Steven M. Marquez, Ph.D. - Related publications

Affiliations: 
Indiana University, Bloomington, Bloomington, IN, United States 
Area:
RNA, Microbial Ecosystems
NOTE: We are testing a new system for identifying relevant work based on semantic analysis that identifies similarities between recently published papers and the current author's publications. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches.
50 most relevant papers in past 60 days:
Year Citation  Score
2021 Hong X, Zheng J, Xie J, Tong X, Liu X, Song Q, Liu S, Liu S. RR3DD: an RNA global structure-based RNA three-dimensional structural classification database. Rna Biology. 1-9. PMID 34663179 DOI: 10.1080/15476286.2021.1989200   
2021 Chan D, Feng C, England WE, Wyman D, Flynn RA, Wang X, Shi Y, Mortazavi A, Spitale RC. Diverse functional elements in RNA predicted transcriptome-wide by orthogonal RNA structure probing. Nucleic Acids Research. PMID 34634799 DOI: 10.1093/nar/gkab885   
2021 Li X, Peng J, Yi C. The epitranscriptome of small non-coding RNAs. Non-Coding Rna Research. 6: 167-173. PMID 34820590 DOI: 10.1016/j.ncrna.2021.10.002   
2021 Bevilacqua PC, Williams AM, Chou HL, Assmann S. RNA Multimerization as an Organizing Force for Liquid-Liquid Phase Separation. Rna (New York, N.Y.). PMID 34706977 DOI: 10.1261/rna.078999.121   
2021 Chen X, Rechavi O. Plant and animal small RNA communications between cells and organisms. Nature Reviews. Molecular Cell Biology. PMID 34707241 DOI: 10.1038/s41580-021-00425-y   
2021 Guo X, Tariq M, Lai Y, Kanwal S, Lv Y, Wang X, Li N, Jiang M, Meng J, Hu J, Yuan J, Luo Z, Ward C, Volpe G, Wang D, et al. Capture of the newly transcribed RNA interactome using click chemistry. Nature Protocols. PMID 34697467 DOI: 10.1038/s41596-021-00609-y   
2021 Choi MH, Nguyen VT, Ravi Kumara GS, Seo YJ. RNA Polymerase-Mediated Stepwise RNA-Primed RNA Polymerization for Site-Specific Multiple Labeling into RNA: A Fluorescence Resonance Energy Transfer Probe Detects the Structural Change of an RNA G-Quadruplex. Acs Synthetic Biology. PMID 34762391 DOI: 10.1021/acssynbio.1c00418   
2021 Jang B, Jang H, Kim H, Kim M, Jeong M, Lee GS, Lee K, Lee H. Protein-RNA interaction guided chemical modification of Dicer substrate RNA nanostructures for superior in vivo gene silencing. Journal of Controlled Release : Official Journal of the Controlled Release Society. PMID 34763005 DOI: 10.1016/j.jconrel.2021.11.009   
2021 Cable J, Heard E, Hirose T, Prasanth KV, Chen LL, Henninger JE, Quinodoz SA, Spector DL, Diermeier SD, Porman AM, Kumar D, Feinberg MW, Shen X, Unfried JP, Johnson R, et al. Noncoding RNAs: biology and applications-a Keystone Symposia report. Annals of the New York Academy of Sciences. PMID 34791665 DOI: 10.1111/nyas.14713   
2021 Soszynska-Jozwiak M, Pszczola M, Piasecka J, Peterson JM, Moss WN, Taras-Goslinska K, Kierzek R, Kierzek E. Universal and strain specific structure features of segment 8 genomic RNA of influenza A virus - application of 4-thiouridine photocrosslinking. The Journal of Biological Chemistry. 101245. PMID 34688660 DOI: 10.1016/j.jbc.2021.101245   
2021 Chen B, Shi H, Zhang J, Zhou C, Han M, Jiang W, Lai Y, Tu X, Li H. CRISPR-based RNA-binding protein mapping in live cells. Biochemical and Biophysical Research Communications. 583: 79-85. PMID 34735883 DOI: 10.1016/j.bbrc.2021.10.059   
2021 Shatoff E, Bundschuh R. dsRBPBind: Modeling the effect of RNA secondary structure on double stranded RNA-protein binding. Bioinformatics (Oxford, England). PMID 34668517 DOI: 10.1093/bioinformatics/btab724   
2021 Zhang S, Sun J, Gu M, Wang G, Wang X. Circular RNA: A promising new star for the diagnosis and treatment of colorectal cancer. Cancer Medicine. PMID 34796685 DOI: 10.1002/cam4.4398   
2021 Zhao Y, Shu R, Liu J. The development and improvement of ribonucleic acid therapy strategies. Molecular Therapy. Nucleic Acids. PMID 34540356 DOI: 10.1016/j.omtn.2021.09.002   
2021 Das AS, Alfonzo JD, Accornero F. The importance of RNA modifications: From cells to muscle physiology. Wiley Interdisciplinary Reviews. Rna. e1700. PMID 34664402 DOI: 10.1002/wrna.1700   
2021 Hohmann KF, Blümler A, Heckel A, Fürtig B. The RNA chaperone StpA enables fast RNA refolding by destabilization of mutually exclusive base pairs within competing secondary structure elements. Nucleic Acids Research. PMID 34614185 DOI: 10.1093/nar/gkab876   
2021 Quinodoz SA, Jachowicz JW, Bhat P, Ollikainen N, Banerjee AK, Goronzy IN, Blanco MR, Chovanec P, Chow A, Markaki Y, Thai J, Plath K, Guttman M. RNA promotes the formation of spatial compartments in the nucleus. Cell. 184: 5775-5790.e30. PMID 34739832 DOI: 10.1016/j.cell.2021.10.014   
2021 Zhang D, Chen SJ, Zhou R. Modeling Noncanonical RNA Base Pairs by a Coarse-Grained IsRNA2 Model. The Journal of Physical Chemistry. B. PMID 34694128 DOI: 10.1021/acs.jpcb.1c07288   
2021 Zhang Z, Chen T, Chen HX, Xie YY, Chen LQ, Zhao YL, Liu BD, Jin L, Zhang W, Liu C, Ma DZ, Chai GS, Zhang Y, Zhao WS, Ng WH, et al. Systematic calibration of epitranscriptomic maps using a synthetic modification-free RNA library. Nature Methods. PMID 34594034 DOI: 10.1038/s41592-021-01280-7   
2021 Wang Y, Yang Y, Ma Z, Wong KC, Li X. EDCNN: Identification of Genome-Wide RNA-binding Proteins Using Evolutionary Deep Convolutional Neural Network. Bioinformatics (Oxford, England). PMID 34694393 DOI: 10.1093/bioinformatics/btab739   
2021 Li L, Luo H, Lim DH, Han L, Li Y, Fu XD, Qi Y. Global profiling of RNA-chromatin interactions reveals co-regulatory gene expression networks in Arabidopsis. Nature Plants. 7: 1364-1378. PMID 34650265 DOI: 10.1038/s41477-021-01004-x   
2021 Fu L, Cao Y, Wu J, Peng Q, Nie Q, Xie X. UFold: fast and accurate RNA secondary structure prediction with deep learning. Nucleic Acids Research. PMID 34792173 DOI: 10.1093/nar/gkab1074   
2021 Sutanto K, Turcotte M. Assessing Global-Local Secondary Structure Fingerprints to Classify RNA Sequences with Deep Learning. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 34633933 DOI: 10.1109/TCBB.2021.3118358   
2021 Zhou M, Wang DO, Li W, Zheng J. RNA adduction derived from electrophilic species in vitro and in vivo. Chemico-Biological Interactions. 351: 109748. PMID 34801539 DOI: 10.1016/j.cbi.2021.109748   
2021 Biswal JK, Ranjan R, Dahiya SS, Mallick S, Mohapatra JK. Regenerated silica-based RNA purification columns to address the short supply of RNA purification kits for COVID-19 diagnosis. Molecular Biology Reports. 48: 6871-6877. PMID 34510319 DOI: 10.1007/s11033-021-06688-0   
2021 Endo M, Kim JI, Shioi NA, Iwai S, Kuraoka I. endonuclease V is a ribonuclease specific for inosine-containing single-stranded RNA. Open Biology. 11: 210148. PMID 34665969 DOI: 10.1098/rsob.210148   
2021 Mulroney L, Wulf M, Schildkraut I, Tzertzinis G, Buswell J, Jain M, Olsen HE, Diekhans M, Corrêa IR, Akeson M, Ettwiller L. Identification of high confidence human poly(A) RNA isoform scaffolds using nanopore sequencing. Rna (New York, N.Y.). PMID 34728536 DOI: 10.1261/rna.078703.121   
2021 Mulroney L, Wulf M, Schildkraut I, Tzertzinis G, Buswell J, Jain M, Olsen HE, Diekhans M, Corrêa IR, Akeson M, Ettwiller L. Identification of high confidence human poly(A) RNA isoform scaffolds using nanopore sequencing. Rna (New York, N.Y.). PMID 34728536 DOI: 10.1261/rna.078703.121   
2021 Luige O, Bose PP, Stulz R, Steunenberg P, Brun O, Andersson S, Murtola M, Strömberg R. Zn-Dependent peptide nucleic acid-based artificial ribonucleases with unprecedented efficiency and specificity. Chemical Communications (Cambridge, England). PMID 34590632 DOI: 10.1039/d1cc04383h   
2021 Roden CA, Gladfelter AS. Design considerations for analyzing protein translation regulation by condensates. Rna (New York, N.Y.). PMID 34670845 DOI: 10.1261/rna.079002.121   
2021 Xiao L, Jun YW, Kool ET. DNA tiling enables precise acylation-based labeling and control of mRNA. Angewandte Chemie (International Ed. in English). PMID 34624169 DOI: 10.1002/anie.202112106   
2021 Hao W, Liu G, Wang W, Shen W, Zhao Y, Sun J, Yang Q, Zhang Y, Fan W, Pei S, Chen Z, Xu D, Qin T. RNA Editing and Its Roles in Plant Organelles. Frontiers in Genetics. 12: 757109. PMID 34659369 DOI: 10.3389/fgene.2021.757109   
2021 Chatterjee B, Shen CJ, Majumder P. RNA Modifications and RNA Metabolism in Neurological Disease Pathogenesis. International Journal of Molecular Sciences. 22. PMID 34769301 DOI: 10.3390/ijms222111870   
2021 Gao J, Klenow L, Parsons L, Malik T, Phue JN, Gao Z, Withers SG, Cipollo J, Daniels R, Wan H. Design of the Recombinant Influenza Neuraminidase Antigen is Crucial for its Biochemical Properties and Protective Efficacy. Journal of Virology. JVI0116021. PMID 34613807 DOI: 10.1128/JVI.01160-21   
2021 Mukherjee S, Frenkel-Morgenstern M. Evolutionary impact of chimeric RNAs on generating phenotypic plasticity in human cells. Trends in Genetics : Tig. PMID 34579972 DOI: 10.1016/j.tig.2021.08.015   
2021 Hong P, Yu M, Tian W. Diverse RNAs in adipose-derived extracellular vesicles and their therapeutic potential. Molecular Therapy. Nucleic Acids. 26: 665-677. PMID 34703651 DOI: 10.1016/j.omtn.2021.08.028   
2021 Kluesner MG, Tasakis RN, Lerner T, Arnold A, Wüst S, Binder M, Webber BR, Moriarity BS, Pecori R. MultiEditR: The first tool for the detection and quantification of RNA editing from Sanger sequencing demonstrates comparable fidelity to RNA-seq. Molecular Therapy. Nucleic Acids. 25: 515-523. PMID 34589274 DOI: 10.1016/j.omtn.2021.07.008   
2021 Morgan M, Kumar L, Li Y, Baptissart M. Post-transcriptional regulation in spermatogenesis: all RNA pathways lead to healthy sperm. Cellular and Molecular Life Sciences : Cmls. PMID 34748024 DOI: 10.1007/s00018-021-04012-4   
2021 Lambert M, Benmoussa A, Diallo I, Ouellet-Boutin K, Dorval V, Majeau N, Joly-Beauparlant C, Droit A, Bergeron A, Têtu B, Fradet Y, Pouliot F, Provost P. Identification of Abundant and Functional dodecaRNAs (doRNAs) Derived from Ribosomal RNA. International Journal of Molecular Sciences. 22. PMID 34575920 DOI: 10.3390/ijms22189757   
2021 Wen J, Rusch M, Brady SW, Shao Y, Edmonson MN, Shaw TI, Powers BB, Tian L, Easton J, Mullighan CG, Gruber T, Ellison D, Zhang J. The landscape of coding RNA editing events in pediatric cancer. Bmc Cancer. 21: 1233. PMID 34789196 DOI: 10.1186/s12885-021-08956-5   
2021 Lahens NF, Brooks TG, Sarantopoulou D, Nayak S, Lawrence C, Mrčela A, Srinivasan A, Schug J, Hogenesch JB, Barash Y, Grant GR. CAMPAREE: a robust and configurable RNA expression simulator. Bmc Genomics. 22: 692. PMID 34563123 DOI: 10.1186/s12864-021-07934-2   
2021 Shi L, Zhang L, Wang L, Liu X, Gao H, Hou X, Zhao F, Yan H, Cai W, Wang L. Identifying long non-coding RNAs and characterizing their functional roles in swine mammary gland from colostrogenesis to lactogenesis. Animal Bioscience. PMID 34727649 DOI: 10.5713/ab.21.0308   
2021 Ali SA, Peffers MJ, Ormseth MJ, Jurisica I, Kapoor M. The non-coding RNA interactome in joint health and disease. Nature Reviews. Rheumatology. 17: 692-705. PMID 34588660 DOI: 10.1038/s41584-021-00687-y   
2021 Radecki P, Uppuluri R, Deshpande K, Aviran S. Accurate detection of RNA stem-loops in structurome data reveals widespread association with protein binding sites. Rna Biology. 1-16. PMID 34606413 DOI: 10.1080/15476286.2021.1971382   
2021 Li X, Wang CY. From bulk, single-cell to spatial RNA sequencing. International Journal of Oral Science. 13: 36. PMID 34782601 DOI: 10.1038/s41368-021-00146-0   
2021 Mańka R, Janas P, Sapoń K, Janas T, Janas T. Role of RNA Motifs in RNA Interaction with Membrane Lipid Rafts: Implications for Therapeutic Applications of Exosomal RNAs. International Journal of Molecular Sciences. 22. PMID 34502324 DOI: 10.3390/ijms22179416   
2021 Pérez-Cañamás M, Hevia E, Katsarou K, Hernández C. Genetic evidence for the involvement of Dicer-like 2 and 4 as well as Argonaute 2 in the response against . The Journal of General Virology. 102. PMID 34623234 DOI: 10.1099/jgv.0.001656   
2021 Zhao EM, Mao AS, de Puig H, Zhang K, Tippens ND, Tan X, Ran FA, Han I, Nguyen PQ, Chory EJ, Hua TY, Ramesh P, Thompson DB, Oh CY, Zigon ES, et al. RNA-responsive elements for eukaryotic translational control. Nature Biotechnology. PMID 34711989 DOI: 10.1038/s41587-021-01068-2   
2021 Zhao J, Hu H, Wang S, Wang L, Wang R. Regulation and Site-Specific Covalent Labeling of via Genetic Encoding Expansion. Genes. 12. PMID 34680884 DOI: 10.3390/genes12101488   
2021 Zhu H, Fu H, Cui T, Ning L, Shao H, Guo Y, Ke Y, Zheng J, Lin H, Wu X, Liu G, He J, Han X, Li W, Zhao X, et al. RNAPhaSep: a resource of RNAs undergoing phase separation. Nucleic Acids Research. PMID 34718740 DOI: 10.1093/nar/gkab985