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Author Gabriela Balderrama Gutierrez

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Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

Francisco Pardo-Palacios, Fairlie Reese, Silvia Carbonell-Sala, Mark Diekhans, Cindy Liang, Dingjie Wang, Brian Williams, Matthew Adams, Amit Behera, Julien Lagarde, Haoran Li, Andrey Prjibelski, Gabriela Balderrama-Gutierrez, Muhammed Hasan Çelik, Maite De María, Nancy Denslow, Natàlia Garcia-Reyero, Stefan Goetz, Margaret Hunter, Jane Loveland, Carlos Menor, David Moraga, Jonathan Mudge, Hazuki Takahashi, Alison Tang, Ingrid Youngworth, Piero Carninci, Roderic Guigó, Hagen Tilgner, Barbara Wold, Christopher Vollmers, Gloria Sheynkman, Adam Frankish, Kin Fai Au, Ana Conesa, Ali Mortazavi, Angela Brooks,

With increased usage of long-read sequencing technologies to perform transcriptome analyses, there becomes a greater need to evaluate different methodologies including library preparation, sequencing platform, and computational analysis tools. Here, we report the study design of a community effort called the Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium, whose ... Read more >>

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Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq

Elisabeth Rebboah, Fairlie Reese, Katherine Williams, Gabriela Balderrama-Gutierrez, Cassandra McGill, Diane Trout, Isaryhia Rodriguez, Heidi Liang, Barbara Wold, Ali Mortazavi,

Alternative RNA isoforms are defined by promoter choice, alternative splicing, and polyA site selection. Although differential isoform expression is known to play a large regulatory role in eukaryotes, it has proved challenging to study with standard short-read RNA-seq because of the uncertainties it leaves about the full-length structure and precise ... Read more >>

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Transcriptome analysis of heterogeneity in mouse model of metastatic breast cancer

Anastasia Ionkina, Gabriela Balderrama-Gutierrez, Kristian Ibanez, Steve Huy Phan, Angelique Cortez, Ali Mortazavi, Jennifer Prescher,

Cancer metastasis is a complex process involving the spread of malignant cells from a primary tumor to distal organs. Understanding this cascade at a mechanistic level could provide critical new insights into the disease and potentially reveal new avenues for treatment. Transcriptome profiling of spontaneous cancer models is an attractive ... Read more >>

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Generation of a humanized Aβ expressing mouse demonstrating aspects of Alzheimer's disease-like pathology.

David Baglietto-Vargas, Stefania Forner, Lena Cai, Alessandra C Martini, Laura Trujillo-Estrada, Vivek Swarup, Marie Minh Thu Nguyen, Kelly Do Huynh, Dominic I Javonillo, Kristine Minh Tran, Jimmy Phan, Shan Jiang, Enikö A Kramár, Cristina Nuñez-Diaz, Gabriela Balderrama-Gutierrez, Franklin Garcia, Jessica Childs, Carlos J Rodriguez-Ortiz, Juan Antonio Garcia-Leon, Masashi Kitazawa, Mohammad Shahnawaz, Dina P Matheos, Xinyi Ma, Celia Da Cunha, Ken C Walls, Rahasson R Ager, Claudio Soto, Antonia Gutierrez, Ines Moreno-Gonzalez, Ali Mortazavi, Andrea J Tenner, Grant R MacGregor, Marcelo Wood, Kim N Green, Frank M LaFerla,

The majority of Alzheimer's disease (AD) cases are late-onset and occur sporadically, however most mouse models of the disease harbor pathogenic mutations, rendering them better representations of familial autosomal-dominant forms of the disease. Here, we generated knock-in mice that express wildtype human Aβ under control of the mouse App locus. ... Read more >>

Nat Commun (Nature communications)
[2021, 12(1):2421]

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An Infection-Tolerant Mammalian Reservoir for Several Zoonotic Agents Broadly Counters the Inflammatory Effects of Endotoxin.

Gabriela Balderrama-Gutierrez, Ana Milovic, Vanessa J Cook, M Nurul Islam, Youwen Zhang, Hippokratis Kiaris, John T Belisle, Ali Mortazavi, Alan G Barbour,

Animals that are competent reservoirs of zoonotic pathogens commonly suffer little morbidity from the infections. To investigate mechanisms of this tolerance of infection, we used single-dose lipopolysaccharide (LPS) as an experimental model of inflammation and compared the responses of two rodents: <i>Peromyscus leucopus</i>, the white-footed deermouse and reservoir for the ... Read more >>

mBio (mBio)
[2021, 12(2):]

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Multi-tissue integrative analysis of personal epigenomes

Joel Rozowsky, Jorg Drenkow, Yucheng Yang, Gamze Gursoy, Timur Galeev, Beatrice Borsari, Charles Epstein, Kun Xiong, Jinrui Xu, Jiahao Gao, Keyang Yu, Ana Berthel, Zhanlin Chen, Fabio Navarro, Jason Liu, Maxwell Sun, James Wright, Justin Chang, Christopher JF Cameron, Noam Shoresh, Elizabeth Gaskell, Jessika Adrian, Sergey Aganezov, Gabriela Balderrama-Gutierrez, Samridhi Banskota, Guillermo Barreto Corona, Sora Chee, Surya Chhetri, Gabriel Conte Cortez Martins, Cassidy Danyko, Carrie Davis, Daniel Farid, Nina Farrell, Idan Gabdank, Yoel Gofin, David Gorkin, Mengting Gu, Vivian Hecht, Benjamin Hitz, Robbyn Issner, Melanie Kirsche, Xiangmeng Kong, Bonita Lam, Shantao Li, Bian Li, Tianxiao Li, Xiqi Li, Khine Zin Lin, Ruibang Luo, Mark Mackiewicz, Jill Moore, Jonathan Mudge, Nicholas Nelson, Chad Nusbaum, Ioann Popov, Henry Pratt, Yunjiang Qiu, Srividya Ramakrishnan, Joe Raymond, Leonidas Salichos, Alexandra Scavelli, Jacob Schreiber, Fritz Sedlazeck, Lei Hoon See, Rachel Sherman, Xu Shi, Minyi Shi, Cricket Alicia Sloan, Seth Strattan, Zhen Tan, Forrest Tanaka, Anna Vlasova, Jun Wang, Jonathan Werner, Brian Williams, Min Xu, Chengfei Yan, Lu Yu, Christopher Zaleski, Jing Zhang, Michael Cherry, Eric Mendenhall, William Noble, Zhiping Weng, Morgan Levine, Alexander Dobin, Barbara Wold, Ali Mortazavi, Bing Ren, Jesse Gillis, Richard Myers, Michael Snyder, Jyoti Choudhary, Aleksandar Milosavljevic, Michael Schatz, Roderic Guigó, Bradley Bernstein, Thomas Gingeras, Mark Gerstein,

Evaluating the impact of genetic variants on transcriptional regulation is a central goal in biological science that has been constrained by reliance on a single reference genome. To address this, we constructed phased, diploid genomes for four cadaveric donors (using long-read sequencing) and systematically charted noncoding regulatory elements and transcriptional ... Read more >>

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Systematic Phenotyping and Characterization of the 5xFAD mouse model of Alzheimer’s Disease

Stefania Forner, Shimako Kawauchi, Gabriela Balderrama-Gutierrez, Enikö Kramár, Dina Matheos, Jimmy Phan, Dominic Javonillo, Kristine Minh Tran, Edna Hingco, Celia da Cunha, Narges Rezaie, Joshua Andrei Alcantara, David Baglietto-Vargas, Camden Jansen, Jonathan Neumann, Marcelo Wood, Grant MacGregor, Ali Mortazavi, Andrea Tenner, Frank LaFerla, Kim Green,

Mouse models of human diseases are invaluable tools for studying pathogenic mechanisms and testing interventions and therapeutics. For disorders such as Alzheimer’s disease in which numerous models are being generated, a challenging first step is to identify the most appropriate model and age to effectively evaluate new therapeutic approaches. Here ... Read more >>

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The infection-tolerant mammalian reservoir of Lyme disease and other zoonoses broadly counters the inflammatory effects of endotoxin

Gabriela Balderrama-Gutierrez, Ana Milovic, Vanessa Cook, Nurul Islam, Youwen Zhang, Hippokratis Kiaris, John Belisle, Ali Mortazavi, Alan Barbour,

<h4>ABSTRACT</h4> Animals that are competent natural reservoirs of zoonotic diseases commonly suffer little morbidity from the pathogens they persistently harbor. The mechanisms of this infection tolerance and the trade-off costs are poorly understood. We used exposure to a single dose of lipopolysaccharide (LPS) endotoxin as an experimental model of inflammation ... Read more >>

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Long-TUC-seq is a robust method for quantification of metabolically labeled full-length isoforms

Sorena Rahmanian, Gabriela Balderrama-Gutierrez, Dana Wyman, Cassandra Joan McGill, Kim Nguyen, Robert Spitale, Ali Mortazavi,

<h4>ABSTRACT</h4> The steady state expression of each gene is the result of a dynamic transcription and degradation of that gene. While regular RNA-seq methods only measure steady state expression levels, RNA-seq of metabolically labeled RNA identifies transcripts that were transcribed during the window of metabolic labeling. Whereas short-read RNA sequencing ... Read more >>

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The genome of Peromyscus leucopus, natural host for Lyme disease and other emerging infections.

Anthony D Long, James Baldwin-Brown, Yuan Tao, Vanessa J Cook, Gabriela Balderrama-Gutierrez, Russell Corbett-Detig, Ali Mortazavi, Alan G Barbour,

The rodent <i>Peromyscus leucopus</i> is the natural reservoir of several tick-borne infections, including Lyme disease. To expand the knowledge base for this key species in life cycles of several pathogens, we assembled and scaffolded the <i>P. leucopus</i> genome. The resulting assembly was 2.45 Gb in total length, with 24 chromosome-length ... Read more >>

Sci Adv (Science advances)
[2019, 5(7):eaaw6441]

Cited: 8 times

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A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification

Dana Wyman, Gabriela Balderrama-Gutierrez, Fairlie Reese, Shan Jiang, Sorena Rahmanian, Stefania Forner, Dina Matheos, Weihua Zeng, Brian Williams, Diane Trout, Whitney England, Shu-Hui Chu, Robert Spitale, Andrea Tenner, Barbara Wold, Ali Mortazavi,

<h4>ABSTRACT</h4> Alternative splicing is widely acknowledged to be a crucial regulator of gene expression and is a key contributor to both normal developmental processes and disease states. While cost-effective and accurate for quantification, short-read RNA-seq lacks the ability to resolve full-length transcript isoforms despite increasingly sophisticated computational methods. Long-read sequencing ... Read more >>

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