Posts classified under: Computational Neuroscience

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.

James Bisley, Ph.D.

Biography

Dr Bisley received his Ph.D. from the University of Melbourne in Australia where he studied the peripheral somatosensory system. He did his first post-doc at the University of Rochester working with Dr Tatiana Pasternak, where he studied the neural mechanisms underlying memory for motion. In 1999, he went to Washington, DC where he worked with Dr Michael E. Goldberg at Georgetown University and the National Eye Institute, studying the neural mechanisms underlying visuo-spatial attention. Dr Bisley moved to Columbia University with Dr Goldberg in 2002 and joined UCLA in 2006.

Michele Basso, Ph.D.

Biography

Dr. Michele A. Basso is a Professor in the Departments of Psychiatry and Biobehavioral Sciences and Neurobiology. She studied Neuroscience at Stony Brook University in NY and was a post-doctoral fellow at the National Eye Institute, NIH. After serving as a faculty member at the University of Wisconsin Madison, she moved to UCLA to join the faculty and direct the Fuster Laboratory of Cognitive Neuroscience. The work performed in her laboratory is aimed at unravelling the neuronal circuits of decision-making in health and disease. Her work spans multiple species and employs multiple technologies designed to understand how memory and sensory information are combined to give rise to our decisions.

Publications

A selected list of publications:

Perugini Alessandra, Basso Michele A   Perceptual decisions based on previously learned information are independent of dopaminergic tone Journal of neurophysiology, 2018; 119(3): 849-861.
Odegaard Brian, Grimaldi Piercesare, Cho Seong Hah, Peters Megan A K, Lau Hakwan, Basso Michele A   Superior colliculus neuronal ensemble activity signals optimal rather than subjective confidence Proceedings of the National Academy of Sciences of the United States of America, 2018; 115(7): E1588-E1597.
Crapse Trinity B, Lau Hakwan, Basso Michele A   A Role for the Superior Colliculus in Decision Criteria Neuron, 2018; 97(1): 181-194.e6.
May Paul J, Basso Michele A   Connections between the zona incerta and superior colliculus in the monkey and squirrel Brain structure & function, 2018; 223(1): 371-390.
Basso Michele A, May Paul J   Circuits for Action and Cognition: A View from the Superior Colliculus Annual review of vision science, 2017; 3(1): 197-226.
Ghitani Nima, Bayguinov Peter O, Basso Michele A, Jackson Meyer B   A sodium afterdepolarization in rat superior colliculus neurons and its contribution to population activity Journal of neurophysiology, 2016; 116(1): 191-200.
Perugini Alessandra, Ditterich Jochen, Basso Michele A   Patients with Parkinson’s Disease Show Impaired Use of Priors in Conditions of Sensory Uncertainty Current biology : CB, 2016; 26(14): 1902-10.
Basso Michele A   Monkey neurophysiology to clinical neuroscience and back again Proceedings of the National Academy of Sciences of the United States of America, 2016; 113(24): 6591-3.
Crapse Trinity B, Basso Michele A   Insights into decision making using choice probability Journal of neurophysiology, 2015; 114(6): 3039-49.
Grimaldi Piercesare, Lau Hakwan, Basso Michele A   There are things that we know that we know, and there are things that we do not know we do not know: Confidence in decision-making Neuroscience and biobehavioral reviews, 2015; 55: 88-97.
Bayguinov Peter O, Ghitani Nima, Jackson Meyer B, Basso Michele A   A hard-wired priority map in the superior colliculus shaped by asymmetric inhibitory circuitry Journal of neurophysiology, 2015; 114(1): 662-76.
Vokoun Corinne R, Huang Xin, Jackson Meyer B, Basso Michele A   Response normalization in the superficial layers of the superior colliculus as a possible mechanism for saccadic averaging The Journal of neuroscience : the official journal of the Society for Neuroscience, 2014; 34(23): 7976-87.
Ghitani Nima, Bayguinov Peter O, Vokoun Corinne R, McMahon Shane, Jackson Meyer B, Basso Michele A   Excitatory synaptic feedback from the motor layer to the sensory layers of the superior colliculus The Journal of neuroscience : the official journal of the Society for Neuroscience, 2014; 34(20): 6822-33.
Mahamed Safraaz, Garrison Tiffany J, Shires Joel, Basso Michele A   Stimulation of the Substantia Nigra Influences the Specification of Memory-Guided Saccades Journal of neurophysiology, 2013; 39(1): .
Powers Alice S, Basso Michele A, Evinger Craig   Blinks slow memory-guided saccades Journal of neurophysiology, 2013; 109(3): 734-41.
Vokoun Corinne R, Jackson Meyer B, Basso Michele A   Circuit dynamics of the superior colliculus revealed by in vitro voltage imaging Annals of the New York Academy of Sciences, 2011; 1233(2): 41-7.
Li Xiaobing, Basso Michele A   Cues to move increased information in superior colliculus tuning curves Journal of neurophysiology, 2011; 106(2): 690-703.
Shires Joel, Joshi Siddhartha, Basso Michele A   Shedding new light on the role of the basal ganglia-superior colliculus pathway in eye movements Current opinion in neurobiology, 2010; 20(6): 717-25.
Vokoun Corinne R, Jackson Meyer B, Basso Michele A   Intralaminar and interlaminar activity within the rodent superior colliculus visualized with voltage imaging The Journal of neuroscience : the official journal of the Society for Neuroscience, 2010; 30(32): 10667-82.
Kim Byounghoon, Basso Michele A   A probabilistic strategy for understanding action selection The Journal of neuroscience : the official journal of the Society for Neuroscience, 2010; 30(6): 2340-55.
Gooding Diane C, Basso Michele A   The tell-tale tasks: a review of saccadic research in psychiatric patient populations Brain and cognition, 2008; 68(3): 371-90.
Liu Ping, Basso Michele A   Substantia nigra stimulation influences monkey superior colliculus neuronal activity bilaterally Journal of neurophysiology, 2008; 100(2): 1098-112.
Basso Michele A   Electrical stimulation of nervous system tissue. Introduction Neuroscience and biobehavioral reviews, 2008; 32(3): 331.
Li Xiaobing, Basso Michele A   Preparing to move increases the sensitivity of superior colliculus neurons The Journal of neuroscience : the official journal of the Society for Neuroscience, 2008; 28(17): 4561-77.
Kim Byounghoon, Basso Michele A   Saccade target selection in the superior colliculus: a signal detection theory approach The Journal of neuroscience : the official journal of the Society for Neuroscience, 2008; 28(12): 2991-3007.
Utter Amy A, Basso Michele A   The basal ganglia: an overview of circuits and function Neuroscience and biobehavioral reviews, 2008; 32(3): 333-42.
Basso Michele A, Liu Ping   Context-dependent effects of substantia nigra stimulation on eye movements Journal of neurophysiology, 2007; 97(6): 4129-42.
Smith Joshua J, Hadzic Vezira, Li Xiaobing, Liu Ping, Day Tiffany, Utter Amy, Kim Byounghoon, Washington Ida M, Basso Michele A   Objective measures of health and well-being in laboratory rhesus monkeys (Macaca mulatta) Journal of medical primatology, 2006; 35(6): 388-96.
Li Xiaobing, Kim Byounghoon, Basso Michele A   Transient pauses in delay-period activity of superior colliculus neurons Journal of neurophysiology, 2006; 95(4): 2252-64.
Li Xiaobing, Basso Michele A   Competitive stimulus interactions within single response fields of superior colliculus neurons The Journal of neuroscience : the official journal of the Society for Neuroscience, 2005; 25(49): 11357-73.
Basso Michele A, Pokorny Jennifer J, Liu Ping   Activity of substantia nigra pars reticulata neurons during smooth pursuit eye movements in monkeys The European journal of neuroscience, 2005; 22(2): 448-64.
Basso Michele A, Uhlrich Daniel, Bickford Martha E   Cortical function: a view from the thalamus Neuron, 2005; 45(4): 485-8.
Williamson Shawn S, Zivotofsky Ari Z, Basso Michele A   Modulation of gaze-evoked blinks depends primarily on extraretinal factors Journal of neurophysiology, 2005; 93(1): 627-32.
Basso Michele A, Wurtz Robert H   Neuronal activity in substantia nigra pars reticulata during target selection The Journal of neuroscience : the official journal of the Society for Neuroscience, 2002; 22(5): 1883-94.

Aaron Blaisdell, Ph.D.

Biography

After receiving his BA and MA in Biological Anthropology (at SUNY Stony Brook and Kent State University, respectively), Dr. Blaisdell realized that animal cognition was even more interesting than dead humans. So he trekked on over to SUNY Binghamton for his Ph.D. in Experimental Psychology with Dr. Ralph Miller, where he studied learning, memory, and temporal cognition in the rat. This was followed by a brief stint as an NRSA Postdoctoral Fellow with Dr. Robert Cook, an expert on Avian Visual Cognition at Tufts University, where he learned how pigeons perceive and think about the world. Since 2001, Dr. Blaisdell has emigrated to the climatological and cultural paradise of sunny LA as Professor in Learning & Behavior and Behavioral Neuroscience in the UCLA Psychology Department. He presides over a comparative cognition lab, studying cognitive processes in rats, pigeons, hermit crabs, and humans. His lab website is http://pigeonrat.psych.ucla.edu.

Publications

A selected list of publications:

Leising Kenneth J, Wong Jared, Blaisdell Aaron P   Extinction and spontaneous recovery of spatial behavior in pigeons Journal of experimental psychology. Animal learning and cognition, 2015; 41(4): 371-7.
Ping Xiaoge, Lee Ji Sun, Garlick Dennis, Jiang Zhigang, Blaisdell Aaron P   Behavioral evidence illuminating the visual abilities of the terrestrial Caribbean hermit crab Coenobita clypeatus Behavioural processes, 2015; 118(4): 47-58.
Leising Kenneth J, Wong Jared, Ruprecht Chad M, Blaisdell Aaron P   Blocking between landmarks during 2-D (touchscreen) and 3-D (ARENA) search tasks with pigeons Learning & behavior, 2014; 42(4): 357-64.
Blaisdell Aaron P, Lau Yan Lam Matthew, Telminova Ekatherina, Lim Hwee Cheei, Fan Boyang, Fast Cynthia D, Garlick Dennis, Pendergrass David C   Food quality and motivation: a refined low-fat diet induces obesity and impairs performance on a progressive ratio schedule of instrumental lever pressing in rats Physiology & behavior, 2014; 128: 220-5.
Bouchekioua Youcef, Miller Holly C, Craddock Paul, Blaisdell Aaron P, Molet Mikael   Spatial integration of boundaries in a 3D virtual environment Acta psychologica, 2013; 144(2): 316-23.
Watanabe Noelle M, Stahlman W David, Blaisdell Aaron P, Garlick Dennis, Fast Cynthia D, Blumstein Daniel T   Quantifying personality in the terrestrial hermit crab: different measures, different inferences Behavioural processes, 2012; 91(2): 133-40.
Biedermann Traci, Garlick Dennis, Blaisdell Aaron P   Food choice in the laboratory pigeon Behavioural processes, 2012; 91(1): 129-32.
Waldmann Michael R, Schmid Martina, Wong Jared, Blaisdell Aaron P   Rats distinguish between absence of events and lack of evidence in contingency learning Animal cognition, 2012; 15(5): 979-90.
Ryan Kelsea M, Blumstein Daniel T, Blaisdell Aaron P, Stahlman W David   Stimulus concordance and risk-assessment in hermit crabs (Coenobita clypeatus): implications for attention Behavioural processes, 2012; 91(1): 26-9.
Leising Kenneth J, Sawa Kosuke, Blaisdell Aaron P   Factors that influence negative summation in a spatial-search task with pigeons Behavioural processes, 2012; 90(3): 357-63.
Cook Robert G, Katz Jeffrey S, Blaisdell Aaron P   Temporal properties of visual search in pigeon target localization Journal of experimental psychology. Animal behavior processes, 2012; 38(2): 209-16.
Fast Cynthia D, Blaisdell Aaron P   Rats are sensitive to ambiguity Psychonomic bulletin & review, 2011; 18(6): 1230-7.
Leising Kenneth J, Garlick Dennis, Blaisdell Aaron P   Overshadowing between landmarks on the touchscreen and in arena with pigeons Journal of experimental psychology. Animal behavior processes, 2011; 37(4): 488-94.
Stahlman W David, Chan Alvin Aaden Yim-Hol, Blumstein Daniel T, Fast Cynthia D, Blaisdell Aaron P   Auditory stimulation dishabituates anti-predator escape behavior in hermit crabs (Coenobita clypeatus) Behavioural processes, 2011; 88(1): 7-11.
Racey Deborah, Young Michael E, Garlick Dennis, Pham Jennifer Ngoc-Minh, Blaisdell Aaron P   Pigeon and human performance in a multi-armed bandit task in response to changes in variable interval schedules Learning & behavior, 2011; 39(3): 245-58.
Garlick Dennis, Gant Dana J, Brakel Linda A W, Blaisdell Aaron P   Attributional and relational processing in pigeons Frontiers in psychology, 2011; 2(3): 14.
Stahlman W David, Blaisdell Aaron P   The Modulation of Operant Variation by the Probability, Magnitude, and Delay of Reinforcement Learning and motivation, 2011; 42(3): 221-236.
Fridman Gene Y, Blair Hugh T, Blaisdell Aaron P, Judy Jack W   Perceived intensity of somatosensory cortical electrical stimulation Experimental brain research. Experimentelle Hirnforschung. Expérimentation cérébrale, 2010; 203(3): 499-515.
Stahlman W David, Young Michael E, Blaisdell Aaron P   Response variability in pigeons in a Pavlovian task Learning & behavior : a Psychonomic Society publication, 2010; 38(2): 111-8.
Stahlman W David, Roberts Seth, Blaisdell Aaron P   Effect of reward probability on spatial and temporal variation Journal of experimental psychology. Animal behavior processes, 2010; 36(1): 77-91.
Leising Kenneth J, Garlick Dennis, Parenteau Michael, Blaisdell Aaron P   Behavioral research in pigeons with ARENA: an automated remote environmental navigation apparatus Behavioural processes, 2009; 81(1): 105-13.
Stahlman W David, Blaisdell Aaron P   Blocking of spatial control by landmarks in rats Behavioural processes, 2009; 81(1): 114-8.
Leising Kenneth J, Blaisdell Aaron P   Associative Basis of Landmark Learning and Integration in Vertebrates Comparative cognition & behavior reviews, 2009; 4(1): 80-102.
Leising Kenneth J, Wong Jared, Waldmann Michael R, Blaisdell Aaron P   The special status of actions in causal reasoning in rats Journal of experimental psychology. General, 2008; 137(3): 514-27.
Badelt Steven W, Blaisdell Aaron P   Capacitive sensors for detecting proximity and response Behavior research methods, 2008; 40(2): 613-21.
Leising Kenneth J, Sawa Kosuke, Blaisdell Aaron P   Temporal integration in Pavlovian appetitive conditioning in rats Learning & behavior : a Psychonomic Society publication, 2007; 35(1): 11-8.
Nakajima Sadahiko, Takahashi Kosuke, Blaisdell Aaron P   An assessment of context-specificity of the CS-preexposure effect in Pavlovian excitatory and inhibitory conditioning Behavioural processes, 2006; 73(1): 84-91.
Cook Robert G, Blaisdell Aaron P   Short-term item memory in successive same-different discriminations Behavioural processes, 2006; 72(3): 255-64.
Blaisdell Aaron P, Sawa Kosuke, Leising Kenneth J, Waldmann Michael R   Causal reasoning in rats Science (New York, N.Y.), 2006; 311(5763): 1020-2.
Roper Karen L, Chaponis Deviney M, Blaisdell Aaron P   Transfer of directed-forgetting cues across discrimination tasks with pigeons Psychonomic bulletin & review, 2005; 12(6): 1005-10.
Sawa Kosuke, Leising Kenneth J, Blaisdell Aaron P   Sensory preconditioning in spatial learning using a touch screen task in pigeons Journal of experimental psychology. Animal behavior processes, 2005; 31(3): 368-75.
Blaisdell, A. P.   Mechanism through methodology: No madness in the method, International Journal of Comparative Psychology, 2005; 18: 23-27.
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Cook Robert G, Levison Deborah G, Gillett Sarah R, Blaisdell Aaron P   Capacity and limits of associative memory in pigeons Psychonomic bulletin & review, 2005; 12(2): 350-8.
Blaisdell Aaron P, Cook Robert G   Two-item same-different concept learning in pigeons Learning & behavior : a Psychonomic Society publication, 2005; 33(1): 67-77.
Blaisdell Aaron P, Cook Robert G   Integration of spatial maps in pigeons Animal cognition, 2005; 8(1): 7-16.
Denniston James C, Blaisdell Aaron P, Miller Ralph R   Temporal coding in conditioned inhibition: analysis of associative structure of inhibition Journal of experimental psychology. Animal behavior processes, 2004; 30(3): 190-202.
Chang Raymond C, Blaisdell Aaron P, Miller Ralph R   Backward conditioning: mediation by the context Journal of experimental psychology. Animal behavior processes, 2003; 29(3): 171-83.
Blaisdell Aaron P   The S-R information stream: where’s the filter? Integrative physiological and behavioral science : the official journal of the Pavlovian Society, 2003; 38(2): 146-65.
Denniston, J. C., Savastano, H. I., Blaisdell, A. P., & Miller, R. R.   Cue competition as a retrieval deficit Learning and Motivation, 2003; 34: 1-31.
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Cook, R. G., Shaw, R., & Blaisdell, A. P.   Dynamic Object Perception by Pigeons: Discrimination of Action in Video Presentations Animal Cognition, 2001; 4: 137-146.
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Blaisdell, A.P., Denniston, J. C., & Miller, R. R.   Recovery from the Overexpectation Effect: Contrasting Performance-focused and Acquisition-focused Models of Retrospective Revaluation Animal Learning & Behavior, 2001; 29: 367-380.
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Blaisdell, A.P., Denniston, J. C., Savastano, H. I., & Miller, R. R.   Counterconditioning of an Overshadowed Cue Attenuates Overshadowing of Aversive Associations Journal of Experimental Psychology: Animal Behavior Processes, 2000; 26: 74-86.
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Blaisdell, A. P., Savastano, H. I., & Miller, R. R.   Overshadowing of Explicitly Unpaired Conditioned Inhibition is Disrupted by Preexposure to the Overshadowed Inhibitor Animal Learning & Behavior, 1999; 27: 346-357.
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Blaisdell, A. P., Gunther, L. M., & Miller, R. R.   Recovery from Blocking Achieved by Extinguishing the Blocking CS Animal Learning & Behavior, 1999; 27: 63-76.
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Blaisdell, AP Denniston, JC Miller, RR   Posttraining shifts in the overshadowing stimulus-unconditioned stimulus interval alleviates the overshadowing deficit Journal of experimental psychology. Animal behavior processes. , 1999; 25(1): 18-27.
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Blaisdell, AP Bristol, AS Gunther, LM Miller, RR   Overshadowing and latent inhibition counteract each other: support for the comparator hypothesis Journal of experimental psychology. Animal behavior processes. , 1998; 24(3): 335-51.
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Friedman, B., Blaisdell, A. P., Escobar, M. E., & Miller, R. R.   Comparator Mechanisms and Conditioned Inhibition: CS Preexposure Disrupts Pavlovian Conditioned Inhibition but not Explicitly Unpaired Inhibition Journal of Experimental Psychology: Animal Behavior Processes, 1998; 24: 453-466.
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Denniston, J. C., Blaisdell, A. P., & Miller, R. R.   Temporal Coding Affects Transfer of Serial and Simultaneous Inhibitors Animal Learning & Behavior, 1998; 26: 336-350.
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Blaisdell, A.P., Denniston, J. C., & Miller, R. R.   Temporal Encoding as a Determinant of Overshadowing Journal of Experimental Psychology: Animal Behavior Processes, 1998; 24: 72-83.
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Blaisdell, A.P., Denniston, J. C., & Miller, R. R.   Unblocking with Qualitative Change of Unconditioned Stimulus Learning and Motivation, 1997; 28: 268-279.
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