Research Papers

Our researchers and clinicians at the Department of Genetics and Genomic Sciences have published research in a number of top journals throughout the world.

Featured Publications

Below are some of the more recent publications from our researchers and faculty.

Chetanya Pandya, Andrew V. Uzilov, Chun Yee Lau, Aye S. Moe, Maya Strahl, Wissam Hamou, Leah C. Newman, Marc Y. Fink, Yevgeniy Antipin, Eric E. Schadt, Robert Sebra, Shuyu D. Li, and Rong Chen (2017) Genomic profiling reveals mutational landscape in parathyroid carcinomas. JCI Insight Read the full study 

Yu-Feng Yvonne Chan, Pei Wang, Nicole Tignor, Nicholas Genes, Erick R Scott, Marcus Badgeley, Samantha Violante, Joel T Dudley, Eric Schadt (2017) The Asthma Mobile Health Study, a large-scale clinical observational study using ResearchKit. Nature Biotechnology Read the full study 

Yu-Feng Yvonne Chan (2017) The Use of Smartphones for Health Research. Academic Medicine Read the full study 

Nicole Tignor, Pei Wang, Nicholas Genes, Erick Scott, Micol Zweig, Yu-Feng Yvonne Chan, and Eric Schadt (2017) Methods for Clustering Time Series Data Acquired From Mobile Health Apps. Pacific Symposium on Biocomputing 2017 Read the full study

John A. Martignetti (2017) Genomic Analysis of Uterine Lavage Fluid Detects Early Endometrial Cancers and Reveals a Prevalent Landscape of Driver Mutations in Women without Histopathologic Evidence of Cancer: A Prospective Cross-Sectional Study. PLOS Medicine Read the full study 

Saskia C Sanderson, Michael D Linderman, Sabrina A Suckiel, Randi Zinberg, Andrew Kasarskis, George A Diaz and Eric E Schadt (2017) Psychological and behavioural impact of returning personal results from whole-genome sequencing: the HealthSeq project. Nature Read the full study

Epel E S, Puterman E, Lin J, Blackburn E H, Lum P Y, Beckmann N D, Zhu J, Lee E, Gilbert A, Rissman R A, Tanzi R E, and Schadt E E (2016) Meditation and vacation effects have an impact on disease-associated molecular phenotypes. Nature Read the full study

Johan Björkegren, et al. (2016) Cardiometabolic risk loci share downstream cis- and trans-gene regulation across tissues and diseases. Science Read the full study

Rong Chen, et al. (2016) Development and Clinical Application of an integrative genomic approach to personalized cancer therapy. Genome Med Read the full study

Zhang J, Lachance V, Schaffner A, Li X, Fedick A, Liao J, Edelmann L, et al. (2016) A Founder Mutation in VPS11 Causes an Autosomal Recessive Leukoencephalopathy Linked to Autophagic Defects. PLOS Genetics Read the full study 

Gracias M, Gaspari S, Mae-Santos P, Tamburini S, Andrade M, Zhang F, Shen N, Zachariou V, Clemente J, Casaccia P, et al. (2016) Microbiota-driven transcriptional changes in prefrontal cortex override genetic differences in social behavior. eLIFE. Read the full study 

Chen R, Shi L, Hakenberg J, Sklar P, Cheng W, Shah H, Fromer M, Bobe J, Levin E, et al. (2016) Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases. Nature Biotechnology Read the full study

Brian A.  Kidd, Gabriel Hoffman, Noah Zimmerman, Li Li, Joseph W. Morgan, Patricia K. Glowe, Gregory J. Botwin, Samir Parekh, Nikolina Babic, Matthew W. Doust, Gregory B. Stock, Eric E. Schadt, and Joel T. Dudley (2016) Evaluation of direct-to-consumer low-volume lab tests in healthy adults. JCI Read the full study 

Jose Clemente, et al. (2016) Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nature Medicine Read the full study

Gang Fang, John Beaulaurier, Shijia Zhu, et al. (2015) Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes. Nature Communications 6 Read the full study

Sanderson S, Linderman M, Suckiel S, Diaz G, Zinberg R, Ferryman K, Wasserstein M, Kasarskis A, Schadt E (2015) Motivations, concerns and preferences of personal genome sequencing research participants: Baseline findings from the HealthSeq project. EJHG 10.1038 Read the full study

Tu Z, Zhang B, Zhu J, Huang T, et al. (2015) contributed to the network analysis in the project The Genotype-Tissue Expression (GTEx) pilot analysis: Multi-tissue gene regulation in humans. Science Read the full study

Jose Clemente, et al. (2015) The Microbiome of Uncontacted Amerindians. Science Advances Read the full study

Harm Van Bakel, Ivan Marazzi, Christopher Basler, Ana Fernandez-Sesma, et al. (2015) Senataxin suppresses the antiviral transcriptional response and controls vital biogenesis. Nature Immunology Read the full study

Brown B, Evans M, Israelow B, Mullokandov G, Agudo J, Sourisseau M, Bashir A, Maldonado A, Dar A, et al. (2014) Hepatitis C virus genetics affects miR-122 requirements and response to miR-122 inhibitors. Nat Commun 5. Read the full study

Zhu J, Huynh JL, Yoo S, Zhang B, Schadt E, Casaccia P, et al. (2014) Common dysregulation network in the human prefrontal cortex underlies two neurodegenerative diseases. Mol Syst Biol 10:743. Read the full study

Brahmachary M, Guilmatre A, Quilez J, Hasson D, Borel C, Warburton P, Sharp AJ, et al. (2014) Digital genotyping of macrosatellites and multicopy genes reveals novel biological functions associated with copy number variation of large tandem repeats. PloS Genet 10 : e1004418 Read the full study

Houten S, Denis S, te Brinke H, Jongejan A, van Kampen AHC, et al. (2014) Mitochondrial NADP(H) deficiency due to a mutation in NADK2 causes dienoyl-CoA reductase deficiency with hyperlysinemia. Hum Mol Genet 23(11) Read the full study

Pinto D, Delaby E, Merico D, Barbosa M, Merikangas A, et al. (2014) Convergence of Genes and Cellular Pathways Dysregulated in Autism Spectrum Disorders. Cell Press. Read the full study

Briese T, Mishra N, Jain K, Zalmout I, Jabado O, et al. (2014) Middle East Respiratory Syndrome Coronavirus Quasispecies That Include Homologues of Human Isolates Revealed through Whole-Genome Analysis and Virus Cultured from Dromedary Camels in Saudi Arabia. mBio 5(3) Read the full study

Auer P, Teumer A, Schick U, O’Shaughnessy A, Lo K, et al. (2014) Rare and low-frequency coding variants in CXCR2 and other genes are associated with hematological traits. Nat Genet. (2014) Read the full study

Dhandapany P, Razzaque M, Muthusami U, Kunnoth S, Edwards J, et al. (2014) RAF1 mutations in childhood-onset dilated cardiomyopathy. Nat. Genet. Read the full study

Sivendran S, Chang R, Pham L, Phelps R, Harcharik S et al. (2014) Dissection of Immune Gene Networks in Primary Melanoma Tumors Critical for Anti-Tumor Surveillance of Patients with Stage II-III Resectable Disease. J Invest Dermatol. Read the full study

Björkegren JLM, Hägg S, Talukdar HA, Foroughi Asl H, Jain RK, et al. (2014) Plasma Cholesterol-Induced Lesion Networks Activated before Regression of Early, Mature, and Advanced Atherosclerosis. PLoS Genet 10(2) Read the full study

Fromer M, Pocklington A, Kavanagh D, Williams H, Dwyer S et al. (2014) De novo mutations in schizophrenia implicate synaptic networks. Nature. Read the full study

Kidd B, Peters L, Schadt E, Dudley J (2014) Unifying immunology with informatics and multiscale biology. Nat Immunol 15(2):118-27 Read the full study

Purcell S, Moran J, Fromer M, Ruderfer D, Solovieff N et al. (2014) A polygenic burden of rare disruptive mutations in schizophrenia. Nature. Read the full study

Parikh A, Lee C, Perinne J, Marchini S, Baccarini A et al. (2014) microRNA-181a has a critical role in ovarian cancer progression through the regulation of the epithelial-mesenchymal transition. Nat Commun 5. Read the full study

Martignetti J, Camacho-Vanegas O, Priedigkeit N, Camacho C, Pereira E, et al. (2014) Personalized Ovarian Cancer Disease Surveillance and Detection of Candidate Therapeutic Drug Target in Circulating Tumor DNA. Neoplasia 16(1). Read the full study

Agudo J, Ruzo A, Tung N, Salmon H, Leboeuf M, et al. (2014) The miR-126-VEGFR2 axis controls the innate response to pathogen-associated nucleic acids. Nat Immunol 15(1):54-62 Read the full study

Huynh J, Garg P, Thin T, Yoo S, Dutta R et al. (2014) Epigenome-wide differences in pathology-free regions of multiple sclerosis?affected brains. Nat Neurosci 17(1):121-130 Read the full study