Pathiraja T, Teo AS, Marquardt JU, Khng A, Heise M, Fei Y, Thieme R, Klein S, Hong JH, Dima SO, Popescu I, Hoppe-Lotichius M, Buettner R, Lautem A, Otto G, Quaas A, Nagarajan N, Rozen S, Teh BT, Goeppert B, Drebber U, Lang H, Tan P, Gockel I, Schumacher J, Hillmer AM
bioRxiv [Preprint]. November 05, 2024. DOI: 10.1101/2024.04.29.591666.
Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny
Hunt M, Hinrichs AS, Anderson D, Karim L, Dearlove BL, Knaggs J, Constantinides B, Fowler PW, Rodger G, Street T, Lumley S, Webster H, Sanderson T, Ruis C, Kotzen B, de Maio N, Amenga-Etego LN, Amuzu DSY, Avaro M, Awandare GA, Ayivor-Djanie R, Barkham T, Bashton M, Batty EM, Bediako Y, De Belder D, Benedetti E, Bergthaler A, Boers SA, Campos J, Carr RAA, Chen YYC, Cuba F, Dattero ME, Dejnirattisai W, Dilthey A, Duedu KO, Endler L, Engelmann I, Francisco NM, Fuchs J, Gnimpieba EZ, Groc S, Gyamfi J, Heemskerk D, Houwaart T, Hsiao NY, Huska M, Hölzer M, Iranzadeh A, Jarva H, Jeewandara C, Jolly B, Joseph R, Kant R, Ki KKK, Kurkela S, Lappalainen M, Lataretu M, Lemieux J, Liu C, Malavige GN, Mashe T, Mongkolsapaya J, Montes B, Mora JAM, Morang'a CM, Mvula B, Nagarajan N, Nelson A, Ngoi JM, da Paixão JP, Panning M, Poklepovich T, Quashie PK, Ranasinghe D, Russo M, San JE, Sanderson ND, Scaria V, Screaton G, Sessions OM, Sironen T, Sisay A, Smith D, Smura T, Supasa P, Suphavilai C, Swann J, Tegally H, Tegomoh B, Vapalahti O, Walker A, Wilkinson RJ, Williamson C, Zair X; IMSSC2 Laboratory Network Consortium; de Oliveira T, Peto TE, Crook D, Corbett-Detig R, Iqbal Z
BMC Bioinformatics. April 16, 2024. DOI: 10.1186/s12859-024-05760-3.
MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes
Peres da Silva R, Suphavilai C, Nagarajan N
ISME J. January 08, 2024. DOI: 10.1093/ismejo/wrae054.
Hypervirulent Klebsiella pneumoniae employs genomic island encoded toxins against bacterial competitors in the gut
Tan YH, Arros P, Berríos-Pastén C, Wijaya I, Chu WHW, Chen Y, Cheam G, Mohamed Naim AN, Marcoleta AE, Ravikrishnan A, Nagarajan N, Lagos R, Gan YH
Microbiol Spectr. April 02, 2024. DOI: 10.1128/spectrum.03969-23.
Comparison of tet(X4)-containing contigs assembled from metagenomic sequencing data with plasmid sequences of isolates from a cohort of healthy subjects
Ding Y, Er S, Tan A, Gounot J-S, Saw W-Y, Tan LWL, Teo YY, Nagarajan N, Seedorf H
Allergy. 2024-06. DOI: 10.1111/all.16044.
The skin microbiome in pediatric atopic dermatitis and food allergy
Tham EH, Chia M, Riggioni C, Nagarajan N, Common JEA, Kong HH
mSphere. February 28, 2024. DOI: 10.1128/msphere.00781-23.
Short-chain fatty acids of various lengths differentially inhibit Klebsiella pneumoniae and Enterobacteriaceae species
Chang KC, Nagarajan N, Gan Y-H
BMC Bioinformatics. January 11, 2024. DOI: 10.1186/s12859-024-05634-8.
Comparative analysis of metagenomic classifiers for long-read sequencing datasets
Marić J, Križanović K, Riondet S, Nagarajan N, Šikić M
2023
Return to topNat Microbiol. 2023-05. DOI: 10.1038/s41564-023-01350-w.
No evidence for a common blood microbiome based on a population study of 9,770 healthy humans
Tan CCS, Ko KKK, Chen H, Liu J, Loh M; SG10K_Health Consortium; Chia M, Nagarajan N
Int J Mol Sci. January 05, 2023. DOI: 10.3390/ijms24021042.
Profiling Microbial Communities in Idiopathic Granulomatous Mastitis
Ong SS, Xu J, Sim CK, Khng AJ, Ho PJ, Kwan PKW, Ravikrishnan A, Tan KB, Tan QT, Tan EY, Tan SM, Putti TC, Lim SH, Tang ELS, Nagarajan N, Karnani N, Li J, Hartman M
Nucleic Acids Res. January 06, 2023. DOI: 10.1093/nar/gkac911.
CREAMMIST: an integrative probabilistic database for cancer drug response prediction
Yingtaweesittikul H, Wu J, Mongia A, Peres R, Ko K, Nagarajan N, Suphavilai C
2022
Return to topNat Commun. October 13, 2022. DOI: 10.1038/s41467-022-33782-z.
Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians
Gounot JS, Chia M, Bertrand D, Saw WY, Ravikrishnan A, Low A, Ding Y, Ng AHQ, Tan LWL, Teo YY, Seedorf H, Nagarajan N
Commun Biol. September 15, 2022. DOI: 10.1038/s42003-022-03940-6.
Genome assembly and chemogenomic profiling of National Flower of Singapore Papilionanthe Miss Joaquim 'Agnes' reveals metabolic pathways regulating floral traits
Lim AH, Low ZJ, Shingate PN, Hong JH, Chong SC, Ng CCY, Liu W, Vaser R, Šikić M, Sung WK, Nagarajan N, Tan P, Teh BT
Nat Microbiol. 2022-10. DOI: 10.1038/s41564-022-01221-w.
Long-term ecological and evolutionary dynamics in the gut microbiomes of carbapenemase-producing Enterobacteriaceae colonized subjects
Kang JTL, Teo JJY, Bertrand D, Ng A, Ravikrishnan A, Yong M, Ng OT, Marimuthu K, Chen SL, Chng KR, Gan YH, Nagarajan N
BMC Ecol Evol. September 03, 2022. DOI: 10.1186/s12862-022-02057-y.
Genomic patterns of divergence in the early and late steps of speciation of the deep-sea vent thermophilic worms of the genus Alvinella
Thomas-Bulle C, Bertrand D, Nagarajan N, Copley RR, Corre E, Hourdez S, Bonnivard É, Claridge-Chang A, Jollivet D
Front Med (Lausanne). August 01, 2022. DOI: 10.3389/fmed.2022.964640.
Clonal serotype 1c multidrug-resistant Shigella flexneri detected in multiple institutions by sentinel-site sequencing
Ko KKK, Chu JJK, Lim KM, Yingtaweesittikul H, Huang W, Tan SYL, Goh KCM, Tan SH, Ng TY, Maiwald M, Chia JWZ, Cao DY, Tan YE, Sim JHC, Koh TH, Nagarajan N, Suphavilai C
Emerg Infect Dis. 2022-08. DOI: 10.3201/eid2808.212542.
Dominant Carbapenemase-Encoding Plasmids in Clinical Enterobacterales Isolates and Hypervirulent Klebsiella pneumoniae, Singapore
Yong M, Chen Y, Oo G, Chang KC, Chu WHW, Teo J, Venkatachalam I, Thevasagayam NM, Sridatta PSR, Koh V, Marcoleta AE, Chen H, Nagarajan N, Kalisvar M, Ng OT, Gan YH
Microbiol Spectr. August 31, 2022. DOI: 10.1128/spectrum.00849-22.
Mutual Exclusion of Methanobrevibacter Species in the Human Gut Microbiota Facilitates Directed Cultivation of a Candidatus Methanobrevibacter Intestini Representative
Low A, Lee JKY, Gounot JS, Ravikrishnan A, Ding Y, Saw WY, Tan LWL, Moong DKN, Teo YY, Nagarajan N, Seedorf H
Microbiol Spectr. June 29, 2022. DOI: 10.1128/spectrum.00791-22.
Emergence of SARS-CoV-2 Spike Mutations during Prolonged Infection in Immunocompromised Hosts
Ko KKK, Yingtaweesittikul H, Tan TT, Wijaya L, Cao DY, Goh SS, Abdul Rahman NB, Chan KXL, Tay HM, Sim JHC, Chan KS, Oon LLE, Nagarajan N, Suphavilai C
NPJ Biofilms Microbiomes. April 11, 2022. DOI: 10.1038/s41522-022-00287-y.
Gut microbiome responses to dietary intervention with hypocholesterolemic vegetable oils
Lim RRX, Park MA, Wong LH, Haldar S, Lim KJ, Nagarajan N, Henry CJ, Jiang YR, Moskvin OV
Nat Methods. 2022-04. DOI: 10.1038/s41592-022-01431-4.
Critical Assessment of Metagenome Interpretation: the second round of challenges
Meyer F, Fritz A, Deng ZL, Koslicki D, Lesker TR, Gurevich A, Robertson G, Alser M, Antipov D, Beghini F, Bertrand D, Brito JJ, Brown CT, Buchmann J, Buluç A, Chen B, Chikhi R, Clausen PTLC, Cristian A, Dabrowski PW, Darling AE, Egan R, Eskin E, Georganas E, Goltsman E, Gray MA, Hansen LH, Hofmeyr S, Huang P, Irber L, Jia H, Jørgensen TS, Kieser SD, Klemetsen T, Kola A, Kolmogorov M, Korobeynikov A, Kwan J, LaPierre N, Lemaitre C, Li C, Limasset A, Malcher-Miranda F, Mangul S, Marcelino VR, Marchet C, Marijon P, Meleshko D, Mende DR, Milanese A, Nagarajan N, Nissen J, Nurk S, Oliker L, Paoli L, Peterlongo P, Piro VC, Porter JS, Rasmussen S, Rees ER, Reinert K, Renard B, Robertsen EM, Rosen GL, Ruscheweyh HJ, Sarwal V, Segata N, Seiler E, Shi L, Sun F, Sunagawa S, Sørensen SJ, Thomas A, Tong C, Trajkovski M, Tremblay J, Uritskiy G, Vicedomini R, Wang Z, Wang Z, Wang Z, Warren A, Willassen NP, Yelick K, You R, Zeller G, Zhao Z, Zhu S, Zhu J, Garrido-Oter R, Gastmeier P, Hacquard S, Häußler S, Khaledi A, Maechler F, Mesny F, Radutoiu S, Schulze-Lefert P, Smit N, Strowig T, Bremges A, Sczyrba A, McHardy AC
Nat Microbiol. 2022-04. DOI: 10.1038/s41564-022-01089-w.
Metagenomics-enabled microbial surveillance
Ko KKK, Chng KR, Nagarajan N
J Allergy Clin Immunol. 2022-10. DOI: 10.1016/j.jaci.2022.01.031.
Shared signatures and divergence in skin microbiomes of children with atopic dermatitis and their caregivers
Chia M, Naim ANM, Tay ASL, Lim K, Chew KL, Yow SJ, Chen J, Common JEA, Nagarajan N, Tham EH
Microbiol Spectr. February 23, 2022. DOI: 10.1128/spectrum.02223-21.
SARS-CoV-2 N Gene G29195T Point Mutation May Affect Diagnostic Reverse Transcription-PCR Detection
Ko KKK, Abdul Rahman NB, Tan SYL, Chan KXL, Goh SS, Sim JHC, Lim KL, Tan WL, Chan KS, Oon LLE, Nagarajan N, Suphavilai C
2021
Return to topFront Med (Lausanne). December 14, 2021. DOI: 10.3389/fmed.2021.790662.
CalmBelt: Rapid SARS-CoV-2 Genome Characterization for Outbreak Tracking
Yingtaweesittikul H, Ko K, Abdul Rahman N, Tan SYL, Nagarajan N, Suphavilai C
Genome Med. December 16, 2021. DOI: 10.1186/s13073-021-01000-y.
Predicting heterogeneity in clone-specific therapeutic vulnerabilities using single-cell transcriptomic signatures
Suphavilai C, Chia S, Sharma A, Tu L, Da Silva RP, Mongia A, DasGupta R, Nagarajan N
PLoS Comput Biol. September 08, 2021. DOI: 10.1371/journal.pcbi.1009343.
BEEM-Static: Accurate inference of ecological interactions from cross-sectional microbiome data
Li C, Av-Shalom TV, Tan JWG, Kwah JS, Chng KR, Nagarajan N
Appl Environ Microbiol. September 28, 2021. DOI: 10.1128/AEM.00488-21.
Extended-Spectrum β-Lactamase-Producing and mcr-1-Positive Escherichia coli from the Gut Microbiota of Healthy Singaporeans
Ding Y, Saw WY, Tan LWL, Moong DKN, Nagarajan N, Teo YY, Seedorf H
Cell. June 24, 2021. DOI: 10.1016/j.cell.2021.05.002.
A global metagenomic map of urban microbiomes and antimicrobial resistance
Danko D, Bezdan D, Afshin EE, Ahsanuddin S, Bhattacharya C, Butler DJ, Chng KR, Donnellan D, Hecht J, Jackson K, Kuchin K, Karasikov M, Lyons A, Mak L, Meleshko D, Mustafa H, Mutai B, Neches RY, Ng A, Nikolayeva O, Nikolayeva T, Png E, Ryon KA, Sanchez JL, Shaaban H, Sierra MA, Thomas D, Young B, Abudayyeh OO, Alicea J, Bhattacharyya M, Blekhman R, Castro-Nallar E, Cañas AM, Chatziefthimiou AD, Crawford RW, De Filippis F, Deng Y, Desnues C, Dias-Neto E, Dybwad M, Elhaik E, Ercolini D, Frolova A, Gankin D, Gootenberg JS, Graf AB, Green DC, Hajirasouliha I, Hastings JJA, Hernandez M, Iraola G, Jang S, Kahles A, Kelly FJ, Knights K, Kyrpides NC, Łabaj PP, Lee PKH, Leung MHY, Ljungdahl PO, Mason-Buck G, McGrath K, Meydan C, Mongodin EF, Moraes MO, Nagarajan N, Nieto-Caballero M, Noushmehr H, Oliveira M, Ossowski S, Osuolale OO, Özcan O, Paez-Espino D, Rascovan N, Richard H, Rätsch G, Schriml LM, Semmler T, Sezerman OU, Shi L, Shi T, Siam R, Song LH, Suzuki H, Court DS, Tighe SW, Tong X, Udekwu KI, Ugalde JA, Valentine B, Vassilev DI, Vayndorf EM, Velavan TP, Wu J, Zambrano MM, Zhu J, Zhu S, Mason CE; International MetaSUB Consortium
BMC Genomics. May 26, 2021. DOI: 10.1186/s12864-021-07702-2.
Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads
Commichaux S, Javkar K, Ramachandran P, Nagarajan N, Bertrand D, Chen Y, Reed E, Gonzalez-Escalona N, Strain E, Rand H, Pop M, Ottesen A
Bioinformatics. August 04, 2021. DOI: 10.1093/bioinformatics/btab299.
TUGDA: task uncertainty guided domain adaptation for robust generalization of cancer drug response prediction from in vitro to in vivo settings
Peres da Silva R, Suphavilai C, Nagarajan N
Int J Infect Dis. 2021-06. DOI: 10.1016/j.ijid.2021.04.012.
Stool metagenome analysis of patients with Klebsiella pneumoniae liver abscess and their domestic partners
Molton JS, Lee IR, Bertrand D, Ding Y, Kalimuddin S, Lye DC, Nagarajan N, Gan YH, Archuleta S
Nat Biotechnol. 2021-04. DOI: 10.1038/s41587-021-00889-5.
Publisher Correction: Determination of isoform-specific RNA structure with nanopore long reads
Aw JGA, Lim SW, Wang JX, Lambert FRP, Tan WT, Shen Y, Zhang Y, Kaewsapsak P, Li C, Ng SB, Vardy LA, Tan MH, Nagarajan N, Wan Y
Lancet Microbe. 2021-04. DOI: 10.1016/S2666-5247(21)00039-2.
COVID-19 drug practices risk antimicrobial resistance evolution
Afshinnekoo E, Bhattacharya C, Burguete-García A, Castro-Nallar E, Deng Y, Desnues C, Dias-Neto E, Elhaik E, Iraola G, Jang S, Łabaj PP, Mason CE, Nagarajan N, Poulsen M, Prithiviraj B, Siam R, Shi T, Suzuki H, Werner J, Zambrano MM, Bhattacharyya M; MetaSUB Consortium
Gut Pathog. February 25, 2021. DOI: 10.1186/s13099-021-00409-5.
Ectopic gut colonization: a metagenomic study of the oral and gut microbiome in Crohn's disease
Hu S, Png E, Gowans M, Ong DEH, de Sessions PF, Song J, Nagarajan N
J Antimicrob Chemother. April 13, 2021. DOI: 10.1093/jac/dkaa561.
Household transmission of carbapenemase-producing Enterobacteriaceae: a prospective cohort study
Marimuthu K, Mo Y, Ling ML, Hernandez-Koutoucheva A, Fenlon SN, Bertrand D, Lye DC, Ang BSP, Perencevich E, Ng OT, Cooper BS, Nagarajan N, Chen SL, Barkham T
Nat Biotechnol. 2021-03. DOI: 10.1038/s41587-020-00755-w.
Author Correction: Determination of isoform-specific RNA structure with nanopore long reads
Aw JGA, Lim SW, Wang JX, Lambert FRP, Tan WT, Shen Y, Zhang Y, Kaewsapsak P, Li C, Ng SB, Vardy LA, Tan MH, Nagarajan N, Wan Y
Nat Biotechnol. 2021-03. DOI: 10.1038/s41587-020-0712-z.
Determination of isoform-specific RNA structure with nanopore long reads
Aw JGA, Lim SW, Wang JX, Lambert FRP, Tan WT, Shen Y, Zhang Y, Kaewsapsak P, Li C, Ng SB, Vardy LA, Tan MH, Nagarajan N, Wan Y
J Allergy Clin Immunol. 2021-04. DOI: 10.1016/j.jaci.2020.09.031.
Atopic dermatitis microbiomes stratify into ecologic dermotypes enabling microbial virulence and disease severity
Tay ASL, Li C, Nandi T, Chng KR, Andiappan AK, Mettu VS, de Cevins C, Ravikrishnan A, Dutertre CA, Wong XFCC, Ng AHQ, Matta SA, Ginhoux F, Rötzschke O, Chew FT, Tang MBY, Yew YW, Nagarajan N, Common JEA
2020
Return to topCell Rep Med. June 23, 2020. DOI: 10.1016/j.xcrm.2020.100039.
Human Tumor-Infiltrating MAIT Cells Display Hallmarks of Bacterial Antigen Recognition in Colorectal Cancer
Li S, Simoni Y, Becht E, Loh CY, Li N, Lachance D, Koo SL, Lim TP, Tan EKW, Mathew R, Nguyen A, Golovato J, Berkson JD, Prlic M, Lee B, Minot SS, Nagarajan N, Dey N, Tan DSW, Tan IB, Newell EW
J Antimicrob Chemother. December 01, 2020. DOI: 10.1093/jac/dkaa372.
Emergence of tigecycline- and eravacycline-resistant Tet(X4)-producing Enterobacteriaceae in the gut microbiota of healthy Singaporeans
Ding Y, Saw WY, Tan LWL, Moong DKN, Nagarajan N, Teo YY, Seedorf H
Emerg Infect Dis. 2020-09. DOI: 10.3201/eid2609.190592.
Duration of Carbapenemase-Producing Enterobacteriaceae Carriage in Hospital Patients
Mo Y, Hernandez-Koutoucheva A, Musicha P, Bertrand D, Lye D, Ng OT, Fenlon SN, Chen SL, Ling ML, Tang WY, Barkham T, Nagarajan N, Cooper BS, Marimuthu K
Nat Ecol Evol. 2020-09. DOI: 10.1038/s41559-020-1236-0.
Metagenome-wide association analysis identifies microbial determinants of post-antibiotic ecological recovery in the gut
Chng KR, Ghosh TS, Tan YH, Nandi T, Lee IR, Ng AHQ, Li C, Ravikrishnan A, Lim KM, Lye D, Barkham T, Raman K, Chen SL, Chai L, Young B, Gan YH, Nagarajan N
Nat Med. 2020-06. DOI: 10.1038/s41591-020-0894-4.
Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment
Chng KR, Li C, Bertrand D, Ng AHQ, Kwah JS, Low HM, Tong C, Natrajan M, Zhang MH, Xu L, Ko KKK, Ho EXP, Av-Shalom TV, Teo JWP, Khor CC; MetaSUB Consortium; Chen SL, Mason CE, Ng OT, Marimuthu K, Ang B, Nagarajan N
Gut Pathog. February 03, 2020. DOI: 10.1186/s13099-020-0346-1.
Gut microbiota changes in children with autism spectrum disorder: a systematic review
Ho LKH, Tong VJW, Syn N, Nagarajan N, Tham EH, Tay SK, Shorey S, Tambyah PA, Law ECN
2019
Return to topPLoS Biol. November 07, 2019. DOI: 10.1371/journal.pbio.3000517.
Boosting natural history research via metagenomic clean-up of crowdsourced feces
Srivathsan A, Nagarajan N, Meier R
Microbiome. August 22, 2019. DOI: 10.1186/s40168-019-0729-z.
An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data
Li C, Chng KR, Kwah JS, Av-Shalom TV, Tucker-Kellogg L, Nagarajan N
Microb Cell Fact. August 19, 2019. DOI: 10.1186/s12934-019-1185-y.
Development and application of a transcriptional sensor for detection of heterologous acrylic acid production in E. coli
Raghavan SS, Chee S, Li J, Poschmann J, Nagarajan N, Jia Wei S, Verma CS, Ghadessy FJ
Nat Biotechnol. 2019-08. DOI: 10.1038/s41587-019-0191-2.
Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes
Bertrand D, Shaw J, Kalathiyappan M, Ng AHQ, Kumar MS, Li C, Dvornicic M, Soldo JP, Koh JY, Tong C, Ng OT, Barkham T, Young B, Marimuthu K, Chng KR, Sikic M, Nagarajan N
Nat Commun. June 17, 2019. DOI: 10.1038/s41467-019-09799-2.
Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen
Menden MP, Wang D, Mason MJ, Szalai B, Bulusu KC, Guan Y, Yu T, Kang J, Jeon M, Wolfinger R, Nguyen T, Zaslavskiy M; AstraZeneca-Sanger Drug Combination DREAM Consortium; Jang IS, Ghazoui Z, Ahsen ME, Vogel R, Neto EC, Norman T, Tang EKY, Garnett MJ, Veroli GYD, Fawell S, Stolovitzky G, Guinney J, Dry JR, Saez-Rodriguez J
Nat Commun. March 29, 2019. DOI: 10.1038/s41467-019-09391-8.
Structure mapping of dengue and Zika viruses reveals functional long-range interactions
Huber RG, Lim XN, Ng WC, Sim AYL, Poh HX, Shen Y, Lim SY, Sundstrom KB, Sun X, Aw JG, Too HK, Boey PH, Wilm A, Chawla T, Choy MM, Jiang L, de Sessions PF, Loh XJ, Alonso S, Hibberd M, Nagarajan N, Ooi EE, Bond PJ, Sessions OM, Wan Y
2018
Return to topMicrobiome. November 29, 2018. DOI: 10.1186/s40168-018-0588-z.
Understanding the microbial basis of body odor in pre-pubescent children and teenagers
Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TMU, Li J, Ong M, Lu Y, Swaile D, Liu P, Liu J, Nagarajan N
Cell. August 09, 2018. DOI: 10.1016/j.cell.2018.07.034.
Comprehensive Characterization of Cancer Driver Genes and Mutations
Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Kwok-Shing Ng P, Jeong KJ, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortés-Ciriano I, Zhou DC, Liang WW, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H; MC3 Working Group; Cancer Genome Atlas Research Network; Lawrence MS, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L
Eur Respir J. July 27, 2018. DOI: 10.1183/13993003.00766-2018.
Immunological corollary of the pulmonary mycobiome in bronchiectasis: the CAMEB study
Mac Aogáin M, Chandrasekaran R, Lim AYH, Low TB, Tan GL, Hassan T, Ong TH, Hui Qi Ng A, Bertrand D, Koh JY, Pang SL, Lee ZY, Gwee XW, Martinus C, Sio YY, Matta SA, Chew FT, Keir HR, Connolly JE, Abisheganaden JA, Koh MS, Nagarajan N, Chalmers JD, Chotirmall SH
Bioinformatics. November 15, 2018. DOI: 10.1093/bioinformatics/bty452.
Predicting Cancer Drug Response using a Recommender System
Suphavilai C, Bertrand D, Nagarajan N
Mol Ecol Resour. April 19, 2018. DOI: 10.1111/1755-0998.12890.
A MinION™-based pipeline for fast and cost-effective DNA barcoding
Srivathsan A, Baloğlu B, Wang W, Tan WX, Bertrand D, Ng AHQ, Boey EJH, Koh JJY, Nagarajan N, Meier R
Cell. April 05, 2018. DOI: 10.1016/j.cell.2018.02.060.
Comprehensive Characterization of Cancer Driver Genes and Mutations
Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Ng PK, Jeong KJ, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortés-Ciriano I, Zhou DC, Liang WW, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H; MC3 Working Group; Cancer Genome Atlas Research Network; Lawrence MS, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L
Cell. April 05, 2018. DOI: 10.1016/j.cell.2018.03.033.
Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics
Ding L, Bailey MH, Porta-Pardo E, Thorsson V, Colaprico A, Bertrand D, Gibbs DL, Weerasinghe A, Huang KL, Tokheim C, Cortés-Ciriano I, Jayasinghe R, Chen F, Yu L, Sun S, Olsen C, Kim J, Taylor AM, Cherniack AD, Akbani R, Suphavilai C, Nagarajan N, Stuart JM, Mills GB, Wyczalkowski MA, Vincent BG, Hutter CM, Zenklusen JC, Hoadley KA, Wendl MC, Shmulevich L, Lazar AJ, Wheeler DA, Getz G; Cancer Genome Atlas Research Network
Nat Commun. March 29, 2018. DOI: 10.1038/s41467-018-03675-1.
Genome-wide identification of natural RNA aptamers in prokaryotes and eukaryotes
Tapsin S, Sun M, Shen Y, Zhang H, Lim XN, Susanto TT, Yang SL, Zeng GS, Lee J, Lezhava A, Ang EL, Zhang LH, Wang Y, Zhao H, Nagarajan N, Wan Y
Cancer Res. January 01, 2018. DOI: 10.1158/0008-5472.CAN-17-1345.
ConsensusDriver Improves upon Individual Algorithms for Predicting Driver Alterations in Different Cancer Types and Individual Patients
Bertrand D, Drissler S, Chia BK, Koh JY, Li C, Suphavilai C, Tan IB, Nagarajan N
Hepatology. 2018-01. DOI: 10.1002/hep.29327.
The liver-gut microbiota axis modulates hepatotoxicity of tacrine in the rat
Yip LY, Aw CC, Lee SH, Hong YS, Ku HC, Xu WH, Chan JMX, Cheong EJY, Chng KR, Ng AHQ, Nagarajan N, Mahendran R, Lee YK, Browne ER, Chan ECY
2017
Return to topPLoS One. October 30, 2017. DOI: 10.1371/journal.pone.0186771.
Measurement of fetal fraction in cell-free DNA from maternal plasma using a panel of insertion/deletion polymorphisms
Barrett AN, Xiong L, Tan TZ, Advani HV, Hua R, Laureano-Asibal C, Soong R, Biswas A, Nagarajan N, Choolani M
BMC Genomics. October 27, 2017. DOI: 10.1186/s12864-017-4217-1.
Single-virion sequencing of lamivudine-treated HBV populations reveal population evolution dynamics and demographic history
Zhu YO, Aw PPK, de Sessions PF, Hong S, See LX, Hong LZ, Wilm A, Li CH, Hue S, Lim SG, Nagarajan N, Burkholder WF, Hibberd M
Nat Genet. 2017-11. DOI: 10.1038/ng.3972.
The draft genome of tropical fruit durian (Durio zibethinus)
Teh BT, Lim K, Yong CH, Ng CCY, Rao SR, Rajasegaran V, Lim WK, Ong CK, Chan K, Cheng VKY, Soh PS, Swarup S, Rozen SG, Nagarajan N, Tan P
Nat Methods. 2017-11. DOI: 10.1038/nmeth.4458.
Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software
Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jørgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvočiūtė M, Hansen LH, Sørensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Don Kang D, Cook JJ, Deltel C, Beckstette M, Lemaitre C, Peterlongo P, Rizk G, Lavenier D, Wu YW, Singer SW, Jain C, Strous M, Klingenberg H, Meinicke P, Barton MD, Lingner T, Lin HH, Liao YC, Silva GGZ, Cuevas DA, Edwards RA, Saha S, Piro VC, Renard BY, Pop M, Klenk HP, Göker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC
PLoS Negl Trop Dis. June 14, 2017. DOI: 10.1371/journal.pntd.0005628.
Comparative genomics of Cryptococcus neoformans var. grubii associated with meningitis in HIV infected and uninfected patients in Vietnam
Day JN, Qihui S, Thanh LT, Trieu PH, Van AD, Thu NH, Chau TTH, Lan NPH, Chau NVV, Ashton PM, Thwaites GE, Boni MF, Wolbers M, Nagarajan N, Tan PBO, Baker S
J Vis Exp. May 24, 2017. DOI: 10.3791/55255.
Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen
Aw JGA, Shen Y, Nagarajan N, Wan Y
Cell Syst. May 24, 2017. DOI: 10.1016/j.cels.2017.04.009.
Mammalian Systems Biotechnology Reveals Global Cellular Adaptations in a Recombinant CHO Cell Line
Yusufi FNK, Lakshmanan M, Ho YS, Loo BLW, Ariyaratne P, Yang Y, Ng SK, Tan TRM, Yeo HC, Lim HL, Ng SW, Hiu AP, Chow CP, Wan C, Chen S, Teo G, Song G, Chin JX, Ruan X, Sung KWK, Hu WS, Yap MGS, Bardor M, Nagarajan N, Lee DY
J Endod. 2017-06. DOI: 10.1016/j.joen.2017.01.020.
Transcriptomics Analysis Reveals Putative Genes Involved in Biofilm Formation and Biofilm-associated Drug Resistance of Enterococcus faecalis
Seneviratne CJ, Suriyanarayanan T, Swarup S, Chia KHB, Nagarajan N, Zhang C
Biotechnol Biofuels. February 03, 2017. DOI: 10.1186/s13068-017-0720-5.
Development of a genetically programed vanillin-sensing bacterium for high-throughput screening of lignin-degrading enzyme libraries
Sana B, Chia KHB, Raghavan SS, Ramalingam B, Nagarajan N, Seayad J, Ghadessy FJ
Genome Res. 2017-05. DOI: 10.1101/gr.214270.116.
Fast and accurate de novo genome assembly from long uncorrected reads
Vaser R, Sović I, Nagarajan N, Šikić M
2016
Return to topNat Microbiol. July 11, 2016. DOI: 10.1038/nmicrobiol.2016.106.
Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare
Chng KR, Tay AS, Li C, Ng AH, Wang J, Suri BK, Matta SA, McGovern N, Janela B, Wong XF, Sio YY, Au BV, Wilm A, De Sessions PF, Lim TC, Tang MB, Ginhoux F, Connolly JE, Lane EB, Chew FT, Common JE, Nagarajan N
Gigascience. August 02, 2016. DOI: 10.1186/s13742-016-0140-7.
INC-Seq: accurate single molecule reads using nanopore sequencing
Li C, Chng KR, Boey EJ, Ng AH, Wilm A, Nagarajan N
EBioMedicine. 2016-06. DOI: 10.1016/j.ebiom.2016.04.034.
Tissue Microbiome Profiling Identifies an Enrichment of Specific Enteric Bacteria in Opisthorchis viverrini Associated Cholangiocarcinoma
Chng KR, Chan SH, Ng AHQ, Li C, Jusakul A, Bertrand D, Wilm A, Choo SP, Tan DMY, Lim KH, Soetinko R, Ong CK, Duda DG, Dima S, Popescu I, Wongkham C, Feng Z, Yeoh KG, Teh BT, Yongvanit P, Wongkham S, Bhudhisawasdi V, Khuntikeo N, Tan P, Pairojkul C, Ngeow J, Nagarajan N
Bioinformatics. October 01, 2016. DOI: 10.1093/bioinformatics/btw357.
@MInter: automated text-mining of microbial interactions
Lim KM, Li C, Chng KR, Nagarajan N
Mol Cell. May 19, 2016. DOI: 10.1016/j.molcel.2016.04.028.
In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation
Aw JG, Shen Y, Wilm A, Sun M, Lim XN, Boon KL, Tapsin S, Chan YS, Tan CP, Sim AY, Zhang T, Susanto TT, Fu Z, Nagarajan N, Wan Y
Genome Biol. May 11, 2016. DOI: 10.1186/s13059-016-0951-y.
OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees
Gao S, Bertrand D, Chia BK, Nagarajan N
Nat Commun. April 15, 2016. DOI: 10.1038/ncomms11307.
Fast and sensitive mapping of nanopore sequencing reads with GraphMap
Sović I, Šikić M, Wilm A, Fenlon SN, Chen S, Nagarajan N
Methods. June 01, 2016. DOI: 10.1016/j.ymeth.2016.02.019.
Predicting microbial interactions through computational approaches
Li C, Lim KM, Chng KR, Nagarajan N
Gigascience. January 19, 2016. DOI: 10.1186/s13742-016-0110-0.
OPTIMA: sensitive and accurate whole-genome alignment of error-prone genomic maps by combinatorial indexing and technology-agnostic statistical analysis
Verzotto D, M Teo AS, Hillmer AM, Nagarajan N
Nat Commun. January 19, 2016. DOI: 10.1038/ncomms10380.
Mutational spectrum of Barrett's stem cells suggests paths to initiation of a precancerous lesion
Yamamoto Y, Wang X, Bertrand D, Kern F, Zhang T, Duleba M, Srivastava S, Khor CC, Hu Y, Wilson LH, Blaszyk H, Rolshud D, Teh M, Liu J, Howitt BE, Vincent M, Crum CP, Nagarajan N, Ho KY, McKeon F, Xian W
J Pathol. 2016-03. DOI: 10.1002/path.4649.
In vitro and in vivo correlates of physiological and neoplastic human Fallopian tube stem cells
Yamamoto Y, Ning G, Howitt BE, Mehra K, Wu L, Wang X, Hong Y, Kern F, Wei TS, Zhang T, Nagarajan N, Basuli D, Torti S, Brewer M, Choolani M, McKeon F, Crum CP, Xian W
2015
Return to topGigascience. December 29, 2015. DOI: 10.1186/s13742-015-0106-1.
Single-molecule optical genome mapping of a human HapMap and a colorectal cancer cell line
Teo AS, Verzotto D, Yao F, Nagarajan N, Hillmer AM
PLoS Genet. November 05, 2015. DOI: 10.1371/journal.pgen.1005614.
Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin
Wu G, Zhao H, Li C, Rajapakse MP, Wong WC, Xu J, Saunders CW, Reeder NL, Reilman RA, Scheynius A, Sun S, Billmyre BR, Li W, Averette AF, Mieczkowski P, Heitman J, Theelen B, Schröder MS, De Sessions PF, Butler G, Maurer-Stroh S, Boekhout T, Nagarajan N, Dawson TL Jr
J Gen Virol. 2015-12. DOI: 10.1099/jgv.0.000298.
Direct whole-genome deep-sequencing of human respiratory syncytial virus A and B from Vietnamese children identifies distinct patterns of inter- and intra-host evolution
Do LAH, Wilm A, van Doorn HR, Lam HM, Sim S, Sukumaran R, Tran AT, Nguyen BH, Tran TTL, Tran QH, Vo QB, Dac NAT, Trinh HN, Nguyen TTH, Binh BTL, Le K, Nguyen MT, Thai QT, Vo TV, Ngo NQM, Dang TKH, Cao NH, Tran TV, Ho LV, Farrar J, de Jong M, Chen S, Nagarajan N, Bryant JE, Hibberd ML
PLoS Negl Trop Dis. September 01, 2015. DOI: 10.1371/journal.pntd.0004044.
Analysis of Dengue Virus Genetic Diversity during Human and Mosquito Infection Reveals Genetic Constraints
Sessions OM, Wilm A, Kamaraj US, Choy MM, Chow A, Chong Y, Ong XM, Nagarajan N, Cook AR, Ooi EE
PLoS Negl Trop Dis. September 01, 2015. DOI: 10.1371/journal.pntd.0004052.
Tracking Dengue Virus Intra-host Genetic Diversity during Human-to-Mosquito Transmission
Sim S, Aw PP, Wilm A, Teoh G, Hue KD, Nguyen NM, Nagarajan N, Simmons CP, Hibberd ML
Cell Rep. July 14, 2015. DOI: 10.1016/j.celrep.2015.06.020.
Recurrent Fusion Genes in Gastric Cancer: CLDN18-ARHGAP26 Induces Loss of Epithelial Integrity
Yao F, Kausalya JP, Sia YY, Teo AS, Lee WH, Ong AG, Zhang Z, Tan JH, Li G, Bertrand D, Liu X, Poh HM, Guan P, Zhu F, Pathiraja TN, Ariyaratne PN, Rao J, Woo XY, Cai S, Mulawadi FH, Poh WT, Veeravalli L, Chan CS, Lim SS, Leong ST, Neo SC, Choi PS, Chew EG, Nagarajan N, Jacques PÉ, So JB, Ruan X, Yeoh KG, Tan P, Sung WK, Hunziker W, Ruan Y, Hillmer AM
Nature. June 11, 2015. DOI: 10.1038/nature14484.
Cloning and variation of ground state intestinal stem cells
Wang X, Yamamoto Y, Wilson LH, Zhang T, Howitt BE, Farrow MA, Kern F, Ning G, Hong Y, Khor CC, Chevalier B, Bertrand D, Wu L, Nagarajan N, Sylvester FA, Hyams JS, Devers T, Bronson R, Lacy DB, Ho KY, Crum CP, McKeon F, Xian W
Nat Methods. 2015-07. DOI: 10.1038/nmeth.3407.
Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection
Ewing AD, Houlahan KE, Hu Y, Ellrott K, Caloian C, Yamaguchi TN, Bare JC, P'ng C, Waggott D, Sabelnykova VY; ICGC-TCGA DREAM Somatic Mutation Calling Challenge participants; Kellen MR, Norman TC, Haussler D, Friend SH, Stolovitzky G, Margolin AA, Stuart JM, Boutros PC
Genome Biol. February 12, 2015. DOI: 10.1186/s13059-015-0589-1.
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
Nucleic Acids Res. April 20, 2015. DOI: 10.1093/nar/gku1393.
Patient-specific driver gene prediction and risk assessment through integrated network analysis of cancer omics profiles
Bertrand D, Chng KR, Sherbaf FG, Kiesel A, Chia BK, Sia YY, Huang SK, Hoon DS, Liu ET, Hillmer A, Nagarajan N
2014
Return to topGenome Biol. December 03, 2014. DOI: 10.1186/s13059-014-0527-7.
The importance of study design for detecting differentially abundant features in high-throughput experiments
Luo H, Li J, Chia BK, Robson P, Nagarajan N
Genome Biol. January 01, 1970. DOI: 10.1186/PREACCEPT-6768001251451949.
BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads
Hong LZ, Hong S, Wong HT, Aw PP, Cheng Y, Wilm A, de Sessions PF, Lim SG, Nagarajan N, Hibberd ML, Quake SR, Burkholder WF
Genome Announc. October 02, 2014. DOI: 10.1128/genomeA.00901-14.
Draft Genome Sequence of Polychlorinated Biphenyl-Dechlorinating Dehalococcoides mccartyi Strain SG1, Which Carries a Circular Putative Plasmid
Wang S, Chng KR, Wu C, Wilm A, Nagarajan N, He J
Genome Res. 2014-10. DOI: 10.1101/gr.164871.113.
Systems consequences of amplicon formation in human breast cancer
Inaki K, Menghi F, Woo XY, Wagner JP, Jacques PÉ, Lee YF, Shreckengast PT, Soon WW, Malhotra A, Teo AS, Hillmer AM, Khng AJ, Ruan X, Ong SH, Bertrand D, Nagarajan N, Karuturi RK, Miranda AH, Liu ET
Proc Natl Acad Sci U S A. August 19, 2014. DOI: 10.1073/pnas.1404845111.
Genomic characterization of three unique Dehalococcoides that respire on persistent polychlorinated biphenyls
Wang S, Chng KR, Wilm A, Zhao S, Yang KL, Nagarajan N, He J
Nat Commun. July 09, 2014. DOI: 10.1038/ncomms5378.
The Opisthorchis viverrini genome provides insights into life in the bile duct
Young ND, Nagarajan N, Lin SJ, Korhonen PK, Jex AR, Hall RS, Safavi-Hemami H, Kaewkong W, Bertrand D, Gao S, Seet Q, Wongkham S, Teh BT, Wongkham C, Intapan PM, Maleewong W, Yang X, Hu M, Wang Z, Hofmann A, Sternberg PW, Tan P, Wang J, Gasser RB
Methods Mol Biol. January 01, 1970. DOI: 10.1007/978-1-4939-0348-1_12.
Next-generation whole genome sequencing of dengue virus
Aw PP, de Sessions PF, Wilm A, Hoang LT, Nagarajan N, Sessions OM, Hibberd ML
2013
Return to topGenome Announc. June 27, 2013. DOI: 10.1128/genomeA.00399-13.
Genome Sequencing of Four Strains of Rickettsia prowazekii, the Causative Agent of Epidemic Typhus, Including One Flying Squirrel Isolate
Bishop-Lilly KA, Ge H, Butani A, Osborne B, Verratti K, Mokashi V, Nagarajan N, Pop M, Read TD, Richards AL
PLoS One. April 08, 2013. DOI: 10.1371/journal.pone.0060811.
Species identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16S rRNA amplicon sequences
Ong SH, Kukkillaya VU, Wilm A, Lay C, Ho EX, Low L, Hibberd ML, Nagarajan N
Nat Genet. 2013-01. DOI: 10.1038/ng.2472.
The draft genome of sweet orange (Citrus sinensis)
Xu Q, Chen LL, Ruan X, Chen D, Zhu A, Chen C, Bertrand D, Jiao WB, Hao BH, Lyon MP, Chen J, Gao S, Xing F, Lan H, Chang JW, Ge X, Lei Y, Hu Q, Miao Y, Wang L, Xiao S, Biswas MK, Zeng W, Guo F, Cao H, Yang X, Xu XW, Cheng YJ, Xu J, Liu JH, Luo OJ, Tang Z, Guo WW, Kuang H, Zhang HY, Roose ML, Nagarajan N, Deng XX, Ruan Y
J Infect Dis. May 01, 2013. DOI: 10.1093/infdis/jis470.
A randomized, double-blind placebo controlled trial of balapiravir, a polymerase inhibitor, in adult dengue patients
Nguyen NM, Tran CN, Phung LK, Duong KT, Huynh Hle A, Farrar J, Nguyen QT, Tran HT, Nguyen CV, Merson L, Hoang LT, Hibberd ML, Aw PP, Wilm A, Nagarajan N, Nguyen DT, Pham MP, Nguyen TT, Javanbakht H, Klumpp K, Hammond J, Petric R, Wolbers M, Nguyen CT, Simmons CP
2012
Return to topGenome Biol. December 13, 2012. DOI: 10.1186/gb-2012-13-12-r115.
Whole-genome reconstruction and mutational signatures in gastric cancer
Nagarajan N, Bertrand D, Hillmer AM, Zang ZJ, Yao F, Jacques PÉ, Teo AS, Cutcutache I, Zhang Z, Lee WH, Sia YY, Gao S, Ariyaratne PN, Ho A, Woo XY, Veeravali L, Ong CK, Deng N, Desai KV, Khor CC, Hibberd ML, Shahab A, Rao J, Wu M, Teh M, Zhu F, Chin SY, Pang B, So JB, Bourque G, Soong R, Sung WK, Tean Teh B, Rozen S, Ruan X, Yeoh KG, Tan PB, Ruan Y
Nucleic Acids Res. 2012-12. DOI: 10.1093/nar/gks918.
LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets
Wilm A, Aw PP, Bertrand D, Yeo GH, Ong SH, Wong CH, Khor CC, Petric R, Hibberd ML, Nagarajan N
PLoS One. September 28, 2012. DOI: 10.1371/journal.pone.0046152.
Long span DNA paired-end-tag (DNA-PET) sequencing strategy for the interrogation of genomic structural mutations and fusion-point-guided reconstruction of amplicons
Yao F, Ariyaratne PN, Hillmer AM, Lee WH, Li G, Teo AS, Woo XY, Zhang Z, Chen JP, Poh WT, Zawack KF, Chan CS, Leong ST, Neo SC, Choi PS, Gao S, Nagarajan N, Thoreau H, Shahab A, Ruan X, Cacheux-Rataboul V, Wei CL, Bourque G, Sung WK, Liu ET, Ruan Y
Nat Biotechnol. 2012-08. DOI: 10.1038/nbt.2303.
Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly
Lam ET, Hastie A, Lin C, Ehrlich D, Das SK, Austin MD, Deshpande P, Cao H, Nagarajan N, Xiao M, Kwok PY
Nat Genet. 2012-05. DOI: 10.1038/ng.2246.
Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes
Zang ZJ, Cutcutache I, Poon SL, Zhang SL, McPherson JR, Tao J, Rajasegaran V, Heng HL, Deng N, Gan A, Lim KH, Ong CK, Huang D, Chin SY, Tan IB, Ng CC, Yu W, Wu Y, Lee M, Wu J, Poh D, Wan WK, Rha SY, So J, Salto-Tellez M, Yeoh KG, Wong WK, Zhu YJ, Futreal PA, Pang B, Ruan Y, Hillmer AM, Bertrand D, Nagarajan N, Rozen S, Teh BT, Tan P
Nat Med. March 18, 2012. DOI: 10.1038/nm.2713.
A common BIM deletion polymorphism mediates intrinsic resistance and inferior responses to tyrosine kinase inhibitors in cancer
Ng KP, Hillmer AM, Chuah CT, Juan WC, Ko TK, Teo AS, Ariyaratne PN, Takahashi N, Sawada K, Fei Y, Soh S, Lee WH, Huang JW, Allen JC Jr, Woo XY, Nagarajan N, Kumar V, Thalamuthu A, Poh WT, Ang AL, Mya HT, How GF, Yang LY, Koh LP, Chowbay B, Chang CT, Nadarajan VS, Chng WJ, Than H, Lim LC, Goh YT, Zhang S, Poh D, Tan P, Seet JE, Ang MK, Chau NM, Ng QS, Tan DS, Soda M, Isobe K, Nöthen MM, Wong TY, Shahab A, Ruan X, Cacheux-Rataboul V, Sung WK, Tan EH, Yatabe Y, Mano H, Soo RA, Chin TM, Lim WT, Ruan Y, Ong ST
2011
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Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences
Gao S, Sung WK, Nagarajan N
Genome Res. 2011-05. DOI: 10.1101/gr.113555.110.
Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes
Hillmer AM, Yao F, Inaki K, Lee WH, Ariyaratne PN, Teo AS, Woo XY, Zhang Z, Zhao H, Ukil L, Chen JP, Zhu F, So JB, Salto-Tellez M, Poh WT, Zawack KF, Nagarajan N, Gao S, Li G, Kumar V, Lim HP, Sia YY, Chan CS, Leong ST, Neo SC, Choi PS, Thoreau H, Tan PB, Shahab A, Ruan X, Bergh J, Hall P, Cacheux-Rataboul V, Wei CL, Yeoh KG, Sung WK, Bourque G, Liu ET, Ruan Y
Nucleic Acids Res. 2011-03. DOI: 10.1093/nar/gkq1232.
GiRaF: robust, computational identification of influenza reassortments via graph mining
Nagarajan N, Kingsford C
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Sequencing and genome assembly using next-generation technologies
Nagarajan N, Pop M
BMC Genomics. April 16, 2010. DOI: 10.1186/1471-2164-11-242.
Finishing genomes with limited resources: lessons from an ensemble of microbial genomes
Nagarajan N, Cook C, Di Bonaventura M, Ge H, Richards A, Bishop-Lilly KA, DeSalle R, Read TD, Pop M
J Comput Biol. 2010-03. DOI: 10.1089/cmb.2009.0173.
Finding biologically accurate clusterings in hierarchical tree decompositions using the variation of information
Navlakha S, White J, Nagarajan N, Pop M, Kingsford C
BMC Bioinformatics. March 24, 2010. DOI: 10.1186/1471-2105-11-152.
Alignment and clustering of phylogenetic markers--implications for microbial diversity studies
White JR, Navlakha S, Nagarajan N, Ghodsi MR, Kingsford C, Pop M
Genome Biol. January 04, 2010. DOI: 10.1186/gb-2010-11-1-r1.
Genomic characterization of the Yersinia genus
Chen PE, Cook C, Stewart AC, Nagarajan N, Sommer DD, Pop M, Thomason B, Thomason MP, Lentz S, Nolan N, Sozhamannan S, Sulakvelidze A, Mateczun A, Du L, Zwick ME, Read TD