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
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