Manolis Kellis (Kamvysselis) manoli@mit.edu |
Spotlight:
Dr Who hack at CSAIL 4/17/2012.
RECOMB Regulatory
and Systems Genomics 2012
in San Francisco Bay
6.881 Computational Personal Genomics
29 mammals in Nature
News: CSAIL - Broad
Olfactory epigenetics
3 papers in Nature on 3/23
Chromatin Dynamics in Human
(News release)
modENCODE paper in Science
Phylogenomics paper in MBE
Chromatin states paper in Nature Biotech
6.047/6.878 Computational Biology:
Genomes, Networks, Evolution
(now with audio track for each lecture)
RECOMB Regulatory Genomics 2010
Positions available
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| Computational Biology - Selected Publications | ||
| Comparative Genomics and Integrative Genomics | ||
| 29 mammals | - | A high-resolution map of evolutionary constraint in the human genome |
| modENCODE | - | Functional elements and regulatory circuits in fly |
| 12flies | - | Evolutionary signatures for systematic genome interpretation in fly |
| HaploReg | - | Interpreting disease-associated SNPs in the human genome |
| 4yeasts | - | Gene identification and motif discovery in yeast |
| 8candida | - | Revealing pathogenic gene families in fungal genomes |
| Other | - | Dog - Neurospora - Drosophila - Platypus - modENCODE - ENCODE - Errors - Schizo |
| Epigenomics and Chromatin regulation | ||
| ChromHMM | - | Automating chromatin-state discovery and characterization |
| Chromatin Dynamics | - | Human chromatin state dynamics, enhancer networks, and disease |
| Chromatin States | - | Combinatorial chromatin patterns for genome annotation |
| Chromatin Regulators | - | From chromatin states to chromatin regulators using ChIP-string |
| Smell neurons | - | Epigenetic signature of monoallelic expression in olfactory neurons |
| Fly landscape | - | Chromatin landscape of Drosophila genes and regulatory elements |
| Human Enhancers | - | Tissue-specific enhancers in multiple human cell types |
| Fly Insulators | - | Genome-wide map of fly boundary elements |
| Other | - | Stalling - Embryo - Yeast - Roadmap - GATA |
| Gene and Genome Evolution | ||
| DupLossCoal | - | Joint modeling of gene duplication, loss, and incomplete lineage sorting |
| Phylogenomics | - | Bayesian gene-tree phylogenomic reconstruction |
| Phylogeny | - | Learning common gene-tree properties to overcome sparse information |
| Sub-gene | - | Domain-level evolution reveals abundant gene fusion and fission events |
| Innovation | - | Three periods of regulatory innovation in vertebrate evolution |
| Duplication | - | Proof and analysis of Whole-Genome Duplication (WGD) in yeast |
| Other | - | FishDup - FlyEvo - Platypus - Candida - Birds |
| Protein-coding genes | ||
| Readthrough | - | Evidence of abundant stop codon readthrough in animal genomes |
| Overlapping | - | Excess synonymous constraint in 10,000 protein-coding exons in human |
| PhyloCSF | - | Phylogenetic evidence of protein-coding evolutionary signatures |
| Drosophila | - | Revisiting fly genome: new genes and exons, unusual gene structures |
| Signatures | - | Comparing evolutionary and single-species metrics |
| Other | - | Revisiting Human and Yeast - CCDS - MassSpec |
| Regulatory non-coding RNAs | ||
| RNAshape | - | RNA folding with soft constraints integrating experimental evidence |
| lincRNAs | - | Chromatin reveals a new class of long intergenic non-coding RNAs |
| RNA families | - | Structural RNA families in the human genome |
| AS-miRNAs | - | Discovery of a new class of anti-sense functional microRNAs |
| microRNAs | - | Comparative identification of microRNAs in fly |
| Other | - | endo-siRNAs - miR-targets - piRNAs - platypus - cancer lncRNAs - Tasmanian |
| Regulatory Motifs | ||
| Parallel Assays | - | Massively parallel dissection of human enhancers |
| Fly CisReg | - | A cis-regulatory map of the Drosophila genome |
| Human Motifs | - | De novo TF/miRNA motif discovery in human |
| Long motifs | - | New class of long motifs in human CNEs, including insulators |
| PSSMs | - | Position-specific constraints match motif information content |
| Heart Beat | - | Motif discovery in cardiogram datasets to predict heart failure |
| Other | - | Yeast Motifs - Motif Pairs |
| Regulatory Networks | ||
| Network Inference | - | Integrative inference of regulatory networks |
| Motif Targets | - | Using motifs to infer regulatory networks in fly |
| Network Motifs | - | Discovering large motifs using symmetry-breaking conditions |
| SubMAP | - | Aligning large pathways with subnetwork mapping |
| Network Evol | - | Post whole-genome duplication (WGD) network evolution |
| Other research (AI, vision, graphics) | ||
| PhD Thesis | - | Received Sprowls award for best PhD thesis in CS |
| Masters Thesis | - | Imagina: Sketch-based image retrieval (applets) |
| Crust | - | 3D surface reconstruction (more info) |
| 3D Morphing | - | Polygon-based 3D model morphing |
| ECI Morph | - | Gaussian morphing 2D convex shapes |
| Chars | - | Character Recognition in Curvature Space |
| Other | - | Mood - RoboLogo - Invest - Webbot - Turing - Evolution - more |
