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1

Gut microbiota changes in children with autism spectrum disorder: a systematic review

Ho, Lucius Kang Hua, Tong, Valerie Jia Wei, Syn, Nicholas, Nagarajan, Niranjan, Tham, Elizabeth Huiwen, Tay, Stacey K., Shorey, Shefaly, Tambyah, Paul Anantharajah, Law, Evelyn Chung Ning

Journal:

Year:

2020

Language:

english

File:

PDF, 1.49 MB

english, 2020

2

Reliability and efficiency of algorithms for computing the significance of the Mann–Whitney test

Niranjan Nagarajan, Uri Keich

Journal:

Computational Statistics

Year:

2009

Language:

english

File:

PDF, 587 KB

english, 2009

3

Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly

Lam, Ernest T, Hastie, Alex, Lin, Chin, Ehrlich, Dean, Das, Somes K, Austin, Michael D, Deshpande, Paru, Cao, Han, Nagarajan, Niranjan, Xiao, Ming, Kwok, Pui-Yan

Journal:

Nature Biotechnology

Year:

2012

Language:

english

File:

PDF, 1.28 MB

english, 2012

4

Sequence assembly demystified

Nagarajan, Niranjan, Pop, Mihai

Journal:

Nature Reviews Genetics

Year:

2013

Language:

english

File:

PDF, 424 KB

english, 2013

5

A novel injectable temperature-sensitive zinc doped chitosan/β-glycerophosphate hydrogel for bone tissue engineering

Niranjan, Ramesh, Koushik, Chandru, Saravanan, Sekaran, Moorthi, Ambigapathi, Vairamani, Mariappanadar, Selvamurugan, Nagarajan

Journal:

International Journal of Biological Macromolecules

Year:

2013

Language:

english

File:

PDF, 837 KB

english, 2013

6

ConsensusDriver Improves upon Individual Algorithms for Predicting Driver Alterations in Different Cancer Types and Individual Patients

Bertrand, Denis, Drissler, Sibyl, Chia, Burton K., Koh, Jia Yu, Li, Chenhao, Suphavilai, Chayaporn, Tan, Iain Beehuat, Nagarajan, Niranjan

Journal:

Cancer Research

Year:

2018

Language:

english

File:

PDF, 1.49 MB

english, 2018

7

Genome-Wide Analysis of Repetitive Elements in Papaya

Niranjan Nagarajan, Rafael Navajas-Pérez, Mihai Pop, Maqsudul Alam, Ray Ming, Andrew H. Paterson, Steven L. Salzberg

Journal:

Tropical Plant Biology

Year:

2008

Language:

english

File:

PDF, 4.28 MB

english, 2008

8

Alignment and clustering of phylogenetic markers - implications for microbial diversity studies

James R White, Saket Navlakha, Niranjan Nagarajan, Mohammad-Reza Ghodsi, Carl Kingsford, Mihai Pop

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.64 MB

english, 2010

9

Finishing genomes with limited resources: lessons from an ensemble of microbial genomes

Niranjan Nagarajan, Christopher Cook, MariaPia Di Bonaventura, Hong Ge, Allen Richards, Kimberly A Bishop-Lilly, Robert DeSalle, Timothy D Read, Mihai Pop

Journal:

Year:

2010

Language:

english

File:

PDF, 1.10 MB

english, 2010

10

Serological evidence of West Nile virus infection in wild migratory and resident water birds in Eastern and Northern India

Niranjan Mishra, S. Kalaiyarasu, S. Nagarajan, Mandava Venkata Subba Rao, Acty George, R. Sridevi, Sthita Pragnya Behera, Shiv Chandra Dubey, Tracy McCracken, Scott H. Newman

Journal:

Comparative Immunology, Microbiology and Infectious Diseases

Year:

2012

Language:

english

File:

PDF, 400 KB

english, 2012

11

Nonstructural Protein 2 (nsP2) of Chikungunya Virus (CHIKV) Enhances Protective Immunity Mediated by a CHIKV Envelope Protein Expressing DNA Vaccine

Bao, Huihui, Ramanathan, Aarti A., Kawalakar, Omkar, Sundaram, Senthil G., Tingey, Colleen, Bian, Charoran B., Muruganandam, Nagarajan, Vijayachari, Paluru, Sardesai, Niranjan Y., Weiner, David B., Ug

Journal:

Viral Immunology

Year:

2013

Language:

english

File:

PDF, 445 KB

english, 2013

12

Whole-genome reconstruction and mutational signatures in gastric cancer

Niranjan Nagarajan, Denis Bertrand, Axel M Hillmer, Zhi Jiang Zang…

Journal:

Year:

2012

Language:

english

File:

PDF, 1.24 MB

english, 2012

13

Genomic characterization of theYersiniagenus

Peter E Chen, Christopher Cook, Andrew C Stewart, Niranjan Nagarajan…

Journal:

Year:

2010

Language:

english

File:

PDF, 1.75 MB

english, 2010

14

A Fast and Numerically Robust Method for Exact Multinomial Goodness-of-Fit Test

Uri Keich and Niranjan Nagarajan

Journal:

Journal of Computational and Graphical Statistics

Year:

2006

Language:

english

File:

PDF, 1.60 MB

english, 2006

15

LPS induces mediators of neuroinflammation, cell proliferation, and GFAP expression in human astrocytoma cells U373MG: the anti-inflammatory and anti-proliferative effect of guggulipid

Niranjan, Rituraj, Nagarajan, Rajasekar, Hanif, Kashif, Nath, Chandishwar, Shukla, Rakesh

Journal:

Neurological Sciences

Year:

2014

Language:

english

File:

PDF, 621 KB

english, 2014

16

[IEEE 2012 IEEE 62nd Electronic Components and Technology Conference (ECTC) - San Diego, CA, USA (2012.05.29-2012.06.1)] 2012 IEEE 62nd Electronic Components and Technology Conference - Robust TSV via-middle and via-reveal process integration accomplished through characterization and management of sources of variation

Kumar, Niranjan, Ramaswami, Sesh, Dukovic, John, Tseng, Jennifer, Ding, Ran, Rajagopalan, Nagarajan, Eaton, Brad, Mishra, Rohit, Yalamanchili, Rao, Wang, Zhihong, Xia, Sherry, Sapre, Kedar, Hua, John,

Year:

2012

Language:

english

File:

PDF, 3.37 MB

english, 2012

17

[IEEE 2008 IEEE International Conference on Bioinformatics and Biomedicine - Philadelphia, PA, USA (2008.11.3-2008.11.5)] 2008 IEEE International Conference on Bioinformatics and Biomedicine - Uncovering Genomic Reassortments among Influenza Strains by Enumerating Maximal Bicliques

Nagarajan, Niranjan, Kingsford, Carl

Year:

2008

Language:

english

File:

PDF, 282 KB

english, 2008

18

Parametric Complexity of Sequence Assembly: Theory and Applications to Next Generation Sequencing

Nagarajan, Niranjan, Pop, Mihai

Journal:

Journal of Computational Biology

Year:

2009

Language:

english

File:

PDF, 325 KB

english, 2009

19

A Fast and Numerically Robust Method for Exact Multinomial Goodness-of-Fit Test

Keich, Uri, Nagarajan, Niranjan

Journal:

Journal of Computational and Graphical Statistics

Year:

2006

Language:

english

File:

PDF, 892 KB

english, 2006

20

Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences

Gao, Song, Sung, Wing-Kin, Nagarajan, Niranjan

Journal:

Journal of Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.74 MB

english, 2011

21

Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information

Navlakha, Saket, White, James, Nagarajan, Niranjan, Pop, Mihai, Kingsford, Carl

Journal:

Journal of Computational Biology

Year:

2010

Language:

english

File:

PDF, 416 KB

english, 2010

22

BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads

Hong, Lewis Z, Hong, Shuzhen, Wong, Han, Aw, Pauline, Cheng, Yan, Wilm, Andreas, de Sessions, Paola F, Lim, Seng, Nagarajan, Niranjan, Hibberd, Martin L, Quake, Stephen R, Burkholder, William F

Journal:

Year:

2014

Language:

english

File:

PDF, 545 KB

english, 2014

23

The importance of study design for detecting differentially abundant features in high-throughput experiments

Luo, Huaien, Li, Juntao, Chia, Burton, Robson, Paul, Nagarajan, Niranjan

Journal:

Year:

2014

Language:

english

File:

PDF, 1.53 MB

english, 2014

24

Species Identification and Profiling of Complex Microbial Communities Using Shotgun Illumina Sequencing of 16S rRNA Amplicon Sequences

Ong, Swee Hoe, Kukkillaya, Vinutha Uppoor, Wilm, Andreas, Lay, Christophe, Ho, Eliza Xin Pei, Low, Louie, Hibberd, Martin Lloyd, Nagarajan, Niranjan, Parkinson, John

Journal:

Year:

2013

Language:

english

File:

PDF, 1.01 MB

english, 2013

25

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

White, James Robert, Nagarajan, Niranjan, Pop, Mihai, Ouzounis, Christos A.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 703 KB

english, 2009

26

The Opisthorchis viverrini genome provides insights into life in the bile duct

Young, Neil D., Nagarajan, Niranjan, Lin, Suling Joyce, Korhonen, Pasi K., Jex, Aaron R., Hall, Ross S., Safavi-Hemami, Helena, Kaewkong, Worasak, Bertrand, Denis, Gao, Song, Seet, Qihui, Wongkham, So

Journal:

Nature Communications

Year:

2014

Language:

english

File:

PDF, 1.24 MB

english, 2014

27

Predicting microbial interactions through computational approaches

Li, Chenhao, Lim, Kun Ming Kenneth, Chng, Kern Rei, Nagarajan, Niranjan

Journal:

Year:

2016

Language:

english

File:

PDF, 1.16 MB

english, 2016

28

OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees

Gao, Song, Bertrand, Denis, Chia, Burton K. H., Nagarajan, Niranjan

Journal:

Year:

2016

Language:

english

File:

PDF, 1.99 MB

english, 2016

29

OPTIMA: sensitive and accurate whole-genome alignment of error-prone genomic maps by combinatorial indexing and technology-agnostic statistical analysis

Verzotto, Davide, M. Teo, Audrey S., Hillmer, Axel M., Nagarajan, Niranjan

Journal:

Year:

2016

Language:

english

File:

PDF, 2.76 MB

english, 2016

30

Single-molecule optical genome mapping of a human HapMap and a colorectal cancer cell line

Teo, Audrey S. M., Verzotto, Davide, Yao, Fei, Nagarajan, Niranjan, Hillmer, Axel M.

Journal:

Year:

2015

Language:

english

File:

PDF, 661 KB

english, 2015

31

@MInter: Automated Text-mining of Microbial Interactions

Lim, Kun Ming Kenneth, Li, Chenhao, Chng, Kern Rei, Nagarajan, Niranjan

Journal:

Year:

2016

Language:

english

File:

PDF, 542 KB

english, 2016

32

In vitro and in vivo correlates of physiological and neoplastic human Fallopian tube stem cells

Yamamoto, Yusuke, Ning, Gang, Howitt, Brooke E, Mehra, Karishma, Wu, Lingyan, Wang, Xia, Hong, Yue, Kern, Florian, Wei, Tay Seok, Zhang, Ting, Nagarajan, Niranjan, Basuli, Debargha, Torti, Suzy, Brewe

Journal:

The Journal of Pathology

Year:

2016

Language:

english

File:

PDF, 3.71 MB

english, 2016

33

Fast and accurate de novo genome assembly from long uncorrected reads

Vaser, Robert, Sović, Ivan, Nagarajan, Niranjan, Šikić, Mile

Journal:

Genome Research

Year:

2017

Language:

english

File:

PDF, 1.48 MB

english, 2017

34

Fast and sensitive mapping of nanopore sequencing reads with GraphMap

Sović, Ivan, Šikić, Mile, Wilm, Andreas, Fenlon, Shannon Nicole, Chen, Swaine, Nagarajan, Niranjan

Journal:

Nature Communications

Year:

2016

Language:

english

File:

PDF, 1.83 MB

english, 2016

35

Development of a genetically programed vanillin-sensing bacterium for high-throughput screening of lignin-degrading enzyme libraries

Sana, Barindra, Chia, Kuan Hui Burton, Raghavan, Sarada S., Ramalingam, Balamurugan, Nagarajan, Niranjan, Seayad, Jayasree, Ghadessy, Farid J.

Journal:

Biotechnology for Biofuels

Year:

2017

Language:

english

File:

PDF, 3.84 MB

english, 2017

36

Transcriptomics Analysis Reveals Putative Genes Involved in Biofilm Formation and Biofilm-associated Drug Resistance of Enterococcus faecalis

Seneviratne, Chaminda J., Suriyanarayanan, Tanujaa, Swarup, Sanjay, Chia, Kuan Hui Burton, Nagarajan, Niranjan, Zhang, Chengfei

Journal:

Journal of Endodontics

Year:

2017

Language:

english

File:

PDF, 1.24 MB

english, 2017

37

Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen

Aw, Jong Ghut Ashley, Shen, Yang, Nagarajan, Niranjan, Wan, Yue

Journal:

Journal of Visualized Experiments

Year:

2017

Language:

english

File:

PDF, 471 KB

english, 2017

38

A MinION-based pipeline for fast and cost-effective DNA barcoding

Srivathsan, Amrita, Baloğlu, Bilgenur, Wang, Wendy, Tan, Wei Xin, Bertrand, Denis, Ng, Amanda Hui Qi, Boey, Esther Jia Hui, Koh, Jayce Jia Yu, Nagarajan, Niranjan, Meier, Rudolf

Journal:

Molecular Ecology Resources

Year:

2018

Language:

english

File:

PDF, 761 KB

english, 2018

39

Predicting Cancer Drug Response Using a Recommender System

Suphavilai, Chayaporn, Bertrand, Denis, Nagarajan, Niranjan

Journal:

Year:

2018

Language:

english

File:

PDF, 1.44 MB

english, 2018

40

Analysis of Dengue Virus Genetic Diversity during Human and Mosquito Infection Reveals Genetic Constraints

Sessions, October M., Wilm, Andreas, Kamaraj, Uma Sangumathi, Choy, Milly M., Chow, Angelia, Chong, Yuwen, Ong, Xin Mei, Nagarajan, Niranjan, Cook, Alex R., Ooi, Eng Eong, Armstrong, Philip M.

Journal:

PLoS Neglected Tropical Diseases

Year:

2015

Language:

english

File:

PDF, 4.29 MB

english, 2015

41

Tracking Dengue Virus Intra-host Genetic Diversity during Human-to-Mosquito Transmission

Sim, Shuzhen, Aw, Pauline P. K., Wilm, Andreas, Teoh, Garrett, Hue, Kien Duong Thi, Nguyen, Nguyet Minh, Nagarajan, Niranjan, Simmons, Cameron P., Hibberd, Martin L., Pimenta, Paulo Filemon

Journal:

PLoS Neglected Tropical Diseases

Year:

2015

Language:

english

File:

PDF, 2.13 MB

english, 2015

42

2009 Swine-Origin Influenza A (H1N1) Resembles Previous Influenza Isolates

Kingsford, Carl, Nagarajan, Niranjan, Salzberg, Steven L., Stekel, Dov J.

Journal:

Year:

2009

Language:

english

File:

PDF, 819 KB

english, 2009

43

Single-virion sequencing of lamivudine-treated HBV populations reveal population evolution dynamics and demographic history

Zhu, Yuan O., Aw, Pauline P. K., de Sessions, Paola Florez, Hong, Shuzhen, See, Lee Xian, Hong, Lewis Z., Wilm, Andreas, Li, Chen Hao, Hue, Stephane, Lim, Seng Gee, Nagarajan, Niranjan, Burkholder, Wi

Journal:

Year:

2017

Language:

english

File:

PDF, 1.64 MB

english, 2017

44

Development and application of a transcriptional sensor for detection of heterologous acrylic acid production in E. coli

Raghavan, Sarada S., Chee, Sharon, Li, Juntao, Poschmann, Jeremie, Nagarajan, Niranjan, Jia Wei, Siau, Verma, Chandra S., Ghadessy, Farid J.

Journal:

Microbial Cell Factories

Year:

2019

Language:

english

File:

PDF, 3.57 MB

english, 2019

45

An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data

Li, Chenhao, Chng, Kern Rei, Kwah, Junmei Samantha, Av-Shalom, Tamar V., Tucker-Kellogg, Lisa, Nagarajan, Niranjan

Journal:

Year:

2019

Language:

english

File:

PDF, 2.51 MB

english, 2019

46

Boosting natural history research via metagenomic clean-up of crowdsourced feces

Srivathsan, Amrita, Nagarajan, Niranjan, Meier, Rudolf

Journal:

Year:

2019

Language:

english

File:

PDF, 2.94 MB

english, 2019

47

Emergence of tigecycline- and eravacycline-resistant tet(X4)-producing Enterobacteriaceae in the gut microbiota of healthy Singaporeans

Ding, Yichen, Saw, Woei-Yuh, Tan, Linda Wei Lin, Moong, Don Kyin Nwe, Nagarajan, Niranjan, Teo, Yik Ying, Seedorf, Henning

Journal:

Journal of Antimicrobial Chemotherapy

Year:

2020

File:

PDF, 373 KB

2020

48

PhyDOSE: Design of follow-up single-cell sequencing experiments of tumors

Weber, Leah L., Aguse, Nuraini, Chia, Nicholas, El-Kebir, Mohammed, Nagarajan, Niranjan

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 5.61 MB

2020

49

Proteomic variations of esophageal squamous cell carcinoma revealed by combining RNA-seq proteogenomics and G-PTM search strategy

Ramesh, Pooja, Nagarajan, Vidhyavathy, Khanchandani, Vartika, Desai, Vasanth Kumar, Niranjan, Vidya

Journal:

Year:

2020

File:

PDF, 668 KB

2020