80 research outputs found
Cube maze
No full textConventional data visualization methods are very narrow in terms of the data typeson which they are applicable. We present a novel way of viewing multi-attributeddataset by grouping subsets of attributes into facets. Cube-Maze interface visually rep-resents each data “entity” as a cube in three dimensional space. Similarity among “datacubes” correspond to 0, 1, and 2 dimensional adjacencies. Our current implementationprovides different modes of “EgoNet” navigation and several interaction filters. Thegraph counterpart for this cube maze representation is a “Labeled Multi Digraph”.M.S.Includes bibliographical referencesby Pritish Sah
Drug Repositioning: Principles, Resources, and Application of Structure-Based Virtual Screening for the Identification of Anticancer Agents
No full textSome hardness escalation results in computational complexity theory
No full textThis electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Thesis: Ph. D., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2020Cataloged from student-submitted PDF of thesis. "February 2020."Includes bibliographical references (pages 92-105).In this thesis, we prove new hardness escalation results in computational complexity theory; a phenomenon where hardness results against seemingly weak models of computation for any problem can be lifted, in a black box manner, to much stronger models of computation by considering a simple gadget composed version of the original problem. For any unsatisfiable CNF formula F that is hard to refute in the Resolution proof system, we show that a gadget-composed version of F is hard to refute in any proof system whose lines are computed by efficient communication protocols. This allows us to prove new lower bounds for: -- Monotone Circuit Size : we get an exponential lower bound for an explicit monotone function computable by linear sized monotone span programs and also in (non-monotone) NC². -- Real Monotone Circuit Size : Our proof technique extends to real communication protocols, which yields similar lower bounds against real monotone circuits. -- Cutting Planes Length : we get exponential lower bound for an explicit CNF contradiction that is refutable with logarithmic Nullstellensatz degree. Finally, we describe an intimate connection between computational models and communication complexity analogs of the sub-classes of TFNP, the class of all total search problems in NP. We show that the communication analog of PPA[subscript p] captures span programs over F[subscript p] for any prime p. This complements previously known results that communication FP captures formulas (Karchmer- Wigderson, 1988) and that communication PLS captures circuits (Razborov, 1995).by Pritish Kamath.Ph. D.Ph.D. Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Scienc
Integrated analysis of dysregulated lncRNA expression in breast cancer cell identified by RNA-seq study
No full textAbstractAmong all the sequencing techniques, RNA sequencing (RNA-seq) has galloped with pace adopting the profiling of transcriptomic data in almost every biological analytics area like gene regulation study, development biology and clinical research. Recently the discovery of differentially expressed genes across different conditions has outshone the barrier of genetic & epigenetic regulations. The present work identified and analyzed differentially expressed novel long non-coding RNAs (lncRNAs) for breast cancer. A complex computational pipeline was adopted for the study which includes analysis of 18498 differentially expressed genes with 4114 up-regulated and 3475 down-regulated transcripts. The overexpression of lnc-MTAP (CDKN2B-AS1), lnc-PCP4 (DSCAM-S1), and lnc-FAM (H19) in breast cells suggests that these lncRNAs may have significant role to play in breast cancer. These results validated the relevance of the dysregulation pattern in cancer cells due to the presence of lncRNAs. The study further opens a new scope for experimental analysis to confirm the aberrant expression pattern of these lncRNAs which may act as potential bio-markers for the diagnosis and early detection of breast cancer
Primary responses to salt stress in a halophyte, smooth cordgrass (Spartina alterniflora Loisel.)
No full textThe response of a grass halophyte Spartina alterniflora at early stages of salt stress was investigated through generation and systematic analysis of expressed sequence tags (ESTs) from both leaf and root tissues. Random EST sequencing produced 1,227 quality ESTs, which were clustered into 127 contigs, and 368 were singletons. Of the 495 unigenes, 27% represented genes for stress response. Comparison of the 368 singletons against the Oryza sativa gene index showed that \u3e85% of these genes had similarity with the rice unigenes. Moreover, the phylogenetic analysis of an EST similar to myo -inositol 1-phosphate synthase of Spartina and some selected grasses and halophytes showed closeness of Spartina with maize and rice. Transcript abundance analysis involving eight known genes of various metabolic pathways and nine transcription factor genes showed temporal and tissue-dependent variation in expression under salinity. Reverse northern analysis of a few selected unknown and ribosomal genes exhibited much higher abundance of transcripts in response to salt stress. The results provide evidence that, in addition to several unknown genes discovered in this study, genes involved in ion transport, osmolyte production, and house-keeping functions may play an important role in the primary responses to salt stress in this grass halophyte. © Springer-Verlag 2008
Unraveling long non-coding RNAs through analysis of high-throughput RNA-sequencing data
No full textExtensive genome-wide transcriptome study mediated by high throughput sequencing technique has revolutionized the study of genetics and epigenetic at unprecedented resolution. The research has revealed that besides protein-coding RNAs, large proportions of mammalian transcriptome includes a heap of regulatory non protein-coding RNAs, the number encoded within human genome is enigmatic. Many taboos developed in the past categorized these non-coding RNAs as ââdark matterâ and âjunksâ. Breaking the myth, RNA-seq-- a recently developed experimental technique is widely being used for studying non-coding RNAs which has acquired the limelight due to their physiological and pathological significance. The longest member of the ncRNA family-- long non-coding RNAs, acts as stable and functional part of a genome, guiding towards the important clues about the varied biological events like cellular-, structural- processes governing the complexity of an organism. Here, we review the most recent and influential computational approach developed to identify and quantify the long non-coding RNAs serving as an assistant for the users to choose appropriate tools for their specific research. Keywords: Transcriptome, High throughput sequencing, Genetic and epigenetic, Long non-coding RNA, RNA-sequencing, RNA-se
Prediction of Blood Brain Barrier Permeability of Ligands Using Sequential Floating Forward Selection and Support Vector Machine
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