Robert R Kitchen

The Dynamic Platelet Transcriptome in Obesity and Weight Loss.

Authors:

Marzieh Ezzaty Mirhashemi Ravi V Shah Robert R Kitchen Jian Rong Aferdita Spahillari Alexander R Pico Olga Vitseva Daniel Levy Danielle Demarco Sajani Shah Mark D Iafrati Martin G Larson Kahraman Tanriverdi Jane E Freedman

Arterioscler Thromb Vasc Biol 2020 Dec 10:ATVBAHA120315186. Epub 2020 Dec 10.

Division of Cardiovascular Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester (M.E.M., O.V., K.T., J.E.F.).

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December 2020

Exploring Predictors of Response to Dacomitinib in -Amplified Recurrent Glioblastoma.

JCO Precis Oncol 2020 8;4. Epub 2020 Jun 8.

Massachusetts General Hospital and Harvard Medical School, Boston, MA.

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June 2020

exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profiling.

Authors:

Joel Rozowsky Robert R Kitchen Jonathan J Park Timur R Galeev James Diao Jonathan Warrell William Thistlethwaite Sai L Subramanian Aleksandar Milosavljevic Mark Gerstein

Cell Syst 2019 04 4;8(4):352-357.e3. Epub 2019 Apr 4.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Department of Computer Science, Yale University, New Haven, CT, USA. Electronic address:

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April 2019

exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids.

Authors:

Oscar D Murillo William Thistlethwaite Joel Rozowsky Sai Lakshmi Subramanian Rocco Lucero Neethu Shah Andrew R Jackson Srimeenakshi Srinivasan Allen Chung Clara D Laurent Robert R Kitchen Timur Galeev Jonathan Warrell James A Diao Joshua A Welsh Kristina Hanspers Anders Riutta Sebastian Burgstaller-Muehlbacher Ravi V Shah Ashish Yeri Lisa M Jenkins Mehmet E Ahsen Carlos Cordon-Cardo Navneet Dogra Stacey M Gifford Joshua T Smith Gustavo Stolovitzky Ashutosh K Tewari Benjamin H Wunsch Kamlesh K Yadav Kirsty M Danielson Justyna Filant Courtney Moeller Parham Nejad Anu Paul Bridget Simonson David K Wong Xuan Zhang Leonora Balaj Roopali Gandhi Anil K Sood Roger P Alexander Liang Wang Chunlei Wu David T W Wong David J Galas Kendall Van Keuren-Jensen Tushar Patel Jennifer C Jones Saumya Das Kei-Hoi Cheung Alexander R Pico Andrew I Su Robert L Raffai Louise C Laurent Matthew E Roth Mark B Gerstein Aleksandar Milosavljevic

Cell 2019 04;177(2):463-477.e15

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address:

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April 2019

Integrative functional genomic analysis of human brain development and neuropsychiatric risks.

Science 2018 12;362(6420)

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December 2018

Isoform-Level Interpretation of High-Throughput Proteomics Data Enabled by Deep Integration with RNA-seq.

Authors:

Becky C Carlyle Robert R Kitchen Jing Zhang Rashaun S Wilson Tukiet T Lam Joel S Rozowsky Kenneth R Williams Nenad Sestan Mark B Gerstein Angus C Nairn

J Proteome Res 2018 10 6;17(10):3431-3444. Epub 2018 Sep 6.

Department of Psychiatry , Yale School of Medicine, Connecticut Mental Health Center , 34 Park Street , New Haven , Connecticut 06519 , United States.

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October 2018

A multiregional proteomic survey of the postnatal human brain.

Authors:

Becky C Carlyle Robert R Kitchen Jean E Kanyo Edward Z Voss Mihovil Pletikos André M M Sousa TuKiet T Lam Mark B Gerstein Nenad Sestan Angus C Nairn

Nat Neurosci 2017 Dec 13;20(12):1787-1795. Epub 2017 Nov 13.

Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.

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December 2017

Molecular and cellular reorganization of neural circuits in the human lineage.

Science 2017 11;358(6366):1027-1032

Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA.

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November 2017

Extending gene ontology in the context of extracellular RNA and vesicle communication.

J Biomed Semantics 2016 12;7:19. Epub 2016 Apr 12.

Department of Reproductive Medicine, University of California, San Diego, La Jolla, CA USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ

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October 2016

The PsychENCODE project.

Authors:

Schahram Akbarian Chunyu Liu James A Knowles Flora M Vaccarino Peggy J Farnham Gregory E Crawford Andrew E Jaffe Dalila Pinto Stella Dracheva Daniel H Geschwind Jonathan Mill Angus C Nairn Alexej Abyzov Sirisha Pochareddy Shyam Prabhakar Sherman Weissman Patrick F Sullivan Matthew W State Zhiping Weng Mette A Peters Kevin P White Mark B Gerstein Anahita Amiri Chris Armoskus Allison E Ashley-Koch Taejeong Bae Andrea Beckel-Mitchener Benjamin P Berman Gerhard A Coetzee Gianfilippo Coppola Nancy Francoeur Menachem Fromer Robert Gao Kay Grennan Jennifer Herstein David H Kavanagh Nikolay A Ivanov Yan Jiang Robert R Kitchen Alexey Kozlenkov Marija Kundakovic Mingfeng Li Zhen Li Shuang Liu Lara M Mangravite Eugenio Mattei Eirene Markenscoff-Papadimitriou Fábio C P Navarro Nicole North Larsson Omberg David Panchision Neelroop Parikshak Jeremie Poschmann Amanda J Price Michael Purcaro Timothy E Reddy Panos Roussos Shannon Schreiner Soraya Scuderi Robert Sebra Mikihito Shibata Annie W Shieh Mario Skarica Wenjie Sun Vivek Swarup Amber Thomas Junko Tsuji Harm van Bakel Daifeng Wang Yongjun Wang Kai Wang Donna M Werling A Jeremy Willsey Heather Witt Hyejung Won Chloe C Y Wong Gregory A Wray Emily Y Wu Xuming Xu Lijing Yao Geetha Senthil Thomas Lehner Pamela Sklar Nenad Sestan

Nat Neurosci 2015 Dec;18(12):1707-12

Yale University, New Haven, Connecticut, USA.

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December 2015

Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry.

Authors:

Erin E Duffy Michael Rutenberg-Schoenberg Catherine D Stark Robert R Kitchen Mark B Gerstein Matthew D Simon

Mol Cell 2015 Sep;59(5):858-66

Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA. Electronic address:

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September 2015

Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies.

Authors:

Sai Lakshmi Subramanian Robert R Kitchen Roger Alexander Bob S Carter Kei-Hoi Cheung Louise C Laurent Alexander Pico Lewis R Roberts Matthew E Roth Joel S Rozowsky Andrew I Su Mark B Gerstein Aleksandar Milosavljevic

J Extracell Vesicles 2015 28;4:27497. Epub 2015 Aug 28.

Bioinformatics Research Laboratory, Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA;

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August 2015

Development of a highly automated and multiplexed targeted proteome pipeline and assay for 112 rat brain synaptic proteins.

Authors:

Christopher M Colangelo Gordana Ivosev Lisa Chung Thomas Abbott Mark Shifman Fumika Sakaue David Cox Robert R Kitchen Lyle Burton Stephen A Tate Erol Gulcicek Ron Bonner Jesse Rinehart Angus C Nairn Kenneth R Williams

Proteomics 2015 Apr 12;15(7):1202-14. Epub 2015 Feb 12.

Yale/NIDA Neuroproteomics Center, New Haven, CT, USA; W.M. Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.

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April 2015

Decoding neuroproteomics: integrating the genome, translatome and functional anatomy.

Authors:

Robert R Kitchen Joel S Rozowsky Mark B Gerstein Angus C Nairn

Nat Neurosci 2014 Nov 28;17(11):1491-9. Epub 2014 Oct 28.

Division of Molecular Psychiatry, Abraham Ribicoff Research Facilities, Connecticut Mental Health Center, Yale University School of Medicine, New Haven, Connecticut, USA.

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November 2014

Comparative analysis of the transcriptome across distant species.

Authors:

Mark B Gerstein Joel Rozowsky Koon-Kiu Yan Daifeng Wang Chao Cheng James B Brown Carrie A Davis LaDeana Hillier Cristina Sisu Jingyi Jessica Li Baikang Pei Arif O Harmanci Michael O Duff Sarah Djebali Roger P Alexander Burak H Alver Raymond Auerbach Kimberly Bell Peter J Bickel Max E Boeck Nathan P Boley Benjamin W Booth Lucy Cherbas Peter Cherbas Chao Di Alex Dobin Jorg Drenkow Brent Ewing Gang Fang Megan Fastuca Elise A Feingold Adam Frankish Guanjun Gao Peter J Good Roderic Guigó Ann Hammonds Jen Harrow Roger A Hoskins Cédric Howald Long Hu Haiyan Huang Tim J P Hubbard Chau Huynh Sonali Jha Dionna Kasper Masaomi Kato Thomas C Kaufman Robert R Kitchen Erik Ladewig Julien Lagarde Eric Lai Jing Leng Zhi Lu Michael MacCoss Gemma May Rebecca McWhirter Gennifer Merrihew David M Miller Ali Mortazavi Rabi Murad Brian Oliver Sara Olson Peter J Park Michael J Pazin Norbert Perrimon Dmitri Pervouchine Valerie Reinke Alexandre Reymond Garrett Robinson Anastasia Samsonova Gary I Saunders Felix Schlesinger Anurag Sethi Frank J Slack William C Spencer Marcus H Stoiber Pnina Strasbourger Andrea Tanzer Owen A Thompson Kenneth H Wan Guilin Wang Huaien Wang Kathie L Watkins Jiayu Wen Kejia Wen Chenghai Xue Li Yang Kevin Yip Chris Zaleski Yan Zhang Henry Zheng Steven E Brenner Brenton R Graveley Susan E Celniker Thomas R Gingeras Robert Waterston

Nature 2014 Aug;512(7515):445-8

1] Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA [2].

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August 2014

Maternal separation with early weaning: a rodent model providing novel insights into neglect associated developmental deficits.

Authors:

Becky C Carlyle Alvaro Duque Robert R Kitchen Kelly A Bordner Daniel Coman Eliza Doolittle Xenophonios Papademetris Fahmeed Hyder Jane R Taylor Arthur A Simen

Dev Psychopathol 2012 Nov;24(4):1401-16

Yale University School of Medicine, CT, USA.

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November 2012

Tissue of origin determines cancer-associated CpG island promoter hypermethylation patterns.

Authors:

Duncan Sproul Robert R Kitchen Colm E Nestor J Michael Dixon Andrew H Sims David J Harrison Bernard H Ramsahoye Richard R Meehan

Genome Biol 2012 Oct 3;13(10):R84. Epub 2012 Oct 3.

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October 2012

Direct integration of intensity-level data from Affymetrix and Illumina microarrays improves statistical power for robust reanalysis.

Authors:

Arran K Turnbull Robert R Kitchen Alexey A Larionov Lorna Renshaw J Michael Dixon Andrew H Sims

BMC Med Genomics 2012 Aug 21;5:35. Epub 2012 Aug 21.

Breakthrough Research Unit, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XR, UK.

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August 2012

Relative impact of key sources of systematic noise in Affymetrix and Illumina gene-expression microarray experiments.

Authors:

Robert R Kitchen Vicky S Sabine Arthur A Simen J Michael Dixon John M S Bartlett Andrew H Sims

BMC Genomics 2011 Dec 1;12:589. Epub 2011 Dec 1.

Applied Bioinformatics of Cancer Group, Breakthrough Breast Cancer Research Unit, Institute of Genetics and Molecular Medicine, Crewe Road South, Edinburgh, Edinburgh, EH4 2XR, UK.

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December 2011

Differential global gene expression in cystic fibrosis nasal and bronchial epithelium.

Authors:

Varrie Ogilvie Margaret Passmore Laura Hyndman Lisa Jones Barbara Stevenson Abigail Wilson Heather Davidson Robert R Kitchen Robert D Gray Pallav Shah Eric W Alton Jane C Davies David J Porteous A Christopher Boyd

Genomics 2011 Nov 2;98(5):327-36. Epub 2011 Jul 2.

Medical Genetics Section, Molecular Medicine Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, UK.

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November 2011