Kreiman:Publications

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PubMed (external link)
PubMed

Journals
Blumberg, J., and Kreiman, G. (2010). How cortical neurons help us see: visual recognition in the human brain. Journal of Clinical Investigation 120:3054-3063. PMCID: PMC2929717 Agam Y, Liu H, Pappanastassiou A, Buia C, Golby AJ, Madsen JR, Kreiman, G. (2010). Robust selectivity to two-object images in human visual cortex. Current Biology 20:872-879. PMCID: PMC2869389 Kim TK*, Hemberg M*, Gray JM*, Costa A, Bear DM, Wu J, Harmin DA, Laptewicz, M, Barbara-Haley K, Kuersten S, Markenscoff-Papadimitriou E, Kuhl D, Bito H, Worley PF, Kreiman G, Greenberg ME. (2010). Widespread transcription at thousands of enhancers during activity-dependent gene expression in neurons. (* = equal contribution) Nature 465:182-187. Singer JM, Sheinberg DL (2010). Temporal cortex neurons encode articulated actions as slow sequences of integrated poses. Journal of Neuroscience 30, 3133-3145. Quian Quiroga R, Kreiman G (2010). Measuring sparseness in the brain. Psychological Reviews, 17:291-297. Liu H, Agam Y, Madsen J, Kreiman G. (2009) Timing, timing, timing: Fast decoding of object inforrmation from intracranial field potentials in human visual cortex. Neuron 62:281-290. PMCID: PMC2921507 NIHMSID: NIHMS226062omr Rasch M, Logothetis NK, Kreiman G (2009). From neurons to circuits: linear estimation of local field potentials. Journal of Neuroscience 29:13785-13796. PMCID: PMC2924964 NIHMSID: NIHMS226152 Horng S, Kreiman G, Ellsworth C, Page D, Blank M, Milen K, Sur M (2009). Differential Gene Expression in the Developing Lateral Geniculate Nucleus and Medial Geniculate Nucleus Reveals Novel Roles for Zic4 and Foxp2 in Visual and Auditory Pathway Development. Journal of Neuroscience 29:13672-13683. Singer J, Kreiman G (2009). Toward unmasking the dynamics of visual perception. Neuron 64:446-447. PMCID: PMC2803075 Flavell SW, Kim TK, Gray JM, Harmin DA, Hemberg M, Hong EJ, Markenscoff-Papadimitriou E, Bear DM, Greenberg ME (2008). Genome-wide analysis of MEF2 transcriptional program reveals synaptic target genes and neuronal activity-dependent polyadenylation site selection. Neuron 60: 1022-1038. PMCID: PMC2630178 Meyers E, Freedman D, Kreiman G, Miller E, Poggio T (2008). Dynamic Population Coding of Category Information in ITC and PFC. Journal of Neurophysiology 100:1407 1419. PMCID: PMC2544466 Quian Quiroga R, Kreiman G, Koch C, Fried I (2008), Trends in Cognitive Science 12:87-91. Leamey C, Glendining K, Kreiman G, Kang N, Kuan H, Fassler R, Sawatari A, Tonegawa S, Sur M. (2008). Differential Gene Expression between Sensory Neocortical Areas: Potential Roles for Ten_m3 and Bcl6 in Patterning Visual and Somatosensory Pathways. Cerebral Cortex, 18:53-66. Kreiman G (2007). Single neuron approaches to human vision and memories. Current Opinion in Neurobiology, 17:471-475. Serre T, Kreiman G, Kouh M, Cadieu C, Knoblich U, Poggio T (2007). A quantitative theory of immediate visual recognition. Progress In Brain Research 165C:33-56. Kreiman G (2007) Brain science: from the very large to the very small. Current Biology 17:R768-R770. Tropea D, Kreiman G, Lyckman A, Mukherjee S, Yu H, Horng S, Sur M. (2006) Distinct gene systems mediating activity-dependent plasticity in visual cortex. Nature Neuroscience 9:660-668. Kreiman G*, Hung C*, Quiroga R, Kraskov A, Poggio T., DiCarlo J. (2006). Selectivity of local field potentials in inferior temporal cortex. Neuron 49:433-445 (*=equal contribution) Hung C*, Kreiman G*, Poggio T, DiCarlo J. (2005) Fast read-out of object information in inferior temporal cortex. Science, 310:863-866. (*=equal contribution) Quian Quiroga R, Reddy L, Kreiman G, Koch C, Fried I (2005) Invariant visual representation by single neurons in the human brain. Nature, 435:1102-1107. Crick F, Koch C, Kreiman G, Fried I (2004) Consciousness and Neurosurgery. Neurosurgery 55:272-282. Yeo G, Holste D, Kreiman G, Burge C (2004). Variation in alternative splicing across human tissues. Genome Biology 5:R74. Kreiman G (2004). Neural coding: computational and biophysical perspectives. Physics of Life Reviews 2:71-102. Kreiman G (2004) Identification of sparsely distributed clusters of cis-regulatory elements in sets of co-expressed genes. Nucleic Acids Research, 32:2889-2900. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, Cooke MP, Walker JR, Hogenesch JB (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proceedings of the National Academy of Sciences USA, 101:6062-6067. Kreiman G, Fried I, Koch C (2002) Single neuron correlates of subjective vision in the human medial temporal lobe. Proceedings of the National Academy of Sciences USA, 99:8378-8383. Rees G, Kreiman G, Koch C (2002). Neural correlates of consciousness in humans. Nature Reviews Neuroscience, 3:261-270. Krahe R, Kreiman G, Gabbiani F, Koch C, Metzner W (2002). Stimulus encoding and feature extraction by multiple pyramidal cells in the hindbrain of weakly electric fish. Journal of Neuroscience, 22:2374-2382. Zirlinger M, Kreiman G, Anderson D (2001). Amygdala-enriched genes identified by microarray technology are restricted to specific amygdaloid sub-nuclei. Proceedings of the National Academy of Sciences USA, 98:5270-5275. Kreiman G (2001), Moveo ergo sum. BioEssays. 23:662. Kreiman G, Koch C, Fried I (2000). Imagery neurons in the human brain. Nature, 408:357-361. Kreiman G, Koch C, Fried I (2000). Category-specific visual responses of single neurons in the human medial temporal lobe. Nature Neuroscience, 3:946-953. Kreiman G, Krahe R, Metzner W, Koch C, Gabbiani F (2000). Robustness and Variability of Neuronal Coding by Amplitude Sensitive Afferents in the Weakly Electric Fish Eigenmannia. Journal of Neurophysiology, 84:189-204. Ouyang Y, Rosenstein A, Kreiman G, Schuman EM, Kennedy, MB (1999). Tetanic stimulation leads to increased accumulation of Ca2+ calmodulin-dependent protein kinase II via dendritic protein synthesis in hippocampal neurons. Journal of Neuroscience, 19:7823-7833. Inon de Iannino N, Briones G, Kreiman G, Ugalde, R (1996). Characterization of the biosynthesis of betha(1-2) cyclc glucan in R. Freddii. Cellular and Molecular Biology, 42:617-629.

Supplementary Material
Kim, T., Hemberg, M., Gray, J., Costa, A., Bear, D., Wu, J., Harmin, D., Laptewicz, M., Barbara-Haley, K., Kuresten, S., Markenscoff-Papdimitriou, E., Kuhl, D., Bito, H., Worley, P., Kreiman, G. and Greenberg, M. Widespread transcription at neuronal activity-regulated enhancers (2010) Nature 465: 182-187 Agam, Y., Liu, H., Papanastassiou, A., Buia, C., Golby, A., Madsen, J. and Kreiman, G. Robost Selectivity to Two-Object Images in Human Visual Cortex (2010) Current Biology 20: 972-879 Liu H, Agam Y, Madsen J, Kreiman G. Timing, timing, timing: Fast decoding of object inforrmation from intracranial field potentials in human visual cortex. Neuron, (2009). Meyers, E., Freedman, D., Kreiman, G., Miller, E., and Poggio, T. Dynamic Population Coding of Category Information in ITC and PFC (2008) Journal of Neurophysiology 100: 1407-1419 Serre T, Kreiman G, Kouh M, Cadieu C, Knoblich U, Poggio T, A quantitative theory of immediate visual recognition. Progress In Brain Research, (2007). 165C: 33-56. Tropea D, Kreiman G, Lyckman A, Mukherjee S, Yu H, Horng S, Sur M. (2006) Distinct gene systems mediating activity-dependent plasticity in visual cortex. Nature Neuroscience 9:660-668 Kreiman, G., Hung, C., Quian Quiroga, R., Kraskov, A., Poggio, T., and DiCarlo, J. (2006). Object selectivity of local field potentials and spikes in the inferior temporal cortex of macaque monkeys. Neuron 49, 433-445 Hung, C., Kreiman, G., Poggio, T., and DiCarlo, J. (2005). Fast Read-out of Object Identity from Macaque Inferior Temporal Cortex. Science 310, 863-866 Invariant visual representation by single neurons in the human brain, R. Quian Quiroga, L. Reddy, G. Kreiman, C. Koch and I. Fried, Nature 2005 435:1102-1107 doi: 10.1038/nature03687 Kreiman, G. (2004). Identification of sparsely distributed clusters of cis-regulatory elements in sets of co-expressed genes. Nucleic Acids Research 32, 2889-2900. Variation in alternative splicing across human tissues, Gene Yeo, Dirk Holste, Gabriel Kreiman and Christopher B Burge, Genome Biology 2004, 5:R74 doi:10.1186/gb-2004-5-10-r74 A gene atlas of the mouse and human protein-encoding transcriptomes, Andrew I. Su, Tim Wiltshire, Serge Batalov, Hilmar Lapp, Keith A. Ching, David Block, Jie Zhang, Richard Soden, Mimi Hayakawa, Gabriel Kreiman, Michael P. Cooke, John R. Walker and John B. Hogenesch, Proceedings of the National Academy of Sciences U S A. 2004 101: 6062–6067. doi: 10.1073/pnas.0400782101. Software and Resources Cisregul (prediction of cis regulatory elements). DOWNLOAD CODE Gene expression atlas in mouse and humans (PNAS 2004 101:6062-6067) Gene Screening Spiker (spike sorting program) Spike Metrics Genebytes.com

Reviews
Kreiman, G. Biological object recognition. Scholarpedia 3, 2667 (2008) R. Quian Quiroga, G. Kreiman, C. Koch, I. Fried, Trends in Cognitive Science 12, 87 (2008). Kreiman, G. (2007). Single neuron approaches to human vision and memories. Current Opinion in Neurobiology 17:471-475. Crick F, Koch C, Kreiman G, Fried I (2004) Consciousness and Neurosurgery. Neurosurgery 55:272-282. Kreiman G (2004). Neural coding: computational and biophysical perspectives. Physics of Life Reviews 2:71-102. Rees G, Kreiman G, Koch C (2002). Neural correlates of consciousness in humans. Nature Reviews Neuroscience, 3:261-270.

Book Chapters
Responses of single neurons in the human brain during flash suppression. Chapter 12 In "Binocular Rivalry", MIT Press, edited by Randolph Blake and David Alais (2005)

Conference Abstracts
2010 Limited extragenic transcription suggests that most conserved non-coding sequences are regulatory factor binding sites, Martin, Hemberg, Jesse M Gray, Nicole Cloonan, Tae-Kyung Kim, Sean MGrimmond, Michael E Greenberg, Gabriel Kreiman, Beyond the Genome, Boston (USA), 2010. Equal contribution Widespread transcription at neuronal activity-regulated enhancers, Tae-Kyung Kim, Martin Hemberg, Jesse M Gray, Allen M Costa, David A Harmin, Eirene Markenscoff-Papadimitriou,Daniel M Bear, Gabriel Kreiman, Michael E Greenberg, Systems Biology: Global Regulation of Gene Expression, invited talk, Cold Spring Harbor (USA), 2010. Equal contribution Neural decoding of natural object categories from intracranial field potentials: A comparison between human and monkey *A. B. ARSLAN, M. CAUCHOIX, D. FIZE, G. KREIMAN, J. R. MADSEN, T. SERRE, J. M. SINGER; Society for Neuroscience, San Diego, 2010 2009 Correlated conservation of tissue-specific gene expression and transcription factor binding sites in human and mouse. Hemberg M, Kreiman G. Cells, Circuits and Computation 2009. Cambridge, MA. Conserved transcription factor binding sites predict tissue-specific gene expression and vice versa, Martin Hemberg, Gabriel Kreiman, Genome informatics, invited talk, Cold Spring Harbor (USA), 2009. Decoding dynamic patterns of neural activity using a 'biologically plausible' fixed set of weights. Meyers E, Freedman D, Kreiman G, Miller EK, Poggio T. Cosyne 2009. When can rates be reliably transmitted in feedforward networks? Burbank K, Kreiman G. Cosyne 2009. 2008 Robust decoding of visual information from the human brain. Liu H, Agam Y, Madsen JR, Kreiman G. Society for Neuroscience Annual Meeting 2008. Stationarity of the neurla code for vision. Blumberg J, Singer J, Liu H, Agam Y, Madsen JR, Kreiman G. Society for Neuroscience Annual Meeting 2008. Examining the neural representation of cluttered scenes in macaque ventral visual cortex. Meyers E, Embark H, Freiwald W, Serre T, Kreiman G, Poggio T. Society for Neuroscience Annual Meeting 2008. 2007 Generalized dynamic theory of alternative splicing regulation. Murugan Rajamanickam and Gabriel Kreiman. RECOMB Satellite Meeting. Boston, 2007. The limits of feed-forward processing in visual object recognition. VSS (Sarasota, 2007) The limits of feed-forward processing in visual object recognition. Cosyne (Salt Lake City, 2007) Reading out visual information from populations of neurons in inferior temporal cortex and prefrontal cortex. Meyers E, Freedman D, Miller E, Kreiman G, Poggio T. Cosyne (Salt Lake City, 2007) Object recognition by decoding spikes and local field potentials. VSS (Sarasota, 2007) Decoding visual information from population of ITC neurons. VSS (Sarasota, 2007) 2006 Role of insuling-like growth factor 1 in activity-dependent plasticity in visual cortex. Society for Neuroscience Annual Meeting (Atlanta 2006). 2005 Using 'read-out' of object identity to understand object coding in the macaque inferior temporal cortex. Cosyne. (Salt Lake City, 2005). Transcription factor binding: does order matter? RECOMB (Boston, 2005) Differential gene expression in the developing lateral geniculate nucleus and medial geniculate nucleus. (Society for Neuroscience, 2005). 2004 Object recognition by selective spike and LFP data in inferior temporal cortex Society for Neuroscience, (San Diego, 2004) Invariant visual representations in the human temporal lobe Society for Neuroscience, (San Diego, 2004) Gene expression in mouse visual cortex after visual input deprivation: gene systems mediating distinct effects of activity Society for Neuroscience, (San Diego, 2004) 2003 Transcriptional regulation in higher eukaryotes. Computational Systems Biology Meeting, MIT. (Maine, 2003). Search for transcriptional regulatory signals in higher eukaryotes. Computational Biology: Function, Pathways, Phylogenies and Populations (Boston, 2003) Dynamics of single neurons during perception and memory tasks in the human medial temporal lobe. 29th Gottingen Neurobiology Conference. 5th German Neuroscience Society Conference (Gottingen, Germany, 2003) In search of the NCC. Insights from single neuron recordings in the human brain. Association for the Scientific Study of Consciousness, (Memphis: ASSC, 2003). 2002 Computational search for differential gene expression and regulation in the medial temporal lobe Society for Neuroscience (Orlando, 2002) Differences in feature extraction by electrosensory neurons for global and local stimuli Society for Neuroscience (Orlando, 2002) Sparse representation of visual information by single neurons in the human medial temporal lobe Cognitive Neuroscience (Orlando, 2002) 2001 Synchrony between single neurons in the human brain during sleep Society for Neuroscience (San Diego, 2001) Single neuron responses in humans during binocular rivalry and flash suppression Society for Neuroscience (San Diego, 2001) Information transmission by multiple pyramidal cells in the hindbrain of weakly electric fish Society for Neuroscience (San Diego, 2001) Imagery neurons in the human brain: a proposed substrate for visual experiential phenomena in epilepsy American Epilepsy Society (Los Angeles, 2001). Epilepsia (2001) 41S:32-32. 2000 Category-specific visual responses of single neurons in the human medial temporal lobe. Society for Neuroscience, (New Orleans, 2000) Feature extraction by multiple pyramidal cells in the hindbrain of weakly electric fish. European Neuroscience Societies Annual Meeting, (Brighton, UK 2000). European Journal of Neuroscience (2000), 12S:90-90. Responses of single neurons in the human brain during visual presentation and imagery. Cognitive Neuroscience Society, (San Francisco, 2000). J. Cogn. Neurosci. (2000) S:70-70. Responses of Single Neurons in the Human Brain During Vision and Visual Imagery 1999 Robustness, variability and modeling of amplitude modulation encoding by P-receptor afferent spike trains of weakly electric fish. Neural Information and Coding Workshop. (Montana, 1999) Stimulus encoding by multiple pyramidal cells in the ELL of weakly electric fish Society for Neuroscience 1999 Flash Suppression: Competition between eyes or patterns? Association for Research in Vision and Opthalmology (Fort Lauderdale, 1999) 1998 Robustness of amplitude modulation encoding by P-receptor afferent spike trains of weakly electric fish Society for Neuroscience 1998 Tetanic Stimulation Increases Both Autophosphorylation and Synthesis of CaMKII in area CA1 of Hippocampal Slices Within 5 Minutes Society for Neuroscience 1998 1997 Tetanic stimulation produces a similar increase in both nonphosphorylated and autophosphorylated CaMKII in dendrites of hippocampal CA1 neurons Society for Neuroscience (New Orleans, 1997)

Commentaries and Memos
Meyers E, Embark H, Freiwald W, Serre T, Kreiman G, Poggio T. Examining neural representations of cluttered scenes. 2010, MIT AI Memo. Boston. CBCL-289 // MIT-CSAIL-TR-2010-034. Singer J, Kreiman G. Toward unmasking the dynamics of visual perception. Neuron (2009) 64:446-447. Quian Quiroga R, Kreiman G. Measuring sparseness in the brain. Psychological Reviews (2010) 117:291-297. Kreiman G. (2007). Brain science: from the very large to the very small. Current Biology17, R768-R770. Serre T, Kouh M, Cadieu C, Knoblich U, Kreiman G, Poggio T. (2005) A theory of object recognition: computations and circuits in the feedforward path of the ventral stream in primate visual cortex, MIT AI Memo 2005-036. Hung CP, Kreiman G, Poggio T, DiCarlo JJ. (2005) Ultra-fast object recognition from few spikes, MIT AI Memo 2005-022 Kreiman, G., Hung, C., Poggio, T., and DiCarlo, J. (2004). Selectivity of local field potentials in macaque inferior temporal cortex. MIT AI Memo 2004-020. Kreiman G. Moveo Ergo Sum. Book Review. BioEssays (2001) 23:662. Comment on book "Consciousness in Brains and Networks" by Roger Cotterill

Theses
On the neuronal activity in the human brain during visual recognition, imagery and binocular rivalry. Gabriel Kreiman. Ph.D. Thesis. Department of Biology, California Institute of Technology (2001). Neural coding and feature extraction of time varying signals. Gabriel Kreiman. M.Sc. Thesis. Computation and Neural Systems Program, California Institute of Technology (2001).

Books
Understanding visual population codes -- towards a common multivariate framework for cell recording and functional imaging