Sofie R Salama

Sofie R Salama

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Sofie R Salama

Sofie R Salama

Publications by authors named "Sofie R Salama"

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29Publications

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Structurally Conserved Primate LncRNAs Are Transiently Expressed during Human Cortical Differentiation and Influence Cell-Type-Specific Genes.

Stem Cell Reports 2019 02 10;12(2):245-257. Epub 2019 Jan 10.

Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA; Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1016/j.stemcr.2018.12.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6372947PMC
February 2019

Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution.

Cell 2019 02;176(4):743-756.e17

Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.01.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6544371PMC
February 2019

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.

Authors:
Daniel J Brat Roel G W Verhaak Kenneth D Aldape W K Alfred Yung Sofie R Salama Lee A D Cooper Esther Rheinbay C Ryan Miller Mark Vitucci Olena Morozova A Gordon Robertson Houtan Noushmehr Peter W Laird Andrew D Cherniack Rehan Akbani Jason T Huse Giovanni Ciriello Laila M Poisson Jill S Barnholtz-Sloan Mitchel S Berger Cameron Brennan Rivka R Colen Howard Colman Adam E Flanders Caterina Giannini Mia Grifford Antonio Iavarone Rajan Jain Isaac Joseph Jaegil Kim Katayoon Kasaian Tom Mikkelsen Bradley A Murray Brian Patrick O'Neill Lior Pachter Donald W Parsons Carrie Sougnez Erik P Sulman Scott R Vandenberg Erwin G Van Meir Andreas von Deimling Hailei Zhang Daniel Crain Kevin Lau David Mallery Scott Morris Joseph Paulauskis Robert Penny Troy Shelton Mark Sherman Peggy Yena Aaron Black Jay Bowen Katie Dicostanzo Julie Gastier-Foster Kristen M Leraas Tara M Lichtenberg Christopher R Pierson Nilsa C Ramirez Cynthia Taylor Stephanie Weaver Lisa Wise Erik Zmuda Tanja Davidsen John A Demchok Greg Eley Martin L Ferguson Carolyn M Hutter Kenna R Mills Shaw Bradley A Ozenberger Margi Sheth Heidi J Sofia Roy Tarnuzzer Zhining Wang Liming Yang Jean Claude Zenklusen Brenda Ayala Julien Baboud Sudha Chudamani Mark A Jensen Jia Liu Todd Pihl Rohini Raman Yunhu Wan Ye Wu Adrian Ally J Todd Auman Miruna Balasundaram Saianand Balu Stephen B Baylin Rameen Beroukhim Moiz S Bootwalla Reanne Bowlby Christopher A Bristow Denise Brooks Yaron Butterfield Rebecca Carlsen Scott Carter Lynda Chin Andy Chu Eric Chuah Kristian Cibulskis Amanda Clarke Simon G Coetzee Noreen Dhalla Tim Fennell Sheila Fisher Stacey Gabriel Gad Getz Richard Gibbs Ranabir Guin Angela Hadjipanayis D Neil Hayes Toshinori Hinoue Katherine Hoadley Robert A Holt Alan P Hoyle Stuart R Jefferys Steven Jones Corbin D Jones Raju Kucherlapati Phillip H Lai Eric Lander Semin Lee Lee Lichtenstein Yussanne Ma Dennis T Maglinte Harshad S Mahadeshwar Marco A Marra Michael Mayo Shaowu Meng Matthew L Meyerson Piotr A Mieczkowski Richard A Moore Lisle E Mose Andrew J Mungall Angeliki Pantazi Michael Parfenov Peter J Park Joel S Parker Charles M Perou Alexei Protopopov Xiaojia Ren Jeffrey Roach Thaís S Sabedot Jacqueline Schein Steven E Schumacher Jonathan G Seidman Sahil Seth Hui Shen Janae V Simons Payal Sipahimalani Matthew G Soloway Xingzhi Song Huandong Sun Barbara Tabak Angela Tam Donghui Tan Jiabin Tang Nina Thiessen Timothy Triche David J Van Den Berg Umadevi Veluvolu Scot Waring Daniel J Weisenberger Matthew D Wilkerson Tina Wong Junyuan Wu Liu Xi Andrew W Xu Lixing Yang Travis I Zack Jianhua Zhang B Arman Aksoy Harindra Arachchi Chris Benz Brady Bernard Daniel Carlin Juok Cho Daniel DiCara Scott Frazer Gregory N Fuller JianJiong Gao Nils Gehlenborg David Haussler David I Heiman Lisa Iype Anders Jacobsen Zhenlin Ju Sol Katzman Hoon Kim Theo Knijnenburg Richard Bailey Kreisberg Michael S Lawrence William Lee Kalle Leinonen Pei Lin Shiyun Ling Wenbin Liu Yingchun Liu Yuexin Liu Yiling Lu Gordon Mills Sam Ng Michael S Noble Evan Paull Arvind Rao Sheila Reynolds Gordon Saksena Zack Sanborn Chris Sander Nikolaus Schultz Yasin Senbabaoglu Ronglai Shen Ilya Shmulevich Rileen Sinha Josh Stuart S Onur Sumer Yichao Sun Natalie Tasman Barry S Taylor Doug Voet Nils Weinhold John N Weinstein Da Yang Kosuke Yoshihara Siyuan Zheng Wei Zhang Lihua Zou Ty Abel Sara Sadeghi Mark L Cohen Jenny Eschbacher Eyas M Hattab Aditya Raghunathan Matthew J Schniederjan Dina Aziz Gene Barnett Wendi Barrett Darell D Bigner Lori Boice Cathy Brewer Chiara Calatozzolo Benito Campos Carlos Gilberto Carlotti Timothy A Chan Lucia Cuppini Erin Curley Stefania Cuzzubbo Karen Devine Francesco DiMeco Rebecca Duell J Bradley Elder Ashley Fehrenbach Gaetano Finocchiaro William Friedman Jordonna Fulop Johanna Gardner Beth Hermes Christel Herold-Mende Christine Jungk Ady Kendler Norman L Lehman Eric Lipp Ouida Liu Randy Mandt Mary McGraw Roger Mclendon Christopher McPherson Luciano Neder Phuong Nguyen Ardene Noss Raffaele Nunziata Quinn T Ostrom Cheryl Palmer Alessandro Perin Bianca Pollo Alexander Potapov Olga Potapova W Kimryn Rathmell Daniil Rotin Lisa Scarpace Cathy Schilero Kelly Senecal Kristen Shimmel Vsevolod Shurkhay Suzanne Sifri Rosy Singh Andrew E Sloan Kathy Smolenski Susan M Staugaitis Ruth Steele Leigh Thorne Daniela P C Tirapelli Andreas Unterberg Mahitha Vallurupalli Yun Wang Ronald Warnick Felicia Williams Yingli Wolinsky Sue Bell Mara Rosenberg Chip Stewart Franklin Huang Jonna L Grimsby Amie J Radenbaugh Jianan Zhang
June 2015

SHAPE Selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data.

RNA 2015 May 24;21(5):1042-52. Epub 2015 Mar 24.

Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark.

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http://dx.doi.org/10.1261/rna.047068.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4408784PMC
May 2015

An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons.

Nature 2014 Dec 28;516(7530):242-5. Epub 2014 Sep 28.

1] Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA [2] Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1038/nature13760DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4268317PMC
December 2014

Double minute chromosomes in glioblastoma multiforme are revealed by precise reconstruction of oncogenic amplicons.

Cancer Res 2013 Oct 12;73(19):6036-45. Epub 2013 Aug 12.

Authors' Affiliations: Five3 Genomics, LLC; Center for Biomolecular Science and Engineering, University of California; Howard Hughes Medical Institute, Santa Cruz, California; Human Oncology & Pathogenesis Program and Department of Neurosurgery; Cytogenetics Laboratory, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York; Departments of Neurology & Neurosurgery, Henry Ford Hospital, Detroit, Michigan; and Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.

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http://dx.doi.org/10.1158/0008-5472.CAN-13-0186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3800429PMC
October 2013

The somatic genomic landscape of glioblastoma.

Cell 2013 Oct;155(2):462-77

Human Oncology and Pathogenesis Program, Brain Tumor Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Department of Neurosurgery, Memorial Sloan-Kettering Cancer Center, Department of Neurological Surgery, Weill Cornell Medical Center, New York, NY 10065, USA. Electronic address:

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https://www.genome.gov/Multimedia/Slides/TCGA2/27_Verhaak.pd
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http://linkinghub.elsevier.com/retrieve/pii/S009286741301208
Publisher Site
http://dx.doi.org/10.1016/j.cell.2013.09.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3910500PMC
October 2013

Gene isoform specificity through enhancer-associated antisense transcription.

PLoS One 2012 24;7(8):e43511. Epub 2012 Aug 24.

Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0043511PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427357PMC
April 2013

Three periods of regulatory innovation during vertebrate evolution.

Science 2011 Aug;333(6045):1019-24

Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1126/science.1202702DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511857PMC
August 2011

FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing.

Nat Methods 2010 Dec 7;7(12):995-1001. Epub 2010 Nov 7.

Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, California, USA.

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http://dx.doi.org/10.1038/nmeth.1529DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3247016PMC
December 2010

Endangered species hold clues to human evolution.

J Hered 2010 Jul-Aug;101(4):437-47. Epub 2010 Mar 23.

Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/jhered/esq016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2884192PMC
October 2010

GC-biased evolution near human accelerated regions.

PLoS Genet 2010 May 20;6(5):e1000960. Epub 2010 May 20.

Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1000960DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873926PMC
May 2010

Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53.

Proc Natl Acad Sci U S A 2007 Nov 14;104(47):18613-8. Epub 2007 Nov 14.

Center for Biomolecular Science and Engineering, and Howard Hughes Medical Institute, University of California, Santa Cruz, CA 95064, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0703637104
Publisher Site
http://dx.doi.org/10.1073/pnas.0703637104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2141825PMC
November 2007

Human genome ultraconserved elements are ultraselected.

Science 2007 Aug;317(5840):915

Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1126/science.1142430DOI Listing
August 2007

Forces shaping the fastest evolving regions in the human genome.

PLoS Genet 2006 Oct 23;2(10):e168. Epub 2006 Aug 23.

Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.0020168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1599772PMC
October 2006

An RNA gene expressed during cortical development evolved rapidly in humans.

Nature 2006 Sep 16;443(7108):167-72. Epub 2006 Aug 16.

Center for Biomolecular Science & Engineering, Department of Molecular, Cell & Developmental Biology, University of California, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1038/nature05113DOI Listing
September 2006

A distal enhancer and an ultraconserved exon are derived from a novel retroposon.

Nature 2006 May 16;441(7089):87-90. Epub 2006 Apr 16.

Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1038/nature04696DOI Listing
May 2006