Posts classified under: Computational and Systems Neuroscience

Loes Olde Loohuis, Ph.D.

Dr. Loes Olde Loohuis’ research focuses on elucidating the underlying molecular mechanisms of severe mental illness, in particular schizophrenia and bipolar disorder, by utilizing and developing computational approaches to leverage  multi-level data (including psychiatric phenotypes, health records and molecular phenotypes).

Xia Yang, Ph.D.

Biography

Dr. Xia Yang received her Ph.D. in Molecular Genetics and Bioinformatics from Georgia State University and had postdoctoral training in Systems Genetics at UCLA. She was Senior Research Scientist at Rosetta Inpharmatics/Merck & Co. and Director of Systems Biology at Sage Bionetworks prior to returning to UCLA as a faculty member.

Research Interests

Our research focuses on developing and applying multitissue multiomics systems biology approaches to dissect the molecular networks underlying diverse complex diseases, ranging from cardiometabolic diseases to neurodegenerative and neurological disorders, and utilize the systems level networks to guide precision medicine. Through integration of genetic, transcriptional, epigenomic, proteomic, gut microbiota, and phenotypic data from human and rodent populations, we investigate how complex interactions between genetic and environmental risk factors perturb tissue- and cell-specific gene networks which in turn induce variations in disease susceptibility. Subsequently, we use the causal molecular networks of diseases as the basis for therapeutic target identification and biomarker discovery.

 

Education

B.S., Pharmacy, Shandong University 1993
Ph.D., Molecular Genetics/Bioinformatics, Georgia State University 2003

 

Selected Publications

Yang X. “Multi-tissue Multi-omics Systems Biology to Dissect Complex Diseases”. Trends in Molecular Medicine, 2020.

Liu W, Venugopal S, Majid S, Ahn IS, Diamante G, Hong J, Yang X*, Chandler SH*. “Single-cell RNA-seq Analysis of the Brainstem of Mutant SOD1 mice Reveals Perturbed Cell Types and Pathways of Amyotrophic Lateral Sclerosis”. Neurobiology of Disease, 141: 104877, 2020.

Rajbhandari P+, Arneson D+, Feng AC, Ahn IS, Diamante G, Zaghari N, Thomas BJ, Vergnes L, Lee SD, Reue K, Smale ST, Yang X, Tontonoz P. “Single Cell Analysis Reveals Immune Cell-Adipocyte Crosstalk Regulating the Transcription of Thermogenic Adipocytes”. eLife 8:e49501, 2019.

Zhang G, Byun HR, Ying Z, Blencowe M, Zhao Y, Hong J, Shu L, Gomez-Pinilla F, Yang X. “Differential Metabolic and Multi-tissue Transcriptomic Responses to Fructose Consumption among Genetically Diverse Mice”. BBA – Molecular Basis of Disease. 1866: 165569, 2020.

Shu L, Meng Q, Tsai B, Diamante G, Chen Y, Mikhail A, Luk H, Ritz B, Allard P, Yang X, “Prenatal Bisphenol A Exposure in Mice Induces Multi-tissue Multi-omics Disruptions Linking to Cardiometabolic Disorders”, Endocrinology, 160 : 409-429, 2019.

Arneson D, Zhuang Y, Byun HR, Ahn IS, Ying Z, Zhang G, Gomez-Pinilla F, Yang X, “Single Cell Molecular Alterations Reveal Pathogenesis and Targets of Concussive Brain Injury”, Nature Communications, 9 : 3894, 2018.

Emilsson V, llkov M, Lamb JR, Finkel N, Gudmundsson EF, Pitts R, Hoover H, Jennings LL, Horman SR, Aspelund T, Shu L, Trifonov V, Gudmundsdottir V, Sigurdsson S, Manolescu A, Zhu J, Lesley SA, To J, Zhang J, Harris TB, Launer LJ, Zhang B, Eiriksdottir G, Yang X, Smith AV, Orth AP, Gudnason V, “Coregulatory Networks of Human Serum Proteins Link Genetics to Disease”, Science, 361 : 769-773, 2018.

Kurt Z, Barrere-Cain R, LaGuardia J, Mehrabian JM, Pan C, Hui ST, Norheim F, Zhou Z, Hasin Y, Lusis AJ, Yang X, “Tissue-specific Pathways and Networks Underlying Sexual Dimorphism in Non-Alcoholic Fatty Liver Disease”, Biology of Sex Differences, 9 : 46- (2018) .

Krishnan KC, Kurt Z, Barrere-Cain R, Sabir S, Das A, Floyd R, Vergnes L, Zhao Y, Che N, Charugundla S, Qi H, Zhou Z, Meng Y, Pan C, Seldin MM, Norheim F, Hui S, Reue K, Lusis, AJ, Yang X., “Integration of Multi-omics Data from Mouse Diversity Panel Highlights Mitochondrial Dysfunction in Non-Alcoholic Fatty Liver Disease”, Cell Systems, 6 : 1-13, 2018.

Shu L, Chen KHK, Zhang G, Huan T, Kurt Z, Zhao Y, Codoni V, Tregouet DA, Yang J, Wilson JG, Luo X, Levy D, Lusis AJ, Liu S, Yang X, “Shared Genetic Regulatory Networks for Cardiovascular Disease and Type 2 Diabetes in Multi-ethnic Populations”, PLOS Genetics, 13 (9): e1007040, 2017.

Avishek Adhikari, Ph.D.

Biography

Dr. Adhikari joined UCLA’s Psychology Department in 2016, following postdoctoral training at Stanford University with Prof. Karl Deisseroth and Ph.D. studies at Columbia University with Prof. Joshua A. Gordon and Prof. Rene Hen.

Dr. Adhikari’s lab investigates how the brain coordinates the constellation of changes related to emotional behaviors, with a focus on fear and anxiety. These multi-faceted changes involve complex and dynamic adaptations in hormonal, physiological and behavioral realms. Dr. Adhikari dissects how interactions between different brain structures control these processes, seeking insights that shed light on the neural basis of pathological anxiety disorders and adaptive aversion to danger. To do so we use a combination of powerful techniques, including electrophysiology, behavioral assays, optogenetics and calcium imaging to monitor and control neural activity and behavior.

Learn more about our research at our lab website

Publications

A selected list of publications:

Ye Li, Allen William E, Thompson Kimberly R, Tian Qiyuan, Hsueh Brian, Ramakrishnan Charu, Wang Ai-Chi, Jennings Joshua H, Adhikari Avishek, Halpern Casey H, Witten Ilana B, Barth Alison L, Luo Liqun, McNab Jennifer A, Deisseroth Karl   Wiring and Molecular Features of Prefrontal Ensembles Representing Distinct Experiences Cell, 2016; 165(7): 1776-88.
Adhikari Avishek, Lerner Talia N, Finkelstein Joel, Pak Sally, Jennings Joshua H, Davidson Thomas J, Ferenczi Emily, Gunaydin Lisa A, Mirzabekov Julie J, Ye Li, Kim Sung-Yon, Lei Anna, Deisseroth Karl   Basomedial amygdala mediates top-down control of anxiety and fear Nature, 2015; 527(7577): 179-85.
Adhikari Avishek   Distributed circuits underlying anxiety Frontiers in behavioral neuroscience, 2014; 8(7): 112.
Gunaydin Lisa A, Grosenick Logan, Finkelstein Joel C, Kauvar Isaac V, Fenno Lief E, Adhikari Avishek, Lammel Stephan, Mirzabekov Julie J, Airan Raag D, Zalocusky Kelly A, Tye Kay M, Anikeeva Polina, Malenka Robert C, Deisseroth Karl   Natural neural projection dynamics underlying social behavior Cell, 2014; 157(7): 1535-51.
Kim Sung-Yon, Adhikari Avishek, Lee Soo Yeun, Marshel James H, Kim Christina K, Mallory Caitlin S, Lo Maisie, Pak Sally, Mattis Joanna, Lim Byung Kook, Malenka Robert C, Warden Melissa R, Neve Rachael, Tye Kay M, Deisseroth Karl   Diverging neural pathways assemble a behavioural state from separable features in anxiety Nature, 2013; 496(7444): 219-23.
Tye Kay M, Mirzabekov Julie J, Warden Melissa R, Ferenczi Emily A, Tsai Hsing-Chen, Finkelstein Joel, Kim Sung-Yon, Adhikari Avishek, Thompson Kimberly R, Andalman Aaron S, Gunaydin Lisa A, Witten Ilana B, Deisseroth Karl   Dopamine neurons modulate neural encoding and expression of depression-related behaviour Nature, 2013; 493(7433): 537-41.
Warden Melissa R, Selimbeyoglu Aslihan, Mirzabekov Julie J, Lo Maisie, Thompson Kimberly R, Kim Sung-Yon, Adhikari Avishek, Tye Kay M, Frank Loren M, Deisseroth Karl   A prefrontal cortex-brainstem neuronal projection that controls response to behavioural challenge Nature, 2012; 492(7429): 428-32.
Nason Malcolm W, Adhikari Avishek, Bozinoski Marjan, Gordon Joshua A, Role Lorna W   Disrupted activity in the hippocampal-accumbens circuit of type III neuregulin 1 mutant mice Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology, 2011; 36(2): 488-96.
Adhikari Avishek, Sigurdsson Torfi, Topiwala Mihir A, Gordon Joshua A   Cross-correlation of instantaneous amplitudes of field potential oscillations: a straightforward method to estimate the directionality and lag between brain areas Journal of neuroscience methods, 2010; 191(2): 191-200.
Resende Rodrigo R, da Costa José L, Kihara Alexandre H, Adhikari Avishek, Lorençon Eudes   Intracellular Ca2+ regulation during neuronal differentiation of murine embryonal carcinoma and mesenchymal stem cells Stem cells and development, 2010; 19(3): 379-94.
Adhikari Avishek, Topiwala Mihir A, Gordon Joshua A   Synchronized activity between the ventral hippocampus and the medial prefrontal cortex during anxiety Neuron, 2010; 65(2): 257-69.
Resende Rodrigo R, Adhikari Avishek   Cholinergic receptor pathways involved in apoptosis, cell proliferation and neuronal differentiation Cell communication and signaling : CCS, 2009; 7(2): 20.
Resende Rodrigo R, Gomes Katia N, Adhikari Avishek, Britto Luiz R G, Ulrich Henning   Mechanism of acetylcholine-induced calcium signaling during neuronal differentiation of P19 embryonal carcinoma cells in vitro Cell calcium, 2008; 43(2): 107-21.
Bechara Etelvino J H, Dutra Fernando, Cardoso Vanessa E S, Sartori Adriano, Olympio Kelly P K, Penatti Carlos A A, Adhikari Avishek, Assunção Nilson A   The dual face of endogenous alpha-aminoketones: pro-oxidizing metabolic weapons Comparative biochemistry and physiology. Toxicology & pharmacology : CBP, 2008; 146(1-2): 88-110.
Adhikari Avishek, Penatti Carlos A A, Resende Rodrigo R, Ulrich Henning, Britto Luiz R G, Bechara Etelvino J H   5-Aminolevulinate and 4, 5-dioxovalerate ions decrease GABA(A) receptor density in neuronal cells, synaptosomes and rat brain Brain research, 2006; 1093(1): 95-104.