Publications by authors named "Ugrappa Nagalakshmi"

16Publications

Multiplexed heritable gene editing using RNA viruses and mobile single guide RNAs.

Nat Plants 2020 06 1;6(6):620-624. Epub 2020 Jun 1.

Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41477-020-0670-yDOI Listing
June 2020

TurboID-Based Proximity Labeling for In Planta Identification of Protein-Protein Interaction Networks.

J Vis Exp 2020 05 17(159). Epub 2020 May 17.

Department of Plant Biology, College of Biological Sciences, University of California, Davis; Genome Center, College of Biological Sciences, University of California, Davis;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3791/60728DOI Listing
May 2020

Plant NLR immune receptor Tm-22 activation requires NB-ARC domain-mediated self-association of CC domain.

PLoS Pathog 2020 04 27;16(4):e1008475. Epub 2020 Apr 27.

MOE Key Laboratory of Bioinformatics, Center for Plant Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.ppat.1008475DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7205312PMC
April 2020

βC1 Protein Induces Autophagy by Disrupting the Interaction of Autophagy-Related Protein 3 with Glyceraldehyde-3-Phosphate Dehydrogenases.

Plant Cell 2020 04 12;32(4):1124-1135. Epub 2020 Feb 12.

MOE Key Laboratory of Bioinformatics, Center for Plant Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, 100084 Beijing, China

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1105/tpc.19.00759DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145496PMC
April 2020

TurboID-based proximity labeling reveals that UBR7 is a regulator of N NLR immune receptor-mediated immunity.

Nat Commun 2019 07 19;10(1):3252. Epub 2019 Jul 19.

Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, 95616, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-019-11202-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6642208PMC
July 2019

Perspectives on intracellular perception of plant viruses.

Mol Plant Pathol 2019 09 8;20(9):1185-1190. Epub 2019 Jul 8.

Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, CA, 95616, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/mpp.12839DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6715608PMC
September 2019

Novel Functional Genomics Approaches: A Promising Future in the Combat Against Plant Viruses.

Phytopathology 2016 10 16;106(10):1231-1239. Epub 2016 Aug 16.

First author: Department of Biological Sciences, Delaware State University, Dover; second author: Department of Plant Biology, College of Biological Sciences, University of California, Davis; and third author: Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1094/PHYTO-03-16-0145-FIDOI Listing
October 2016

RNA sequencing.

Methods Mol Biol 2011 ;759:125-32

Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-61779-173-4_8DOI Listing
December 2011

RNA-Seq: a method for comprehensive transcriptome analysis.

Curr Protoc Mol Biol 2010 Jan;Chapter 4:Unit 4.11.1-13

Molecular, Cellular, and Developmental Biology Department, Yale University, New Haven, Connecticut, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/0471142727.mb0411s89DOI Listing
January 2010

Mismatch oligonucleotides in human and yeast: guidelines for probe design on tiling microarrays.

BMC Genomics 2008 Dec 31;9:635. Epub 2008 Dec 31.

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2164-9-635DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2642824PMC
December 2008

The transcriptional landscape of the yeast genome defined by RNA sequencing.

Science 2008 Jun 1;320(5881):1344-9. Epub 2008 May 1.

Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.1158441DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2951732PMC
June 2008

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007