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Resource: The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data
- Hsin-Yen Larry Wu,
- Isaiah D. Kaufman,
- and Polly Yingshan Hsu
Genome Res. September 2025 35: 2130-2142; Published in Advance July 22, 2025, doi:10.1101/gr.280480.125
...provide examples of multiomic comparisons that reveal insights that connect the transcriptome, translatome, and degradome. In summary, ggRibo is an advanced single-gene viewer that offers a valuable resource for studying gene expression regulation through its intuitive and flexible platform...
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Research: A prospective trial comparing programmable targeted long-read sequencing and short-read genome sequencing for genetic diagnosis of cerebellar ataxia
- Haloom Rafehi,
- Liam G. Fearnley,
- Justin Read,
- Penny Snell,
- Kayli C. Davies,
- Liam Scott,
- Greta Gillies,
- Genevieve C. Thompson,
- Tess A. Field,
- Aleena Eldo,
- Simon Bodek,
- Ernest Butler,
- Luke Chen,
- John Drago,
- Himanshu Goel,
- Anna Hackett,
- G. Michael Halmagyi,
- Andrew Hannaford,
- Katya Kotschet,
- Kishore R. Kumar,
- Smitha Kumble,
- Matthew Lee-Archer,
- Abhishek Malhotra,
- Mark Paine,
- Michael Poon,
- Kate Pope,
- Katrina Reardon,
- Steven Ring,
- Anne Ronan,
- Matthew Silsby,
- Renee Smyth,
- Chloe Stutterd,
- Mathew Wallis,
- John Waterston,
- Thomas Wellings,
- Kirsty West,
- Christine Wools,
- Kathy H.C. Wu,
- David J. Szmulewicz,
- Martin B. Delatycki,
- Melanie Bahlo,
- and Paul J. Lockhart
Genome Res. April 2025 35: 769-785; Published in Advance February 27, 2025, doi:10.1101/gr.279634.124
...was the 22 REs listed in Table 1. This included the 17 REs associated with CA and five additional pathogenic REs that cause neurological movement disorders that could possibly be a differential diagnosis for our cohort. In addition, these five REs are also commonly tested with single gene assays at our...
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Research: Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders
- Susan M. Hiatt,
- James M.J. Lawlor,
- Lori H. Handley,
- Donald R. Latner,
- Zachary T. Bonnstetter,
- Candice R. Finnila,
- Michelle L. Thompson,
- Lori Beth Boston,
- Melissa Williams,
- Ivan Rodriguez Nunez,
- Jerry Jenkins,
- Whitley V. Kelley,
- E. Martina Bebin,
- Michael A. Lopez,
- Anna C.E. Hurst,
- Bruce R. Korf,
- Jeremy Schmutz,
- Jane Grimwood,
- and Gregory M. Cooper
Genome Res. November 2024 34: 1747-1762; Published in Advance September 19, 2024, doi:10.1101/gr.279227.124
...Long-read sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders Susan M. Hiatt1, James M.J. Lawlor1, Lori H. Handley1, Donald R. Latner1, Zachary T. Bonnstetter1, Candice R. Finnila1, Michelle L. Thompson1, Lori Beth Boston1, Melissa Williams1, Ivan Rodriguez...
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Research: Identification of a transcriptional signature found in multiple models of ASD and related disorders
- Samuel Thudium,
- Katherine Palozola,
- Éloïse L'Her,
- and Erica Korb
Genome Res. September 2022 32: 1642-1654; Published in Advance September 14, 2022, doi:10.1101/gr.276591.122
...single-gene sets. In summary, the approaches used here define transcriptional signatures that encode critical neuronal developmental proteins, contain unique chromatin features, and are present throughout multiple experimental models of ASD.DiscussionHere we defined transcriptional signatures...
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Method: A general framework for identifying oligogenic combinations of rare variants in complex disorders
- Vijay Kumar Pounraja and
- Santhosh Girirajan
Genome Res. May 2022 32: 904-915; Published in Advance March 17, 2022, doi:10.1101/gr.276348.121
...clinical diagnosis information for intellectual disability, anxiety, attention deficit hyperactivity disorders (ADHD), schizophrenia, and language and sleep disorders were encoded as binary variables for the SPARK samples; full-scale intelligence quotient (IQ) scores were available for the SSC cohort...
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Research: Gene by environment interaction mouse model reveals a functional role for 5-hydroxymethylcytosine in neurodevelopmental disorders
- Ligia A. Papale,
- Andy Madrid,
- Qi Zhang,
- Kailei Chen,
- Lara Sak,
- Sündüz Keleş,
- and Reid S. Alisch
Genome Res. February 2022 32: 266-279; Published in Advance December 23, 2021, doi:10.1101/gr.276137.121
...neurodevelopmental disorders. We tested adult Cntnap2 heterozygous mice (Cntnap2+/−; lacking behavioral or neuropathological abnormalities) subjected to a prenatal stress and found that prenatally stressed Cntnap2+/− female mice show repetitive behaviors and altered sociability, similar to the homozygote phenotype...
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Method: The discovery of integrated gene networks for autism and related disorders
- Fereydoun Hormozdiari,
- Osnat Penn,
- Elhanan Borenstein,
- and Evan E. Eichler
Genome Res. January 2015 25: 142-154; Published in Advance November 5, 2014, doi:10.1101/gr.178855.114
...it with other seed pathways, as long as the score of the resultingmodule does not decrease and the constraints regarding the PPI density and coexpression are satisfied. Repeating this step produces a set of potentially overlapping modules. Last, a local search routine is performed in which single genes...
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Perspective: The Mendelian disorders of the epigenetic machinery
- Hans Tomas Bjornsson
Genome Res. October 2015 25: 1473-1481; doi:10.1101/gr.190629.115
...of the gene RUNX2 (Vega et al. 2004; Balemans et al. 2014), and both conditions lead to a particular limb abnormality (brachydactyly). Finally, sometimes the shared abnormalities appear to disrupt the function of target networks rather than single genes. For instance, three of the Mendelian disorders...
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Resource: Gene expression imputation and cell-type deconvolution in human brain with spatiotemporal precision and its implications for brain-related disorders
- Guangsheng Pei,
- Yin-Ying Wang,
- Lukas M. Simon,
- Yulin Dai,
- Zhongming Zhao,
- and Peilin Jia
Genome Res. January 2021 31: 146-158; Published in Advance December 3, 2020, doi:10.1101/gr.265769.120
..., bipolar disorder–related genes were enriched in Ex1 (P = 5.7 × 10−3) and In4 (P = 0.04). Of note, neuron In4 was enriched for prenatal front amygdala and hippocampus regions (Fig. 6C), and the amygdala, hippocampus, and prefrontal cortex regions were previously reported to be related with bipolar disorder...
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Method: OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities
- Siavash Raeisi Dehkordi,
- Zhaoyang Jia,
- Joey Estabrook,
- Jen Hauenstein,
- Neil Miller,
- Naz Güleray-Lafci,
- Jürgen Neesen,
- Alex Hastie,
- Alka Chaubey,
- Andy Wing Chun Pang,
- Paul Dremsek,
- and Vineet Bafna
Genome Res. December 2025 35: 2671-2681; Published in Advance November 14, 2025, doi:10.1101/gr.280536.125
...an individual's genotype. Karyotype analysis, which includes identifying aneuploidies and structural rearrangements, is essential for understanding genetic risk factors, informing diagnosis and treatment, and guiding genetic counseling in constitutional disorders. The current karyotyping standard relies...
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