Sofia Kirke Forslund, PhD - Related publications

2012-2018 SCB EMBL, Heidelberg 
 2018- ECRC MDC, Berlin 
Metagenomics, evolution, antibiotic resistance, cardiometabolic health, orthology
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50 most relevant papers in past 60 days:
Year Citation  Score
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 Shan Y, Pei X, Yong S, Li J, Qin Q, Zeng S, Yu J. Analysis of the complete chloroplast genomes of and (Lamiaceae). Mitochondrial Dna. Part B, Resources. 6: 2672-2680. PMID 34435116 DOI: 10.1080/23802359.2021.1920491   
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 Awan F, Ali MM, Hamid M, Awan MH, Mushtaq MH, Kalsoom S, Ijaz M, Mehmood K, Liu Y. Epi-Gene: An R-Package for Easy Pan-Genome Analysis. Biomed Research International. 2021: 5585586. PMID 34595238 DOI: 10.1155/2021/5585586   
2021 Huang Z, Zhou X, Stanton C, Ross RP, Zhao J, Zhang H, Yang B, Chen W. Comparative Genomics and Specific Functional Characteristics Analysis of . Microorganisms. 9. PMID 34576887 DOI: 10.3390/microorganisms9091992   
2021 Safder I, Shao G, Sheng Z, Hu P, Tang S. Genome-wide identification studies - A primer to explore new genes in plant species. Plant Biology (Stuttgart, Germany). PMID 34558163 DOI: 10.1111/plb.13340   
2021 Izatt L, Owens MM, Pierce H, Wilcox S, Park SM. A Practical Guide to Genetic Testing in Endocrinology. Clinical Endocrinology. PMID 34528717 DOI: 10.1111/cen.14596   
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   
2021 Gaikani H, Giaever G, Nislow C. Chemical-Genetic Interactions as a Means to Characterize Drug Synergy. Methods in Molecular Biology (Clifton, N.J.). 2381: 243-263. PMID 34590281 DOI: 10.1007/978-1-0716-1740-3_14   
2021 Hao Z, Li Y, Jiang Y, Xu J, Li J, Luo L. Genome Sequence Analysis of the Fungal Pathogen Using Oxford Nanopore Technology. Journal of Fungi (Basel, Switzerland). 7. PMID 34575738 DOI: 10.3390/jof7090699   
2021 David S. A current guide to candidate gene association studies. Trends in Genetics : Tig. PMID 34400010 DOI: 10.1016/j.tig.2021.07.009   
2021 Huang Y, Sun M, Zhuang L, He J. Molecular Phylogenetic Analysis of the Family in Vertebrates. Genes. 12. PMID 34440364 DOI: 10.3390/genes12081190   
2021 Patino LH, Castillo-Castañeda A, Muñoz M, Muskus C, Rivero-Rodríguez M, Pérez-Doria A, Bejarano EE, Ramírez JD. Revisiting the heterogeneous global genomic population structure of . Microbial Genomics. 7. PMID 34491157 DOI: 10.1099/mgen.0.000640   
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 Heckel DG. Perspectives on gene copy number variation and pesticide resistance. Pest Management Science. PMID 34480789 DOI: 10.1002/ps.6631   
2021 Tan Y, Wang C, Schneider T, Li H, de Souza RF, Tang X, Swisher Grimm KD, Hsieh TF, Wang X, Li X, Zhang D. Comparative Phylogenomic Analysis Reveals Evolutionary Genomic Changes and Novel Toxin Families in Endophytic Pathogens. Microbiology Spectrum. e0050921. PMID 34523996 DOI: 10.1128/Spectrum.00509-21   
2021 Jiang X, Xu Z, Zhang T, Li Y, Li W, Tan H. Whole-Genome-Based Geographic Surveillance: A Visualized and Expandable Webtool. Frontiers in Microbiology. 12: 687259. PMID 34408729 DOI: 10.3389/fmicb.2021.687259   
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 Chen Y, Liu B, Zhao Y, Yu W, Si W. Whole-Genome Duplication and Purifying Selection Contributes to the Functional Redundancy of Auxin Response Factor () Genes in Foxtail Millet ( L.). International Journal of Genomics. 2021: 2590665. PMID 34414231 DOI: 10.1155/2021/2590665   
2021 Abbott M, McKenzie L, Moran BVG, Heidenreich S, Hernández R, Hocking-Mennie L, Clark C, Gomes J, Lampe A, Baty D, McGowan R, Miedzybrodzka Z, Ryan M. Continuing the sequence? Towards an economic evaluation of whole genome sequencing for the diagnosis of rare diseases in Scotland. Journal of Community Genetics. PMID 34415556 DOI: 10.1007/s12687-021-00541-4   
2021 Lee I, Ha SM, Baek MG, Kim DW, Yi H, Chun J. VicPred: A Genotype Prediction Tool. Frontiers in Microbiology. 12: 691895. PMID 34566903 DOI: 10.3389/fmicb.2021.691895   
2021 Hodor P, Pope CE, Whitlock KB, Hoffman LR, Limbrick DL, McDonald PJ, Hauptman JS, Ojemann JG, Simon TD. Molecular Characterization of Microbiota in Cerebrospinal Fluid From Patients With CSF Shunt Infections Using Whole Genome Amplification Followed by Shotgun Sequencing. Frontiers in Cellular and Infection Microbiology. 11: 699506. PMID 34490140 DOI: 10.3389/fcimb.2021.699506   
2021 Wu T, Hu E, Xu S, Chen M, Guo P, Dai Z, Feng T, Zhou L, Tang W, Zhan L, Fu X, Liu S, Bo X, Yu G. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. Innovation (New York, N.Y.). 2: 100141. PMID 34557778 DOI: 10.1016/j.xinn.2021.100141   
2021 Lee JH, Siddique MI, Kwon JK, Kang BC. Comparative Genomic Analysis Reveals Genetic Variation and Adaptive Evolution in the Pathogenicity-Related Genes of . Frontiers in Microbiology. 12: 694136. PMID 34484141 DOI: 10.3389/fmicb.2021.694136   
2021 Lee CY, Lee YF, Lai LC, Tsai MH, Lu TP, Chuang EY. MiDSystem: A Comprehensive Online System for De Novo Assembly and Analysis of Microbial Genomes. New Biotechnology. PMID 34411700 DOI: 10.1016/j.nbt.2021.08.002   
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 Díaz R, Torres-Miranda A, Orellana G, Garrido D. Comparative Genomic Analysis of Novel subsp. Strains Reveals Functional Divergence in the Human Gut Microbiota. Microorganisms. 9. PMID 34576801 DOI: 10.3390/microorganisms9091906   
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 Hutter CR, Cobb KA, Portik DM, Travers SL, Wood PL, Brown RM. FrogCap: A modular sequence capture probe-set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales. Molecular Ecology Resources. PMID 34569723 DOI: 10.1111/1755-0998.13517   
2021 Flores Ramos S, Brugger SD, Escapa IF, Skeete CA, Cotton SL, Eslami SM, Gao W, Bomar L, Tran TH, Jones DS, Minot S, Roberts RJ, Johnston CD, Lemon KP. Genomic Stability and Genetic Defense Systems in , a Candidate Beneficial Bacterium from the Human Microbiome. Msystems. e0042521. PMID 34546072 DOI: 10.1128/mSystems.00425-21   
2021 Liu Y, Huang L, Hu H, Cai M, Liang X, Li X, Zhang Z, Xie Y, Xiao C, Chen S, Chen D, Yong T, Pan H, Gao X, Wu Q. Whole-genome assembly of Ganoderma leucocontextum (Ganodermataceae, Fungi) discovered from the Tibetan Plateau of China. G3 (Bethesda, Md.). PMID 34586388 DOI: 10.1093/g3journal/jkab337   
2021 Ulaszewski B, Meger J, Mishra B, Thines M, Burczyk J. Complete Chloroplast Genomes of L. Reveal Sequence Conservation in the Inverted Repeat and the Presence of Allelic Variation in NUPTs. Genes. 12. PMID 34573338 DOI: 10.3390/genes12091357   
2021 Zhang L, Wang S, Su C, Harris AJ, Zhao L, Su N, Wang JR, Duan L, Chang ZY. Comparative Chloroplast Genomics and Phylogenetic Analysis of (Zygophyllaceae) of China. Frontiers in Plant Science. 12: 723622. PMID 34630471 DOI: 10.3389/fpls.2021.723622   
2021 Campbell JF, Athanassiou CG, Hagstrum DW, Zhu KY. : A Model Insect for Fundamental and Applied Research. Annual Review of Entomology. PMID 34614365 DOI: 10.1146/annurev-ento-080921-075157   
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 Huang CH, Chen CC, Lin YC, Chen CH, Lee AY, Liou JS, Gu CT, Huang L. The Gene as a Genome-Wide Taxonomic Marker for High Resolution Discrimination of and Its Closely Related Taxa. Microorganisms. 9. PMID 34442649 DOI: 10.3390/microorganisms9081570   
2021 Deng A, Sun Z, Wang T, Cui D, Li L, Liu S, Huang F, Wen T. Simultaneous Multiplex Genome Engineering Accelerated Natural Transformation in . Frontiers in Microbiology. 12: 714449. PMID 34484154 DOI: 10.3389/fmicb.2021.714449   
2021 Chen W, Ren ZH, Tang N, Chai G, Zhang H, Zhang Y, Ma J, Wu Z, Shen X, Huang X, Luo GZ, Ji Q. Targeted genetic screening in bacteria with a Cas12k-guided transposase. Cell Reports. 36: 109635. PMID 34469724 DOI: 10.1016/j.celrep.2021.109635   
2021 Kesawat MS, Kherawat BS, Singh A, Dey P, Kabi M, Debnath D, Saha D, Khandual A, Rout S, Manorama, Ali A, Palem RR, Gupta R, Kadam AA, Kim HU, et al. Genome-Wide Identification and Characterization of the Brassinazole-resistant () Gene Family and Its Expression in the Various Developmental Stage and Stress Conditions in Wheat ( L.). International Journal of Molecular Sciences. 22. PMID 34445448 DOI: 10.3390/ijms22168743   
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 Chen H, Li X, Wang Y, Zhu C, Huang H, Yang W, Li G. De Novo Transcriptomic Characterization Enables Novel Microsatellite Identification and Marker Development in . Life (Basel, Switzerland). 11. PMID 34440547 DOI: 10.3390/life11080803   
2021 Wilcox E, Harrison SM, Lockhart E, Voelkerding K, Lubin IM, , Rehm HL, Kalman L, Funke B. Creation of an Expert Curated Variant List for Clinical Genomic Test Development and Validation: A ClinGen and GeT-RM Collaborative Project. The Journal of Molecular Diagnostics : Jmd. PMID 34384894 DOI: 10.1016/j.jmoldx.2021.07.018   
2021 Ross K, Varani AM, Snesrud E, Huang H, Alvarenga DO, Zhang J, Wu C, McGann P, Chandler M. TnCentral: a Prokaryotic Transposable Element Database and Web Portal for Transposon Analysis. Mbio. e0206021. PMID 34517763 DOI: 10.1128/mBio.02060-21   
2021 Pratt BM, Won H. Advances in profiling chromatin architecture shed light on the regulatory dynamics underlying brain disorders. Seminars in Cell & Developmental Biology. PMID 34483043 DOI: 10.1016/j.semcdb.2021.08.013   
2021 Lewis S, Nash A, Li Q, Ahn TH. Comparison of 16S and whole genome dog microbiomes using machine learning. Biodata Mining. 14: 41. PMID 34419136 DOI: 10.1186/s13040-021-00270-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 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 Lupski JR. Clan genomics: From OMIM phenotypic traits to genes and biology. American Journal of Medical Genetics. Part A. PMID 34405553 DOI: 10.1002/ajmg.a.62434   
2021 Wold J, Koepfli KP, Galla SJ, Eccles D, Hogg CJ, Le Lec MF, Guhlin J, Santure AW, Steeves TE. Expanding the conservation genomics toolbox: incorporating structural variants to enhance genomic studies for species of conservation concern. Molecular Ecology. PMID 34424587 DOI: 10.1111/mec.16141   
2021 Galla SJ, Brown L, Couch-Lewis Y, Cubrinovska I, Eason D, Gooley RM, Hamilton JA, Heath JA, Hauser SS, Latch EK, Matocq MD, Richardson A, Wold JR, Hogg CJ, Santure AW, et al. The relevance of pedigrees in the conservation genomics era. Molecular Ecology. PMID 34553796 DOI: 10.1111/mec.16192