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1. Full Text On the impact of uncertain gene tree rooting on duplication-transfer-loss reconciliation
by Kundu, Soumya and Bansal, Mukul S
BMC bioinformatics, ISSN 1471-2105, 08/2018, Volume 19, Issue Suppl 9, pp. 290 - 290
Phylogenetics | Gene trees | Microbial evolution | Reconciliation | Horizontal gene transfer | Gene Duplication | Multigene Family | Uncertainty | Algorithms | Gene Transfer, Horizontal | Software | Phylogeny | Genomics - methods | Evolution, Molecular | Gene families | Computer programs | Impact analysis | Microorganisms | Reproduction (copying) | Computer applications | Evolution | Rooting | Bioinformatics | Index Medicus
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2. Full Text Linear-time algorithms for phylogenetic tree completion under Robinson-Foulds distance
by Bansal, Mukul S
Algorithms for molecular biology, ISSN 1748-7188, 04/2020, Volume 15, Issue 1, pp. 6 - 6
Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Biochemical Research Methods | Science & Technology | Mathematical & Computational Biology | Leaves | Biological effects | Algorithms | Evolutionary biology | Similarity measures | Computer applications | Phylogenetics | Distance measurement | Phylogeny | Optimal phylogenetic tree completion | Robinson–Foulds distance | Distance measures
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3. Full Text TreeFix: Statistically Informed Gene Tree Error Correction Using Species Trees
by Yi-Chieh Wu and Matthew D. Rasmussen and Mukul S. Bansal and Manolis Kellis
Systematic biology, ISSN 1063-5157, 1/2013, Volume 62, Issue 1, pp. 110 - 120
Datasets | Biological taxonomies | Genes | Reconciliation | Phylogenetics | Evolution | Genomes | Topology | Hybridity | Cost efficiency | Life Sciences & Biomedicine | Evolutionary Biology | Science & Technology | Reproducibility of Results | Animals | Fungi - classification | Classification - methods | Drosophila - classification | Software | Phylogeny | Fungi - genetics | Drosophila - genetics | Insects | Information | Index Medicus | Gene tree error correction | phylogenetics | Regular | reconciliation
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4. Full Text SaGePhy: an improved phylogenetic simulation framework for gene and subgene evolution
by Kundu, Soumya and Bansal, Mukul S
Bioinformatics, ISSN 1367-4803, 09/2019, Volume 35, Issue 18, pp. 3496 - 3498
Statistics & Probability | Biochemistry & Molecular Biology | Physical Sciences | Computer Science, Interdisciplinary Applications | Life Sciences & Biomedicine | Technology | Biochemical Research Methods | Computer Science | Mathematics | Biotechnology & Applied Microbiology | Science & Technology | Mathematical & Computational Biology | Index Medicus
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5. Full Text IGTP: A software package for large-scale gene tree parsimony analysis
by Chaudhary, Ruchi and Bansal, Mukul S and Wehe, André and Fernández-Baca, David and Eulenstein, Oliver
BMC bioinformatics, ISSN 1471-2105, 11/2010, Volume 11, Issue 1, pp. 574 - 574
Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Biochemical Research Methods | Science & Technology | Mathematical & Computational Biology | Gene Duplication | Algorithms | Databases, Genetic | Software | Phylogeny | Genome | Genomics - methods | Evolution, Molecular | Trees | Flowers & plants | Genes | Index Medicus
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6. Full Text Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss
by Bansal, Mukul S and Alm, Eric J and Kellis, Manolis
Bioinformatics, ISSN 1367-4803, 06/2012, Volume 28, Issue 12, pp. i283 - i291
Gene Duplication | Multigene Family | Algorithms | Gene Deletion | Genomics | Gene Transfer, Horizontal | Software | Phylogeny | Evolution, Molecular | Index Medicus | Ismb 2012 Proceedings Papers Committee July 15 to July 19, 2012, Long Beach, Ca, Usa | Original Papers
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7. Full Text Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models
by Bansal, Mukul S and Burleigh, J Gordon and Eulenstein, Oliver
BMC bioinformatics, ISSN 1471-2105, 01/2010, Volume 11, Issue 1, pp. S42 - S42
Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Biochemical Research Methods | Science & Technology | Mathematical & Computational Biology | Gene Duplication | Algorithms | Phylogeny | Genome | Evolution, Molecular | Trees | Studies | Problems | Genes | Evolution | Bioinformatics | Heuristic | Indexing in process | Index Medicus
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8. Full Text Genome-Scale Phylogenetics: Inferring the Plant Tree of Life from 18,896 Gene Trees
by J. Gordon Burleigh and Mukul S. Bansal and Oliver Eulenstein and Stefanie Hartmann and André Wehe and Todd J. Vision
Systematic biology, ISSN 1063-5157, 3/2011, Volume 60, Issue 2, pp. 117 - 125
Datasets | Taxa | Biological taxonomies | Genes | Phylogenetics | Gene duplication | Phylogeny | Topology | Quartets | Angiosperms | plant phylogeny | gene tree parsimony | phylogenomics | Gene tree-species tree reconciliation | Life Sciences & Biomedicine | Evolutionary Biology | Science & Technology | Algorithms | Plants - genetics | Genomics | Classification - methods | Plants - classification | Expressed Sequence Tags | Trees | Proteins | Studies | Genomes | Software | Flowers & plants | Index Medicus | Gene tree–species tree reconciliation | Regular
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9. Full Text RANGER-DTL 2.0: rigorous reconstruction of gene-family evolution by duplication, transfer and loss
by Bansal, Mukul S and Kellis, Manolis and Kordi, Misagh and Kundu, Soumya
Bioinformatics, ISSN 1367-4803, 09/2018, Volume 34, Issue 18, pp. 3214 - 3216
Statistics & Probability | Biochemistry & Molecular Biology | Physical Sciences | Computer Science, Interdisciplinary Applications | Life Sciences & Biomedicine | Technology | Biochemical Research Methods | Computer Science | Mathematics | Biotechnology & Applied Microbiology | Science & Technology | Mathematical & Computational Biology | Applications Notes
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10. Full Text Robinson-Foulds supertrees
by Bansal, Mukul S and Burleigh, J Gordon and Eulenstein, Oliver and Fernández-Baca, David
Algorithms for molecular biology, ISSN 1748-7188, 02/2010, Volume 5, Issue 1, pp. 18 - 18
Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Biochemical Research Methods | Science & Technology | Mathematical & Computational Biology | Heuristic programming | Trees (Graph theory) | Usage | Algorithms | Molecular systematics | Research | Methods | Trees | Studies | Computer science | Accuracy | Evolution | Manuscripts | Heuristic | Problem solving | Leaves | Data processing | Phylogeny
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11. Full Text Tree fix: Statistically informed gene tree error correction using species trees
by Wu, Yi-Chieh and Rasmussen, Matthew D and Bansal, Mukul S and Kellis, Manolis
Systematic biology, ISSN 1063-5157, 01/2013, Volume 62, Issue 1, pp. 110 - 120
Gene tree error correction | phylogenetics | reconciliation
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12. Full Text Systematic Detection of Large-Scale Multi-Gene Horizontal Transfer in Prokaryotes
by Kloub, Lina and Gosselin, Sean and Fullmer, Matthew and Graf, Joerg and Gogarten, J Peter and Bansal, Mukul S
Molecular biology and evolution, ISSN 0737-4038, 02/2021
Index Medicus
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13. Full Text Integrative analysis of 111 reference human epigenomes
by Roadmap Epigenomics Consortium, Epigenomics Consortium and Kundaje, Anshul and Meuleman, Wouter and Ernst, Jason and Bilenky, Misha and Yen, Angela and Heravi-Moussavi, Alireza and Kheradpour, Pouya and Zhang, Zhizhuo and Wang, Jianrong and Ziller, Michael J and Amin, Viren and Whitaker, John W and Schultz, Matthew D and Ward, Lucas D and Sarkar, Abhishek and Quon, Gerald and Sandstrom, Richard S and Eaton, Matthew L and Wu, Yi-Chieh and Pfenning, Andreas R and Wang, Xinchen and Claussnitzer, Melina and Liu, Yaping and Coarfa, Cristian and Harris, R. Alan and Shoresh, Noam and Epstein, Charles B and Gjoneska, Elizabeta and Leung, Danny and Xie, Wei and Hawkins, R. David and Lister, Ryan and Hong, Chibo and Gascard, Philippe and Mungall, Andrew J and Moore, Richard and Chuah, Eric and Tam, Angela and Canfield, Theresa K and Hansen, R. Scott and Kaul, Rajinder and Sabo, Peter J and Bansal, Mukul S and Carles, Annaick and Dixon, Jesse R and Farh, Kai-How and Feizi, Soheil and Karlic, Rosa and Kim, Ah-Ram and Kulkarni, Ashwinikumar and Li, Daofeng and Lowdon, Rebecca and Elliott, Ginell and Mercer, Tim R and Neph, Shane J and Onuchic, Vitor and Polak, Paz and Rajagopal, Nisha and Ray, Pradipta and Sallari, Richard C and Siebenthall, Kyle T and Sinnott-Armstrong, Nicholas A and Stevens, Michael and Thurman, Robert E and Wu, Jie and Zhang, Bo and Zhou, Xin and Beaudet, Arthur E and Boyer, Laurie A and De Jager, Philip L and Farnham, Peggy J and Fisher, Susan J and Haussler, David and Jones, Steven J. M and Li, Wei and Marra, Marco A and McManus, Michael T and Sunyaev, Shamil and Thomson, James A and Tlsty, Thea D and Tsai, Li-Huei and Wang, Wei and Waterland, Robert A and Zhang, Michael Q and Chadwick, Lisa H and Bernstein, Bradley E and Costello, Joseph F and Ecker, Joseph R and Hirst, Martin and Meissner, Alexander and Milosavljevic, Aleksandar and Ren, Bing and Stamatoyannopoulos, John A and Wang, Ting and Kellis, Manolis and Roadmap Epigenomics Consortium
Nature (London), ISSN 0028-0836, 02/2015, Volume 518, Issue 7539, pp. 317 - 329
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Chromatin - metabolism | Humans | Reference Values | RNA - genetics | Organ Specificity - genetics | DNA Methylation | Base Sequence | Cell Lineage - genetics | Chromatin - chemistry | Genome-Wide Association Study | Datasets as Topic | Epigenomics | Chromosomes, Human - genetics | Cells, Cultured | Chromosomes, Human - metabolism | DNA - metabolism | Genome, Human - genetics | Chromosomes, Human - chemistry | DNA - genetics | DNA - chemistry | Epigenesis, Genetic - genetics | Enhancer Elements, Genetic - genetics | Genetic Variation - genetics | Histones - metabolism | Chromatin - genetics | Genetic research | Epigenetic inheritance | Research | Human genome | DNA methylation | Enzymes | Genomes | Gene expression | Genomics | Deoxyribonucleic acid--DNA | Index Medicus
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