Chris Sander, PhD - Related publications

1986-1997 Biocomputing EMBL Heidelberg 
 1995-1998 Research European Bioinformatics Institute (EBI), UK 
 2002-2015 Computational Biology Center Memorial Sloan Kettering Cancer Center, Rockville Centre, NY, United States 
 2016- Cell Biology Harvard Medical School 
computational biology, structural biology, cancer biology, evolutionary biology
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Wu H, Chen Z, Wu Y, Zhang H, Liu Q. Integrating Protein-Protein Interaction Networks and Somatic Mutation Data to Detect Driver Modules in Pan-Cancer. Interdisciplinary Sciences, Computational Life Sciences. PMID 34491536 DOI: 10.1007/s12539-021-00475-y   
2021 Fang LT, Zhu B, Zhao Y, Chen W, Yang Z, Kerrigan L, Langenbach K, de Mars M, Lu C, Idler K, Jacob H, Zheng Y, Ren L, Yu Y, Jaeger E, ... , et al. Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing. Nature Biotechnology. 39: 1151-1160. PMID 34504347 DOI: 10.1038/s41587-021-00993-6   
2021 Xiao W, Ren L, Chen Z, Fang LT, Zhao Y, Lack J, Guan M, Zhu B, Jaeger E, Kerrigan L, Blomquist TM, Hung T, Sultan M, Idler K, Lu C, et al. Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing. Nature Biotechnology. 39: 1141-1150. PMID 34504346 DOI: 10.1038/s41587-021-00994-5   
2021 Leong PPT, Mihajlović A, Bogdanović N, Breberina L, Xi L. Reconstructing and counting genomic fragments through tagmentation-based haploid phasing. Scientific Reports. 11: 18907. PMID 34556684 DOI: 10.1038/s41598-021-97852-w   
2021 Bastidas Torres AN, Melchers RC, Van Grieken L, Out-Luiting JJ, Mei H, Agaser C, Kuipers TB, Quint KD, Willemze R, Vermeer MH, Tensen CP. Whole-genome profiling of primary cutaneous anaplastic large cell lymphoma. Haematologica. PMID 34382383 DOI: 10.3324/haematol.263251   
2021 Cooley NP, Wright ES. Accurate annotation of protein coding sequences with IDTAXA. Nar Genomics and Bioinformatics. 3: lqab080. PMID 34541527 DOI: 10.1093/nargab/lqab080   
2021 Georgakopoulos-Soares I, Yizhar-Barnea O, Mouratidis I, Hemberg M, Ahituv N. Absent from DNA and protein: genomic characterization of nullomers and nullpeptides across functional categories and evolution. Genome Biology. 22: 245. PMID 34433494 DOI: 10.1186/s13059-021-02459-z   
2021 Huang G, Zhang H, Qu Y, Huang K, Gong X, Wei J, Du H. ARMT: An automatic RNA-seq data mining tool based on comprehensive and integrative analysis in cancer research. Computational and Structural Biotechnology Journal. 19: 4426-4434. PMID 34471489 DOI: 10.1016/j.csbj.2021.08.009   
2021 Horak P, Leichsenring J, Goldschmid H, Kreutzfeldt S, Kazdal D, Teleanu V, Endris V, Gieldon L, Allgäuer M, Volckmar AL, Dikow N, Renner M, Kirchner M, Penzel R, Ploeger C, et al. Assigning evidence to actionability: An introduction to variant interpretation in precision cancer medicine. Genes, Chromosomes & Cancer. PMID 34331337 DOI: 10.1002/gcc.22987   
2021 Park J, Wang HH. Systematic dissection of σ sequence diversity and function in bacteria. Cell Reports. 36: 109590. PMID 34433066 DOI: 10.1016/j.celrep.2021.109590   
2021 Kim N, Eum HH, Lee HO. Clinical Perspectives of Single-Cell RNA Sequencing. Biomolecules. 11. PMID 34439827 DOI: 10.3390/biom11081161   
2021 Zhou P, Wang L, Liu H, Li C, Li Z, Wang J, Tan X. CyanoOmicsDB: an integrated omics database for functional genomic analysis of cyanobacteria. Nucleic Acids Research. PMID 34614159 DOI: 10.1093/nar/gkab891   
2021 Terzian P, Olo Ndela E, Galiez C, Lossouarn J, Pérez Bucio RE, Mom R, Toussaint A, Petit MA, Enault F. PHROG: families of prokaryotic virus proteins clustered using remote homology. Nar Genomics and Bioinformatics. 3: lqab067. PMID 34377978 DOI: 10.1093/nargab/lqab067   
2021 Pozdeyev N, Fishbein L, Gay LM, Sokol ES, Hartmaier R, Ross JS, Darabi S, Demeure MJ, Kar A, Foust LJ, Koc K, Bowles DW, Leong S, Wierman ME, Kiseljak-Vassiliades K. Targeted genomic analysis of 364 adrenocortical carcinomas. Endocrine-Related Cancer. 28: 671-681. PMID 34410225 DOI: 10.1530/ERC-21-0040   
2021 Huang D, Zhou Y, Yi X, Fan X, Wang J, Yao H, Sham PC, Hao J, Chen K, Li MJ. VannoPortal: multiscale functional annotation of human genetic variants for interrogating molecular mechanism of traits and diseases. Nucleic Acids Research. PMID 34570217 DOI: 10.1093/nar/gkab853   
2021 Jiang L, Guo F, Tang J, Yu H, Ness S, Duan M, Mao P, Zhao YY, Guo Y. SBSA: an online service for somatic binding sequence annotation. Nucleic Acids Research. PMID 34606615 DOI: 10.1093/nar/gkab877   
2021 Al-Zain AM, Symington LS. The dark side of homology-directed repair. Dna Repair. 106: 103181. PMID 34311272 DOI: 10.1016/j.dnarep.2021.103181   
2021 Umarov R, Li Y, Arakawa T, Takizawa S, Gao X, Arner E. ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation. Plos Computational Biology. 17: e1009376. PMID 34491989 DOI: 10.1371/journal.pcbi.1009376   
2021 Guerrini MM, Oguchi A, Suzuki A, Murakawa Y. Cap analysis of gene expression (CAGE) and noncoding regulatory elements. Seminars in Immunopathology. PMID 34468849 DOI: 10.1007/s00281-021-00886-5   
2021 Wright BW, Molloy MP, Jaschke PR. Overlapping genes in natural and engineered genomes. Nature Reviews. Genetics. PMID 34611352 DOI: 10.1038/s41576-021-00417-w   
2021 Lv W, Li T, Wang S, Wang H, Li X, Zhang S, Wang L, Xu Y, Wei W. The Application of the CRISPR/Cas9 System in the Treatment of Hepatitis B Liver Cancer. Technology in Cancer Research & Treatment. 20: 15330338211045206. PMID 34605326 DOI: 10.1177/15330338211045206   
2021 Xia L, Wang Z, Wu X, Zeng T, Luo W, Hu X, Ni Y, Che G, Liu L, Zhang W, Xie D, Li W. Multiplatform discovery and regulatory function analysis of structural variations in non-small cell lung carcinoma. Cell Reports. 36: 109660. PMID 34496260 DOI: 10.1016/j.celrep.2021.109660   
2021 Hassan KA, Maher C, Elbourne LD, Henderson PJ, Paulsen IT. Increasing the PACE of characterising novel transporters by functional genomics. Current Opinion in Microbiology. 64: 1-8. PMID 34492595 DOI: 10.1016/j.mib.2021.08.005   
2021 Kang L, Michalak P, Hallerman E, Moncrief ND. A Draft Genome Assembly for the Eastern Fox Squirrel, Sciurus niger. G3 (Bethesda, Md.). PMID 34550334 DOI: 10.1093/g3journal/jkab315   
2021 Stephens Z, O'Brien D, Dehankar M, Roberts LR, Iyer RK, Kocher JP. Exogene: A performant workflow for detecting viral integrations from paired-end next-generation sequencing data. Plos One. 16: e0250915. PMID 34550971 DOI: 10.1371/journal.pone.0250915   
2021 Kim P, Tan H, Liu J, Yang M, Zhou X. FusionAI: Predicting fusion breakpoint from DNA sequence with deep learning. Iscience. 24: 103164. PMID 34646994 DOI: 10.1016/j.isci.2021.103164   
2021 Liu N, Low WY, Alinejad-Rokny H, Pederson S, Sadlon T, Barry S, Breen J. Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C. Epigenetics & Chromatin. 14: 41. PMID 34454581 DOI: 10.1186/s13072-021-00417-4   
2021 Sajib AM, Agarwal P, Patton DJ, Nance RL, Stahr NA, Kretzschmar WP, Sandey M, Smith BF. In vitro functional genetic modification of canine adenovirus type 2 genome by CRISPR/Cas9. Laboratory Investigation; a Journal of Technical Methods and Pathology. PMID 34417549 DOI: 10.1038/s41374-021-00654-x   
2021 Fedrizzi T, Ciani Y, Lorenzin F, Cantore T, Gasperini P, Demichelis F. Fast mutual exclusivity algorithm nominates potential synthetic lethal gene pairs through brute force matrix product computations. Computational and Structural Biotechnology Journal. 19: 4394-4403. PMID 34429855 DOI: 10.1016/j.csbj.2021.08.001   
2021 Wang S, Xu X, Wei C, Li S, Zhao J, Zheng Y, Liu X, Zeng X, Yuan W, Peng S. Molecular evolutionary characteristics of SARS-CoV-2 emerging in the United States. Journal of Medical Virology. PMID 34506640 DOI: 10.1002/jmv.27331   
2021 Jensen TJ, Goodman AM, Ellison CK, Holden KA, Kato S, Kim L, Daniels GA, Fitzgerald K, McCarthy E, Nakashe P, Mazloom AR, Almasri E, McLennan G, Grosu DS, Eisenberg M, et al. Genome-wide sequencing of cell-free DNA enables detection of copy number alterations in cancer patients where tissue biopsy is not feasible. Molecular Cancer Therapeutics. PMID 34465593 DOI: 10.1158/1535-7163.MCT-20-1066   
2021 Sun H, Cao S, Mashl RJ, Mo CK, Zaccaria S, Wendl MC, Davies SR, Bailey MH, Primeau TM, Hoog J, Mudd JL, Dean DA, Patidar R, Chen L, Wyczalkowski MA, ... , et al. Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidatesfor targeted treatment. Nature Communications. 12: 5086. PMID 34429404 DOI: 10.1038/s41467-021-25177-3   
2021 Zhang H, Qin C, An C, Zheng X, Wen S, Chen W, Liu X, Lv Z, Yang P, Xu W, Gao W, Wu Y. Application of the CRISPR/Cas9-based gene editing technique in basic research, diagnosis, and therapy of cancer. Molecular Cancer. 20: 126. PMID 34598686 DOI: 10.1186/s12943-021-01431-6   
2021 Osia B, Alsulaiman T, Jackson T, Kramara J, Oliveira S, Malkova A. Cancer cells are highly susceptible to accumulation of templated insertions linked to MMBIR. Nucleic Acids Research. PMID 34379776 DOI: 10.1093/nar/gkab685   
2021 Avsec Ž, Agarwal V, Visentin D, Ledsam JR, Grabska-Barwinska A, Taylor KR, Assael Y, Jumper J, Kohli P, Kelley DR. Effective gene expression prediction from sequence by integrating long-range interactions. Nature Methods. 18: 1196-1203. PMID 34608324 DOI: 10.1038/s41592-021-01252-x   
2021 D'Huys L, Vitale R, Ruppeka-Rupeika E, Goyvaerts V, Ruckebusch C, Hofkens J. Assessing the Resolution of Methyltransferase-Mediated DNA Optical Mapping. Acs Omega. 6: 21276-21283. PMID 34471732 DOI: 10.1021/acsomega.1c01381   
2021 Rahman MM, Kader SB, Rizvi SMS. Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. Heliyon. 7: e07866. PMID 34458642 DOI: 10.1016/j.heliyon.2021.e07866   
2021 Iacobucci I, Kimura S, Mullighan CG. Biologic and Therapeutic Implications of Genomic Alterations in Acute Lymphoblastic Leukemia. Journal of Clinical Medicine. 10. PMID 34501239 DOI: 10.3390/jcm10173792   
2021 Kumar P, Das S, Tigga R, Pandey R, Bhattacharya SN, Taneja B. Whole genome sequences of two clinical isolates from India emerging as threats during therapeutic treatment of dermatophytosis. 3 Biotech. 11: 402. PMID 34458064 DOI: 10.1007/s13205-021-02950-1   
2021 Di Sera T, Velinder M, Ward A, Qiao Y, Georges S, Miller C, Pitman A, Richards W, Ekawade A, Viskochil D, Carey JC, Pace L, Bale J, Clardy SL, Andrews A, et al. Gene.iobio: an interactive web tool for versatile, clinically-driven variant interrogation and prioritization. Scientific Reports. 11: 20307. PMID 34645894 DOI: 10.1038/s41598-021-99752-5   
2021 Basher ARMA, Mclaughlin RJ, Hallam SJ. Metabolic Pathway Prediction Using Non-Negative Matrix Factorization with Improved Precision. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 34520674 DOI: 10.1089/cmb.2021.0258   
2021 Stanton RA, Vlachos N, Halpin AL. GAMMA: a tool for the rapid identification, classification, and annotation of translated gene matches from sequencing data. Bioinformatics (Oxford, England). PMID 34415321 DOI: 10.1093/bioinformatics/btab607   
2021 Liu Y, Hu H, Cai M, Liang X, Wu X, Wang A, Chen X, Li X, Xiao C, Huang L, Xie Y, Wu Q. Whole genome sequencing of an edible and medicinal mushroom, Russula griseocarnosa, and its association with mycorrhizal characteristics. Gene. 145996. PMID 34634440 DOI: 10.1016/j.gene.2021.145996   
2021 Yuan XL, Zhang CS, Kong FY, Zhang ZF, Wang FL. Genome Analysis of JM01 Provides Insights into Its Pathogenicity Mechanisms. Plants (Basel, Switzerland). 10. PMID 34451665 DOI: 10.3390/plants10081620   
2021 Fioretti T, Di Iorio V, Lombardo B, De Falco F, Cevenini A, Cattaneo F, Testa F, Pastore L, Simonelli F, Esposito G. Molecular Characterization of Choroideremia-Associated Deletions Reveals an Unexpected Regulation of Gene Transcription. Genes. 12. PMID 34440285 DOI: 10.3390/genes12081111   
2021 Dorado G, Gálvez S, Rosales TE, Vásquez VF, Hernández P. Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing - Review. Biomolecules. 11. PMID 34439777 DOI: 10.3390/biom11081111   
2021 Stringer DN, Bertozzi T, Meusemann K, Delean S, Guzik MT, Tierney SM, Mayer C, Cooper SJB, Javidkar M, Zwick A, Austin AD. Development and evaluation of a custom bait design based on 469 single-copy protein-coding genes for exon capture of isopods (Philosciidae: Haloniscus). Plos One. 16: e0256861. PMID 34534224 DOI: 10.1371/journal.pone.0256861   
2021 Martínez-Cárdenas A, Cruz-Zamora Y, Fajardo-Hernández CA, Villanueva-Silva R, Cruz-García F, Raja HA, Figueroa M. Genome Mining and Molecular Networking-Based Metabolomics of the Marine Facultative sp. MEXU 27854. Molecules (Basel, Switzerland). 26. PMID 34500798 DOI: 10.3390/molecules26175362   
2021 Prabh N, Tautz D. Frequent lineage-specific substitution rate changes support an episodic model for protein evolution. G3 (Bethesda, Md.). PMID 34542594 DOI: 10.1093/g3journal/jkab333   
2021 Mongad DS, Chavan NS, Narwade NP, Dixit K, Shouche YS, Dhotre DP. MicFunPred: A conserved approach to predict functional profiles from 16S rRNA gene sequence data. Genomics. PMID 34450292 DOI: 10.1016/j.ygeno.2021.08.016