Search Results - "Ramaswami, Gokul"

RADAR: a rigorously annotated database of A-to-I RNA editing by Ramaswami, Gokul, Li, Jin Billy

“…We present RADAR--a rigorously annotated database of A-to-I RNA editing (available at http://RNAedit.com). The identification of A-to-I RNA editing sites has…”
Get full text

Identification of human RNA editing sites: A historical perspective by Ramaswami, Gokul, Li, Jin Billy

“…•Historical review of methods to identify A-to-I RNA editing sites.•Our ability to identify editing sites is heavily dependent on the DNA sequencing…”
Get full text

RNA editing by ADAR1 prevents MDA5 sensing of endogenous dsRNA as nonself by Liddicoat, Brian J., Piskol, Robert, Chalk, Alistair M., Ramaswami, Gokul, Higuchi, Miyoko, Hartner, Jochen C., Li, Jin Billy, Seeburg, Peter H., Walkley, Carl R.

“…Adenosine-to-inosine (A-to-I) editing is a highly prevalent posttranscriptional modification of RNA, mediated by ADAR (adenosine deaminase acting on RNA)…”
Get full text

Accurate identification of human Alu and non-Alu RNA editing sites by Ramaswami, Gokul, Lin, Wei, Piskol, Robert, Tan, Meng How, Davis, Carrie, Li, Jin Billy

“…A computational framework is reported for the accurate and sensitive identification of RNA editing sites from whole-genome DNA and RNA sequences from the same…”
Get full text

Genetic Control of Expression and Splicing in Developing Human Brain Informs Disease Mechanisms by Walker, Rebecca L., Ramaswami, Gokul, Hartl, Christopher, Mancuso, Nicholas, Gandal, Michael J., de la Torre-Ubieta, Luis, Pasaniuc, Bogdan, Stein, Jason L., Geschwind, Daniel H.

“…Tissue-specific regulatory regions harbor substantial genetic risk for disease. Because brain development is a critical epoch for neuropsychiatric disease…”
Get full text

Editing of Cellular Self-RNAs by Adenosine Deaminase ADAR1 Suppresses Innate Immune Stress Responses by George, Cyril X., Ramaswami, Gokul, Li, Jin Billy, Samuel, Charles E.

“…Adenosine deaminases acting on double-stranded RNA (ADARs) catalyze the deamination of adenosine (A) to produce inosine (I) in double-stranded (ds) RNA…”
Get full text

Gene co-expression network analysis in human spinal cord highlights mechanisms underlying amyotrophic lateral sclerosis susceptibility by Wang, Jerry C., Ramaswami, Gokul, Geschwind, Daniel H.

“…Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease defined by motor neuron (MN) loss. Multiple genetic risk factors have been identified,…”
Get full text

Shared molecular neuropathology across major psychiatric disorders parallels polygenic overlap by Gandal, Michael J, Haney, Jillian R, Parikshak, Neelroop N, Leppa, Virpi, Ramaswami, Gokul, Hartl, Chris, Schork, Andrew J, Appadurai, Vivek, Buil, Alfonso, Werge, Thomas M, Liu, Chunyu, White, Kevin P, Horvath, Steve, Geschwind, Daniel H

“…The predisposition to neuropsychiatric disease involves a complex, polygenic, and pleiotropic genetic architecture. However, little is known about how genetic…”
Get full text

Integrative genomics identifies a convergent molecular subtype that links epigenomic with transcriptomic differences in autism by Ramaswami, Gokul, Won, Hyejung, Gandal, Michael J., Haney, Jillian, Wang, Jerry C., Wong, Chloe C. Y., Sun, Wenjie, Prabhakar, Shyam, Mill, Jonathan, Geschwind, Daniel H.

“…Autism spectrum disorder (ASD) is a phenotypically and genetically heterogeneous neurodevelopmental disorder. Despite this heterogeneity, previous studies have…”
Get full text

Broad transcriptomic dysregulation occurs across the cerebral cortex in ASD by Gandal, Michael J., Haney, Jillian R., Wamsley, Brie, Yap, Chloe X., Parhami, Sepideh, Emani, Prashant S., Chang, Nathan, Chen, George T., Hoftman, Gil D., de Alba, Diego, Ramaswami, Gokul, Hartl, Christopher L., Bhattacharya, Arjun, Luo, Chongyuan, Jin, Ting, Wang, Daifeng, Kawaguchi, Riki, Quintero, Diana, Ou, Jing, Wu, Ye Emily, Parikshak, Neelroop N., Swarup, Vivek, Belgard, T. Grant, Gerstein, Mark, Pasaniuc, Bogdan, Geschwind, Daniel H.

“…Neuropsychiatric disorders classically lack defining brain pathologies, but recent work has demonstrated dysregulation at the molecular level, characterized by…”
Get full text

Learning cis-regulatory principles of ADAR-based RNA editing from CRISPR-mediated mutagenesis by Liu, Xin, Sun, Tao, Shcherbina, Anna, Li, Qin, Jarmoskaite, Inga, Kappel, Kalli, Ramaswami, Gokul, Das, Rhiju, Kundaje, Anshul, Li, Jin Billy

“…Adenosine-to-inosine (A-to-I) RNA editing catalyzed by ADAR enzymes occurs in double-stranded RNAs. Despite a compelling need towards predictive understanding…”
Get full text

Coexpression network architecture reveals the brain-wide and multiregional basis of disease susceptibility by Hartl, Christopher L., Ramaswami, Gokul, Pembroke, William G., Muller, Sandrine, Pintacuda, Greta, Saha, Ashis, Parsana, Princy, Battle, Alexis, Lage, Kasper, Geschwind, Daniel H.

“…Gene networks have yielded numerous neurobiological insights, yet an integrated view across brain regions is lacking. We leverage RNA sequencing in 864 samples…”
Get full text

A transition zone complex regulates mammalian ciliogenesis and ciliary membrane composition by Reiter, Jeremy F, Garcia-Gonzalo, Francesc R, Corbit, Kevin C, Sirerol-Piquer, María Salomé, Ramaswami, Gokul, Otto, Edgar A, Noriega, Thomas R, Seol, Allen D, Robinson, Jon F, Bennett, Christopher L, Josifova, Dragana J, García-Verdugo, José Manuel, Katsanis, Nicholas, Hildebrandt, Friedhelm

“…Jeremy Reiter and colleagues show that Tctn1 is a component of a transition zone complex that regulates ciliogenesis and ciliary membrane composition. They…”
Get full text

Molecular definition of a metastatic lung cancer state reveals a targetable CD109–Janus kinase–Stat axis by Chuang, Chen-Hua, Greenside, Peyton G, Rogers, Zoë N, Brady, Jennifer J, Yang, Dian, Ma, Rosanna K, Caswell, Deborah R, Chiou, Shin-Heng, Winters, Aidan F, Grüner, Barbara M, Ramaswami, Gokul, Spencley, Andrew L, Kopecky, Kimberly E, Sayles, Leanne C, Sweet-Cordero, E Alejandro, Li, Jin Billy, Kundaje, Anshul, Winslow, Monte M

“…In vivo screening of pro-metastatic factors in a genetically engineered mouse model of lung cancer uncovered the CD109–JAK–STAT3 axis as a key contributor of…”
Get full text

Quantifying RNA allelic ratios by microfluidic multiplex PCR and sequencing by Zhang, Rui, Li, Xin, Ramaswami, Gokul, Smith, Kevin S, Turecki, Gustavo, Montgomery, Stephen B, Li, Jin Billy

“…For allele-specific expression and RNA editing studies, targeted RNA sequencing using microfluidic multiplexed PCR (mmPCR-seq) gives robust high-throughput…”
Get full text

A-to-I RNA editing in the rat brain is age-dependent, region-specific and sensitive to environmental stress across generations by Zaidan, Hiba, Ramaswami, Gokul, Golumbic, Yaela N, Sher, Noa, Malik, Assaf, Barak, Michal, Galiani, Dalia, Dekel, Nava, Li, Jin B, Gaisler-Salomon, Inna

“…Adenosine-to-inosine (A-to-I) RNA editing is an epigenetic modification catalyzed by adenosine deaminases acting on RNA (ADARs), and is especially prevalent in…”
Get full text

Transcriptional characterization of iPSC-derived microglia as a model for therapeutic development in neurodegeneration by Ramaswami, Gokul, Yuva-Aydemir, Yeliz, Akerberg, Brynn, Matthews, Bryan, Williams, Jenna, Golczer, Gabriel, Huang, Jiaqi, Al Abdullatif, Ali, Huh, Dann, Burkly, Linda C., Engle, Sandra J., Grossman, Iris, Sehgal, Alfica, Sigova, Alla A., Fremeau, Robert T., Liu, Yuting, Bumcrot, David

“…Microglia are the resident immune cells in the brain that play a key role in driving neuroinflammation, a hallmark of neurodegenerative disorders. Inducible…”
Get full text

Author Correction: Transcriptional characterization of iPSC-derived microglia as a model for therapeutic development in neurodegeneration by Ramaswami, Gokul, Yuva-Aydemir, Yeliz, Akerberg, Brynn, Matthews, Bryan, Williams, Jenna, Golczer, Gabriel, Huang, Jiaqi, Al Abdullatif, Ali, Huh, Dann, Burkly, Linda C., Engle, Sandra J., Grossman, Iris, Sehgal, Alfica, Sigova, Alla A., Fremeau, Robert T., Liu, Yuting, Bumcrot, David

Get full text

RNA editing underlies genetic risk of common inflammatory diseases by Li, Qin, Gloudemans, Michael J., Geisinger, Jonathan M., Fan, Boming, Aguet, François, Sun, Tao, Ramaswami, Gokul, Li, Yang I., Ma, Jin-Biao, Pritchard, Jonathan K., Montgomery, Stephen B., Li, Jin Billy

Get full text

Reliable Identification of Genomic Variants from RNA-Seq Data by Piskol, Robert, Ramaswami, Gokul, Li, Jin Billy

“…Identifying genomic variation is a crucial step for unraveling the relationship between genotype and phenotype and can yield important insights into human…”
Get full text