|
13 Mar 2025
|
BMRC
|
Genome Institute of Singapore
|
A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines
|
Ying Chen,
Nadia M. Davidson,
Yuk Kei Wan,
Fei Yao,
Yan Su,
Hasindu Gamaarachchi,
Andre Sim,
Harshil Patel,
Hwee Meng Low,
Christopher Hendra,
Laura Wratten,
Christopher Hakkaart,
Chelsea Sawyer,
Viktoriia Iakovleva,
Puay Leng Lee,
Lixia Xin,
Hui En Vanessa Ng,
Jia Min Loo,
Xuewen Ong,
Hui Qi Amanda Ng,
Jiaxu Wang,
Wei Qian Casslynn Koh,
Suk Yeah Polly Poon,
Dominik Stanojevic,
Hoang-Dai Tran,
Kok Hao Edwin Lim,
Shen Yon Toh,
Philip Andrew Ewels,
Huck-Hui Ng,
N. Gopalakrishna Iyer,
Alexandre Thiery,
Wee Joo Chng,
Leilei Chen,
Ramanuj DasGupta,
Mile Sikic,
Yun-Shen Chan,
Boon Ooi Patrick Tan,
Yue Wan,
Wai Leong Tam,
Qiang Yu,
Chiea Chuan Khor,
Torsten Wüstefeld,
Alexander Lezhava,
Ploy N. Pratanwanich,
Michael I. Love,
Wee Siong Sho Goh,
Sarah B. Ng,
Alicia Oshlack,
,
N. Gopalakrishna Iyer,
Qiang Yu,
Jonathan Göke
|
Nature Methods
|
|
11 Dec 2023
|
BMRC
|
Genome Institute of Singapore
|
The Helicobacter pylori Genome Project: insights into H. pylori population structure from analysis of a worldwide collection of complete genomes
|
Kaisa Thorell,
Zilia Y. Muñoz-Ramírez,
Difei Wang,
Santiago Sandoval-Motta,
Rajiv Boscolo Agostini,
Silvia Ghirotto,
Roberto C. Torres,
,
Judith Romero-Gallo,
Uma Krishna,
Richard M. Peek,
M. Blanca Piazuelo,
Naïma Raaf,
Federico Bentolila,
Hafeza Aftab,
Junko Akada,
Takashi Matsumoto,
Freddy Haesebrouck,
Rony P. Colanzi,
Thais F. Bartelli,
Diana Noronha Nunes,
Adriane Pelosof,
Claudia Zitron Sztokfisz,
Emmanuel Dias-Neto,
Paulo Pimentel Assumpção,
Ivan Tishkov,
Laure Brigitte Kouitcheu Mabeku,
Karen J. Goodman,
Janis Geary,
Taylor J. Cromarty,
Nancy L. Price,
Douglas Quilty,
Alejandro H. Corvalan,
Carolina A. Serrano,
Robinson Gonzalez,
Arnoldo Riquelme,
Apolinaria García-Cancino,
Cristian Parra-Sepúlveda,
Giuliano Bernal,
Francisco Castillo,
Alisa M. Goldstein,
Nan Hu,
Philip R. Taylor,
Maria Mercedes Bravo,
Alvaro Pazos,
Luis E. Bravo,
Keith T. Wilson,
James G. Fox,
Vanessa Ramírez-Mayorga,
Silvia Molina-Castro,
Sundry Durán-Bermúdez,
Christian Campos-Núñez,
Manuel Chaves-Cervantes,
Evariste Tshibangu-Kabamba,
Ghislain Disashi Tumba,
Antoine Tshimpi-Wola,
Patrick de Jesus Ngoma-Kisoko,
Dieudonné Mumba Ngoyi,
Modesto Cruz,
Celso Hosking,
José Jiménez Abreu,
Christine Varon,
Lucie Benejat,
Ousman Secka,
Alexander Link,
Peter Malfertheiner,
Michael Buenor Adinortey,
Ansumana Sandy Bockarie,
Cynthia Ayefoumi Adinortey,
Eric Gyamerah Ofori,
Dionyssios N. Sgouras,
Beatriz Martinez-Gonzalez,
Spyridon Michopoulos,
Sotirios Georgopoulos,
Elisa Hernandez,
Braulio Volga Tacatic,
Mynor Aguilar,
Ricardo L. Dominguez,
Douglas R. Morgan,
Hjördís Harðardóttir,
Anna Ingibjörg Gunnarsdóttir,
Hallgrímur Guðjónsson,
Jón Gunnlaugur Jónasson,
Einar S. Björnsson,
Mamatha Ballal,
Vignesh Shetty,
Muhammad Miftahussurur,
Titong Sugihartono,
Ricky Indra Alfaray,
Langgeng Agung Waskito,
Kartika Afrida Fauzia,
Ari Fahrial Syam,
Hasan Maulahela,
Reza Malekzadeh,
Masoud Sotoudeh,
Avi Peretz,
Maya Azrad,
Avi On,
Valli De Re,
Stefania Zanussi,
Renato Cannizzaro,
Vincenzo Canzonieri,
Takaya Shimura,
Kengo Tokunaga,
Takako Osaki,
Shigeru Kamiya,
Khaled Jadallah,
Ismail Matalka,
Nurbek Igissinov,
Mariia Satarovna Moldobaeva,
Attokurova Rakhat,
Il Ju Choi,
Jae Gyu Kim,
Nayoung Kim,
Minkyo Song,
Mārcis Leja,
Reinis Vangravs,
Ģirts Šķenders,
Dace Rudzīte,
Aiga Rūdule,
Aigars Vanags,
Ilze Kikuste,
Juozas Kupcinskas,
Jurgita Skieceviciene,
Laimas Jonaitis,
Gediminas Kiudelis,
Paulius Jonaitis,
Vytautas Kiudelis,
Greta Varkalaite,
Jamuna Vadivelu,
Mun Fai Loke,
Kumutha Malar Vellasamy,
Roberto Herrera-Goepfert,
Juan Octavio Alonso-Larraga,
Than Than Yee,
Kyaw Htet,
Takeshi Matsuhisa,
Pradeep Krishna Shrestha,
Shamshul Ansari,
Olumide Abiodun,
Christopher Jemilohun,
Kolawole Oluseyi Akande,
Oluwatosin Olu-Abiodun,
Francis Ajang Magaji,
Ayodele Omotoso,
Chukwuemeka Chukwunwendu Osuagwu,
Uchenna Okonkwo,
Opeyemi O. Owoseni,
Carlos Castaneda,
Miluska Castillo,
Billie Velapatino,
Robert H. Gilman,
Paweł Krzyżek,
Grażyna Gościniak,
Dorota Pawełka,
Izabela Korona-Glowniak,
Halina Cichoz-Lach,
Monica Oleastro,
Ceu Figueiredo,
Jose C. Machado,
Rui M. Ferreira,
Dmitry S. Bordin,
Maria A. Livzan,
Vladislav V. Tsukanov,
Patrick Tan,
Khay Guan Yeoh,
Feng Zhu,
Reid Ally,
Rainer Haas,
Milagrosa Montes,
María Fernández-Reyes,
Esther Tamayo,
Jacobo Lizasoain,
Luis Bujanda,
Sergio Lario,
María José Ramírez-Lázaro,
Xavier Calvet,
Eduard Brunet-Mas,
María José Domper-Arnal,
Sandra García-Mateo,
Daniel Abad-Baroja,
Pedro Delgado-Guillena,
Leticia Moreira,
Josep Botargues,
Isabel Pérez-Martínez,
Eva Barreiro-Alonso,
Virginia Flores,
Javier P. Gisbert,
Edurne Amorena Muro,
Pedro Linares,
Vicente Martin,
Laura Alcoba,
Tania Fleitas-Kanonnikoff,
Hisham N. Altayeb,
Lars Engstrand,
Helena Enroth,
Peter M. Keller,
Karoline Wagner,
Daniel Pohl,
Yi-Chia Lee,
Jyh-Ming Liou,
Ming-Shiang Wu,
Bekir Kocazeybek,
Suat Sarıbas,
İhsan Tasçı,
Süleyman Demiryas,
Nuray Kepil,
Luis Quiel,
Miguel Villagra,
Morgan Norton,
Deborah Johnson,
Robert J. Huang,
Joo Ha Hwang,
Wendy Szymczak,
Saranathan Rajagopalan,
Emmanuel Asare,
William R. Jacobs,
Haejin In,
Roni Bollag,
Aileen Lopez,
Edward J. Kruse,
Joseph White,
David Y. Graham,
Charlotte Lane,
Yang Gao,
Patricia I. Fields,
Benjamin D. Gold,
Marcia Cruz-Correa,
María González-Pons,
Luz M. Rodriguez,
Vo Phuoc Tuan,
Ho Dang Quy Dung,
Tran Thanh Binh,
Tran Thi Huyen Trang,
Vu Van Khien,
Xiongfong Chen,
Castle Raley,
Bailey Kessing,
Yongmei Zhao,
Bao Tran,
Andrés J. Gutiérrez-Escobar,
Yunhu Wan,
Belynda Hicks,
Bin Zhu,
Kai Yu,
Bin Zhu,
Meredith Yeager,
Amy Hutchinson,
Kedest Teshome,
Kristie Jones,
Wen Luo,
Quentin Jehanne,
Yukako Katsura,
Patricio Gonzalez-Hormazabal,
Xavier Didelot,
Sam Sheppard,
Eduardo Tarazona-Santos,
Leonardo Mariño-Ramírez,
John T. Loh,
Steffen Backert,
Michael Naumann,
Christian C. Abnet,
Annemieke Smet,
Douglas E. Berg,
Álvaro Chiner-Oms,
Iñaki Comas,
Francisco José Martínez-Martínez,
Roxana Zamudio,
Philippe Lehours,
Francis Megraud,
Koji Yahara,
Martin J. Blaser,
Tamas Vincze,
Richard D. Morgan,
Richard J. Roberts,
Stephen J. Chanock,
John P. Dekker,
Javier Torres,
Timothy L. Cover,
Mehwish Noureen,
Wolfgang Fischer,
Filipa F. Vale,
Joshua L. Cherry,
Naoki Osada,
Masaki Fukuyo,
Masanori Arita,
Yoshio Yamaoka,
Ichizo Kobayashi,
Ikuo Uchiyama,
Daniel Falush,
M. Constanza Camargo,
Charles S. Rabkin
|
Nature Communications
|
|
29 Nov 2023
|
BMRC
|
Genome Institute of Singapore
|
Identification of constrained sequence elements across 239 primate genomes
|
Lukas F. K. Kuderna,
Jacob C. Ulirsch,
Sabrina Rashid,
Mohamed Ameen,
Laksshman Sundaram,
Glenn Hickey,
Anthony J. Cox,
Hong Gao,
Arvind Kumar,
Francois Aguet,
Matthew J. Christmas,
Hiram Clawson,
Maximilian Haeussler,
Mareike C. Janiak,
Martin Kuhlwilm,
Joseph D. Orkin,
Thomas Bataillon,
Shivakumara Manu,
Alejandro Valenzuela,
Juraj Bergman,
Marjolaine Rouselle,
Felipe Ennes Silva,
Lidia Agueda,
Julie Blanc,
Marta Gut,
Dorien de Vries,
Ian Goodhead,
R. Alan Harris,
Muthuswamy Raveendran,
Axel Jensen,
Idriss S. Chuma,
Julie E. Horvath,
Christina Hvilsom,
David Juan,
Peter Frandsen,
Joshua G. Schraiber,
Fabiano R. de Melo,
Fabrício Bertuol,
Hazel Byrne,
Iracilda Sampaio,
Izeni Farias,
João Valsecchi,
Malu Messias,
Maria N. F. da Silva,
Mihir Trivedi,
Rogerio Rossi,
Tomas Hrbek,
Nicole Andriaholinirina,
Clément J. Rabarivola,
Alphonse Zaramody,
Clifford J. Jolly,
Jane Phillips-Conroy,
Gregory Wilkerson,
Christian Abee,
Joe H. Simmons,
Eduardo Fernandez-Duque,
Sree Kanthaswamy,
Fekadu Shiferaw,
Dongdong Wu,
Long Zhou,
Yong Shao,
Guojie Zhang,
Julius D. Keyyu,
Sascha Knauf,
Minh D. Le,
Esther Lizano,
Stefan Merker,
Arcadi Navarro,
Tilo Nadler,
Chiea Chuen Khor,
Jessica Lee,
Patrick Tan,
Weng Khong Lim,
Andrew C. Kitchener,
Dietmar Zinner,
Ivo Gut,
Amanda D. Melin,
Katerina Guschanski,
Mikkel Heide Schierup,
Robin M. D. Beck,
Ioannis Karakikes,
Kevin C. Wang,
Govindhaswamy Umapathy,
Christian Roos,
Jean P. Boubli,
Adam Siepel,
Anshul Kundaje,
Benedict Paten,
Kerstin Lindblad-Toh,
Jeffrey Rogers,
Tomas Marques Bonet,
Kyle Kai-How Farh
|
Nature
|
|
24 Nov 2023
|
BMRC
|
Genome Institute of Singapore
|
Integrative multiomics enhancer activity profiling identifies therapeutic vulnerabilities in cholangiocarcinoma of different etiologies
|
Jing Han Hong,
Chern Han Yong,
Hong Lee Heng,
Jason Yongsheng Chan,
Mai Chan Lau,
Jianfeng Chen,
Jing Yi Lee,
Abner Herbert Lim,
Zhimei Li,
Peiyong Guan,
Pek Lim Chu,
Arnoud Boot,
Sheng Rong Ng,
Xiaosai Yao,
Felicia Yu Ting Wee,
Jeffrey Chun Tatt Lim,
Wei Liu,
Peili Wang,
Rong Xiao,
Xian Zeng,
Yichen Sun,
Joanna Koh,
Xiu Yi Kwek,
Cedric Chuan Young Ng,
Poramate Klanrit,
Yaojun Zhang,
Jiaming Lai,
David Wai Meng Tai,
Chawalit Pairojkul,
Simona Dima,
Irinel Popescu,
Sen-Yung Hsieh,
Ming-Chin Yu,
Joe Yeong,
Sarinya Kongpetch,
Apinya Jusakul,
Watcharin Loilome,
Patrick Tan,
Jing Tan,
Bin Tean Teh
|
Gut
|
|
2 Jun 2023
|
BMRC
|
Genome Institute of Singapore
|
The landscape of tolerated genetic variation in humans and primates
|
Hong Gao,
Tobias Hamp,
Jeffrey Ede,
Joshua G. Schraiber,
Jeremy McRae,
Moriel Singer-Berk,
Yanshen Yang,
Anastasia S. D. Dietrich,
Petko P. Fiziev,
Lukas F. K. Kuderna,
Laksshman Sundaram,
Yibing Wu,
Aashish Adhikari,
Yair Field,
Chen Chen,
Serafim Batzoglou,
Francois Aguet,
Gabrielle Lemire,
Rebecca Reimers,
Daniel Balick,
Mareike C. Janiak,
Martin Kuhlwilm,
Joseph D. Orkin,
Shivakumara Manu,
Alejandro Valenzuela,
Juraj Bergman,
Marjolaine Rousselle,
Felipe Ennes Silva,
Lidia Agueda,
Julie Blanc,
Marta Gut,
Dorien de Vries,
Ian Goodhead,
R. Alan Harris,
Muthuswamy Raveendran,
Axel Jensen,
Idriss S. Chuma,
Julie E. Horvath,
Christina Hvilsom,
David Juan,
Peter Frandsen,
Fabiano R. de Melo,
Fabrício Bertuol,
Hazel Byrne,
Iracilda Sampaio,
Izeni Farias,
João Valsecchi do Amaral,
Mariluce Messias,
Maria N. F. da Silva,
Mihir Trivedi,
Rogerio Rossi,
Tomas Hrbek,
Nicole Andriaholinirina,
Clément J. Rabarivola,
Alphonse Zaramody,
Clifford J. Jolly,
Jane Phillips-Conroy,
Gregory Wilkerson,
Christian Abee,
Joe H. Simmons,
Eduardo Fernandez-Duque,
Sree Kanthaswamy,
Fekadu Shiferaw,
Dongdong Wu,
Long Zhou,
Yong Shao,
Guojie Zhang,
Julius D. Keyyu,
Sascha Knauf,
Minh D. Le,
Esther Lizano,
Stefan Merker,
Arcadi Navarro,
Thomas Bataillon,
Tilo Nadler,
Chiea Chuen Khor,
Jessica Lee,
Patrick Tan,
Weng Khong Lim,
Andrew C. Kitchener,
Dietmar Zinner,
Ivo Gut,
Amanda Melin,
Katerina Guschanski,
Mikkel Heide Schierup,
Robin M. D. Beck,
Govindhaswamy Umapathy,
Christian Roos,
Jean P. Boubli,
Monkol Lek,
Shamil Sunyaev,
Anne O’Donnell-Luria,
Heidi L. Rehm,
Jinbo Xu,
Jeffrey Rogers,
Tomas Marques-Bonet,
Kyle Kai-How Farh
|
Science
|
|
1 Jun 2023
|
BMRC
|
Genome Institute of Singapore
|
A global catalog of whole-genome diversity from 233 primate species
|
Lukas F. K. Kuderna,
Hong Gao,
Mareike C. Janiak,
Martin Kuhlwilm,
Joseph D. Orkin,
Thomas Bataillon,
Shivakumara Manu,
Alejandro Valenzuela,
Juraj Bergman,
Marjolaine Rousselle,
Felipe Ennes Silva,
Lidia Agueda,
Julie Blanc,
Marta Gut,
Dorien de Vries,
Ian Goodhead,
R. Alan Harris,
Muthuswamy Raveendran,
Axel Jensen,
Idrissa S. Chuma,
Julie E. Horvath,
Christina Hvilsom,
David Juan,
Peter Frandsen,
Joshua G. Schraiber,
Fabiano R. de Melo,
Fabrício Bertuol,
Hazel Byrne,
Iracilda Sampaio,
Izeni Farias,
João Valsecchi,
Malu Messias,
Maria N. F. da Silva,
Mihir Trivedi,
Rogerio Rossi,
Tomas Hrbek,
Nicole Andriaholinirina,
Clément J. Rabarivola,
Alphonse Zaramody,
Clifford J. Jolly,
Jane Phillips-Conroy,
Gregory Wilkerson,
Christian Abee,
Joe H. Simmons,
Eduardo Fernandez-Duque,
Sree Kanthaswamy,
Fekadu Shiferaw,
Dongdong Wu,
Long Zhou,
Yong Shao,
Guojie Zhang,
Julius D. Keyyu,
Sascha Knauf,
Minh D. Le,
Esther Lizano,
Stefan Merker,
Arcadi Navarro,
Tilo Nadler,
Chiea Chuen Khor,
Jessica Lee,
Patrick Tan,
Weng Khong Lim,
Andrew C. Kitchener,
Dietmar Zinner,
Ivo Gut,
Amanda D. Melin,
Katerina Guschanski,
Mikkel Heide Schierup,
Robin M. D. Beck,
Govindhaswamy Umapathy,
Christian Roos,
Jean P. Boubli,
Jeffrey Rogers,
Kyle Kai-How Farh,
Tomas Marques Bonet
|
Science
|
|
19 Jan 2023
|
BMRC
|
Bioinformatics Institute
|
The Singapore National Precision Medicine Strategy
|
Eleanor Wong,
Nicolas Bertin,
Maxime Hebrard,
Roberto Tirado-Magallanes,
Claire Bellis,
Weng Khong Lim,
Chee Yong Chua,
Philomena Mei Lin Tong,
Raymond Chua,
Kenneth Mak,
Tit Meng Lim,
Wei Yang Cheong,
Kwee Eng Thien,
Khean Teik Goh,
Jin-Fang Chai,
Jimmy Lee,
Joseph Jao-Yiu Sung,
Tien Yin Wong,
Calvin Woon Loong Chin,
Peter D. Gluckman,
Liuh Ling Goh,
Kenneth Hon Kim Ban,
Tin Wee Tan,
,
Rob M. van Dam,
Yik Ying Teo,
Marie Loh,
Paul Eillot,
Eng Sing Lee,
Joanne Ngeow,
Elio Riboli,
Rinkoo Dalan,
Irfahan Kassam,
Lakshmi Narayanan Lakshmanan,
Tock Han Lim,
Hong Kiat Ng,
Theresia Mina,
Darwin Tay,
Charumathi Sabanayagam,
Yih Chung Tham,
Tyler Rim,
Tin Aung,
Miao Ling Chee,
Hengtong Li,
Miao Li Chee,
Khung Keong Yeo,
Stuart Alexander Cook,
Chee Jian Pua,
Chengxi Yang,
Yap Seng Chong,
Johan Gunnar Eriksson,
Kok Hian Tan,
Fabian Yap,
Chia Wei Lim,
Pi Kuang Tsai,
Wen Jie Chew,
Wey Ching Sim,
Li-xian Grace Toh,
Clarabelle Bitong Lin,
Yee Yen Sia,
Tat Hung Koh,
Wee Yang Meah,
Joanna Hui Juan Tan,
Justin Jeyakani,
Jack Ow,
Shimin Ang,
Ashar J. Malik,
Dimitar Kenanov,
Xueling Sim,
Ching-Yu Cheng,
Sonia Davila,
Neerja Karnani,
Khai Pang Leong,
Jianjun Liu,
Shyam Prabhakar,
Sebastian Maurer-Stroh,
Chandra Shekhar Verma,
Pavitra Krishnaswamy,
Rick Siow Mong Goh,
Irenaeus Chia,
Clarissa Ho,
Doreen Low,
Suchin Virabhak,
Jacklyn Yong,
Weiling Zheng,
Shih Wee Seow,
Yee Kwang Seck,
Mingshi Koh,
John C. Chambers,
E. Shyong Tai,
Patrick Tan
|
Nature Genetics
|
|
29 Jul 2022
|
SERC
|
Institute for Infocomm Research
|
High-Resolution Digital Phenotypes From Consumer Wearables and Their Applications in Machine Learning of Cardiometabolic Risk Markers: Cohort Study
|
Weizhuang Zhou,
Yu En Chan,
Chuan Sheng Foo,
Jingxian Zhang,
Jing Xian Teo,
Sonia Davila,
Weiting Huang,
Jonathan Yap,
Stuart Cook,
Patrick Tan,
Calvin Woon-Loong Chin,
Khung Keong Yeo,
Weng Khong Lim,
Pavitra Krishnaswamy
|
Journal of Medical Internet Research
|
|
8 Mar 2022
|
BMRC
|
Institute of Molecular and Cell Biology
|
Single-Cell Atlas of Lineage States, Tumor Microenvironment, and Subtype-Specific Expression Programs in Gastric Cancer
|
Vikrant Kumar,
Kalpana Ramnarayanan,
Raghav Sundar,
Nisha Padmanabhan,
Supriya Srivastava,
Mayu Koiwa,
Tadahito Yasuda,
Vivien Koh,
Kie Kyon Huang,
Su Ting Tay,
Shamaine Wei Ting Ho,
Angie Lay Keng Tan,
Takatsugu Ishimoto,
Guowei Kim,
Asim Shabbir,
Qingfeng Chen,
Biyan Zhang,
Shengli Xu,
Kong-Peng Lam,
Huey Yew Jeffrey Lum,
Ming Teh,
Wei Peng Yong,
Jimmy Bok Yan So,
Patrick Tan
|
Cancer Discovery
|
|
25 Aug 2021
|
BMRC
|
Institute of Molecular and Cell Biology
|
Epigenetic promoter alterations in GI tumour immune-editing and resistance to immune checkpoint inhibition
|
Raghav Sundar,
Kie-Kyon Huang,
Vikrant Kumar,
Kalpana Ramnarayanan,
Deniz Demircioğlu,
Zhisheng Her,
Xuewen Ong,
Zul Fazreen Bin Adam Isa,
Manjie Xing,
Angie Lay-Keng Tan,
David Wai Meng Tai,
Su Pin Choo,
Weiwei Zhai,
Jia Qi Lim,
Meghna Das Thakur,
Luciana Molinero,
Edward Cha,
Marcella Fasso,
Monica Niger,
Filippo Pietrantonio,
Jeeyun Lee,
Anand D Jeyasekharan,
Aditi Qamra,
Radhika Patnala,
Arne Fabritius,
Mark De Simone,
Joe Yeong,
Cedric Chuan Young Ng,
Sun Young Rha,
Yukiya Narita,
Kei Muro,
Yu Amanda Guo,
Anders Jacobsen Skanderup,
Jimmy Bok Yan So,
Wei Peng Yong,
Qingfeng Chen,
Jonathan Göke,
Patrick Tan
|
Gut
|