Tech Reports in Computer Science and Engineering
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Item Nervous system maps on the C. elegans genome(2020-09-28) Cherniak, Christopher; Mokhtarzada, Zekeria; Rodriguez-Esteban, RaulThis project begins from a synoptic point of view, focusing upon the large-scale (global) landscape of the genome. This is along the lines of combinatorial network optimization in computational complexity theory [1]. Our research program here in turn originated along parallel lines in computational neuroanatomy [2,3,4,5]. Rather than mapping body structure onto the genome, the present report focuses upon statistically significant mappings of the Caenorhabditis elegans nervous system onto its genome. Via published datasets, evidence is derived for a "wormunculus", on the model of a homunculus representation, but on the C. elegans genome. The main method of testing somatic-genomic position-correlations here is via public genome databases, with r^2 analyses and p evaluations. These findings appear to yield some of the basic structural and functional organization of invertebrate nucleus and chromosome architecture. The design rationale for somatic maps on the genome in turn may be efficient interconnections. A next question this study raises: How do these various somatic maps mesh (interrelate, interact) with each other?Item Cell Maps on the Human Genome(2018-06-01) Cherniak, Christopher; Rodriguez-Esteban, RaulSub-cellular organization is significantly mapped onto the human genome: Evidence is reported for a "cellunculus" -- on the model of a homunculus, on the H. sapiens genome. We have previously described a statistically significant, global, supra-chromosomal representation of the human body that appears to extend over the entire genome. Here, we extend the genome mapping model, zooming down to the typical individual animal cell. Basic cell structure turns out to map onto the total genome, mirrored via genes that express in particular cell organelles (e.g., “nuclear membrane”); evidence also suggests similar cell maps appear on individual chromosomes that map the dorsoventral body axis.Item Body Maps on Human Chromosomes(2015-11-08) Cherniak, Christopher; Rodriguez-Esteban, RaulAn exploration of the hypothesis that human genes are organized somatotopically: For each autosomal chromosome, its tissue-specific genes tend to have relative positions on the chromosome that mirror corresponding positions of the tissues in the body. In addition, there appears to be a division of labor: Such a homunculus representation on a chromosome holds significantly for either the anteroposterior or the dorsoventral body axis. In turn, anteroposterior and dorsoventral chromosomes tend to occupy separate zones in the spermcell nucleus. One functional rationale of such largescale organization is for efficient interconnections in the genome.Item Body Maps on the Human Genome(2010-12-01) Cherniak, Christopher; Rodriguez-Esteban, RaulThe human genome possesses large-scale structure: In particular, body tissue genes map somatotopically onto the complete chromosome set. The synoptic picture is that genes highly expressed in particular tissues are not randomly distributed on the genome. Rather, they form a "genome homunculus": a multi-dimensional, genome-wide body representation extending across chromosome territories (each chromosome's preferred nucleus locale) of the entire spermcell nucleus. The antero-posterior axis of the body corresponds to the head-tail axis of the nucleus, and the dorso-ventral body axis to the central-peripheral nucleus axis. Somatotopic maps in cerebral cortex have been reported for over a century. This pervasive genome mapping merits further attention.Item Global Layout Optimization of Olfactory Cortex and of Amygdala of Rat(2005-06) Rodriguez-Esteban, Raul; Cherniak, ChristopherPrinciples of connection minimization in the nervous system apply not only to complete neural systems but also to smaller subsystems such as rat olfactory cortex and rat amygdala. These subsystems have a three-dimensional organization, rather than previously-studied two-dimensional and one-dimensional schemes. Nonetheless, wire-cost savings show optimality at similar levels, suggesting neural optimization principles are widespread, followed at multiple scales of the nervous system.Item Global Optimization of Cerebral Cortex Layout (II)(2003-11-25) Cherniak, Christopher; Mokhtarzada, Zekeria; Rodriguez-Esteban, Raul; Changizi, B. K.Supplementary supporting material for: UMIACS-TR-2003-102 CS-TR-4534 Global Optimization of Cerebral Cortex Layout (I) C. Cherniak, Z. Mokhtarzada, R. Rodriguez-Esteban, B. Changizi.Item Global Optimization of Cerebral Cortex Layout (I)(2003-11-25) Cherniak, Christopher; Mokhtarzada, Zekeria; Rodriguez-Esteban, Raul; Changizi, B. K.Functional areas of mammalian cerebral cortex seem positioned to minimize costs of their interconnections, down to a best-in-a-billion optimality level. The optimization problem here, originating in microcircuit design, is: Given connections among components, what is the physical placement of the components on a surface that minimizes total length of connections? Because of unfeasibility of measuring longrange "wirelength" in the cortex, a simpler adjacency cost was validated. To deal with incomplete information on brain networks, a Size Law was developed that predicts optimization patterns in subnetworks. Macaque and cat cortex rank better in this connection optimization than the wiring of comparably structured computer chips, but somewhat worse than the macroeconomic commodity-flow network among U.S. states. However, cortex wiring conforms to the Size Law better than the macroeconomic patterns, which may indicate cortex optimizing mechanisms involve more global processes. [ See also Supplementary Material: CS-TR-4535 ] UMIACS-TR-2003-102)