Publications
NIAGADS Publications
Title | Authors | Year | Journal | Link |
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A comprehensive database of high-throughput sequencing-based RNA secondary structure prbing data (Structure Surfer). | Nathan D. Berkowitz, Ian M. Silverman, D. Micah Childress, Hilal Kazan, Li-San Wang and Brian D. Gregory | 2016 | BMC Bioinformatics. 2016 17:215 |
PubMed Central: |
DASHR: database of small human noncoding RNAs | Yuk Yee Leung, Pavel P. Kuksa, Alexandre Amlie-Wolf, Otto Valladares, Lyle H. Ungar, Sampath Kannan, Brian D. Gregory, and Li-San Wang | 2015 | Nucleic Acids Res. 2016 Jan 4; 44(Database issue): D216–D222. |
PubMed Central: |
Transcriptomic Changes Due to Cytoplasmic TDP-43 Expression Reveal Dysregulation of Histone Transcripts and Nuclear Chromatin | Alexandre Amlie-Wolf, Paul Ryvkin, Rui Tong, Isabelle Dragomir, EunRan Suh, Yan Xu, Vivianna M. Van Deerlin, Brian D. Gregory, Linda K. Kwong, John Q. Trojanowski, Virginia M.-Y. Lee, Li-San Wang, and Edward B. Lee | 2015 | PLoS One. 2015; 10(10): e0141836. |
PubMed Central: |
HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements | Yih-Chii Hwang, Chiao-Feng Lin, Otto Valladares, John Malamon, Pavel P. Kuksa, Qi Zheng, Brian D. Gregory, and Li-San Wang | 2015 | Bioinformatics. 2015 Apr 15; 31(8): 1290–1292. |
PubMed Central: |
Using machine learning and high-throughput RNA sequencing to classify the precursors of small non-coding RNAs | Paul Ryvkin, Yuk Yee Leung, Lyle H. Ungar, Brian D. Gregory, and Li-San Wang | 2014 | Methods. 2014 May 1; 67(1): 28–35. |
PubMed Central: |
High-throughput identification of long-range regulatory elements and their target promoters in the human genome | Yih-Chii Hwang, Qi Zheng, Brian D. Gregory, and Li-San Wang | 2013 | Nucleic Acids Res. 2013 May; 41(9): 4835–4846. |
PubMed Central: |
CoRAL: predicting non-coding RNAs from small RNA-sequencing data | Yuk Yee Leung, Paul Ryvkin, Lyle H. Ungar, Brian D. Gregory, and Li-San Wang | 2013 | Nucleic Acids Res. 2013 Aug; 41(14): e137. |
PubMed Central: |
Analyzing Copy Number Variation using SNP Array Data: Protocols for Calling CNV and Association Tests | Chiao-Feng Lin, Adam C Naj, and Li-San Wang | 2013 | Curr Protoc Hum Genet. 2013 Oct 18; 79: Unit–1.27. |
PubMed Central: |
DRAW+SneakPeek: Analysis workflow and quality metric management for DNA-seq experiments | Chiao-Feng Lin, Otto Valladares, D. Micah Childress, Egor Klevak, Evan T. Geller, Yih-Chii Hwang, Ellen A. Tsai, Gerard D. Schellenberg, and Li-San Wang | 2013 | Bioinformatics. 2013 Oct 1; 29(19): 2498–2500. |
PubMed Central: |
HAMR: high-throughput annotation of modified ribonucleotides | Paul Ryvkin, Yuk Yee Leung, Ian M. Silverman, Micah Childress, Otto Valladares, Isabelle Dragomir, Brian D. Gregory, and Li-San Wang | 2013 | RNA. 2013 Dec; 19(12): 1684–1692. |
PubMed Central: |
List of Other Publications Acknowledging NIAGADS*
These papers acknowledge NIAGADS or come from ADGC Special Analysis Groups supported by NIAGADS.
Title | Authors | Year | Journal | Link |
---|---|---|---|---|
Weighted burden analysis of exome-sequenced late-onset Alzheimer's cases and controls provides further evidence for a role for for PSEN1 and suggests involvement of the PI3K/Akt/GSK-3? and WNT signalling pathways |
David Curtis, Kaushiki Bakaya, Leona Sharma, and Sreejan Bandyopadhyay | 2020 | Annals of Human Genetics | PMID: 32020597 |
Human whole genome genotype and transcriptome data for Alzheimer’s and other neurodegenerative diseases | Allen M and Carrasquillo MM et al. | 2016 | Sci Data. 2016 Oct 11;3:160089 | PMID: 27727239 |
Rare TREM2 variants associated with Alzheimer’s disease display reduced cell surface expression | Sirkis DW, Bonham LW et al. | 2016 | Acta Neuropathol Commun. 2016 Sep 2;4(1):98 | PMID: 27589997 |
A loss of function variant in CASP7 protects against Alzheimer’s disease in homozygous APOE ε4 allele carriers | Ayers KL et al. | 2016 | BMC Genomics. 2016; 17(Suppl 2) | PubMed Central: PMC4928152 |
Age‐dependent effects of APOE ε4 in preclinical Alzheimer's disease | Bonham LW, Geier EG et al. | 2016 | Ann Clin Transl Neurol. 2016 Sep; 3(9) | PubMed Central: PMC5018579 |
JBrowse: a dynamic web platform for genome visualization and analysis | Buels R | 2016 | Genome Biol. 2016; 17: 66 | PMID: 27072794 |
Assessment of the genetic variance of late-onset Alzheimer's disease | Ridge PG et al. | 2016 | Neurobiol Aging. 2016 May; 41:200.e13-20. | PMID: 27036079 |
Association Between Genetic Traits for Immune-Mediated Diseases and Alzheimer Disease | Yokoyama JS et al. | 2016 | JAMA Neurol. 2016 Jun 1;73(6):691-7. | PMID: 27088644 |
Interaction between variants in CLU and MS4A4E modulates Alzheimer's disease risk | Ebbert MT et al. | 2016 | Alzheimers Dement. 2016 Feb;12(2):121-9. | PMID: 26449541 |
A novel Alzheimer disease locus located near the gene encoding tau protein | Jun G et al. | 2016 | Mol Psychiatry. 2016 Jan;21(1):108-17. | PMID: 25778476 |
Alzheimer’s Disease Risk Polymorphisms Regulate Gene Expression in the ZCWPW1 and the CELF1 Loci | Karch CM et al. | 2016 | PLoS One. 2016 Feb 26;11(2):e0148717. | PMID: 26919393 |
Genome-wide linkage analyses of non-Hispanic white families identify novel loci for familial late-onset Alzheimer’s disease | Kunkle BW et al. | 2016 | Alzheimers Dement. 2016 Jan;12(1):2-10. | PMID: 26365416 |
The executive prominent/memory prominent spectrum in Alzheimer’s disease is highly heritable | Mez J et al. | 2016 | Neurobiol Aging. 2016 May;41:115-21. | PMID: 27103524 |
Defining the Genetic Architecture of Alzheimer’s Disease: Where Next | Sims R and Williams J | 2016 | Neurodegener Dis. 2016;16(1-2):6-11. | PMID: 26550988 |
A multiancestral genome-wide exome array study of Alzheimer disease, frontotemporal dementia, and progressive supranuclear palsy | Chen JA et al. | 2015 | JAMA Neurol. 2015 Apr;72(4):414-22 | PMID: 25706306 |
Big Data for Advancing Dementia Research: An Evaluation of Data Sharing Practices in Research on Age-related Neurodegenerative Diseases | Deetjen U et al. | 2015 | OECD Digital Economy Papers, No. 246 | DOI: 10.1787/20716826 |
Genetic overlap between Alzheimer’s disease and Parkinson's disease at the MAPT locus | Desikan RS et al. | 2015 | Mol Psychiatry. 2015 Dec;20(12):1588-95. | PMID: 25687773 |
Association of Long Runs of Homozygosity With Alzheimer Disease Among African American Individuals | Ghani M | 2015 | JAMA Neurol. 2015 Nov;72(11):1313-23. | PMID: 26366463 |
Genetics of CD33 in Alzheimer’s disease and acute myeloid leukemia | Malik M et al. | 2015 | Hum Mol Genet. 2015 Jun 15;24(12):3557-70. | PMID: 25762156 |
PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences | Mirarab S et al. | 2015 | J Comput Biol. 2015 May;22(5):377-86. | PMID: 25549288 |
Genetic diagnosis and prognosis of Alzheimer’s disease: challenges and opportunities | Reitz C | 2015 | Expert Rev Mol Diagn. 2015 Mar;15(3):339-48. | PMID: 25634383 |
Next-generation gene discovery for variants of large impact on lipid traits | Rosenthal E et al. | 2015 | Curr Opin Lipidol. 2015 Apr;26(2):114-9. | PMID: 25636063 |
Polygenic Overlap Between C-Reactive Protein, Plasma Lipids, and Alzheimer Disease* | Desikan RS et al. | 2015 | Circulation. 2015 Jun 9;131(23):2061-9. | PMID: 25862742 |
Genetically predicted body mass index and Alzheimer’s disease-related phenotypes in three large samples: Mendelian randomization analyses* | Mukherjee S et al. | 2015 | Alzheimers Dement. 2015 Dec;11(12):1439-51. | PMID: 26079416 |
Rare coding variants in the phospholipase D3 gene confer risk for Alzheimer’s disease | Cruchaga C et al. | 2014 | Nature. 2014 Jan 23;505(7484):550-4. | PMID: 24336208 |
Next generation sequencing techniques in neurological diseases: redefining clinical and molecular associations | Guerreiro R et al. | 2014 | Hum Mol Genet. 2014 Sep 15;23(R1):R47-53. | PMID: 24794858 |
Genomics in neurological disorders | Han G et al. | 2014 | Genomics Proteomics Bioinformatics. 2014 Aug;12(4):156-63. | PMID: 25108264 |
Alzheimer’s disease genetics: from the bench to the clinic | Karch CM et al. | 2014 | Neuron. 2014 Jul 2;83(1):11-26. | PMID: 24991952 |
Genome-wide association study of CSF levels of 59 Alzheimer’s disease candidate proteins: significant associations with proteins involved in amyloid processing and inflammation* | Kauwe JS et al. | 2014 | PLoS Genet. 2014 Oct 23;10(10):e1004758. | PMID: 25340798 |
Association of MAPT haplotypes with Alzheimer’s disease risk and MAPT brain gene expression levels* | Allen M et al. | 2014 | Alzheimers Res Ther. 2014 Jul 1;6(4):39. | PMID: 25324900 |
Genetic variants in a “cAMP element binding protein” (CREB)-dependent histone acetylation pathway influence memory performance in cognitively healthy elderly individuals* | Barral S et al. | 2014 | Neurobiol Aging. 2014 Dec;35(12):2881.e7-2881.e10. | PMID: 25150575 |
Independent and epistatic effects of variants in VPS10-d receptors on Alzheimer disease risk and processing of the amyloid precursor protein (APP) | Reitz C et al. | 2013 | Transl Psychiatry. 2013 May 14;3:e256. | PMID: 23673467 |
Variants in the ATP-binding cassette transporter (ABCA7), apolipoprotein E ϵ4,and the risk of late-onset Alzheimer disease in African Americans | Reitz C et al. | 2013 | JAMA. 2013 Apr 10;309(14):1483-92. | PMID: 23571587 |
Alzheimer’s disease: analyzing the missing heritability | Ridge PG et al. | 2013 | PLoS One. 2013 Nov 7;8(11):e79771. | PMID: 24244562 |
Exceptional memory performance in the Long Life Family Study* | Barral S et al. | 2013 | Neurobiol Aging. 2013 Nov;34(11):2445-8. | PMID: 23759147 |
Alzheimer’s disease risk genes and the age-at-onset phenotype | Thambisetty M et al. | 2013 | Neurobiol Aging. 2013 Nov;34(11):2696.e1-5. | PMID: 23870418 |
Brain expression genome-wide association study (eGWAS) identifies human disease-associated variants | Zou F et al. | 2012 | PLoS Genet. 2012;8(6):e1002707. | PMID: 22685416 |
*Indicates NIAGADS-supported ADGC SAG publication