Jessica M. Maia's research works | Columbia University, NY (CU) and other places

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Fig 1. Scatterplot of Principal Component 1 (PC1) vs Principal...

Fig 2. Results of genome-wide association study of certolizumab pegol...

Fig 3. Fine mapping of regions with suggestive associations with DAS28...

Fig 4. Quantile-quantile (QQ) plots of results from candidate SNP...

Fig 5. Manhattan plots of significance scores from single-variant...

A genome-wide screen for variants influencing certolizumab pegol response in a moderate to severe rheumatoid arthritis population

Article

Full-text available

Apr 2022

Certolizumab pegol (CZP) is a PEGylated Fc-free tumor necrosis factor (TNF) inhibitor antibody approved for use in the treatment of rheumatoid arthritis (RA), Crohn’s disease, psoriatic arthritis, axial spondyloarthritis and psoriasis. In a clinical trial of patients with severe RA, CZP improved disease symptoms in approximately half of patients. H...

S3 Table

Data

Jul 2017

List of genes showing likely-gene-disrupting indels in GAERS genome as compared to BN reference genome. (XLSX)

S1 Table

Data

Jul 2017

List of genes showing gain or loss of stop codon, or splice acceptor/donor site in GAERS compared to BN reference genome. (XLSX)

S5 Table

Data

Jul 2017

Copy number variations (CNVs) between GAERS, NEC and BN genome predicted using ERDS. (XLSX)

S2 Table

Data

Jul 2017

List of genes showing missense codon specific to NEC compared to BN reference genome (i.e., absent in GAERS). (XLSX)

Evaluating whole genome sequence data from the Genetic Absence Epilepsy Rat from Strasbourg and its related non-epileptic strain

Article

Full-text available

Jul 2017

Objective The Genetic Absence Epilepsy Rats from Strasbourg (GAERS) are an inbreed Wistar rat strain widely used as a model of genetic generalised epilepsy with absence seizures. As in humans, the genetic architecture that results in genetic generalized epilepsy in GAERS is poorly understood. Here we present the strain-specific variants found among...

S4 Table

Data

Jul 2017

List of genes showing likely-gene-disrupting indels in NEC genome as compared to BN reference genome. (XLSX)

S6 Table

Data

Jul 2017

non-intergenic copy number variants (CNVs) specific to GAERS or NEC genome predicted using ERDS. (XLSX)

Figure S6

Data

Jun 2013

Same as Figure 2 except that weight is shown on the log10 scale. (PDF)

Figure S3

Data

Full-text available

Jun 2013

Distributions of the simulated liability values for exome sequencing samples. Dashed line marks median of the distribution of all samples, which was used to classify samples to cases and controls. (A): NOD2 data, where 12% of samples were risk allele carriers. (B): ITPA data, where 39% of samples were risk allele carriers. (PDF)

Figure S5

Data

Jun 2013

Distributions of standardized variant effect estimates from Bayesian liability model with phastCons weight and with r×phastCons weight. In each scenario (plot), effect estimates of Bayesian with phastCons weight (or r×phastCons) were collected from 200 replicates to form a distribution density. (PDF)

Text S1

Data

Full-text available

Jun 2013

Gibbs sampling in Bayesian liability regression model. (PDF)

Figure S 4: Heatmap plots showing the number of non-causal variants...

Figure S4

Data

Full-text available

Jun 2013

Heatmap plots showing the number of non-causal variants that were falsely identified as causal in each of the 200 replicates. Numbers on the right side of each plot are false positive rates averaged across replicates for different methods. (PDF)

Text S2

Data

Jun 2013

Exome sequencing data processing and quality control. (PDF)

Figure S 1: Upper: pairwise LD (r 2 ) of the 100 candidate variants in...

Figure S1

Data

Full-text available

Jun 2013

Upper: pairwise LD (r2) of the 100 candidate variants in NOD2 region in the exome sequencing data. Lower: LD (r) between each candidate variant and the GWAS signal. Causal variants are marked in red color. (PDF)

Text S3

Data

Full-text available

Jun 2013

Using simulation to demonstrate effect of clustering variants on power. (PDF)

Figure S 2: Same as Figure S1 but for the 338 candidate variants in...

Figure S2

Data

Full-text available

Jun 2013

Same as Figure S1 but for the 338 candidate variants in ITPA region. (PDF)

Leveraging Prior Information to Detect Causal Variants via Multi-Variant Regression

Article

Full-text available

Jun 2013

Author Summary The decline in DNA sequencing cost permits the interrogation of potentially all variants across the entire allele frequency spectrum for their associations with complex human diseases and traits. However, the identification of causal variants remains challenging. Existing single variant tests do not distinguish between causal associa...

Using ERDS to Infer Copy-Number Variants in High-Coverage Genomes

Article

Aug 2012

Although there are many methods available for inferring copy-number variants (CNVs) from next-generation sequence data, there remains a need for a system that is computationally efficient but that retains good sensitivity and specificity across all types of CNVs. Here, we introduce a new method, estimation by read depth with single-nucleotide varia...

Prioritizing Genetic Variants for Causality on the Basis of Preferential Linkage Disequilibrium

Article

Aug 2012

To date, the widely used genome-wide association studies (GWASs) of the human genome have reported thousands of variants that are significantly associated with various human traits. However, in the vast majority of these cases, the causal variants responsible for the observed associations remain unknown. In order to facilitate the identification of...

Exome Sequencing Followed by Large-Scale Genotyping Suggests a Limited Role for Moderately Rare Risk Factors of Strong Effect in Schizophrenia

Article

Aug 2012

Schizophrenia is a severe psychiatric disorder with strong heritability and marked heterogeneity in symptoms, course, and treatment response. There is strong interest in identifying genetic risk factors that can help to elucidate the pathophysiology and that might result in the development of improved treatments. Linkage and genome-wide association...

Exome Sequencing Followed by Large-Scale Genotyping Fails to Identify Single Rare Variants of Large Effect in Idiopathic Generalized Epilepsy

Article

Full-text available

Aug 2012

Idiopathic generalized epilepsy (IGE) is a complex disease with high heritability, but little is known about its genetic architecture. Rare copy-number variants have been found to explain nearly 3% of individuals with IGE; however, it remains unclear whether variants with moderate effect size and frequencies below what are reliably detected with ge...

A whole-genome analysis of premature termination codons

Article

Jul 2011

We sequenced the genomes of ten unrelated individuals and identified heterozygous stop codon-gain variants in protein-coding genes: we then sequenced their transcriptomes and assessed the expression levels of the stop codon-gain alleles. An ANOVA showed statistically significant differences between their expression levels (p=4×10(-16)). This differ...

Supplementary Data

Data

May 2011

SVA: Software for Annotating and Visualizing Sequenced Human Genomes

Article

Full-text available

May 2011

Here we present Sequence Variant Analyzer (SVA), a software tool that assigns a predicted biological function to variants identified in next-generation sequencing studies and provides a browser to visualize the variants in their genomic contexts. SVA also provides for flexible interaction with software implementing variant association tests allowin...

A Genome-wide Comparison of the Functional Properties of Rare and Common Genetic Variants in Humans

Article

Mar 2011

One of the longest running debates in evolutionary biology concerns the kind of genetic variation that is primarily responsible for phenotypic variation in species. Here, we address this question for humans specifically from the perspective of population allele frequency of variants across the complete genome, including both coding and noncoding re...

Figure S1

Data

Sep 2010

Location of identified variants observed across all 20 genomes. These graphs show the functional distribution of SNVs (A) and indels (B) based on their location in relation to annotated transcripts. (1.65 MB TIF)

Table S7

Data

Sep 2010

Comparison of transition to transversion ratios and homozygote to heterozygote ratios. (0.05 MB DOC)

Table S2

Data

Sep 2010

Variants identified for each individual genome. (0.04 MB DOC)

Table S5

Data

Sep 2010

Number of indels identified in whole-genome sequencing studies and in dbSNP. (0.06 MB DOC)

Table S3

Data

Sep 2010

Overlap of SNVs identified by sequencing with those that are included in the dbSNP database, HapMap, or are on the Illumina 1M chip, version 1. (0.06 MB DOC)

Table S6

Data

Sep 2010

Transition to transversion ratios and homozygote to heterozygote ratios. (0.04 MB DOC)

Table S14

Data

Sep 2010

Prioritization of all genes enriched for protein truncating variants in hemophilia samples. (0.04 MB DOC)

Table S1

Data

Sep 2010

General characteristics for each genome. (0.06 MB DOC)

Table S13

Data

Sep 2010

Causal variants of type A hemophilia observed in this study. (0.04 MB DOC)

Text S1

Data

Sep 2010

Supplementary methods. (0.04 MB DOC)

Table S4

Data

Sep 2010

Overlap of dbSNP and SNVs identified by sequencing. (0.05 MB DOC)

Table S11

Data

Sep 2010

Comparison of individual average number of coding indels, restricted to exome captured regions and canonical genes and transcripts. (0.04 MB DOC)

Figure S3

Data

Sep 2010

F8 variants. This image shows the positions of the F8 variants that were observed in our dataset. Image modified from Ge et al. and Hubbard et al. (0.09 MB TIF)

Table S9

Data

Sep 2010

SNVs by their function and predicted number of homozygotes. (0.07 MB DOC)

Table S12

Data

Sep 2010

Validating protein-truncating variants using Sanger sequencing. (0.05 MB DOC)

Table S8

Data

Sep 2010

Comparison of SNV calls made from whole-genome sequence versus genotype data. (0.05 MB DOC)

Figure S2

Data

Sep 2010

Position of protein truncating variants within coding sequences. These graphs show the relative locations of stop-gain SNVs (A) and frameshift indels (B) within protein-coding sequences. A relative location near 0.1 (left side of x-axis) indicates that the variant is near the N-terminus, while a location near 1.0 (right side of x-axis) indicates th...

Table S10

Data

Sep 2010

Indels by their function and homozygosity. (0.06 MB DOC)

The Characterization of Twenty Sequenced Human Genomes

Article

Full-text available

Sep 2010

We present the analysis of twenty human genomes to evaluate the prospects for identifying rare functional variants that contribute to a phenotype of interest. We sequenced at high coverage ten "case" genomes from individuals with severe hemophilia A and ten "control" genomes. We summarize the number of genetic variants emerging from a study of this...

Text S1

Data

Jun 2010

Supplementary methods and figures. (3.28 MB DOC)

Whole-Genome Sequencing of a Single Proband Together with Linkage Analysis Identifies a Mendelian Disease Gene

Article

Full-text available

Jun 2010

Author Summary Metachondromatosis (MC) is an autosomal dominant condition characterized by exostoses (osteochondromas), commonly of the hands and feet, and enchondromas of long bone metaphyses and iliac crests. MC exostoses may regress or even resolve over time, and short stature is not characteristic of MC. Here, we sequenced the whole genome of a...

Research Screening the human exome: a comparison of whole genome and whole transcriptome sequencing

Article

Full-text available

May 2010

There is considerable interest in the development of methods to efficiently identify all coding variants present in large sample sets of humans. There are three approaches possible: whole-genome sequencing, whole-exome sequencing using exon capture methods, and RNA-Seq. While whole-genome sequencing is the most complete, it remains sufficiently exp...

Additional file 1

Data

May 2010

Supplemental figures S1 to S4. Showing the specificity at different read depth levels and the overlap with dbSNP entries at different coverage levels and different expression levels.

Rare Deletions at 16p13.11 Predispose to a Diverse Spectrum of Sporadic Epilepsy Syndromes

Article

Full-text available

May 2010

Deletions at 16p13.11 are associated with schizophrenia, mental retardation, and most recently idiopathic generalized epilepsy. To evaluate the role of 16p13.11 deletions, as well as other structural variation, in epilepsy disorders, we used genome-wide screens to identify copy number variation in 3812 patients with a diverse spectrum of epilepsy s...

Diversification in the genetic architecture of gene expression and transcriptional networks in organ differentiation of Populus

Article

Full-text available

May 2010

A fundamental goal of systems biology is to identify genetic elements that contribute to complex phenotypes and to understand how they interact in networks predictive of system response to genetic variation. Few studies in plants have developed such networks, and none have examined their conservation among functionally specialized organs. Here we u...

Host Determinants of HIV-1 Control in African Americans

Article

Full-text available

Mar 2010

We performed a whole-genome association study of human immunodeficiency virus type 1 (HIV-1) set point among a cohort of African Americans (n=515), and an intronic single-nucleotide polymorphism (SNP) in the HLA-B gene showed one of the strongest associations. We use a subset of patients to demonstrate that this SNP reflects the effect of the HLA-B...

Rare deletions at 16p13. 11 predispose to a diverse spectrum of sporadic epilepsy syndromes

Article

Jan 2010

A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB

Article

Full-text available

Oct 2009

Psychiatric disorders such as schizophrenia are commonly accompanied by cognitive impairments that are treatment resistant and crucial to functional outcome. There has been great interest in studying cognitive measures as endophenotypes for psychiatric disorders, with the hope that their genetic basis will be clearer. To investigate this, we perfor...

Correction: A Genome-Wide Investigation of SNPs and CNVs in Schizophrenia

Article

Full-text available

Mar 2009

Table S3

Data

Feb 2009

Pathway analysis for genes disrupted by large rare copy number variations in schizophrenia patients and controls. (0.12 MB DOC)

Figure S4

Data

Feb 2009

The expression of ADAMTSL3 in the mouse forebrain as depicted in the Allen Brain Atlas. Highlighted is high expression in the pyramidal cell layer of the hippocampal formation (including CA1 and CA3 regions). We used information provided by the Allen Mouse Brain Atlas (http://www.brain-map.org) to determine the likelihood that a gene classified as...

Figure S3

Data

Feb 2009

Evidence of the genetic control of ADAMTSL3 exon 30 alternative splicing in human brain tissue. Correlation of the ADAMTSL3 rs950169 genotype with the relative abundance of transcripts in the prefrontal cortex of control (•) and Alzheimer's disease brain tissue (◊). Bars indicate the means of combined controls and Alzheimer's disease patients trans...

Text S1

Data

Full-text available

Feb 2009

Supplementary methods and results. (0.09 MB PDF)

Figure S1

Data

Feb 2009

Schematic of exons 29–30 of the ADAMTSL3 gene and evidence of the presence of four alternative transcripts. A. Exons 29 and 30 are depicted as blue boxes and the PLAC domain coding part of gene is striped. The alternative splice donor site (ASD) and alternative splice acceptor site (ASA) are indicated by the black lines, while the locations of ADAM...

Table S1

Data

Feb 2009

Association results in this dataset presented for the Aberdeen cohort for loci implicated in O'Donovan et al. [1]. (0.04 MB DOC)

Figure S2

Data

Feb 2009

Evidence of the genetic control of ADAMTSL3 exon 30 alternative splicing in human brain tissue. Correlation of the ADAMTSL3 rs950169 genotype with the relative abundance of transcripts containing shorter exon 30 due to usage of alternative splice acceptor site (RSD-ASA) and full reference exon 30 (RSD-RSA) in the prefrontal cortex of control (•) an...

Table S2

Data

Feb 2009

Association results in this dataset for SNPs previously implicated in schizophrenia GWAS studies. (0.15 MB DOC)

A Genome-Wide Investigation of SNPs and CNVs in Schizophrenia

Article

Full-text available

Feb 2009

We report a genome-wide assessment of single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) in schizophrenia. We investigated SNPs using 871 patients and 863 controls, following up the top hits in four independent cohorts comprising 1,460 patients and 12,995 controls, all of European origin. We found no genome-wide significant asso...

Tissue-Specific Genetic Control of Splicing: Implications for the Study of Complex Traits

Article

Full-text available

Jan 2009

Author Summary Although humans have a relatively small complement of genes, the proteins encoded by those genes and their biologic function are far more complex. The increased complexity is achieved in part through processes that create different messages from the same gene sequence (alternative splicing) and that regulate the expression of those...

Table S1

Data

Dec 2008

Sample Demographics (48 KB RTF)

Table S2

Data

Dec 2008

Lower Confidence cis-Acting SNPs That Were Shown in This Study to Influence Transcript Level Expression (321 KB RTF)

Table S4

Data

Dec 2008

Table of Associations between Consensus Site SNPs and Adjacent Exons (285 KB RTF)

Table S3

Data

Dec 2008

Lower Confidence cis-Acting SNPs That Were Shown in This Study to Influence Exon-Level Expression (4.3 MB RTF)

Table S5

Data

Dec 2008

A List of Genome-wide Association Studies Interrogated for Significant Associations That Affect Expression and Splicing in the SNPExpress Database. Full references are provided below this table. (459 KB RTF)