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2021

2021,  
Nature Communications

Common variants in Alzheimer's disease and risk stratification by polygenic risk scores

de Rojas, I., et al.
2021,  
Scientific Reports

Reconcile the debate over protective effects of BCG vaccine against COVID-19

Fu, W., et al.
2021,  
JAMA neurology

Novel Alzheimer Disease Risk Loci and Pathways in African American Individuals Using the African Genome Resources Panel: A Meta-analysis

Kunkle, BW., et al.
2021,  
Methods in Molecular Biology (Clifton, N.J.)

Using INFERNO to Infer the Molecular Mechanisms Underlying Noncoding Genetic Associations

Amlie-Wolf, A., et al.

2020

2020,  
Nature Genetics

An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer's disease

Nativio, R., et al.
2020,  
Neurobiology of Aging

LRP10 variants in progressive supranuclear palsy

Vergouw, LJM., et al.
2020,  
Alzheimer's & Dementia: The Journal of the Alzheimer's Association

Circulating ethanolamine plasmalogen indices in Alzheimer's disease: Relation to diagnosis, cognition, and CSF tau

Kling, MA., et al.
2020,  
Brain: A Journal of Neurology

Genetic variants and functional pathways associated with resilience to Alzheimer's disease

Dumitrescu, L., et al.
2020,  
Molecular Psychiatry

Whole exome sequencing study identifies novel rare and common Alzheimer's-Associated variants involved in immune response and transcriptional regulation

Bis, JC., et al.
2020,  
Bioinformatics (Oxford, England)

SparkINFERNO: a scalable high-throughput pipeline for inferring molecular mechanisms of non-coding genetic variants

Kuksa, PP., et al.
2020,  
NAR genomics and bioinformatics

HIPPIE2: a method for fine-scale identification of physically interacting chromatin regions

Kuksa, PP., et al.
2020,  
Nature Communications

Exceptionally low likelihood of Alzheimer's dementia in APOE2 homozygotes from a 5,000-person neuropathological study

Reiman, EM., et al.
2020,  
Computational and Structural Biotechnology Journal

HiPR: High-throughput probabilistic RNA structure inference

Kuksa, PP., et al.
2020,  
Journal of Alzheimer's disease: JAD

A Coordinated Approach by Public Domain Bioinformatics Resources to Aid the Fight Against Alzheimer's Disease Through Expert Curation of Key Protein Targets

Breuza, L., et al.

2019

2019,  
Genomics

Quality control and integration of genotypes from two calling pipelines for whole genome sequence data in the Alzheimer's disease sequencing project

Naj, AC., et al.
2019,  
Bioinformatics (Oxford, England)

VCPA: genomic variant calling pipeline and data management tool for Alzheimer's Disease Sequencing Project

Leung, YY., et al.
2019,  
Bioinformatics (Oxford, England)

DASHR 2.0: integrated database of human small non-coding RNA genes and mature products

Kuksa, PP., et al.
2019,  
Oncogene

Targeting EIF4E signaling with ribavirin in infant acute lymphoblastic leukemia

Urtishak, KA., et al.
2019,  
Nature Genetics

Genetic meta-analysis of diagnosed Alzheimer's disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing

Kunkle, BW., et al.
2019,  
Journal of Alzheimer's disease: JAD

Inferring the Molecular Mechanisms of Noncoding Alzheimer's Disease-Associated Genetic Variants

Amlie-Wolf, A., et al.

2018

2018,  
Nucleic Acids Research

INFERNO: inferring the molecular mechanisms of noncoding genetic variants

Amlie-Wolf, A., et al.
2018,  
Bioinformatics (Oxford, England)

Functional annotation of genomic variants in studies of late-onset Alzheimer's disease

Butkiewicz, M., et al.
2018,  
Bioinformatics (Oxford, England)

Integrative DNA copy number detection and genotyping from sequencing and array-based platforms

Zhou, Z., et al.
2018,  
Molecular Neurodegeneration

Replication of progressive supranuclear palsy genome-wide association study identifies SLCO1A2 and DUSP10 as new susceptibility loci

Sanchez-Contreras, MY., et al.
2018,  
Nucleic Acids Research

SPAR: small RNA-seq portal for analysis of sequencing experiments

Kuksa, PP., et al.
2018,  
Nature Neuroscience

Dysregulation of the epigenetic landscape of normal aging in Alzheimer's disease

Nativio, R., et al.
2018,  
Annals of Clinical and Translational Neurology

Whole genome sequencing of Caribbean Hispanic families with late-onset Alzheimer's disease

Vardarajan, BN., et al.
2018,  
Dementia and Geriatric Cognitive Disorders

Genetic Variation in Genes Underlying Diverse Dementias May Explain a Small Proportion of Cases in the Alzheimer's Disease Sequencing Project

Blue, EE., et al.

2017

2017,  
Genome Biology

McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes

Hafez, D., et al.
2017,  
JAMA neurology

Apolipoprotein E Genotype and Sex Risk Factors for Alzheimer Disease: A Meta-analysis

Neu, SC., et al.
2017,  
JAMA neurology

Early-Onset Alzheimer Disease and Candidate Risk Genes Involved in Endolysosomal Transport

Kunkle, BW., et al.
2017,  
Nature Genetics

Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease

Sims, R., et al.
2017,  
Alzheimer's & Dementia: The Journal of the Alzheimer's Association

Transethnic genome-wide scan identifies novel Alzheimer's disease loci

Jun, GR., et al.
2017,  
Methods in Molecular Biology (Clifton, N.J.)

In Silico Identification of RNA Modifications from High-Throughput Sequencing Data Using HAMR

Kuksa, PP., et al.

2016

2016,  
PLoS genetics

Rare Functional Variant in TM2D3 is Associated with Late-Onset Alzheimer's Disease

Jakobsdottir, J., et al.
2016,  
Pediatric Blood & Cancer

Unique Familial MLL(KMT2A)-Rearranged Precursor B-Cell Infant Acute Lymphoblastic Leukemia in Non-twin Siblings

Urtishak, KA., et al.
2016,  
Neurology. Genetics

ABCA7 frameshift deletion associated with Alzheimer disease in African Americans

Cukier, HN., et al.
2016,  
BMC bioinformatics

A comprehensive database of high-throughput sequencing-based RNA secondary structure probing data (Structure Surfer)

Berkowitz, ND., et al.
2016,  
Neurobiology of Aging

Assessment of the genetic variance of late-onset Alzheimer's disease

Ridge, PG., et al.
2016,  
Alzheimer's & Dementia: The Journal of the Alzheimer's Association

Global and local ancestry in African-Americans: Implications for Alzheimer's disease risk

Hohman, TJ., et al.
2016,  
Nucleic Acids Research

DASHR: database of small human noncoding RNAs

Leung, YY., et al.
2016,  
Alzheimer's & Dementia: The Journal of the Alzheimer's Association

Genome-wide linkage analyses of non-Hispanic white families identify novel loci for familial late-onset Alzheimer's disease

Kunkle, BW., et al.
2016,  
Frontiers in Aging Neuroscience

Changes in the Transcriptome of Human Astrocytes Accompanying Oxidative Stress-Induced Senescence

Crowe, EP., et al.

2015

2015,  
Alzheimer's & Dementia: The Journal of the Alzheimer's Association

The role of TREM2 R47H as a risk factor for Alzheimer's disease, frontotemporal lobar degeneration, amyotrophic lateral sclerosis, and Parkinson's disease

Lill, CM., et al.
2015,  
Alzheimer's & Dementia: The Journal of the Alzheimer's Association

Genetically predicted body mass index and Alzheimer's disease-related phenotypes in three large samples: Mendelian randomization analyses

Mukherjee, S., et al.
2015,  
JAMA neurology

Association of Long Runs of Homozygosity With Alzheimer Disease Among African American Individuals

Ghani, M., et al.
2015,  
The Plant Cell

Chemical Modifications Mark Alternatively Spliced and Uncapped Messenger RNAs in Arabidopsis

Vandivier, LE., et al.
2015,  
Alzheimer's & Dementia (Amsterdam, Netherlands)

Identifying amyloid pathology-related cerebrospinal fluid biomarkers for Alzheimer's disease in a multicohort study

Leung, YY., et al.
2015,  
Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences

Solutions to Peto's paradox revealed by mathematical modelling and cross-species cancer gene analysis

Caulin, AF., et al.
2015,  
Nature Communications

Genome-wide association study of corticobasal degeneration identifies risk variants shared with progressive supranuclear palsy

Kouri, N., et al.
2015,  
Journal of Computational Biology: A Journal of Computational Molecular Cell Biology

PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences

Mirarab, S., et al.
2015,  
Bioinformatics (Oxford, England)

HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements

Hwang, Y., et al.
2015,  
JAMA neurology

Rarity of the Alzheimer disease-protective APP A673T variant in the United States

Wang, L., et al.
2015,  
Journal of Neuropathology and Experimental Neurology

Reassessment of risk genotypes (GRN, TMEM106B, and ABCC9 variants) associated with hippocampal sclerosis of aging pathology

Nelson, PT., et al.
2015,  
PloS One

Transcriptomic Changes Due to Cytoplasmic TDP-43 Expression Reveal Dysregulation of Histone Transcripts and Nuclear Chromatin

Amlie-Wolf, A., et al.

2014

2014,  
Nature

Synaptic, transcriptional and chromatin genes disrupted in autism

De Rubeis, S., et al.
2014,  
JAMA neurology

Effects of multiple genetic loci on age at onset in late-onset Alzheimer disease: a genome-wide association study

Naj, AC., et al.
2014,  
Journal of Immunology (Baltimore, Md.: 1950)

IL-18 synergizes with IL-7 to drive slow proliferation of naive CD8 T cells by costimulating self-peptide-mediated TCR signals

Walsh, MC., et al.
2014,  
Methods (San Diego, Calif.)

Using machine learning and high-throughput RNA sequencing to classify the precursors of small non-coding RNAs

Ryvkin, P., et al.
2014,  
Acta Neuropathologica

ABCC9 gene polymorphism is associated with hippocampal sclerosis of aging pathology

Nelson, PT., et al.
2014,  
PloS One

Gene-wide analysis detects two new susceptibility genes for Alzheimer's disease

Escott-Price, V., et al.

2013

2013,  
The Journal of Comparative Neurology

Comparative survey of the topographical distribution of signature molecular lesions in major neurodegenerative diseases

Arnold, SE., et al.
2013,  
RNA (New York, N.Y.)

HAMR: high-throughput annotation of modified ribonucleotides

Ryvkin, P., et al.
2013,  
Nature Genetics

Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease

Lambert, JC., et al.
2013,  
Current Protocols in Human Genetics

Analyzing copy number variation using SNP array data: protocols for calling CNV and association tests

Lin, C., et al.
2013,  
Bioinformatics (Oxford, England)

DRAW+SneakPeek: analysis workflow and quality metric management for DNA-seq experiments

Lin, C., et al.
2013,  
Nucleic Acids Research

CoRAL: predicting non-coding RNAs from small RNA-sequencing data

Leung, YY., et al.
2013,  
Genes & Development

Rap1 relocalization contributes to the chromatin-mediated gene expression profile and pace of cell senescence

Platt, JM., et al.
2013,  
Nucleic Acids Research

High-throughput identification of long-range regulatory elements and their target promoters in the human genome

Hwang, Y., et al.
2013,  
JAMA

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,  
Blood

Potent obatoclax cytotoxicity and activation of triple death mode killing across infant acute lymphoblastic leukemia

Urtishak, KA., et al.
2013,  
Neuron

Rare complete knockouts in humans: population distribution and significant role in autism spectrum disorders

Lim, ET., et al.
2013,  
Neurobiology of Aging

Cellular, synaptic, and biochemical features of resilient cognition in Alzheimer's disease

Arnold, SE., et al.
2013,  
Journal of Alzheimer's disease: JAD

Frequency and clinicopathological characteristics of presenilin 1 Gly206Ala mutation in Puerto Rican Hispanics with dementia

Arnold, SE., et al.
2013,  
PloS One

SORL1 is genetically associated with late-onset Alzheimer's disease in Japanese, Koreans and Caucasians

Miyashita, A., et al.
2013,  
PloS One

Analysis of nonlinear gene expression progression reveals extensive pathway and age-specific transitions in aging human brains

Cao, K., et al.

2012

2012,  
BMC evolutionary biology

Evolutionary genomics of host-use in bifurcating demes of RNA virus phi-6

Turner, PE., et al.
2012,  
Human Molecular Genetics

Evidence for a role of the rare p.A152T variant in MAPT in increasing the risk for FTD-spectrum and Alzheimer's diseases

Coppola, G., et al.
2012,  
Archives of Neurology

Comparison of cerebrospinal fluid levels of tau and Aβ 1-42 in Alzheimer disease and frontotemporal degeneration using 2 analytical platforms

Irwin, DJ., et al.
2012,  
Nucleic Acids Research

SAVoR: a server for sequencing annotation and visualization of RNA structures

Li, F., et al.
2012,  
Bioinformatics (Oxford, England)

DACTAL: divide-and-conquer trees (almost) without alignments

Nelesen, S., et al.
2012,  
Nature

Patterns and rates of exonic de novo mutations in autism spectrum disorders

Neale, BM., et al.
2012,  
Nature

The microRNA miR-34 modulates ageing and neurodegeneration in Drosophila

Liu, N., et al.
2012,  
Cell Reports

Global analysis of RNA secondary structure in two metazoans

Li, F., et al.
2012,  
Translational Psychiatry

Plasma biomarkers of depressive symptoms in older adults

Arnold, SE., et al.
2012,  
Journal of Alzheimer's disease: JAD

Comparison of xMAP and ELISA assays for detecting cerebrospinal fluid biomarkers of Alzheimer's disease

Wang, L., et al.

2011

2011,  
Journal of Immunology (Baltimore, Md.: 1950)

Selection of individual VH genes occurs at the pro-B to pre-B cell transition

Meng, W., et al.
2011,  
IEEE/ACM transactions on computational biology and bioinformatics

The impact of multiple protein sequence alignment on phylogenetic estimation

Wang, L., et al.
2011,  
Nature Genetics

Identification of common variants influencing risk of the tauopathy progressive supranuclear palsy

Höglinger, GU., et al.
2011,  
Nature Genetics

Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease

Naj, AC., et al.

2010

2010,  
Archives of Neurology

Meta-analysis confirms CR1, CLU, and PICALM as alzheimer disease risk loci and reveals interactions with APOE genotypes

Jun, G., et al.
2010,  
BMC neurology

Genome-wide association reveals genetic effects on human Aβ42 and τ protein levels in cerebrospinal fluids: a case control study

Han, M., et al.
2010,  
PLoS genetics

Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis

Zheng, Q., et al.
2010,  
PloS One

Age-correlated gene expression in normal and neurodegenerative human brain tissues

Cao, K., et al.
2010,  
BMC medical genetics

Population-based study of genetic variation in individuals with autism spectrum disorders from Croatia

Wang, L., et al.
2010,  
Bioinformatics (Oxford, England)

Correcting population stratification in genetic association studies using a phylogenetic approach

Li, M., et al.
2010,  
Nucleic Acids Research

Altered gene expression in the Werner and Bloom syndromes is associated with sequences having G-quadruplex forming potential

Johnson, JE., et al.
2010,  
Alzheimer's & Dementia: The Journal of the Alzheimer's Association

Design of comprehensive Alzheimer's disease centers to address unmet national needs

Trojanowski, JQ., et al.
2010,  
Nature Genetics

Common variants at 7p21 are associated with frontotemporal lobar degeneration with TDP-43 inclusions

Van Deerlin, VM., et al.
2010,  
Methods in Molecular Biology (Clifton, N.J.)

Computational approaches to the detection and analysis of sequences with intramolecular G-quadruplex forming potential

Ryvkin, P., et al.

2009

2009,  
Nature

Enhancing CD8 T-cell memory by modulating fatty acid metabolism

Pearce, EL., et al.
2009,  
BMC bioinformatics

A Bayesian approach to efficient differential allocation for resampling-based significance testing

Jensen, ST., et al.
2009,  
PloS One

Genomic landscape of a three-generation pedigree segregating affective disorder

Yang, S., et al.

2008

2008,  
Nucleic Acids Research

Genomic distribution and functional analyses of potential G-quadruplex-forming sequences in Saccharomyces cerevisiae

Hershman, SG., et al.

2007

2007,  
Nucleic Acids Research

TREMOR--a tool for retrieving transcriptional modules by incorporating motif covariance

Singh, LN., et al.

2006

2006,  
Journal of Molecular Evolution

Distance-based genome rearrangement phylogeny

Wang, L., et al.

2005

2005,  
PLoS biology

The cobweb of life revealed by genome-scale estimates of horizontal gene transfer

Ge, F., et al.
2005,  
Bioinformatics (Oxford, England)

Enhanced position weight matrices using mixture models

Hannenhalli, S.

2002

2002,  
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

Fast phylogenetic methods for the analysis of genome rearrangement data: an empirical study

Wang, L., et al.
2002,  
Bioinformatics (Oxford, England)

Statistically based postprocessing of phylogenetic analysis by clustering

Stockham, C., et al.