• UC Davis

MacDonald III AG, Goghari VM, Hicks BM, Flory JD, Carter CS, Manuck SB (2005). A convergent-divergent approach to context processing, general intellectual functioning and genetic liability in schizophrenia. Neuropsychology 19:814-821.
Becker TM, Kerns KG, Macdonald AW 3 rd, and Carter CS (2008). Prefrontal dysfunction in first-degree relatives of schizophrenia patients during a Stroop task. Neuropsychopharmacology 33(11):2619-2625.
Goghari,VM, RehmK, Carter CS, MacDonald III AM Sulcal thickness as a vulnerability factor for schizophrenia. (2007) British J Psychiatry 191:229-233.
Minzenberg MJ, Watrous AJ, Yoon JH, Ursu S, Carter CS (2008). Modafinil shifts human locus coeruleus to low-tonic, high phasic activity during functional MRI. Science 322(4908):1700-1702.
Yoon JH, Minzenberg MJ, Ursu S, Walters R, Wendelken C, Ragland JD, Carter CS (2008): Association of dorsolateral prefrontal cortex dysfunction with disrupted coordinated brain activity in schizophrenia: relationship with impaired cognition, behavioral disorganization, and global function. American Journal of Psychiatry165(8):1006-1014.

• UC Irvine

Potkin SG, Turner JA, Fallon JA, Lakatos A, Keator DB, Guffanti G, Macciardi F. Gene discovery through imaging genetics: identification of two novel genes associated with schizophrenia. Mol Psych, (2009) 14, 416–428
Potkin SG, Turner JA, Guffanti G, Lakatos A, Fallon JH, Nguyen DD, Mathalon D, Ford J, Lauriello J, Macciardi F; FBIRN. A genome-wide association study of schizophrenia using brain activation as a quantitative phenotype. Schizophr Bull, 35(1):96-108, 2009.
Potkin SG, Ford JM. Widespread Cortical Dysfunction in Schizophrenia: The FBIRN Imaging Consortium. Schizophr Bull, 35(1):15-8, 2009.
Tura E, Turner JA, Fallon JH, Kennedy JL, Potkin SG. Multivariate analyses suggest genetic impacts on neurocircuitry in schizophrenia. Neuroreport 19(6):603-7, 2008.
Begg CB, Haile RW, Borg A, Malone KE, Concannon P, Thomas DC, Langholz B, Bernstein L, Olsen JH,
Lynch CF, Anton-Culver H, Capanu M, Liang X, Hummer AJ, Sima C, Bernstein JL. Variation of breast cancer risk among BRCA1/2 carriers. JAMA 2008; Jan 9, 299:194-201.
Yarosh W, Barrientos T, Esmailpour T, Lin L, Carpenter PM, Osann K, Anton-Culver H, Huang T. TBX3 is overexpressed in breast cancer and represses p14 ARF by interacting with histone deacetylases. Cancer Res 2008; Feb 1, 68:693-9.
Atz M, Walsh D, Cartagena P, Li J, Evans S, Choudary P, Overman K, Stein R,Tomita H, Potkin S, Myers R, Watson SJ, Jones EG, Akil H, Bunney WE Jr, Vawter MP; Members of National Institute of Mental Health Conte Center and Pritzker Neuropsychiatric Disorders Research Consortium. Methodological considerations for gene expression profiling of human brain. J Neurosci Methods. 163(2):295-309 (2007)
Sequeira A, Meng F, Rollins B, Myers RM, Jones EG, Watson SJ, Akil H, Schatzberg AF, Barchas J, Bunney WE, and Vawter MP. “Coding SNPs Included in Exon Arrays for the Study of Psychiatric Disorders.” Molecular Psychiatry 13, 363-365 (2008).
Gokoffski. K.K., H.-H. Wu, C.L. Beites, J. Kim, E. Silman, B. Jin, E. Goka, A. J. Celeste, M.M. Matzuk, A.D. Lander, and A.L. Calof (2009) Differential actions of activin and GDF11 on proliferation and fate choice by neural stem/progenitor cells. In revision.
Kawauchi, S., R. Santos, M.E. Lopez-Burks, C.M. Young, M.P. Hoang, A. Chua, T. Lao, M.S. Lechner, L. Kitzes, B. Hallgrimsson, A.L. Calof and A.D. Lander (2009) Multiple organ system defects and transcriptional dysregulation in the Nipbl+/- mouse, a model of Cornelia de Lange Syndrome. In revision
English, A.W., Y.-H. Jen, A. Mulligan, D. Cucoranu, M. J. Sabatier, H. Saiyed, G. Schwartz, J. Spector, and A. D. Lander (2009) Axon regeneration after peripheral nerve injury is enhanced in syndecan and glypican knockout mice. Submitted.
Fallon, J.H. and Keator, D.B. (2008) Commentary on In Silico Modeling System: A National Research Resource for Simulation of Complex Brain Disorders. Alzheimer's & Dementia: J. Alzheimer's Association.
Melonakos J, Al-Hakim, R., Fallon, J.H., and Tannenbaum, A. (2005) Knowledge-Based Segmentation of Brain MRI Scans Using the Insight Toolkit. Insight Journal (NAMIC/BIRN).
Turner , J.A., Smyth , P., Macciardi , F., Fallon , J.H., Kennedy, J.L., Potkin, S.G. (2006) Imaging phenotypes and genotypes in schizophrenia. Neuroscience 4 (1).
Potkin , SG, F. Macciardi, L. Friedman, J. Turner, J.H. Fallon, W. Bunney, D. Keator, D. Goldstein, N. Schork (2006) Brain Imaging As A Strategy for Genome Wide Scan Data Reduction for Neuropsychiatric Illness. American Society of Human Genetics.
Shao, L., Vawter, M.P. (2008). Shared gene expression alterations in schizophrenia and bipolar disorder. Biol Psychiatry. Jan 10 [Epub ahead of print].

• UC Los Angeles

Hyun Min Kang, Noah A. Zaitlen, Claire M. Wade, Andrew Kirby, David Heckerman, Mark J. Daly, and Eleazar Eskin. ``Efficient Control of Population Structure in Model Organism Association Mapping.'' Genetics. 178(3):1709-23, 2008.
Eleazar Eskin. ``Increasing Power in Association Studies by using Linkage Disequilibrium Structure and Molecular Function as Prior Information.'' Genome Research. 18(4):653-60 Special Issue Proceedings of the 12th Annual Conference on Research in Computational Biology (RECOMB-2008), 2008.
Noah Zaitlen, Hyun Min Kang, Eleazar Eskin, Eran Halperin.``Leveraging the HapMap Correlation Structure in Association Studies.'' American Journal of Human Genetics. 80(4):683-91, 2007.
David A. Hinds, Laura L. Stuve, Geoffrey B. Nilsen, Eran Halperin, Eleazar Eskin, Dennis G. Ballinger, Kelly A. Frazer, David R. Cox. ``Whole-Genome Patterns of Common DNA Variation in Three Human Populations'' Science 18 February 2005: 307(5712):1072-1079.
Kelly A. Frazer, Eleazar Eskin, Hyun Min Kang, Molly A. Bogue, David A. Hinds, Erica J. Beilharz, Robert V. Gupta, Julie Montgomery, Matt M. Morenzoni, Geoffrey B. Nilsen, Charit L. Pethiyagoda, Laura L. Stuve, Frank M. Johnson, Mark J. Daly, Claire M. Wade & David R. Cox. ``A sequence-based variation map of 8.27 million SNPs in inbred mouse strains.'' Nature 448(7157):1050-3. 2007.
Abrahams BS, Tentler D, Perederiy JV, Oldham MC, Coppola G, Geschwind DH (2007). Genome-wide analyses of human perisylvian cerebral cortical patterning. Proc Natl Acad Sci 104(45): 17849–54.
Sebat J, Lakshmi B, Malhotra D, et al. (2007). Strong association of de novo copy number mutations with autism. Science 316(5823):445-9.
Alarcón M, Abrahams BS, Stone JL, Duvall JA, Perederiy JV, Bomar JM, Sebat J, Wigler M, Martin CL, Ledbetter DH, Nelson SF, Cantor RM, Geschwind DH (2008). Linkage, association, and gene-expression analyses identify CNTNAP2 as an autism-susceptibility gene. Am J Hum Genet 82(1):150-9.

• UC San Diego

Malo N, Libiger O, Schork NJ. Accommodating linkage disequilibrium in genetic-association analyses via ridge regression. Am J Hum Genet. 2008 Feb;82(2):375-85. PMID: 18252218. This paper describes an approach to genetic association analysis that accommodates linkage disequilibrium between sequence variations and that can handle more variations than subjects in a simultaneous analysis of all those variations.
Torkamani A, Schork NJ. Predicting Functional Regulatory Polymorphisms. Bioinformatics. 2008 Jun 18. [Epub ahead of print] PMID: 18562267. This paper describes a method for inferring the likely regulatory functional significance of DNA sequence variations.
Neivergelt CM, Libiger O, Schork NJ. Generalized molecular analysis of variance. PLOS Genetics Apr 6;3(4):e51. PMID: 17411342. This paper proposes a general strategy to investigating the relationship between genetic background and an arbitrary phenotype. It’s strength lies in the fact that it does not make any assumptions about the origins of the subjects, the number of subpopulations, etc. and can accommodate covariates.
Schork NJ, Nath SK, Fallin, D, Chakravarti A. Linkage Disequilibrium Analysis of Bi-allelic DNA Markers, Human Quantitative Trait Loci, and Threshold-Defined Cases and Controls. Am J Hum Genet 2000 67:1208-18. PMID: 11032785. This paper describes an approach to association mapping of human quantitative traits that exploits the use of extreme individuals. It is an approach that is often used in human genetic studies.
Macfall J, Fischl B, Dale A. Reliability in multi-site structural MRI studies: effects of gradient non-linearity correction on phantom and human data. Neuroimage 2006;30(2):436-443.
Taylor S, Jang KL, Stewart SH, Stein MB. Etiology of the dimensions of anxiety sensitivity: A behavioral-genetic analysis. J.Anxiety Disord 22:899-914, 2008
Stein MB, Schork NJ, Gelernter J. Gene-by-environment (serotonin transporter and childhood maltreatment) interaction for anxiety sensitivity, an intermediate phenotype for anxiety disorders. Neuropsychopharmacology 33:312-319, 2008

• UC San Francisco

Brown GG, McCarthy G, Bischoff-Grethe A, Ozyurt B, Greve D, Potkin SG, Turner JA, Notestine R, Calhoun VD, Ford JM, Mathalon D, Manoach DS, Gadde S, Glover GH, Wible CG, Belger A, Gollub RL, Lauriello J, O'Leary D, Lim KO: Brain-performance correlates of working memory retrieval in schizophrenia: a cognitive modeling approach. Schizophr Bull 2009; 35(1):32-46
Wible CG, Lee K, Molina I, Hashimoto R, Preus AP, Roach BJ, Ford JM, Mathalon DH, McCarthey G, Turner JA, Potkin SG, O'Leary D, Belger A, Diaz M, Voyvodic J, Brown GG, Notestine R, Greve D, Lauriello J: fMRI activity correlated with auditory hallucinations during performance of a working memory task: data from the FBIRN consortium study. Schizophr Bull 2009; 35(1):47-57
Agosta F, Vossel KA, Miller BL, et al. Apolipoprotein E epsilon4 is associated with disease-specific effects on brain atrophy in Alzheimer's disease and frontotemporal dementia. Proc Natl Acad Sci U S A Feb 10 2009;106(6):2018-2022.
Du AT, Schuff N, Kramer JH, Rosen HJ, Gorno-Tempini ML, Rankin K, Miller BL, Weiner MW. Different regional patterns of cortical thinning in Alzheimer's disease and frontotemporal dementia. Brain Apr 2007;130(Pt 4):1159-1166.
Wilson SM, Brambati SM, Henry RG, et al. The neural basis of surface dyslexia in semantic dementia. Brain Jan 2009;132(Pt 1):71-86.
Jahng GH, Zhu XP, Matson GB, Weiner MW, Schuff N. Improved perfusion-weighted MRI by a novel double inversion with proximal labeling of both tagged and control acquisitions. Magn Reson Med Feb 2003;49(2):307-314.
Zhu XP, Du AT, Jahng GH, Soher BJ, Maudsley AA, Weiner MW, Schuff N. Magnetic resonance spectroscopic imaging reconstruction with deformable shape-intensity models. Magn Reson Med Sep 2003;50(3):474-482.
Li KL, Zhu X, Hylton N, Jahng GH, Weiner MW, Schuff N. Four-phase single-capillary stepwise model for kinetics in arterial spin labeling MRI. Magn Reson Med Mar 2005;53(3):511-518.
Hayasaka S, Du AT, Duarte A, Kornak J, Jahng GH, Weiner MW, Schuff N. A non-parametric approach for co-analysis of multi-modal brain imaging data: application to Alzheimer's disease. Neuroimage Apr 15 2006;30(3):768-779.
Young K, Schuff N. Measuring structural complexity in brain images. Neuroimage Feb 15 2008;39(4):1721-1730.
Morra JH, Tu Z, Apostolova LG, et al. Validation of a fully automated 3D hippocampal segmentation method using subjects with Alzheimer's disease mild cognitive impairment, and elderly controls. Neuroimage Oct 15 2008;43(1):59-68.