Publications

NIAGADS Publications

Title Authors Year Journal Link
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:

PMC4869249

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:

PMC4702848

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:

PMC4624943

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:

PMC4393516

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:

PMC3991776

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:

PMC3643598

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:

PMC3737537

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:

PMC4015338

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:

PMC3777113

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:

PMC3884653

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-3𝛃 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