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List of works by Joel S. Bader

"Perfect" designer chromosome V and behavior of a ring derivative

scientific article

3D organization of synthetic and scrambled chromosomes.

scientific article published in March 2017

A DNA integrity network in the yeast Saccharomyces cerevisiae

scientific article (publication date: 10 March 2006)

A Robust Toolkit for Functional Profiling of the Yeast Genome

scientific article published on 01 November 2004

A comprehensive synthetic genetic interaction network governing yeast histone acetylation and deacetylation

scientific article

A protein interaction map of Drosophila melanogaster

scientific article (publication date: 5 December 2003)

A systems biology analysis of the Drosophila phagosome

scientific article

Analysis of VEGF--a regulated gene expression in endothelial cells to identify genes linked to angiogenesis

scientific article published in 2011

Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets

scientific article

Analytical approximations for the amplitude and period of a relaxation oscillator

scientific article published on 14 January 2009

Angiogenesis-associated crosstalk between collagens, CXC chemokines, and thrombospondin domain-containing proteins

scientific article published on 18 May 2011

Assembling DNA fragments by USER fusion

scientific article

Assembling large DNA segments in yeast

scientific article published in January 2012

BRCA1 and S phase DNA repair pathways restrict LINE-1 retrotransposition in human cells

scientific article published on 10 February 2020

Between-tumor and within-tumor heterogeneity in invasive potential

scientific article published on 21 January 2020

Bug mapping and fitness testing of chemically synthesized chromosome X.

scientific article

CLONEQC: lightweight sequence verification for synthetic biology

scientific article

Commensurate distances and similar motifs in genetic congruence and protein interaction networks in yeast

scientific article

Comparisons of tyrosine phosphorylated proteins in cells expressing lung cancer-specific alleles of EGFR and KRAS

scholarly article

Comprehensive evaluation of imputation performance in African Americans

scientific article

Constructing the angiome: a global angiogenesis protein interaction network

scientific article

DNA Pooling: a tool for large-scale association studies

scientific article

Decoding transcriptional regulatory interactions

scientific article published on December 2006

Design of a synthetic yeast genome.

scientific article

Design-A-Gene with GeneDesign

article

Differential transport of DNA by a rectified Brownian motion device

scientific article published on 01 January 2000

Dynamic networks from hierarchical bayesian graph clustering

scientific article

Engineering the ribosomal DNA in a megabase synthetic chromosome

scientific article published in March 2017

Family-based association tests for quantitative traits using pooled DNA

Finding friends and enemies in an enemies-only network: a graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions

scientific article published on 2 October 2008

Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK

retracted paper

Gaining confidence in high-throughput protein interaction networks

scientific article published on 14 December 2003

Gene synthesis demystified

scientific article published on 26 December 2008

Gene-based tests of association

scientific article

GeneDesign 3.0 is an updated synthetic biology toolkit

scientific article

Genetic Determinants of Intrinsic Antibiotic Tolerance in Mycobacterium avium

scientific article published on 15 September 2021

Genetic Interaction Motif Finding by expectation maximization--a novel statistical model for inferring gene modules from synthetic lethality

scientific article

Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization

scientific article

Genetic interaction mapping informs integrative structure determination of protein complexes

scientific article published on 01 December 2020

Genome analysis of Mycobacterium avium subspecies hominissuis strain 109

scientific article published on 04 December 2018

Genome sequencing in microfabricated high-density picolitre reactors

scientific article

Genome-wide association meta-analysis of PR interval identifies 47 novel loci associated with atrial and atrioventricular electrical activity

Global synthetic-lethality analysis and yeast functional profiling

scientific article

Grand network convergence ⬇️

scientific article published on June 17, 2011

Greedily building protein networks with confidence

scientific article published on October 2003

HapZipper: sharing HapMap populations just got easier

scientific article

Heterozygous diploid and interspecies SCRaMbLEing.

scientific article

HistoneHits: a database for histone mutations and their phenotypes

scientific article published on 13 February 2009

How networks change with time

scientific article

Human Proteinpedia enables sharing of human protein data

scientific article

Identifying the essential genes of Mycobacterium avium subsp. hominissuis with Tn-Seq using a rank-based filter procedure

scientific article published on 23 January 2020

Inhibiting the stringent response blocks entry into quiescence and reduces persistence

scientific article published on 20 March 2019

Metabolic flux correlations, genetic interactions, and disease

scientific article

Modeling intercellular transfer of biomolecules through tunneling nanotubes

scientific article published on 16 February 2013

Morphology-guided transcriptomic analysis of human pancreatic cancer organoids reveals microenvironmental signals that enhance invasion

scientific article published in 2023

NeMo: Network Module identification in Cytoscape

scientific article

New connections, new components, real dynamics

scientific article published on 4 August 2009

Next-generation large-scale binary protein interaction network for Drosophila

preprint published on 3 August 2022

Next-generation large-scale binary protein interaction network for Drosophila melanogaster

scientific article published on 15 April 2023

Novel peptide-specific quantitative structure-activity relationship (QSAR) analysis applied to collagen IV peptides with antiangiogenic activity

scientific article published on 13 September 2011

PR interval genome-wide association meta-analysis identifies 50 loci associated with atrial and atrioventricular electrical activity

scientific article published in Nature Communications

Precision and recall estimates for two-hybrid screens

scientific article published on 17 December 2008

Predicting functional associations from metabolism using bi-partite network algorithms

scientific article

Priors, population sizes, and power in genome-wide hypothesis tests

scientific article published in 2023

Probabilistic inference of molecular networks from noisy data sources

scientific article

Probing nucleosome function: a highly versatile library of synthetic histone H3 and H4 mutants

scientific article

Profiling diverse compounds by flux- and electrophysiology-based primary screens for inhibition of human Ether-à-go-go related gene potassium channels

scientific article

RNA interference analysis of Legionella in Drosophila cells: exploitation of early secretory apparatus dynamics

scientific article published on 28 April 2006

Resolving the structure of interactomes with hierarchical agglomerative clustering

scientific article (publication date: 15 February 2011)

Response to Dr Stephen Cooper's ‘On the use of metaphor to understand, explain, or rationalize redundant genes in yeast’

article

Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond.

scientific article

Synthetic chromosome arms function in yeast and generate phenotypic diversity by design

scientific article published on 14 September 2011

Systems approaches for pharmacogenetics and pharmacogenomics

Systems biology. When proteomes collide

scientific article

Teaching synthetic biology, bioinformatics and engineering to undergraduates: the interdisciplinary Build-a-Genome course

scientific article

Temporal profiling of the secretome during adipogenesis in humans

scientific article

The Build-a-Genome course

scientific article published in January 2012

The NIH Protein Capture Reagents Program (PCRP): a standardized protein affinity reagent toolbox

scientific article published in September 2016

The minimum information required for reporting a molecular interaction experiment (MIMIx).

scientific article published on August 2007

The relative power of SNPs and haplotype as genetic markers for association tests.

scientific article

Theory of correlated hops in surface diffusion

scientific article published in Physical Review Letters

Tissue matrix arrays for high-throughput screening and systems analysis of cell function

scientific article

Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps

scientific article

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