• Publications
Legend: # Corresponding Authors, * First Authors

2021

  1. "Ectopic gut colonization: a metagenomic study of the oral and gut microbiome in Crohn’s disease" 2021 Gut Pathogens
    Shijia Hu*, Eileen Png, Michelle Gowans, David EH Ong, Paola Florez de Sessions, Jie Song, Niranjan Nagarajan
    Abstract
    2.  
  2. "Stool metagenome analysis of patients with Klebsiella pneumoniae liver abscess and their domestic partners" 2021 International Journal of Infectious Diseases
    James S Molton*, I Russel Lee, Denis Bertrand, Ying Ding, Shirin Kalimuddin, David C Lye, Niranjan Nagarajan, Yunn-Hwen Gan, Sophia Archuleta
    Abstract
    3.  
  3. "COVID-19 drug practices risk antimicrobial resistance evolution" 2021 The Lancet Microbe
    Ebrahim Afshinnekoo, Chandrima Bhattacharya, Ana Burguete-García, Eduardo Castro-Nallar, Youping Deng, Christelle Desnues, Emmanuel Dias-Neto, Eran Elhaik, Gregorio Iraola, Soojin Jang, Paweł P Łabaj, Christopher E Mason, Niranjan Nagarajan, Michael Poulsen, Bharath Prithiviraj, Rania Siam, Tieliu Shi, Haruo Suzuki, Johannes Werner, Maria Mercedes Zambrano, Malay Bhattacharyya
    Abstract
    4.  
  4. "Atopic dermatitis microbiomes stratify into ecological dermotypes enabling microbial virulence and disease severity" 2021 Journal of Allergy and Clinical Immunology
    Angeline SL Tay*, Chenhao Li*, Tannistha Nandi*, Kern Rei Chng, Anand Kumar Andiappan, Vijaya Saradhi Mettu, Camille de Cevins, Aarthi Ravikrishnan, Charles-Antoine Dutertre, XF Colin C Wong, Amanda Hui Qi Ng, Sri Anusha Matta, Florent Ginhoux, Olaf Rötzschke, Fook Tim Chew, Mark BY Tang, Yik Weng Yew, Niranjan Nagarajan#, John EA Common#
    Abstract
    5.  
  5. "Determination of isoform-specific RNA structure with nanopore long reads" 2021 Nature Biotechnology
    Jong Ghut Ashley Aw*, Shaun W. Lim, Jia Xu Wang, Finnlay R. P. Lambert, Wen Ting Tan, Yang Shen, Yu Zhang, Pornchai Kaewsapsak, Chenhao Li, Sarah B. Ng, Leah A. Vardy, Meng How Tan, Niranjan Nagarajan#, Yue Wan#
    Abstract
    6.  
  6. "Household transmission of carbapenemase-producing Enterobacteriaceae: a prospective cohort study" 2021 Journal of Antimicrobial Chemotherapy
    Kalisvar Marimuthu, Yin Mo, Moi Lin Ling, Anastasia Hernandez-Koutoucheva, Shannon N Fenlon, Denis Bertrand, David Chien Lye, Brenda Sze Peng Ang, Eli Perencevich, Oon Tek Ng, Ben S Cooper, Niranjan Nagarajan, Swaine L Chen, Timothy Barkham#
    Abstract
    7.  

2020

  1. "Gut microbiota changes in children with autism spectrum disorder: a systematic review" 2020 Gut pathogens
    Lucius Kang Hua Ho*, Valerie Jia Wei Tong, Nicholas Syn, Niranjan Nagarajan, Elizabeth Huiwen Tham, Stacey K. Tay, Shefaly Shorey, Paul Anantharajah Tambyah & Evelyn Chung Ning Law#
    Abstract
    2.  
  2. "Duration of Carbapenemase-Producing Enterobacteriaceae Carriage in Hospital Patients" 2020 Emerging infectious diseases
    Yin Mo#, Anastasia Hernandez-Koutoucheva, Patrick Musicha, Denis Bertrand, David Lye, Oon Tek Ng, Shannon N Fenlon, Swaine L Chen, Moi Lin Ling, Wen Ying Tang, Timothy Barkham, Niranjan Nagarajan, Ben S Cooper, Kalisvar Marimuthu
    Abstract
    3.  
  3. "Metagenome-wide association analysis identifies microbial determinants of post-antibiotic ecological recovery in the gut" 2020 Nature Ecology & Evolution
    Chng KR*, Ghosh TS*, Tan YH*, Nandi T*, Lee RI, Ng AHQ, Li C, Ravikrishnan A, Lim KM, Lye D, Barkham T, Raman K, Chen SL, Chai L, Young B, Gan YH#, Nagarajan N#
    Abstract
    4.  
  4. "Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment." 2020 Nature Medicine
    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, Woon JPT, Khor CC, MetaSUB Consortium, Chen SL, Mason CE, Ng OT, Marimuthu K, Ang B, Nagarajan N#
    Abstract
    5.  
  5. "Gut microbiota changes in children with autism spectrum disorder: a systematic review." 2020 Gut Pathogen 12 (1), 6
    Ho LK, Tong VJ, Syn N, Nagarajan N, Tham EH, Tay SK, Shorey S, Tambyah PA, Law EC#
    Abstract
    6.  

2019

  1. "Boosting natural history research via metagenomic clean-up of crowdsourced feces." 2019 PLoS Biology 17 (11)
    Srivathsan A, Nagarajan N, Meier R#
    Abstract
    2.  
  2. "Global genetic cartography of urban metagenomes and anti-microbial resistance." 2019 BioRxiv, 724526
    Danko D, Bezdan D, Afshinnekoo E, Ahsanuddin S, Bhattacharya C, Butler DJ, Chng KR, Png E, Ng AHQ, Nagaranjan N, … , Mason CE#, The International MetaSUB Consortium
    Abstract
    3.  
  3. "An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data." 2019 Microbiome 7 (1), 1-14
    Li C, Chng KR, Kwah JS, Av-Shalom TV, Tucker-Kellogg L, Nagarajan N
    Abstract
    4.  
  4. "Development and application of a transcriptional sensor for detection of heterologous acrylic acid production in E. coli." 2019 Microbial Cell Factories 18 (1), 1-12
    Raghavan SS, Chee S, Li J, Poschmann J, Nagarajan N, Wei SJ, Verma CS, Ghadessy FJ
    Abstract
    5.  
  5. "Graphmap2-splice-aware RNA-seq mapper for long reads." 2019 BioRxiv, 720458
    Maric J, Sovic I, Krizanovic K, Nagarajan N, Sikic M
    Abstract
    6.  
  6. "Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes." 2019 Nature Biotechnology 37 (8), 937-944
    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
    Abstract
    7.  
  7. "Carriage duration of carbapenemase-producing Enterobacteriaceae in a hospital cohort-implications for infection control measures." 2019 MedRxiv, 19001479
    Mo Y, Hernandez-Koutoucheva A, Musicha P, Bertrand D, Lye D, Ng OT, Fenlon SN, Chen SL, Ling ML, Tang WY, Barkham T, Nagaranjan N, Cooper BS, Marimuthu K
    Abstract
    8.  
  8. "Structure mapping of dengue and Zika viruses reveals functional long-range interactions." 2019 Nature Communications 10 (1), 1-13
    Huber RG, Lim XN, Ng WC, Sim AY, 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
    Abstract
    9.  

2018

  1. "Understanding the microbial basis of body odor in pre-pubescent children and teenagers." 2018 Microbiome 6 (1), 1-14
    Lam TH, Verzotto D, Brahma P, Ng AHQ, Hu P, Schnell D, Tiesman J, Kong R, Ton TM, Li J, Ong M, Lu Y, Swaile D, Liu P, Liu J, Nagarajan N
    Abstract
    2.  
  2. "Predicting cancer drug response using a recommender system." 2018 Bioinformatics 34 (22), 3907-3914
    Suphavilai C, Bertrand D, Nagarajan N
    Abstract
    3.  
  3. "Immunological corollary of the pulmonary mycobiome in bronchiectasis: the CAMEB study." 2018 European Respiratory Journal 52 (1)
    Mac Aogáin M, Chandrasekaran R, Lim AY, Low TB, Tan GL, Hassan T, Ong TH, Ng AHQ, 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 M, Nagarajan N, Chalmers JD, Chotirmall SH
    Abstract
    4.  
  4. "Gut microbiome recovery after antibiotic usage is mediated by specific bacterial species." 2018 BioRxiv, 350470
    Nandi T, Lee IR, Ghosh T, Ng AHQ, Chng KR, Li C, Tan YH, Lye D, Barkham T, Chen S, Gan YH, Young B, Nagarajan N
    Abstract
    5.  
  5. "A Min ION™‐based pipeline for fast and cost‐effective DNA barcoding." 2018 Molecular Ecology Resources 18 (5), 1035-1049
    Srivathsan A, Baloğlu B, Wang W, Tan WX, Bertrand D, Ng AHQ, Boey EJ, Koh JJ, Nagarajan N, Meier R
    Abstract
    6.  
  6. "Perspective on oncogenic processes at the end of the beginning of cancer genomics." 2018 Cell 173 (2), 305-320. e10
    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
    Abstract
    7.  
  7. "Comprehensive characterization of cancer driver genes and mutations." 2018 Cell 173 (2), 371-385. e18
    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
    Abstract
    8.  
  8. "Genome-wide identification of natural RNA aptamers in prokaryotes and eukaryotes." 2018 Nature Communications 9 (1), 1-10
    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
    Abstract
    9.  
  9. "ConsensusDriver improves upon individual algorithms for predicting driver alterations in different cancer types and individual patients." 2018 Cancer Research 78 (1), 290-301
    Bertrand D, Drissler S, Chia BK, Koh JY, Li C, Suphavilai C, Tan IB, Nagarajan N
    Abstract
    10.  

2017

  1. "Measurement of fetal fraction in cell-free DNA from maternal plasma using a panel of insertion/deletion polymorphisms." 2017 PloS One 12 (10)
    Barrett AN, Xiong L, Tan TZ, Advani HV, Hua R, Laureano-Asibal C, Soong R, Biswas A, Nagarajan N, Choolani M
    Abstract
    2.  
  2. "Single-virion sequencing of lamivudine-treated HBV populations reveal population evolution dynamics and demographic history." 2017 BMC Genomics 18 (1), 829
    Zhu YO, Aw PP, de Sessions PF, Hong S, See LX, Hong LZ, Wilm A, Li CH, Hue S, Lim SG, Nagarajan N, Burkholder WF, Hibberd M
    Abstract
    3.  
  3. "The draft genome of tropical fruit durian (Durio zibethinus)." 2017 Nature Genetics 49 (11), 1633
    Teh BT, Lim K, Yong CH, Ng CC, Rao SR, Rajasegaran V, Lim WK, Ong CK, Chan K, Cheng VK, Soh PS, Swarup S, Rozen SG, Nagarajan N, Tan P
    Abstract
    4.  
  4. "Critical assessment of metagenome interpretation—a benchmark of metagenomics software." 2017 Nature Methods 14 (11), 1063-1071
    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 R15, 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
    Abstract
    5.  
  5. "The liver–gut microbiota axis modulates hepatotoxicity of tacrine in the rat." 2017 Hepatology 67 (1), 282-295
    Yip LY, Aw CC, Lee SH, Hong YS, Ku HC, Xu WH, Chan JM, Cheong EJ, Chng KR, Ng AHQ, Nagarajan N, Mahendran R, Lee YK, Browne ER, Chan ECY
    Abstract
    6.  
  6. "Comparative genomics of Cryptococcus neoformans var. grubii associated with meningitis in HIV infected and uninfected patients in Vietnam." 2017 PLoS Neglected Tropical Diseases 11 (6), e0005628
    Day JN, Qihui S, Thanh LT, Trieu PH, Van AD, Thu NH, Chau TT, Lan NP, Chau NV, Ashton PM, Thwaites GE, Boni MF, Wolbers M, Nagarajan N, Tan PBO, Baker S
    Abstract
    7.  
  7. "Transcriptomics analysis reveals putative genes involved in biofilm formation and biofilm-associated drug resistance of Enterococcus faecalis." 2017 Journal of Endodontics 43 (6), 949-955
    Seneviratne CJ, Suriyanarayanan T, Swarup S, Chia KH, Nagarajan N, Zhang C
    Abstract
    8.  
  8. "Fast and accurate de novo genome assembly from long uncorrected reads." 2017 Genome Research 27 (5), 737-746
    Vaser R, Sović I, Nagarajan N, Šikić M
    Abstract
    9.  
  9. "Mapping RNA-RNA interactions globally using biotinylated psoralen." 2017 JoVE (Journal of Visualized Experiments), e55255
    Aw JG, Shen Y, Nagarajan N, Wan Y
    Abstract
    10.  
  10. "Mammalian systems biotechnology reveals global cellular adaptations in a recombinant CHO cell line." 2017 Cell Systems 4 (5), 530-542. e6
    Yusufi FN, Lakshmanan M, Ho YS, Loo BL, Ariyaratne P, Yang Y, Ng SK, Tan TR, 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
    Abstract
    11.  
  11. "Development of a genetically programed vanillin-sensing bacterium for high-throughput screening of lignin-degrading enzyme libraries." 2017 Biotechnology for Biofuels 10 (1), 32
    Sana B, Chia KH, Raghavan SS, Ramalingam B, Nagarajan N, Seayad J, Ghadessy FJ
    Abstract
    12.  

2016

  1. "@MInter: automated text-mining of microbial interactions." 2016 Bioinformatics 32 (19), 2981-2987
    Lim KM, Li C, Chng KR, Nagarajan N#
    Abstract
    2.  
  2. "INC-Seq: accurate single molecule reads using nanopore sequencing." 2016 Gigascience 5 (1), s13742-016-0140-7
    Li C, Chng KR, Boey EJ, Ng AHQ, Wilm A, Nagarajan N
    Abstract
    3.  
  3. "Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare" 2016 Nature Microbiololgy 1 (9), 16106
    Chng KR, Tay ASL, Li C, Ng AHQ, Wang J, Suri BK, Matta AS, McGovern N, Janela B, Wong XFC, Sio YY, Au BV, Wilm A, De Sessions PF, Lim TC, Tang MBY, Ginhoux F, Connolly JE, Lane EB, Chew FT, Common JEA#, Nagarajan N#
    Abstract
    4.  
  4. "Tissue microbiome profiling identifies an enrichment of specific enteric bacteria In Opisthorchis viverrini associated cholangiocarcinoma" 2016 EBioMedicine 8, 195-202
    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 KH, Teh BT, Yongvanit P, Wongkham S, Bhudhisawasdi V, Khuntikeo N, Tan P, Pairojkul C#, Ngeow J#, Nagarajan N#
    Abstract
    5.  
  5. "Predicting microbial interactions through computational approaches." 2016 Methods 102, 12-19
    Li C, Lim KM, Chng KR, Nagarajan N#
    Abstract
    6.  
  6. "In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation." 2016 Molecular Cell 62 (4), 603-617
    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#
    Abstract
    7.  
  7. "OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees." 2016 Genome Biology 17(1), 102
    Gao S, Bertrand D, Chia BK, Nagarajan N#
    Abstract
    8.  
  8. "Fast and sensitive mapping of nanopore sequencing reads with GraphMap." 2016 Nature Communications 7 : 11307
    Sović I, Šikić M, Wilm A, Fenlon SN, Chen S, Nagarajan N#
    Abstract
    9.  
  9. "In vitro and in vivo correlates of physiological and neoplastic human Fallopian tube stem cells." 2016 The Journal of Pathology 238 (4), 519-530
    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
    Abstract
    10.  
  10. "OPTIMA: sensitive and accurate whole-genome alignment of error-prone genomic maps by combinatorial indexing and technology-agnostic statistical analysis." 2016 GigaScience 5 : 2 Epub 2016 Jan 19
    Verzotto D, M Teo AS, Hillmer AM, Nagarajan N#
    Abstract
    11.  
  11. "Mutational spectrum of Barrett\'s stem cells suggests paths to initiation of a precancerous lesion." 2016 Nature Communications 7 : 10380
    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
    Abstract
    12.  

2015

  1. "Patient-specific driver gene prediction and risk assessment through integrated network analysis of cancer omics profiles." 2015 Jan 8 Nucleic Acids Research 43(7), e44-e44.
    Bertrand D, Chng KR, Sherbaf FG, Kiesel A, Chia BK, Sia YY, Huang SK, Hoon DS, Liu ET, Hillmer A, Nagarajan N#
    Abstract
    2.  
  2. "Recurrent Fusion Genes in Gastric Cancer: CLDN18-ARHGAP26 Induces Loss of Epithelial Integrity." 2015 Jul 14 Cell Rep 12(2) : 272-85 Epub 2015 Jul 2
    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
    Abstract
    3.  
  3. "High-depth sequencing of over 750 genes supports linear progression of primary tumors and metastases in most patients with liver-limited metastatic colorectal cancer." 2015 Genome Biology 16(1) : 32 Epub 2015 Feb 12
    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
    Abstract
    4.  
  4. "Cloning and variation of ground state intestinal stem cells." 2015 Jun 11 Nature 522(7555) : 173-8 Epub 2015 Jun 3
    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
    Abstract
    5.  
  5. "Index-based map-to-sequence alignment in large eukaryotic genomes." 2015 BioRxiv 017194
    Verzotto D, Hillmer AM, Teo ASM, Nagarajan N#
    Abstract
    6.  
  6. "Analysis of Dengue Virus Genetic Diversity during Human and Mosquito Infection Reveals Genetic Constraints." 2015 Sep PLoS Neglected Tropical Diseases 9(9) : e0004044 Epub 2015 Sep 1
    Sessions OM, Wilm A, Kamaraj US, Choy MM, Chow A, Chong Y, Ong XM, Nagarajan N, Cook AR, Ooi EE
    Abstract
    7.  
  7. "Tracking Dengue Virus Intra-host Genetic Diversity during Human-to-Mosquito Transmission." 2015 Sep PLoS Neglected Tropical Diseases 9(9) : e0004052 Epub 2015 Sep 1
    Sim S, Aw PP, Wilm A, Teoh G, Hue KD, Nguyen NM, Nagarajan N, Simmons CP, Hibberd ML
    Abstract
    8.  
  8. "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." 2015 Sep 25 The Journal of General Virology 96(Pt 12), 3470.
    Do LA, Wilm A, van Doorn HR, Lam HM, Sim S, Sukumaran R, Tran AT, Nguyen BH, Tran TT, Tran QH, Vo QB, Tran Dac NA, Trinh HN, Nguyen TT, Le Binh BT, Le K, Nguyen MT, Thai QT, Vo TV, Ngo NQ, Dang TK, Cao NH, Tran TV, Ho LV, Farrar J, De Jong M, Chen S, Nagarajan N, Bryant JE, Hibberd ML
    Abstract
    9.  
  9. "Single-molecule optical genome mapping of a human HapMap and a colorectal cancer cell line." 2015 GigaScience 4 : 65 Epub 2015 Dec 29
    Teo AS, Verzotto D, Yao F, Nagarajan N, Hillmer AM
    Abstract
    10.  
  10. "Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin." 2015 Nov PLoS Genetics 11(11) : e1005614 Epub 2015 Nov 5
    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#
    Abstract
    11.  
  11. "In Vitro and In Vivo Correlates of Physiologic and Neoplastic Human Fallopian Tube Stem Cells." 2015 Sep 28 The Journal of Pathology 238(4), 519-530
    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
    Abstract
    12.  

2014

  1. "Next-generation whole genome sequencing of dengue virus." 2014 In: Padmanabhan R., Vasudevan S. (eds) Dengue. Methods in Molecular Biology (Methods and Protocols), vol 1138, 1138 : 175-95, Humana Press, New York, NY
    Aw PP, de Sessions PF, Wilm A, Hoang LT, Nagarajan N, Sessions OM, Hibberd ML
    Abstract
    2.  
  2. "Genomic characterization of three unique Dehalococcoides that respire on persistent polychlorinated biphenyls." 2014 Jul 15 Proceedings of the National Academy of Sciences 111(33), 12103-12108
    Wang S, Chng KR, Wilm A, Zhao S, Yang KL, Nagarajan N#, He J#
    Abstract
    3.  
  3. "The Opisthorchis viverrini genome provides insights into life in the bile duct." 2014 Nature Communications 5(1), 1-11
    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
    Abstract
    4.  
  4. "Systems consequences of amplicon formation in human breast cancer." 2014 Sep 3 Genome Research 24(10), 1559-1571
    Inaki K, Menghi F, Woo XY, Wagner JP, Jacques PE, Lee YF, Shreckengast PT, Soon WW, Malhotra A, Teo AS, Hillmer AM, Khng AJ, Ruan X, Ong SH, Bertrand D, Nagarajan N, Karuturi RK, Hidalgo Miranda A, Liu ET
    Abstract
    5.  
  5. "Draft Genome Sequence of Polychlorinated Biphenyl-Dechlorinating Dehalococcoides mccartyi Strain SG1, Which Carries a Circular Putative Plasmid." 2014 Genome Announcements 2(5), e00901-14
    Wang S, Chng KR, Wu C, Wilm A, Nagarajan N, He J
    Abstract
    6.  
  6. "BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads." 2014 Nov 19 Genome Biology 15(11) : 517
    Hong LZ, Hong S, Wong H, Aw P, Yan C, Wilm A, de Sessions PF, Lim S, Nagarajan N, Hibberd ML, Quake SR, Burkholder WF
    Abstract
    7.  
  7. "The importance of study design for detecting differentially abundant features in high-throughput experiments." 2014 Genome Biology 15(12) : 527 Epub 2014 Dec 3
    Luo H, Li J, Chia BK, Robson P, Nagarajan N#
    Abstract
    8.  
  8. "Papaya Repeat Database." 2014 In: Ming R., Moore P. (eds) Genetics and Genomics of Papaya. Plant Genetics and Genomics: Crops and Models, vol 10, 225-240. Springer, New York, NY
    Nagarajan N, Navajas-Pérez R
    Abstract
    9.  

2013

  1. "Sequence assembly demystified." 2013 Jan 29 Nature Reviews Genetics 14(3), 157-167 Epub 2013 Jan 29
    Nagarajan N, Pop M
    Abstract
    2.  
  2. "Species Identification and Profiling of Complex Microbial Communities Using Shotgun Illumina Sequencing of 16S rRNA Amplicon Sequences." 2013 PLoS One 8(4) : e60811 Epub 2013 Apr 8
    Ong SH, Kukkillaya VU, Wilm A, Lay C, Ho EX, Low L, Hibberd ML, Nagarajan N#
    Abstract
    3.  
  3. "Genome Sequencing of Four Strains of Rickettsia prowazekii, the Causative Agent of Epidemic Typhus, Including One Flying Squirrel Isolate." 2013 Genome Announcements 1(3), e00399-13
    Bishop-Lilly KA, Ge H, Butani A, Osborne B, Verratti K, Mokashi V, Nagarajan N, Pop M, Read TD, Richards AL
    Abstract
    4.  

2012

  1. "A common BIM deletion polymorphism mediates intrinsic resistance and inferior responses to tyrosine kinase inhibitors in cancer." 2012 Nat Med 18(4) : 521-8 Epub 2012 Mar 18
    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, 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
    Abstract
    2.  
  2. "Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes." 2012 Apr 8 Nat Genet 44(5), 570 Epub 2012 Apr 8
    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
    Abstract
    3.  
  3. "Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly." 2012 Jul 15 Nat Biotechnol 30(8), 771 Epub 2012 Jul 15
    Lam ET, Hastie A, Lin C, Ehrlich D, Das SK, Austin MD, Deshpande P, Cao H, Nagarajan N, Xiao M, Kwok PY
    Abstract
    4.  
  4. "A randomized, double-blind placebo controlled trial of balapiravir, a polymerase inhibitor, in adult dengue patients." 2012 Jul 17 The Journal of infectious diseases 207(9), 1442-1450
    Nguyet NM, Chau TN, Lam PK, Kien DT, Huy HL, Farrar J, Quyen TH, Hien TT, Van Vinh Chau N, Merson L, Long HT, Hibberd ML, Aw PP, Wilm A, Nagarajan N, Dung NT, Mai PP, Truong NT, Javanbaht H, Klumpp K, Hammond J, Petric R, Wolbers M, Chinh NT, Simmons CP
    Abstract
    5.  
  5. "FinIS: Improved in silico finishing using an exact quadratic programming formulation." 2012 In: Raphael B., Tang J. (eds) Algorithms in Bioinformatics. WABI 2012. Lecture Notes in Computer Science, vol 7534. Springer, Berlin, Heidelberg
    Gao S, Bertrand D, Nagarajan N#
    Abstract
    6.  
  6. "LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets." 2012 Oct 12 Nucleic Acids Res 40(22), 11189-11201
    Wilm A, Aw PP, Bertrand D, Yeo GH, Ong SH, Wong CH, Khor CC, Petric R, Hibberd ML, Nagarajan N#
    Abstract
    7.  
  7. "Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons." 2012 PLoS One 7(9) : e46152 Epub 2012 Sep 28
    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
    Abstract
    8.  
  8. "The draft genome of sweet orange (Citrus sinensis)." 2012 Dec 16 Nat Genet 45(1) : 59-66 Epub 2012 Nov 25
    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
    Abstract
    9.  
  9. "Whole-genome reconstruction and mutational signatures in gastric cancer." 2012 Dec 13 Genome Biol 13(12) : R115 Epub 2012 Dec 13
    Nagarajan N#, Bertrand D*, Hillmer AM*, Zang ZJ*, Yao F, Jacques PE, 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, Teh BT, Rozen S, Ruan X, Yeoh KG, Tan PB#, Ruan Y#
    Abstract
    10.  

2011

  1. "Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes." 2011 May Genome Res 21(5) : 665-75 Epub 2011 Apr 5
    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, Kum ar 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
    Abstract
    2.  
  2. "Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences." 2011 Sep 19 Journal of Computational Biology 18(11), 1681-1691
    Gao S, Sung WK, Nagarajan N#
    Abstract
    3.  

2010

  1. "Genomic characterization of the Yersinia genus." 2010 Jan 4 Genome Biology 11(1) : R1 Epub 2010 Jan 4
    Chen PE, Cook C, Stewart AC, Nagarajan N, Sommer DD, Pop M, Thomason B, Kiley MP, Lentz S, Nolan N, Sozhamannan S, Sulakvelidze A, Mateczun A, Du L, Zwick ME, Read TD
    Abstract
    2.  
  2. "Alignment and clustering of phylogenetic markers - implications for microbial diversity studies." 2010 Mar 24 BMC Bioinformatics 11(1) : 152 Epub 2010 Mar 24
    White JR, Navlakha S, Nagarajan N, Ghodsi MR, Kingsford C, Pop M
    Abstract
    3.  
  3. "Finishing genomes with limited resources: lessons from an ensemble of microbial genomes." 2010 Apr 16 BMC Genomics 11(1) : 242 Epub 2010 Apr 16
    Nagarajan N, Cook C, Di Bonaventura M, Ge H, Richards A, Bishop-Lilly KA, Desalle R, Read TD, Pop M
    Abstract
    4.  
  4. "Sequencing and genome assembly using next-generation technologies." 2010 Methods Mol Biol 673 : 1-17
    Nagarajan N, Pop M
    Abstract
    5.  
  5. "GiRaF: robust, computational identification of influenza reassortments via graph mining." 2010 Dec 21 Nucleic Acids Research 39(6), e34-e34.
    Nagarajan N#, Kingsford C
    Abstract
    6.  

2009 and earlier (i.e. pre- Nagarajan Lab papers)

  1. "2009 Swine-origin influenza A (H1N1) resembles previous influenza isolates." 2009 PLoS ONE 4(7) : e6402 Epub 2009 Jul 28.
    Kingsford C*, Nagarajan N*, Salzberg SL
    Abstract
    2.  
  2. "Parametric complexity of sequence assembly: theory and applications to next generation sequencing." 2009 Jul J Comput Biol 16(7) : 897-908
    Nagarajan N, Pop M
    Abstract
    3.  
  3. "Complete genome sequence of Aggregatibacter (Haemophilus) aphrophilus NJ8700." 2009 Jul J Bacteriol 191(14) : 4693-4 Epub 2009 May 15
    Di Bonaventura MP, DeSalle R, Pop M, Nagarajan N, Figurski DH, Fine DH, Kaplan JB, Planet PJ
    Abstract
    4.  
  4. "Statistical methods for detecting differentially abundant features in clinical metagenomic samples." 2009 Apr PLoS Comput Biol 5(4) : e1000352 Epub 2009 Apr 10
    White JR, Nagarajan N, Pop M
    Abstract
    5.  
  5. "Finding biologically accurate clusterings in hierarchical decompostions using the variation of information." 2009 Journal of Computational Biology 17(3), 503-516
    Navlakha S, White JR, Nagarajan N, Pop M, Kingsford C
    Abstract
    6.  
  6. "Reliability and efficiency of algorithms for computing the significance of the Mann-Whitney test." 2009 Computational Statistics 24:4 605-622
    Nagarajan N, Keich U
    Abstract
    7.  
  7. "The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)." 2008 Apr 24 Nature 452(7190) : 991-6
    Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, … , Nagarajan N, … , Shippen DE, dePamphilis CW, Palmer JD, Freeling M, Paterson AH, Gonsalves D, Wang L, Alam M
    Abstract
    8.  
  8. "Scaffolding and validation of bacterial genome assemblies using optical restriction maps." 2008 May 15 Bioinformatics 24(10) : 1229-35 Epub 2008 Mar 20
    Nagarajan N, Read TD, Pop M
    Abstract
    9.  
  9. "FAST: Fourier transform based algorithms for significance testing of ungapped multiple alignments." 2008 Feb 15 Bioinformatics 24(4) : 577-8 Epub 2008 Jan 6
    Nagarajan N, Keich U
    Abstract
    10.  
  10. "Uncovering genomic reassortments among Influenza strains by enumerating maximal bicliques." 2008 IEEE International Conference on Bioinformatics and Biomedicine Philadelphia, PA, 223-230
    Nagarajan N, Kingsford C
    Abstract
    11.  
  11. "Genome-wide analysis of repetitive elements in papaya." 2008 Tropical Plant Biology 1(3-4) : 191-201
    Nagarajan N, Navajas-Perez R, Pop M, Alam M, Ming R, Paterson AH and Salzberg SL
    Abstract
    12.  
  12. "Apples to apples: improving the performance of motif finders and their significance analysis in the Twilight Zone." 2006 Bioinformatics 22(14) : e393-401
    Ng P, Nagarajan N, Jones N, Keich U
    Abstract
    13.  
  13. "Refining motif finders with E-value calculations." 2006 RECOMB Regulatory Genomics, 73-84
    Nagarajan N, Ng P, Keich U
    Abstract
    14.  
  14. "A fast and numerically robust method for exact multinomial goodness-of-fit test." 2006 Journal of Computational and Graphical Statistics 15(4) : 779-802
    Keich U, Nagarajan N
    Abstract
    15.  
  15. "Computing the P-value of the information content from an alignment of multiple sequences." 2005 Bioinformatics 21 Suppl 1 : i311-8
    Nagarajan N, Jones N, Keich U
    Abstract
    16.  
  16. "Automatic prediction of protein domains from sequence information using a hybrid learning system." 2004 Bioinformatics 20(9) : 1335-60 Epub 1970 Jan 1
    Nagarajan N, Yona G
    Abstract
    17.  
  17. "A faster reliable algorithm to estimate the p-value of the multinomial LLR statistic." 2004 In: Jonassen I., Kim J. (eds) Algorithms in Bioinformatics. WABI 2004. Lecture Notes in Computer Science, vol 3240. Springer, Berlin, Heidelberg
    Keich U, Nagarajan N
    Abstract
    18.  
  18. "A multi-expert system for the automatic detection of protein domains from sequence information." 2003 In RECOMB Proceedings of the seventh annual international conference on Research in computational molecular biology, 224-234.
    Nagarajan N, Yona G
    Abstract
    19.