Steffen Schmidt - Related publications

Bioinformatics Max Planck Institute for Developmental Biology, Tübingen, Baden-Württemberg, Germany 
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50 most relevant papers in past 60 days:
Year Citation  Score
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 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 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 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 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 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 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 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 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 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 Jiang M, Zhu Y, Wu Q, Zhang H. Complete chloroplast genome of a rare and endangered plant species : genomic features and phylogenetic relationship within Orchidaceae. Mitochondrial Dna. Part B, Resources. 6: 2872-2879. PMID 34532575 DOI: 10.1080/23802359.2021.1972049   
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 Yan SM, Sherman RM, Taylor DJ, Nair DR, Bortvin AN, Schatz MC, McCoy RC. Local adaptation and archaic introgression shape global diversity at human structural variant loci. Elife. 10. PMID 34528508 DOI: 10.7554/eLife.67615   
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 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 Ma Y, Chen Z, Yu J. Pseudogenes and their potential functions in hematopoiesis. Experimental Hematology. PMID 34517065 DOI: 10.1016/j.exphem.2021.09.001   
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 Jiang T, Yin Z, Cai R, Yu H, Lu Q, Zhao S, Tian Y, Yan Y, Chen X, Guo J. Chromosomal-level Genome Assembly of a True Bug, Aspongopus chinensis Dallas, 1851 (Hemiptera: Dinidoridae). Genome Biology and Evolution. PMID 34623414 DOI: 10.1093/gbe/evab232   
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 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 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 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 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 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 Takeda I, Araki M, Ishiguro KI, Ohga T, Takada K, Yamaguchi Y, Hashimoto K, Kai T, Nakagata N, Imasaka M, Yoshinobu K, Araki K. Gene trapping reveals a new transcriptionally active genome element: The chromosome-specific clustered trap region. Genes to Cells : Devoted to Molecular & Cellular Mechanisms. PMID 34418226 DOI: 10.1111/gtc.12890   
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 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 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 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 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 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 Tassia MG, David KT, Townsend JP, Halanych KM. TIAMMAt: Leveraging biodiversity to revise protein domain models, evidence from innate immunity. Molecular Biology and Evolution. PMID 34459919 DOI: 10.1093/molbev/msab258   
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 Rivard EL, Ludwig AG, Patel PH, Grandchamp A, Arnold SE, Berger A, Scott EM, Kelly BJ, Mascha GC, Bornberg-Bauer E, Findlay GD. A putative de novo evolved gene required for spermatid chromatin condensation in Drosophila melanogaster. Plos Genetics. 17: e1009787. PMID 34478447 DOI: 10.1371/journal.pgen.1009787   
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 He J, Zhao C, Guo Y, Zhang H, Zhao B, Chu Z. Completely mitochondrial genome of . Mitochondrial Dna. Part B, Resources. 6: 2708-2709. PMID 34435128 DOI: 10.1080/23802359.2021.1945966   
2021 Wakao S, Shih PM, Guan K, Schackwitz W, Ye J, Patel D, Shih RM, Dent RM, Chovatia M, Sharma A, Martin J, Wei CL, Niyogi KK. Discovery of photosynthesis genes through whole-genome sequencing of acetate-requiring mutants of Chlamydomonas reinhardtii. Plos Genetics. 17: e1009725. PMID 34492001 DOI: 10.1371/journal.pgen.1009725   
2021 Pang J, Hu W, Wang W, Li J, Mao K. The complete chloroplast genome of , a Critically Endangered species in New Caledonia. Mitochondrial Dna. Part B, Resources. 6: 2648-2649. PMID 34409167 DOI: 10.1080/23802359.2021.1964399   
2021 Li X, Li Y, Sylvester SP, Zang M, El-Kassaby YA, Fang Y. Evolutionary patterns of nucleotide substitution rates in plastid genomes of . Ecology and Evolution. 11: 13401-13414. PMID 34646478 DOI: 10.1002/ece3.8063   
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 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 Heckel DG. Perspectives on gene copy number variation and pesticide resistance. Pest Management Science. PMID 34480789 DOI: 10.1002/ps.6631   
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 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 Zhou Q, Jiao L, Li W, Hu Z, Li Y, Zhang H, Yang M, Xu L, Yan Y. A Novel Cre/-Based Genetic Tool for Repeated, Targeted and Markerless Gene Integration in . International Journal of Molecular Sciences. 22. PMID 34639080 DOI: 10.3390/ijms221910739   
2021 Smit SJ, Vivier MA, Young PR. Seeing the Forest through the (Phylogenetic) Trees: Functional Characterisation of Grapevine Terpene Synthase () Paralogues and Orthologues. Plants (Basel, Switzerland). 10. PMID 34451565 DOI: 10.3390/plants10081520   
2021 Han L, Lan T, Li D, Li H, Deng L, Peng Z, He S, Zhou Y, Han R, Li L, Lu Y, Lu H, Wang Q, Yang S, Zhu Y, et al. Chromosome-scale assembly and whole-genome sequencing of 266 giant panda roundworms provide insights into their evolution, adaptation and potential drug targets. Molecular Ecology Resources. PMID 34549895 DOI: 10.1111/1755-0998.13504   
2021 Guo Y, Wariss HM, Zhang R. The complete chloroplast genome of (L.) Goldblatt & J. C. Manning (Leguminosae), an important medicinal plant species from Southern Africa. Mitochondrial Dna. Part B, Resources. 6: 2767-2769. PMID 34471699 DOI: 10.1080/23802359.2021.1967811   
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