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publications.yml
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scholar_user: s65iHisAAAAJ
author_name: Niranjan Nagarajan
publications:
- title: Fast and accurate de novo genome assembly from long uncorrected reads
authors:
- Robert Vaser
- Ivan Sović
- Niranjan Nagarajan
- Mile Šikić
keywords: []
doi: https://doi.org/10.1101/gr.214270.116
- title: Comprehensive characterization of cancer driver genes and mutations
authors:
- Matthew H Bailey
- Collin Tokheim
- Eduard Porta-Pardo
- Sohini Sengupta
- Denis Bertrand
- Amila Weerasinghe
- Antonio Colaprico
- Michael C Wendl
- Jaegil Kim
- Brendan Reardon
- Patrick Kwok-Shing Ng
- Kang Jin Jeong
- Song Cao
- Zixing Wang
- Jianjiong Gao
- Qingsong Gao
- Fang Wang
- Eric Minwei Liu
- Loris Mularoni
- Carlota Rubio-Perez
- Niranjan Nagarajan
- Isidro Cortés-Ciriano
- Daniel Cui Zhou
- Wen-Wei Liang
- Julian M Hess
- Venkata D Yellapantula
- David Tamborero
- Abel Gonzalez-Perez
- Chayaporn Suphavilai
- Jia Yu Ko
- Ekta Khurana
- Peter J Park
- Eliezer M Van Allen
- Han Liang
- Samantha J Caesar-Johnson
- John A Demchok
- Ina Felau
- Melpomeni Kasapi
- Martin L Ferguson
- Carolyn M Hutter
- Heidi J Sofia
- Roy Tarnuzzer
- Zhining Wang
- Liming Yang
- Jean C Zenklusen
- Jiashan Julia Zhang
- Sudha Chudamani
- Jia Liu
- Laxmi Lolla
- Rashi Naresh
- Todd Pihl
- Qiang Sun
- Yunhu Wan
- Ye Wu
- Juok Cho
- Timothy DeFreitas
- Scott Frazer
- Nils Gehlenborg
- Gad Getz
- David I Heiman
- Michael S Lawrence
- Pei Lin
- Sam Meier
- Michael S Noble
- Gordon Saksena
- Doug Voet
- Hailei Zhang
- Brady Bernard
- Nyasha Chambwe
- Varsha Dhankani
- Theo Knijnenburg
- Roger Kramer
- Kalle Leinonen
- Yuexin Liu
- Michael Miller
- Sheila Reynolds
- Ilya Shmulevich
- Vesteinn Thorsson
- Wei Zhang
- Rehan Akbani
- Bradley M Broom
- Apurva M Hegde
- Zhenlin Ju
- Rupa S Kanchi
- Anil Korkut
- Jun Li
- Shiyun Ling
- Wenbin Liu
- Yiling Lu
- Gordon B Mills
- Kwok-Shing Ng
- Arvind Rao
- Michael Ryan
- Jing Wang
- John N Weinstein
- Jiexin Zhang
- Adam Abeshouse
- Joshua Armenia
- Debyani Chakravarty
- Walid K Chatila
- Ino de Bruijn
- Benjamin E Gross
- Zachary J Heins
- Ritika Kundra
- Konnor La
- Marc Ladanyi
- Augustin Luna
- Moriah G Nissan
- Angelica Ochoa
- Sarah M Phillips
- Ed Reznik
- Francisco Sanchez-Vega
- Chris Sander
- Nikolaus Schultz
- Robert Sheridan
- S Onur Sumer
- Yichao Sun
- Barry S Taylor
- Jioajiao Wang
- Hongxin Zhang
- Pavana Anur
- Myron Peto
- Paul Spellman
- Christopher Benz
- Joshua M Stuart
- Christopher K Wong
- Christina Yau
- D Neil Hayes
- Joel S Parker
- Matthew D Wilkerson
- Adrian Ally
- Miruna Balasundaram
- Reanne Bowlby
- Denise Brooks
- Rebecca Carlsen
- Eric Chuah
- Noreen Dhalla
- Robert Holt
- Steven JM Jones
- Katayoon Kasaian
- Darlene Lee
- Yussanne Ma
- Marco A Marra
- Michael Mayo
- Richard A Moore
- Andrew J Mungall
- Karen Mungall
- A Gordon Robertson
- Sara Sadeghi
- Jacqueline E Schein
keywords: []
doi: https://doi.org/10.1016/j.cell.2018.02.060
- title: Statistical methods for detecting differentially abundant features in clinical
metagenomic samples
authors:
- James Robert White
- Niranjan Nagarajan
- Mihai Pop
keywords: []
doi: https://doi.org/10.1371/journal.pcbi.1000352
- title: 'LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering
cell-population heterogeneity from high-throughput sequencing datasets'
authors:
- Andreas Wilm
- Pauline Poh Kim Aw
- Denis Bertrand
- Grace Hui Ting Yeo
- Swee Hoe Ong
- Chang Hua Wong
- Chiea Chuen Khor
- Rosemary Petric
- Martin Lloyd Hibberd
- Niranjan Nagarajan
keywords: []
doi: https://doi.org/10.1093/nar/gks918
- title: The draft genome of the transgenic tropical fruit tree papaya (Carica papaya
Linnaeus)
authors:
- Ray Ming
- Shaobin Hou
- Yun Feng
- Qingyi Yu
- Alexandre Dionne-Laporte
- Jimmy H Saw
- Pavel Senin
- Wei Wang
- Benjamin V Ly
- Kanako LT Lewis
- Steven L Salzberg
- Lu Feng
- Meghan R Jones
- Rachel L Skelton
- Jan E Murray
- Cuixia Chen
- Wubin Qian
- Junguo Shen
- Peng Du
- Moriah Eustice
- Eric Tong
- Haibao Tang
- Eric Lyons
- Robert E Paull
- Todd P Michael
- Kerr Wall
- Danny W Rice
- Henrik Albert
- Ming-Li Wang
- Yun J Zhu
- Michael Schatz
- Niranjan Nagarajan
- Ricelle A Acob
- Peizhu Guan
- Andrea Blas
- Ching Man Wai
- Christine M Ackerman
- Yan Ren
- Chao Liu
- Jianmei Wang
- Jianping Wang
- Jong-Kuk Na
- Eugene V Shakirov
- Brian Haas
- Jyothi Thimmapuram
- David Nelson
- Xiyin Wang
- John E Bowers
- Andrea R Gschwend
- Arthur L Delcher
- Ratnesh Singh
- Jon Y Suzuki
- Savarni Tripathi
- Kabi Neupane
- Hairong Wei
- Beth Irikura
- Maya Paidi
- Ning Jiang
- Wenli Zhang
- Gernot Presting
- Aaron Windsor
- Rafael Navajas-Pérez
- Manuel J Torres
- F Alex Feltus
- Brad Porter
- Yingjun Li
- A Max Burroughs
- Ming-Cheng Luo
- Lei Liu
- David A Christopher
- Stephen M Mount
- Paul H Moore
- Tak Sugimura
- Jiming Jiang
- Mary A Schuler
- Vikki Friedman
- Thomas Mitchell-Olds
- Dorothy E Shippen
- Claude W Depamphilis
- Jeffrey D Palmer
- Michael Freeling
- Andrew H Paterson
- Dennis Gonsalves
- Lei Wang
- Maqsudul Alam
keywords: []
doi: https://doi.org/10.1038/nature06856
- title: The draft genome of sweet orange (Citrus sinensis)
authors:
- Qiang Xu
- Ling-Ling Chen
- Xiaoan Ruan
- Dijun Chen
- Andan Zhu
- Chunli Chen
- Denis Bertrand
- Wen-Biao Jiao
- Bao-Hai Hao
- Matthew P Lyon
- Jiongjiong Chen
- Song Gao
- Feng Xing
- Hong Lan
- Ji-Wei Chang
- Xianhong Ge
- Yang Lei
- Qun Hu
- Yin Miao
- Lun Wang
- Shixin Xiao
- Manosh Kumar Biswas
- Wenfang Zeng
- Fei Guo
- Hongbo Cao
- Xiaoming Yang
- Xi-Wen Xu
- Yun-Jiang Cheng
- Juan Xu
- Ji-Hong Liu
- Oscar Junhong Luo
- Zhonghui Tang
- Wen-Wu Guo
- Hanhui Kuang
- Hong-Yu Zhang
- Mikeal L Roose
- Niranjan Nagarajan
- Xiu-Xin Deng
- Yijun Ruan
keywords: []
doi: https://doi.org/10.1038/ng.2472
- title: Critical assessment of metagenome interpretation—a benchmark of metagenomics
software
authors:
- Alexander Sczyrba
- Peter Hofmann
- Peter Belmann
- David Koslicki
- Stefan Janssen
- Johannes Dröge
- Ivan Gregor
- Stephan Majda
- Jessika Fiedler
- Eik Dahms
- Andreas Bremges
- Adrian Fritz
- Ruben Garrido-Oter
- Tue Sparholt Jørgensen
- Nicole Shapiro
- Philip D Blood
- Alexey Gurevich
- Yang Bai
- Dmitrij Turaev
- Matthew Z DeMaere
- Rayan Chikhi
- Niranjan Nagarajan
- Christopher Quince
- Fernando Meyer
- Monika Balvočiūtė
- Lars Hestbjerg Hansen
- Søren J Sørensen
- Burton KH Chia
- Bertrand Denis
- Jeff L Froula
- Zhong Wang
- Robert Egan
- Dongwan Don Kang
- Jeffrey J Cook
- Charles Deltel
- Michael Beckstette
- Claire Lemaitre
- Pierre Peterlongo
- Guillaume Rizk
- Dominique Lavenier
- Yu-Wei Wu
- Steven W Singer
- Chirag Jain
- Marc Strous
- Heiner Klingenberg
- Peter Meinicke
- Michael D Barton
- Thomas Lingner
- Hsin-Hung Lin
- Yu-Chieh Liao
- Genivaldo Gueiros Z Silva
- Daniel A Cuevas
- Robert A Edwards
- Surya Saha
- Vitor C Piro
- Bernhard Y Renard
- Mihai Pop
- Hans-Peter Klenk
- Markus Göker
- Nikos C Kyrpides
- Tanja Woyke
- Julia A Vorholt
- Paul Schulze-Lefert
- Edward M Rubin
- Aaron E Darling
- Thomas Rattei
- Alice C McHardy
keywords: []
doi: https://doi.org/10.1038/nmeth.4458
- title: Genome mapping on nanochannel arrays for structural variation analysis and
sequence assembly
authors:
- Ernest T Lam
- Alex Hastie
- Chin Lin
- Dean Ehrlich
- Somes K Das
- Michael D Austin
- Paru Deshpande
- Han Cao
- Niranjan Nagarajan
- Ming Xiao
- Pui-Yan Kwok
keywords: []
doi: https://doi.org/10.1038/nbt.2303
- title: Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations
in cell adhesion and chromatin remodeling genes
authors:
- Zhi Jiang Zang
- Ioana Cutcutache
- Song Ling Poon
- Shen Li Zhang
- John R McPherson
- Jiong Tao
- Vikneswari Rajasegaran
- Hong Lee Heng
- Niantao Deng
- Anna Gan
- Kiat Hon Lim
- Choon Kiat Ong
- DaChuan Huang
- Sze Yung Chin
- Iain Beehuat Tan
- Cedric Chuan Young Ng
- Willie Yu
- Yingting Wu
- Minghui Lee
- Jeanie Wu
- Dianne Poh
- Wei Keat Wan
- Sun Young Rha
- Jimmy So
- Manuel Salto-Tellez
- Khay Guan Yeoh
- Wai Keong Wong
- Yi-Jun Zhu
- P Andrew Futreal
- Brendan Pang
- Yijun Ruan
- Axel M Hillmer
- Denis Bertrand
- Niranjan Nagarajan
- Steve Rozen
- Bin Tean Teh
- Patrick Tan
keywords: []
doi: https://doi.org/10.1038/ng.2246
- title: A common BIM deletion polymorphism mediates intrinsic resistance and inferior
responses to tyrosine kinase inhibitors in cancer
authors:
- King Pan Ng
- Axel M Hillmer
- Charles TH Chuah
- Wen Chun Juan
- Tun Kiat Ko
- Audrey SM Teo
- Pramila N Ariyaratne
- Naoto Takahashi
- Kenichi Sawada
- Yao Fei
- Sheila Soh
- Wah Heng Lee
- John WJ Huang
- John C Allen Jr
- Xing Yi Woo
- Niranjan Nagarajan
- Vikrant Kumar
- Anbupalam Thalamuthu
- Wan Ting Poh
- Ai Leen Ang
- Hae Tha Mya
- Gee Fung How
- Li Yi Yang
- Liang Piu Koh
- Balram Chowbay
- Chia-Tien Chang
- Veera S Nadarajan
- Wee Joo Chng
- Hein Than
- Lay Cheng Lim
- Yeow Tee Goh
- Shenli Zhang
- Dianne Poh
- Patrick Tan
- Ju-Ee Seet
- Mei-Kim Ang
- Noan-Minh Chau
- Quan-Sing Ng
- Daniel SW Tan
- Manabu Soda
- Kazutoshi Isobe
- Markus M Nöthen
- Tien Y Wong
- Atif Shahab
- Xiaoan Ruan
- Valère Cacheux-Rataboul
- Wing-Kin Sung
- Eng Huat Tan
- Yasushi Yatabe
- Hiroyuki Mano
- Ross A Soo
- Tan Min Chin
- Wan-Teck Lim
- Yijun Ruan
- S Tiong Ong
keywords: []
doi: https://doi.org/10.1038/nm.2713
- title: Sequence assembly demystified
authors:
- Niranjan Nagarajan
- Mihai Pop
keywords: []
doi: https://doi.org/10.1038/nrg3367
- title: Fast and sensitive mapping of nanopore sequencing reads with GraphMap
authors:
- Ivan Sović
- Mile Šikić
- Andreas Wilm
- Shannon Nicole Fenlon
- Swaine Chen
- Niranjan Nagarajan
keywords: []
doi: https://doi.org/10.1038/ncomms11307
- title: Perspective on oncogenic processes at the end of the beginning of cancer
genomics
authors:
- Li Ding
- Matthew H Bailey
- Eduard Porta-Pardo
- Vesteinn Thorsson
- Antonio Colaprico
- Denis Bertrand
- David L Gibbs
- Amila Weerasinghe
- Kuan-lin Huang
- Collin Tokheim
- Isidro Cortés-Ciriano
- Reyka Jayasinghe
- Feng Chen
- Lihua Yu
- Sam Sun
- Catharina Olsen
- Jaegil Kim
- Alison M Taylor
- Andrew D Cherniack
- Rehan Akbani
- Chayaporn Suphavilai
- Niranjan Nagarajan
- Joshua M Stuart
- Gordon B Mills
- Matthew A Wyczalkowski
- Benjamin G Vincent
- Carolyn M Hutter
- Jean Claude Zenklusen
- Katherine A Hoadley
- Michael C Wendl
- Alexander J Lazar
- David A Wheeler
- Gad Getz
- Samantha J Caesar-Johnson
- John A Demchok
- Ina Felau
- Melpomeni Kasapi
- Martin L Ferguson
- Heidi J Sofia
- Roy Tarnuzzer
- Zhining Wang
- Liming Yang
- Jean C Zenklusen
- Jiashan Julia Zhang
- Sudha Chudamani
- Jia Liu
- Laxmi Lolla
- Rashi Naresh
- Todd Pihl
- Qiang Sun
- Yunhu Wan
- Ye Wu
- Juok Cho
- Timothy DeFreitas
- Scott Frazer
- Nils Gehlenborg
- David I Heiman
- Michael S Lawrence
- Pei Lin
- Sam Meier
- Michael S Noble
- Gordon Saksena
- Doug Voet
- Hailei Zhang
- Brady Bernard
- Nyasha Chambwe
- Varsha Dhankani
- Theo Knijnenburg
- Roger Kramer
- Kalle Leinonen
- Yuexin Liu
- Michael Miller
- Sheila Reynolds
- Ilya Shmulevich
- Wei Zhang
- Bradley M Broom
- Apurva M Hegde
- Zhenlin Ju
- Rupa S Kanchi
- Anil Korkut
- Jun Li
- Han Liang
- Shiyun Ling
- Wenbin Liu
- Yiling Lu
- Kwok-Shing Ng
- Arvind Rao
- Michael Ryan
- Jing Wang
- John N Weinstein
- Jiexin Zhang
- Adam Abeshouse
- Joshua Armenia
- Debyani Chakravarty
- Walid K Chatila
- Ino de Bruijn
- Jianjiong Gao
- Benjamin E Gross
- Zachary J Heins
- Ritika Kundra
- Konnor La
- Marc Ladanyi
- Augustin Luna
- Moriah G Nissan
- Angelica Ochoa
- Sarah M Phillips
- Ed Reznik
- Francisco Sanchez-Vega
- Chris Sander
- Nikolaus Schultz
- Robert Sheridan
- S Onur Sumer
- Yichao Sun
- Barry S Taylor
- Jioajiao Wang
- Hongxin Zhang
- Pavana Anur
- Myron Peto
- Paul Spellman
- Christopher Benz
- Christopher K Wong
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