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1. Full Text FastME 2.0: A comprehensive, accurate, and fast distance-based phylogeny inference program
by Lefort, Vincent and Desper, Richard and Gascuel, Olivier
Molecular Biology and Evolution, ISSN 0737-4038, 10/2015, Volume 32, Issue 10, pp. 2798 - 2800
FastME provides distance algorithms to infer phylogenies. FastME is based on balanced minimum evolution, which is the very principle of Neighbor Joining (NJ).... 
NNI and SPR topological moves | phylogeny inference | distance-based | fast algorithms | (balanced) minimum evolution | MATRIX | MINIMUM-EVOLUTION METHOD | BIOCHEMISTRY & MOLECULAR BIOLOGY | ALGORITHMS | EVOLUTIONARY BIOLOGY | TREES | GENETICS & HEREDITY | THEORETICAL FOUNDATION | Models, Theoretical | Algorithms | Phylogeny | Bioinformatics | Computer Science | Resources
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2. Full Text Fast and accurate phylogeny reconstruction algorithms based on the Minimum-Evolution principle
by Desper, Richard and Gascuel, Olivier
Journal of Computational Biology, ISSN 1066-5277, 2002, Volume 9, Issue 5, pp. 687 - 705
The Minimum Evolution (ME) approach to phylogeny estimation has been shown to be statistically consistent when it is used in conjunction with ordinary... 
Phylogenetic inference | Topological accuracy | Computational speed | Distance methods | Minimum evolution | topological accuracy | computational speed | phylogenetic inference | SEQUENCE DATA | BIOCHEMICAL RESEARCH METHODS | distance methods | minimum evolution | STATISTICS & PROBABILITY | SIMULATION | LEAST-SQUARES | RATES | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | TREES | MODELS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | SUBSTITUTIONS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | Models, Genetic | Algorithms | Phylogeny | Computer Simulation | Evolution, Molecular
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3. Full Text Theoretical Foundation of the Balanced Minimum Evolution Method of Phylogenetic Inference and Its Relationship to Weighted Least-Squares Tree Fitting
by Desper, Richard and Gascuel, Olivier
Molecular Biology and Evolution, ISSN 0737-4038, 03/2004, Volume 21, Issue 3, pp. 587 - 598
Due to its speed, the distance approach remains the best hope for building phylogenies on very large sets of taxa. Recently (R. Desper and O. Gascuel, J. Comp.... 
Method comparison using simulations | Least-squares | Minimum evolution | Distance-based phylogenetic inference | Consistency | Least-Squares Analysis | Models, Genetic | Algorithms | Phylogeny | Computer Simulation | Evolution, Molecular
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4. FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program
by Vincent Lefort and Richard Desper and Olivier Gascuel
Molecular Biology and Evolution, ISSN 0737-4038, 10/2015, Volume 32, Issue 10, p. 2798
  FastME provides distance algorithms to infer phylogenies. FastME is based on balanced minimum evolution, which is the very principle of Neighbor Joining... 
Proteins | Algorithms | Evolutionary biology | Phylogenetics | Deoxyribonucleic acid--DNA
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5. Full Text FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program: Table 1
by Lefort, Vincent and Desper, Richard and Gascuel, Olivier
Molecular Biology and Evolution, ISSN 0737-4038, 10/2015, Volume 32, Issue 10, pp. 2798 - 2800
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6. Full Text Synthesis, structure, magnetic properties and kinetics of formation of a cluster containing a {Cu3(μ3-OH)} core supported by a triazole-based ligand
by Jasim M. Al-Karawi, Ahmed and Maatta, Eric and Desper, John and Maurmann, Leila and Henderson, Richard A and Buchholz, Axel and Plass, Winfried
Journal of Coordination Chemistry, ISSN 0095-8972, 02/2016, Volume 69, Issue 3, pp. 458 - 474
The trinuclear copper complex, [Cu 3 (μ 3 -OH)(CTMB) 3 (NO 3 ) 2 (CH 3 CN) 2 ]·5CH 3 CN·H 2 O (1) {CTMB = cyclohexotriazole-3-(4-methoxybenzamide)}, has been... 
Cu | 3 | OH)} core | magnetic properties | trinuclear copper(II) | kinetic of complex formation | μ | HEXACOPPER(II) COMPLEX | CRYSTAL-STRUCTURE | X-RAY-STRUCTURE | METAL-ORGANIC FRAMEWORK | CU(II) COMPLEXES | CU-II | SECONDARY BUILDING UNITS | CHEMISTRY, INORGANIC & NUCLEAR | MU-OH CORE | {Cu-3(-OH)} core | TRINUCLEAR COPPER(II) HYDROXO | COORDINATION POLYMERS | Ligands | Magnetism | Exchange | PHASES | LIGANDS | PROPERTIES | MAGNETIC PROPERTIES | TRIAZOLE | KINETICS | Clusters | Formations | Coordination compounds | Copper
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7. Full Text Somatic Deletions in Hereditary Breast Cancers Implicate 13q21 as a Putative Novel Breast Cancer Susceptibility Locus
by Tommi Kainu and Suh-Hang Hank Juo and Richard Desper and Alejandro A. Schaffer and Elizabeth Gillanders and Ester Rozenblum and Diana Freas-Lutz and Don Weaver and Dietrich Stephan and Joan Bailey-Wilson and Olli-P. Kallioniemi and Mika Trikkonen and Kirsi Syrjakoski and Tuula Kuukasjarvi and Pasi Koivisto and Ritva Karhu and Kaija Holli and Adalgeir Arason and Gudrun Johannesdottir and Jon Thor Bergthorsson and Hrefna Johannsdottir and Valgardur Egilsson and Rosa Bjork Barkardottir and Oskar Johannsson and Karin Haraldsson and Therese Sandberg and Eva Holmberg and Henrik Gronberg and Hakan Olsson and Ake Borg and Paula Vehmanen and Hannaleena Eerola and Paivi Heikkila and Seppo Pyrhonen and Heli Nevanlinna and Onkologi och Patologi, MV and Lund University and Oncology and Pathology, MV and Lunds universitet
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 8/2000, Volume 97, Issue 17, pp. 9603 - 9608
A significant proportion of familial breast cancers cannot be explained by mutations in the BRCA1 or BRCA2 genes. We applied a strategy to identify... 
Biological Sciences | Lod score | Comparative genomic hybridization | University hospitals | Medical genetics | Genetic loci | Breast cancer | Chromosomes | Human genetics | Tumors | Cancer | DISTINCT REGIONS | GERM-LINE MUTATIONS | TUMOR PROGRESSION | CHROMOSOME 13Q | FAMILIAL BREAST | PEUTZ-JEGHERS-SYNDROME | MULTIDISCIPLINARY SCIENCES | PROSTATE-CANCER | LINKAGE ANALYSIS | ALLELIC LOSS | COMPARATIVE GENOMIC HYBRIDIZATION | Chromosomes, Human, Pair 13 - genetics | Genes, BRCA1 - genetics | Humans | Hybrid Cells | Middle Aged | Male | Germ-Line Mutation - genetics | Lod Score | Haplotypes - genetics | Female | Neoplasm Proteins - genetics | Chromosome Deletion | Genetic Predisposition to Disease - genetics | Nucleic Acid Hybridization | Genotype | Chromosome Mapping | Transcription Factors - genetics | Disease Progression | Breast Neoplasms - genetics | Breast Neoplasms - pathology | Pedigree | BRCA2 Protein | Aged | Models, Genetic | Genome, Human | Genetic aspects | Clinical Medicine | Medical and Health Sciences | Klinisk medicin | Cancer and Oncology | Medicin och hälsovetenskap | Cancer och onkologi
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8. Full Text Evaluation of the Clonal Relationship between Primary and Metastatic Renal Cell Carcinoma by Comparative Genomic Hybridization
by Bissig, Heidi and Richter, Jan and Desper, Richard and Meier, Verena and Schraml, Peter and Schäffer, Alejandro A and Sauter, Guido and Mihatsch, Michael J and Moch, Holger
The American Journal of Pathology, ISSN 0002-9440, 1999, Volume 155, Issue 1, pp. 267 - 274
The outcome of patients with renal cell carcinoma is limited by the development of metastasis after nephrectomy. To evaluate the genetic basis underlying... 
BREAST-CANCER | GROWTH-FACTOR RECEPTOR | BLADDER-CANCER | PRIMARY TUMORS | SOLID TUMORS | DNA-CONTENT | COPY NUMBER CHANGES | INTRATUMOR HETEROGENEITY | PATHOLOGY | CYTOGENETIC ANALYSIS | GENETIC-DIFFERENCES | Nucleic Acid Hybridization | Carcinoma, Renal Cell - pathology | Humans | Carcinoma, Renal Cell - genetics | Proteins - genetics | Ubiquitin-Protein Ligases | Chromosome Aberrations - genetics | Ligases | Carcinoma, Renal Cell - secondary | Gene Deletion | Kidney Neoplasms - pathology | Von Hippel-Lindau Tumor Suppressor Protein | Tumor Suppressor Proteins | Regular
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9. Full Text Tumor classification using phylogenetic methods on expression data
by Desper, Richard and Khan, Javed and Schäffer, Alejandro A
Journal of Theoretical Biology, ISSN 0022-5193, 2004, Volume 228, Issue 4, pp. 477 - 496
Tumor classification is a well-studied problem in the field of bioinformatics. Developments in the field of DNA chip design have now made it possible to... 
Phylogenetic trees | Breast cancer | Gene expression data | Small round blue cell tumors | Microarrays | Tumor classification | gene expression data | phylogenetic trees | PROFILES | RECONSTRUCTION | breast cancer | PATTERNS | CANCER | microarrays | MOLECULAR CLASSIFICATION | tumor classification | small round blue cell tumors | TREES | MAPS | BIOLOGY | GENE-EXPRESSION | CLASS PREDICTION | Breast Neoplasms - classification | Gene Expression | Algorithms | Neoplasms - genetics | Oligonucleotide Array Sequence Analysis - methods | Humans | Neoplasms - classification | DNA, Neoplasm - genetics | Phylogeny
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10. Full Text Genetic differences detected by comparative genomic hybridization in head and neck squamous cell carcinomas from different tumor sites: construction of oncogenetic trees for tumor progression
by Huang, Qiang and Yu, Guo Pei and McCormick, Steven A and Mo, Juan and Datta, Bhakti and Mahimkar, Manoj and Lazarus, Philip and Schäffer, Alejandro A and Desper, Richard and Schantz, Stimson P
Genes, Chromosomes and Cancer, ISSN 1045-2257, 06/2002, Volume 34, Issue 2, pp. 224 - 233
For a better understanding of genetic alterations in head and neck squamous cell carcinoma (HNSCC), we applied comparative genomic hybridization (CGH) in the... 
BREAST-CANCER | FREQUENT | GAINS | AMPLIFICATION | SOLID TUMORS | ONCOLOGY | COPY NUMBER CHANGES | DNA | OLIGONUCLEOTIDE-PRIMED PCR | GENETICS & HEREDITY | IMBALANCES | CHROMOSOMAL-ABERRATIONS | Laryngeal Neoplasms - genetics | Oncogenes - genetics | Nucleic Acid Hybridization | Carcinoma, Squamous Cell - genetics | Carcinoma, Squamous Cell - pathology | Humans | Gene Dosage | Disease Progression | Head and Neck Neoplasms - pathology | Laryngeal Neoplasms - pathology | Pharyngeal Neoplasms - genetics | Chromosome Aberrations - statistics & numerical data | Mouth Neoplasms - pathology | Head and Neck Neoplasms - genetics | Pharyngeal Neoplasms - pathology | Mouth Neoplasms - genetics
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11. Full Text A newly discovered human α-globin gene
by Goh, Sung-Ho and Lee, Y. Terry and Bhanu, Natarajan V and Cam, Margaret C and Desper, Richard and Martin, Brian M and Moharram, Ramy and Gherman, Robert B and Miller, Jeffery L
Blood, ISSN 0006-4971, 08/2005, Volume 106, Issue 4, pp. 1466 - 1472
A previously undefined transcript with significant homology to the pseudo-alpha 2 region of the at-globin locus on human chromosome 16 was detected as part of... 
HUMAN GENOME | ALIGNMENT | AMINO-ACID-SEQUENCES | D-CHAINS | PSEUDOGENE | HIGH-ALTITUDE RESPIRATION | CLUSTER | PROTEINS | HEMATOLOGY | EXPRESSION | MINOR HEMOGLOBIN COMPONENT | Humans | RNA, Messenger - genetics | Gene Expression Regulation | Molecular Sequence Data | RNA, Messenger - analysis | Gene Expression Profiling | Erythrocytes - chemistry | Phylogeny | Reticulocytes - chemistry | Cell Differentiation - genetics | Globins - genetics | Cloning, Molecular | Conserved Sequence | Red Cells
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12. Full Text Construction and analysis of tree models for chromosomal classification of diffuse large B-cell lymphomas
by Hui-Yong Jiang Zhong-Xi Huang Xue-Feng Zhang Richard Desper Tong Zhao
世界胃肠病学杂志：英文版, ISSN 1007-9327, 2007, Volume 13, Issue 11, pp. 1737 - 1742
AIM： To construct tree models for classification of diffuse large B-cell lymphomas （DLBCL） by chromosome copy numbers, to compare them with cDNA microarray... 
树型模型 | 亚型 | 染色体 | 弥漫性B细胞淋巴瘤 | 比较基因杂交 | 肿瘤发生 | Subclassification | Comparative gene hybridization | Tree model | Tumorigenesis | Lymphoma | SURVIVAL | subclassification | RECONSTRUCTION | lymphoma | PHYLOGENETIC TREES | CANCER | CYTOGENETIC ANALYSIS | GENE | COPY NUMBER CHANGES | comparative gene hybridization | NON-HODGKINS-LYMPHOMA | tumorigenesis | tree model | COMPARATIVE GENOMIC HYBRIDIZATION | GASTROENTEROLOGY & HEPATOLOGY | EXPRESSION | Gene Expression Profiling - classification | Gene Dosage - genetics | Nucleic Acid Hybridization | Oligonucleotide Array Sequence Analysis | Models, Biological | Humans | Lymphoma, Large B-Cell, Diffuse - classification | DNA, Neoplasm - genetics | Decision Trees | Chromosome Aberrations - classification | Lymphoma, Large B-Cell, Diffuse - genetics | Rapid Communication
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13. Full Text Construction of evolutionary tree models for renal cell carcinoma from comparative genomic hybridization data
by Jiang, Feng and Jiang, F and Desper, Richard and Desper, R and Papadimitriou, C.H and Papadimitriou, Christos H and Schaffer, A.A and Schäffer, Alejandro A and Kallioniemi, Olli-P and Kallioniemi, O.-P and Richter, Jan and Richter, J and Schraml, P and Schraml, Peter and Sauter, G and Sauter, Guido and Mihatsch, M.J and Mihatsch, Michael J and Moch, Holger and Moch, H
Cancer Research, ISSN 0008-5472, 2000, Volume 60, Issue 22, pp. 6503 - 6509
Renal cell carcinoma is characterized by an accumulation of complex chromosomal alterations during tumor progression. Chromosome 3p deletions are known to... 
BLADDER-CANCER | INTRATUMORAL HETEROGENEITY | INTERPHASE CYTOGENETICS | SOLID TUMORS | ONCOLOGY | SHORT ARM | SEQUENCE COPY NUMBER | ALLELIC LOSS | RETINOBLASTOMA GENE | CORTICAL NEOPLASMS | CHROMOSOMAL IMBALANCES | Nucleic Acid Hybridization - methods | Kidney Neoplasms - genetics | Prognosis | Carcinoma, Renal Cell - pathology | Humans | Carcinoma, Renal Cell - genetics | Chromosome Aberrations | Survival Analysis | Kidney Neoplasms - pathology | Models, Genetic | Retrospective Studies | DNA, Neoplasm - genetics | Decision Trees | Neoplasm Staging | Evolution, Molecular
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14. Full Text Graph Models of Oncogenesis with an Application to Melanoma
by RADMACHER, MICHAEL D and SIMON, RICHARD and DESPER, RICHARD and TAETLE, RAYMOND and SCHÄFFER, ALEJANDRO A and NELSON, MARK A
Journal of Theoretical Biology, ISSN 0022-5193, 10/2001, Volume 212, Issue 4, pp. 535 - 548
We describe several analytical techniques for use in developing genetic models of oncogenesis including: methods for the selection of important genetic events,... 
CUTANEOUS MALIGNANT-MELANOMA | TREE MODELS | NONRANDOM CHROMOSOME-ABNORMALITIES | OVARIAN ADENOCARCINOMA | 11Q23 | COMPARATIVE GENOMIC HYBRIDIZATION | CANCER | BIOLOGY, MISCELLANEOUS | Melanoma - genetics | Humans | Models, Genetic | Cytogenetic Analysis | Models, Statistical | Chromosome Breakage | Disease Progression | Models | Methylation | Carcinogenesis | Melanoma | chromosome 6 | chromosome 7 | chromosome 1 | chromosome 9
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15. Full Text 8p12–23 and +20q Are Predictors of Subtypes and Metastatic Pathways in Colorectal Cancer: Construction of Tree Models Using Comparative Genomic Hybridization Data
by Li, Xiaobo and Chen, Jian and Lü, Bingjian and Peng, Sihua and Desper, Richard and Lai, Maode
OMICS: A Journal of Integrative Biology, ISSN 1536-2310, 01/2011, Volume 15, Issue 1-2, pp. 37 - 47
A substantial body of evidence suggests the genetic heterogeneous pattern and multiple pathways in colorectal cancer initiation and progression. In this study,... 
Original Articles | HEPATOCELLULAR-CARCINOMA | ONCOGENESIS | COPY NUMBER CHANGES | NEOPLASTIC PROGRESSION | ABNORMALITIES | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENETICS & HEREDITY | TUMOR-SUPPRESSOR | CLASSIFICATION | PHYLOGENETIC TREES | RENAL-CELL CARCINOMA | GENETIC ALTERATIONS | Neoplasm Metastasis - genetics | Nucleic Acid Hybridization | Colorectal Neoplasms - genetics | Humans | Chromosome Aberrations | Chromosomes, Human, Pair 8 | Colorectal Neoplasms - pathology | Complications and side effects | Chromosome abnormalities | Genes | Colorectal cancer | Physiological aspects | Genetic aspects | Research | Diagnosis | Risk factors
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16. Full Text Construction of tree models for pathogenesis of nasopharyngeal carcinoma
by Huang, Zhongxi and Desper, Richard and Schäffer, Alejandro A and Yin, Zhihua and Li, Xin and Yao, Kaitai
Genes, Chromosomes and Cancer, ISSN 1045-2257, 08/2004, Volume 40, Issue 4, pp. 307 - 315
Pathogenesis of nasopharyngeal carcinoma (NPC) is a multistep and multipathway process that cannot be fully explained by a fixed linear progression model. We... 
PROMOTER HYPERMETHYLATION | SOLID TUMORS | ONCOLOGY | COPY NUMBER CHANGES | SHORT ARM | GENETICS & HEREDITY | COMPARATIVE GENOMIC HYBRIDIZATION | PHYLOGENETIC TREES | CANCER | CELL CARCINOMA | ABNORMAL EXPRESSION | GENETIC ALTERATIONS | Nasopharyngeal Neoplasms - genetics | Predictive Value of Tests | Genetic Predisposition to Disease - genetics | Humans | Carcin