Literature DB >> 25618354

Chemical genomic profiling via barcode sequencing to predict compound mode of action.

Jeff S Piotrowski1, Scott W Simpkins, Sheena C Li, Raamesh Deshpande, Sean J McIlwain, Irene M Ong, Chad L Myers, Charlie Boone, Raymond J Andersen.   

Abstract

Chemical genomics is an unbiased, whole-cell approach to characterizing novel compounds to determine mode of action and cellular target. Our version of this technique is built upon barcoded deletion mutants of Saccharomyces cerevisiae and has been adapted to a high-throughput methodology using next-generation sequencing. Here we describe the steps to generate a chemical genomic profile from a compound of interest, and how to use this information to predict molecular mechanism and targets of bioactive compounds.

Entities:  

Mesh：

Year:  2015        PMID： 25618354      PMCID： PMC4497522          DOI： 10.1007/978-1-4939-2269-7_23

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  14 in total

1.  Chemogenomic profiling: identifying the functional interactions of small molecules in yeast.

Authors:  Guri Giaever; Patrick Flaherty; Jochen Kumm; Michael Proctor; Corey Nislow; Daniel F Jaramillo; Angela M Chu; Michael I Jordan; Adam P Arkin; Ronald W Davis
Journal:  Proc Natl Acad Sci U S A       Date:  2004-01-12       Impact factor: 11.205

2.  Exploring the mode-of-action of bioactive compounds by chemical-genetic profiling in yeast.

Authors:  Ainslie B Parsons; Andres Lopez; Inmar E Givoni; David E Williams; Christopher A Gray; Justin Porter; Gordon Chua; Richelle Sopko; Renee L Brost; Cheuk-Hei Ho; Jiyi Wang; Troy Ketela; Charles Brenner; Julie A Brill; G Esteban Fernandez; Todd C Lorenz; Gregory S Payne; Satoru Ishihara; Yoshikazu Ohya; Brenda Andrews; Timothy R Hughes; Brendan J Frey; Todd R Graham; Raymond J Andersen; Charles Boone
Journal:  Cell       Date:  2006-08-11       Impact factor: 41.582

3.  Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe.

Authors:  Dong-Uk Kim; Jacqueline Hayles; Dongsup Kim; Valerie Wood; Han-Oh Park; Misun Won; Hyang-Sook Yoo; Trevor Duhig; Miyoung Nam; Georgia Palmer; Sangjo Han; Linda Jeffery; Seung-Tae Baek; Hyemi Lee; Young Sam Shim; Minho Lee; Lila Kim; Kyung-Sun Heo; Eun Joo Noh; Ah-Reum Lee; Young-Joo Jang; Kyung-Sook Chung; Shin-Jung Choi; Jo-Young Park; Youngwoo Park; Hwan Mook Kim; Song-Kyu Park; Hae-Joon Park; Eun-Jung Kang; Hyong Bai Kim; Hyun-Sam Kang; Hee-Moon Park; Kyunghoon Kim; Kiwon Song; Kyung Bin Song; Paul Nurse; Kwang-Lae Hoe
Journal:  Nat Biotechnol       Date:  2010-05-16       Impact factor: 54.908

4.  Quantitative phenotyping via deep barcode sequencing.

Authors:  Andrew M Smith; Lawrence E Heisler; Joseph Mellor; Fiona Kaper; Michael J Thompson; Mark Chee; Frederick P Roth; Guri Giaever; Corey Nislow
Journal:  Genome Res       Date:  2009-07-21       Impact factor: 9.043

5.  Unbiased screening of marine sponge extracts for anti-inflammatory agents combined with chemical genomics identifies girolline as an inhibitor of protein synthesis.

Authors:  Shan-Yu Fung; Vladimir Sofiyev; Julia Schneiderman; Aaron F Hirschfeld; Rachel E Victor; Kate Woods; Jeff S Piotrowski; Raamesh Deshpande; Sheena C Li; Nicole J de Voogd; Chad L Myers; Charlie Boone; Raymond J Andersen; Stuart E Turvey
Journal:  ACS Chem Biol       Date:  2013-10-29       Impact factor: 5.100

6.  Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research.

Authors:  Masanari Kitagawa; Takeshi Ara; Mohammad Arifuzzaman; Tomoko Ioka-Nakamichi; Eiji Inamoto; Hiromi Toyonaga; Hirotada Mori
Journal:  DNA Res       Date:  2006-01-09       Impact factor: 4.458

7.  Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples.

Authors:  Andrew M Smith; Lawrence E Heisler; Robert P St Onge; Eveline Farias-Hesson; Iain M Wallace; John Bodeau; Adam N Harris; Kathleen M Perry; Guri Giaever; Nader Pourmand; Corey Nislow
Journal:  Nucleic Acids Res       Date:  2010-05-11       Impact factor: 16.971

8.  Functional profiling of the Saccharomyces cerevisiae genome.

Authors:  Guri Giaever; Angela M Chu; Li Ni; Carla Connelly; Linda Riles; Steeve Véronneau; Sally Dow; Ankuta Lucau-Danila; Keith Anderson; Bruno André; Adam P Arkin; Anna Astromoff; Mohamed El-Bakkoury; Rhonda Bangham; Rocio Benito; Sophie Brachat; Stefano Campanaro; Matt Curtiss; Karen Davis; Adam Deutschbauer; Karl-Dieter Entian; Patrick Flaherty; Francoise Foury; David J Garfinkel; Mark Gerstein; Deanna Gotte; Ulrich Güldener; Johannes H Hegemann; Svenja Hempel; Zelek Herman; Daniel F Jaramillo; Diane E Kelly; Steven L Kelly; Peter Kötter; Darlene LaBonte; David C Lamb; Ning Lan; Hong Liang; Hong Liao; Lucy Liu; Chuanyun Luo; Marc Lussier; Rong Mao; Patrice Menard; Siew Loon Ooi; Jose L Revuelta; Christopher J Roberts; Matthias Rose; Petra Ross-Macdonald; Bart Scherens; Greg Schimmack; Brenda Shafer; Daniel D Shoemaker; Sharon Sookhai-Mahadeo; Reginald K Storms; Jeffrey N Strathern; Giorgio Valle; Marleen Voet; Guido Volckaert; Ching-yun Wang; Teresa R Ward; Julie Wilhelmy; Elizabeth A Winzeler; Yonghong Yang; Grace Yen; Elaine Youngman; Kexin Yu; Howard Bussey; Jef D Boeke; Michael Snyder; Peter Philippsen; Ronald W Davis; Mark Johnston
Journal:  Nature       Date:  2002-07-25       Impact factor: 49.962

9.  The genetic landscape of a cell.

Authors:  Michael Costanzo; Anastasia Baryshnikova; Jeremy Bellay; Yungil Kim; Eric D Spear; Carolyn S Sevier; Huiming Ding; Judice L Y Koh; Kiana Toufighi; Sara Mostafavi; Jeany Prinz; Robert P St Onge; Benjamin VanderSluis; Taras Makhnevych; Franco J Vizeacoumar; Solmaz Alizadeh; Sondra Bahr; Renee L Brost; Yiqun Chen; Murat Cokol; Raamesh Deshpande; Zhijian Li; Zhen-Yuan Lin; Wendy Liang; Michaela Marback; Jadine Paw; Bryan-Joseph San Luis; Ermira Shuteriqi; Amy Hin Yan Tong; Nydia van Dyk; Iain M Wallace; Joseph A Whitney; Matthew T Weirauch; Guoqing Zhong; Hongwei Zhu; Walid A Houry; Michael Brudno; Sasan Ragibizadeh; Balázs Papp; Csaba Pál; Frederick P Roth; Guri Giaever; Corey Nislow; Olga G Troyanskaya; Howard Bussey; Gary D Bader; Anne-Claude Gingras; Quaid D Morris; Philip M Kim; Chris A Kaiser; Chad L Myers; Brenda J Andrews; Charles Boone
Journal:  Science       Date:  2010-01-22       Impact factor: 47.728

10.  Genome-wide analysis of barcoded Saccharomyces cerevisiae gene-deletion mutants in pooled cultures.

Authors:  Sarah E Pierce; Ron W Davis; Corey Nislow; Guri Giaever
Journal:  Nat Protoc       Date:  2007       Impact factor: 13.491
View more
  17 in total

1.  Chemical Genomics, Structure Elucidation, and in Vivo Studies of the Marine-Derived Anticlostridial Ecteinamycin.

Authors:  Thomas P Wyche; René F Ramos Alvarenga; Jeff S Piotrowski; Megan N Duster; Simone R Warrack; Gabriel Cornilescu; Travis J De Wolfe; Yanpeng Hou; Doug R Braun; Gregory A Ellis; Scott W Simpkins; Justin Nelson; Chad L Myers; James Steele; Hirotada Mori; Nasia Safdar; John L Markley; Scott R Rajski; Tim S Bugni
Journal:  ACS Chem Biol       Date:  2017-07-26       Impact factor: 5.100

2.  Coculture of Marine Invertebrate-Associated Bacteria and Interdisciplinary Technologies Enable Biosynthesis and Discovery of a New Antibiotic, Keyicin.

Authors:  Navid Adnani; Marc G Chevrette; Srikar N Adibhatla; Fan Zhang; Qing Yu; Doug R Braun; Justin Nelson; Scott W Simpkins; Bradon R McDonald; Chad L Myers; Jeff S Piotrowski; Christopher J Thompson; Cameron R Currie; Lingjun Li; Scott R Rajski; Tim S Bugni
Journal:  ACS Chem Biol       Date:  2017-11-22       Impact factor: 5.100

3.  Using BEAN-counter to quantify genetic interactions from multiplexed barcode sequencing experiments.

Authors:  Scott W Simpkins; Raamesh Deshpande; Justin Nelson; Sheena C Li; Jeff S Piotrowski; Henry Neil Ward; Yoko Yashiroda; Hiroyuki Osada; Minoru Yoshida; Charles Boone; Chad L Myers
Journal:  Nat Protoc       Date:  2019-02       Impact factor: 13.491

4.  Decyl Gallate as a Possible Inhibitor of N-Glycosylation Process in Paracoccidioides lutzii.

Authors:  Ana Carolina Alves de Paula E Silva; Haroldo Cesar de Oliveira; Liliana Scorzoni; Caroline Maria Marcos; Claudia Tavares Dos Santos; Ana Marisa Fusco-Almeida; Ana Carolina Guerta Salina; Alexandra Ivo Medeiros; Fausto Almeida; Sheena Claire Li; Charles Boone; Maria J S Mendes-Giannini
Journal:  Antimicrob Agents Chemother       Date:  2019-10-22       Impact factor: 5.191

5.  A New Natural Product Analog of Blasticidin S Reveals Cellular Uptake Facilitated by the NorA Multidrug Transporter.

Authors:  Jack R Davison; Katheryn M Lohith; Xiaoning Wang; Kostyantyn Bobyk; Sivakoteswara R Mandadapu; Su-Lin Lee; Regina Cencic; Justin Nelson; Scott Simpkins; Karen M Frank; Jerry Pelletier; Chad L Myers; Jeff Piotrowski; Harold E Smith; Carole A Bewley
Journal:  Antimicrob Agents Chemother       Date:  2017-05-24       Impact factor: 5.191

6.  Leveraging Genetic-Background Effects in Saccharomyces cerevisiae To Improve Lignocellulosic Hydrolysate Tolerance.

Authors:  Maria Sardi; Nikolay Rovinskiy; Yaoping Zhang; Audrey P Gasch
Journal:  Appl Environ Microbiol       Date:  2016-09-16       Impact factor: 4.792

7.  A global genetic interaction network maps a wiring diagram of cellular function.

Authors:  Michael Costanzo; Benjamin VanderSluis; Elizabeth N Koch; Anastasia Baryshnikova; Carles Pons; Guihong Tan; Wen Wang; Matej Usaj; Julia Hanchard; Susan D Lee; Vicent Pelechano; Erin B Styles; Maximilian Billmann; Jolanda van Leeuwen; Nydia van Dyk; Zhen-Yuan Lin; Elena Kuzmin; Justin Nelson; Jeff S Piotrowski; Tharan Srikumar; Sondra Bahr; Yiqun Chen; Raamesh Deshpande; Christoph F Kurat; Sheena C Li; Zhijian Li; Mojca Mattiazzi Usaj; Hiroki Okada; Natasha Pascoe; Bryan-Joseph San Luis; Sara Sharifpoor; Emira Shuteriqi; Scott W Simpkins; Jamie Snider; Harsha Garadi Suresh; Yizhao Tan; Hongwei Zhu; Noel Malod-Dognin; Vuk Janjic; Natasa Przulj; Olga G Troyanskaya; Igor Stagljar; Tian Xia; Yoshikazu Ohya; Anne-Claude Gingras; Brian Raught; Michael Boutros; Lars M Steinmetz; Claire L Moore; Adam P Rosebrock; Amy A Caudy; Chad L Myers; Brenda Andrews; Charles Boone
Journal:  Science       Date:  2016-09-23       Impact factor: 47.728

8.  Ecological and Genetic Barriers Differentiate Natural Populations of Saccharomyces cerevisiae.

Authors:  Katie J Clowers; Justin Heilberger; Jeff S Piotrowski; Jessica L Will; Audrey P Gasch
Journal:  Mol Biol Evol       Date:  2015-05-06       Impact factor: 16.240

9.  Mechanism of imidazolium ionic liquids toxicity in Saccharomyces cerevisiae and rational engineering of a tolerant, xylose-fermenting strain.

Authors:  Quinn Dickinson; Scott Bottoms; Li Hinchman; Sean McIlwain; Sheena Li; Chad L Myers; Charles Boone; Joshua J Coon; Alexander Hebert; Trey K Sato; Robert Landick; Jeff S Piotrowski
Journal:  Microb Cell Fact       Date:  2016-01-20       Impact factor: 5.328

10.  Controlling microbial contamination during hydrolysis of AFEX-pretreated corn stover and switchgrass: effects on hydrolysate composition, microbial response and fermentation.

Authors:  Jose Serate; Dan Xie; Edward Pohlmann; Charles Donald; Mahboubeh Shabani; Li Hinchman; Alan Higbee; Mick Mcgee; Alex La Reau; Grace E Klinger; Sheena Li; Chad L Myers; Charles Boone; Donna M Bates; Dave Cavalier; Dustin Eilert; Lawrence G Oates; Gregg Sanford; Trey K Sato; Bruce Dale; Robert Landick; Jeff Piotrowski; Rebecca Garlock Ong; Yaoping Zhang
Journal:  Biotechnol Biofuels       Date:  2015-11-14       Impact factor: 6.040
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.