| Year |
Citation |
Score |
| 2020 |
Patton RD, Sanjeev M, Woodward LA, Mabin JW, Bundschuh R, Singh G. Chemical crosslinking enhances RNA immunoprecipitation for efficient identification of binding sites of proteins that photo-crosslink poorly with RNA. Rna (New York, N.Y.). PMID 32467309 DOI: 10.1261/Rna.074856.120 |
0.372 |
|
| 2020 |
Shatoff E, Bundschuh R. Single nucleotide polymorphisms affect RNA-protein interactions at a distance through modulation of RNA secondary structures. Plos Computational Biology. 16: e1007852. PMID 32379750 DOI: 10.1371/Journal.Pcbi.1007852 |
0.345 |
|
| 2020 |
Walker LA, Sovic MG, Chiang CL, Hu E, Denninger JK, Chen X, Kirby ED, Byrd JC, Muthusamy N, Bundschuh R, Yan P. CLEAR: coverage-based limiting-cell experiment analysis for RNA-seq. Journal of Translational Medicine. 18: 63. PMID 32039730 DOI: 10.1186/S12967-020-02247-6 |
0.357 |
|
| 2020 |
Del Valle Morales D, Trotman JB, Bundschuh R, Schoenberg DR. Inhibition of cytoplasmic cap methylation identifies 5' TOP mRNAs as recapping targets and reveals recapping sites downstream of native 5' ends. Nucleic Acids Research. PMID 31996904 DOI: 10.1093/Nar/Gkaa046 |
0.307 |
|
| 2019 |
Baez WD, Roy B, McNutt ZA, Shatoff EA, Chen S, Bundschuh R, Fredrick K. Global analysis of protein synthesis in Flavobacterium johnsoniae reveals the use of Kozak-like sequences in diverse bacteria. Nucleic Acids Research. PMID 31602466 DOI: 10.1093/Nar/Gkz855 |
0.346 |
|
| 2019 |
Brehove M, Shatoff E, Donovan BT, Jipa CM, Bundschuh R, Poirier MG. DNA sequence influences hexasome orientation to regulate DNA accessibility. Nucleic Acids Research. 47: 5617-5633. PMID 31216039 DOI: 10.1093/Nar/Gkz283 |
0.31 |
|
| 2019 |
Baez WD, Wiese KJ, Bundschuh R. Behavior of random RNA secondary structures near the glass transition. Physical Review. E. 99: 022415. PMID 30934369 DOI: 10.1103/Physreve.99.022415 |
0.625 |
|
| 2019 |
Dodbele S, Moreland B, Gardner SM, Bundschuh R, Jackman JE. 5'-end sequencing in Saccharomyces cerevisiae offers new insights into 5'-ends of tRNA and snoRNAs. Febs Letters. PMID 30908619 DOI: 10.1002/1873-3468.13364 |
0.364 |
|
| 2018 |
Zhao D, Baez W, Fredrick K, Bundschuh R. RiboProP: A Probabilistic Ribosome Positioning Algorithm for Ribosome Profiling. Bioinformatics (Oxford, England). PMID 30304369 DOI: 10.1093/Bioinformatics/Bty854 |
0.334 |
|
| 2018 |
Kiss DL, Baez WD, Huebner K, Bundschuh R, Schoenberg DR. Loss of fragile histidine triad (Fhit) protein expression alters the translation of cancer-associated mRNAs. Bmc Research Notes. 11: 178. PMID 29540221 DOI: 10.1186/S13104-018-3278-9 |
0.346 |
|
| 2017 |
Papaioannou D, Nicolet D, Volinia S, Mrózek K, Yan P, Bundschuh R, Carroll AJ, Kohlschmidt J, Blum W, Powell BL, Uy GL, Kolitz JE, Wang ES, Eisfeld AK, Orwick SJ, et al. Prognostic and biologic significance of long non-coding RNA profiling in younger adults with cytogenetically normal acute myeloid leukemia. Haematologica. PMID 28473620 DOI: 10.3324/Haematol.2017.166215 |
0.338 |
|
| 2016 |
Moreland B, Oman K, Curfman J, Yan P, Bundschuh R. Methyl-CpG/MBD2 Interaction Requires Minimum Separation and Exhibits Minimal Sequence Specificity. Biophysical Journal. 111: 2551-2561. PMID 28002732 DOI: 10.1016/J.Bpj.2016.11.014 |
0.321 |
|
| 2016 |
Liyanarachchi S, Li W, Yan P, Bundschuh R, Brock P, Senter L, Ringel MD, de la Chapelle A, He H. Genome-wide expression screening discloses long noncoding RNAs involved in thyroid carcinogenesis. The Journal of Clinical Endocrinology and Metabolism. jc20161991. PMID 27459529 DOI: 10.1210/Jc.2016-1991 |
0.308 |
|
| 2016 |
Kiss DL, Oman KM, Dougherty JA, Mukherjee C, Bundschuh R, Schoenberg DR. Cap homeostasis is independent of poly(A) tail length. Nucleic Acids Research. 44: 304-14. PMID 26673707 DOI: 10.1093/Nar/Gkv1460 |
0.302 |
|
| 2016 |
Papaioannou D, Petri A, Thrue CA, Volinia S, Kroll K, Pearlly Y, Bundschuh R, Singh G, Kauppinen S, Bloomfield CD, Dorrance A, Garzon R. HOXB-AS3 Regulates Cell Cycle Progression and Interacts with the Drosophila Splicing Human Behavior (DSHB) Complex in NPM1-Mutated Acute Myeloid Leukemia Blood. 128: 1514-1514. DOI: 10.1182/Blood.V128.22.1514.1514 |
0.349 |
|
| 2015 |
Schaap P, Barrantes I, Minx P, Sasaki N, Anderson RW, Bénard M, Biggar KK, Buchler NE, Bundschuh R, Chen X, Fronick C, Fulton L, Golderer G, Jahn N, Knoop V, et al. The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-component and Metazoan-type Tyrosine Kinase Signaling. Genome Biology and Evolution. PMID 26615215 DOI: 10.1093/Gbe/Evv237 |
0.649 |
|
| 2015 |
Lin YH, Bundschuh R. RNA structure generates natural cooperativity between single-stranded RNA binding proteins targeting 5' and 3'UTRs. Nucleic Acids Research. 43: 1160-9. PMID 25550422 DOI: 10.1093/Nar/Gku1320 |
0.376 |
|
| 2014 |
Balakrishnan R, Oman K, Shoji S, Bundschuh R, Fredrick K. The conserved GTPase LepA contributes mainly to translation initiation in Escherichia coli. Nucleic Acids Research. 42: 13370-83. PMID 25378333 DOI: 10.1093/Nar/Gku1098 |
0.309 |
|
| 2014 |
Kroll KW, Mokaram NE, Pelletier AR, Frankhouser DE, Westphal MS, Stump PA, Stump CL, Bundschuh R, Blachly JS, Yan P. Quality Control for RNA-Seq (QuaCRS): An Integrated Quality Control Pipeline. Cancer Informatics. 13: 7-14. PMID 25368506 DOI: 10.4137/Cin.S14022 |
0.302 |
|
| 2014 |
Frankhouser DE, Murphy M, Blachly JS, Park J, Zoller MW, Ganbat JO, Curfman J, Byrd JC, Lin S, Marcucci G, Yan P, Bundschuh R. PrEMeR-CG: inferring nucleotide level DNA methylation values from MethylCap-seq data. Bioinformatics (Oxford, England). 30: 3567-74. PMID 25178460 DOI: 10.1093/Bioinformatics/Btu583 |
0.326 |
|
| 2014 |
Chen C, Bundschuh R. Quantitative models for accelerated protein dissociation from nucleosomal DNA. Nucleic Acids Research. 42: 9753-60. PMID 25114052 DOI: 10.1093/Nar/Gku719 |
0.476 |
|
| 2014 |
Madina BR, Kumar V, Metz R, Mooers BHM, Bundschuh R, Cruz-Reyes J. Native mitochondrial RNA-binding complexes in kinetoplastid RNA editing differ in guide RNA composition Rna. 20: 1142-1152. PMID 24865612 DOI: 10.1261/Rna.044495.114 |
0.373 |
|
| 2014 |
Bundschuh R. Unified approach to partition functions of RNA secondary structures. Journal of Mathematical Biology. 69: 1129-50. PMID 24177391 DOI: 10.1007/S00285-013-0737-8 |
0.397 |
|
| 2013 |
Lin YH, Bundschuh R. Interplay between single-stranded binding proteins on RNA secondary structure. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 88: 052707. PMID 24329296 DOI: 10.1103/Physreve.88.052707 |
0.375 |
|
| 2013 |
Bernot KM, Siebenaler RF, Whitman SP, Zorko NA, Marcucci GG, Santhanam R, Ahmed EH, Ngangana M, McConnell KK, Nemer JS, Brook DL, Kulp SK, Chen CS, Frankhouser D, Yan P, ... Bundschuh R, et al. Toward personalized therapy in AML: in vivo benefit of targeting aberrant epigenetics in MLL-PTD-associated AML. Leukemia. 27: 2379-82. PMID 23660685 DOI: 10.1038/Leu.2013.147 |
0.427 |
|
| 2012 |
Trimarchi MP, Murphy M, Frankhouser D, Rodriguez BA, Curfman J, Marcucci G, Yan P, Bundschuh R. Enrichment-based DNA methylation analysis using next-generation sequencing: sample exclusion, estimating changes in global methylation, and the contribution of replicate lanes. Bmc Genomics. 13: S6. PMID 23281662 DOI: 10.1186/1471-2164-13-S8-S6 |
0.304 |
|
| 2012 |
Chen C, Bundschuh R. Systematic investigation of insertional and deletional RNA-DNA differences in the human transcriptome. Bmc Genomics. 13: 616. PMID 23148664 DOI: 10.1186/1471-2164-13-616 |
0.564 |
|
| 2012 |
Rodriguez BA, Frankhouser D, Murphy M, Trimarchi M, Tam HH, Curfman J, Huang R, Chan MW, Lai HC, Parikh D, Ball B, Schwind S, Blum W, Marcucci G, Yan P, ... Bundschuh R, et al. Methods for high-throughput MethylCap-Seq data analysis. Bmc Genomics. 13: S14. PMID 23134780 DOI: 10.1186/1471-2164-13-S6-S14 |
0.311 |
|
| 2012 |
Mukherjee C, Patil DP, Kennedy BA, Bakthavachalu B, Bundschuh R, Schoenberg DR. Identification of cytoplasmic capping targets reveals a role for cap homeostasis in translation and mRNA stability. Cell Reports. 2: 674-84. PMID 22921400 DOI: 10.1016/J.Celrep.2012.07.011 |
0.323 |
|
| 2012 |
Chen C, Frankhouser D, Bundschuh R. Comparison of insertional RNA editing in Myxomycetes. Plos Computational Biology. 8: e1002400. PMID 22383871 DOI: 10.1371/Journal.Pcbi.1002400 |
0.564 |
|
| 2011 |
Bundschuh R, Altmüller J, Becker C, Nürnberg P, Gott JM. Complete characterization of the edited transcriptome of the mitochondrion of Physarum polycephalum using deep sequencing of RNA Nucleic Acids Research. 39: 6044-6055. PMID 21478163 DOI: 10.1093/Nar/Gkr180 |
0.371 |
|
| 2011 |
Li Y, Chia N, Lauria M, Bundschuh R. A performance enhanced PSI-BLAST based on hybrid alignment. Bioinformatics (Oxford, England). 27: 31-7. PMID 21115441 DOI: 10.1093/Bioinformatics/Btq621 |
0.551 |
|
| 2009 |
McCauley M, Forties R, Gerland U, Bundschuh R. Anomalous scaling in nanopore translocation of structured heteropolymers. Physical Biology. 6: 036006. PMID 19411739 DOI: 10.1088/1478-3975/6/3/036006 |
0.387 |
|
| 2009 |
Lin J, Bundschuh R, Meller A. Single-molecule Studies of RNA Unzipping Kinetics Using Nanopores Biophysical Journal. 96: 545a. DOI: 10.1016/J.Bpj.2008.12.2949 |
0.395 |
|
| 2008 |
Beargie C, Liu T, Corriveau M, Lee HY, Gott J, Bundschuh R. Genome annotation in the presence of insertional RNA editing. Bioinformatics (Oxford, England). 24: 2571-8. PMID 18819938 DOI: 10.1093/Bioinformatics/Btn487 |
0.36 |
|
| 2008 |
Bundschuh R, Bruinsma R. Melting of branched RNA molecules. Physical Review Letters. 100: 148101. PMID 18518073 DOI: 10.1103/Physrevlett.100.148101 |
0.376 |
|
| 2008 |
Lee MM, Chan MK, Bundschuh R. Simple is beautiful: a straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches. Bioinformatics (Oxford, England). 24: 1339-43. PMID 18403442 DOI: 10.1093/Bioinformatics/Btn130 |
0.318 |
|
| 2008 |
Djordjevic M, Bundschuh R. Formation of the open complex by bacterial RNA polymerase--a quantitative model. Biophysical Journal. 94: 4233-48. PMID 18281386 DOI: 10.1529/Biophysj.107.116970 |
0.362 |
|
| 2008 |
Itaya A, Bundschuh R, Archual AJ, Joung JG, Fei Z, Dai X, Zhao PX, Tang Y, Nelson RS, Ding B. Small RNAs in tomato fruit and leaf development. Biochimica Et Biophysica Acta. 1779: 99-107. PMID 18078843 DOI: 10.1016/J.Bbagrm.2007.09.003 |
0.373 |
|
| 2008 |
Lee MM, Bundschuh R, Chan MK. Distant homology detection using a LEngth and STructure-based sequence Alignment Tool (LESTAT). Proteins. 71: 1409-19. PMID 18076050 DOI: 10.1002/Prot.21830 |
0.368 |
|
| 2007 |
Messer PW, Bundschuh R, Vingron M, Arndt PF. Effects of long-range correlations in DNA on sequence alignment score statistics. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 14: 655-68. PMID 17683266 DOI: 10.1089/Cmb.2007.R008 |
0.338 |
|
| 2007 |
Bundschuh R. Computational approaches to insertional RNA editing. Methods in Enzymology. 424: 173-95. PMID 17662841 DOI: 10.1016/S0076-6879(07)24008-X |
0.321 |
|
| 2007 |
Itaya A, Zhong X, Bundschuh R, Qi Y, Wang Y, Takeda R, Harris AR, Molina C, Nelson RS, Ding B. A structured viroid RNA serves as a substrate for dicer-like cleavage to produce biologically active small RNAs but is resistant to RNA-induced silencing complex-mediated degradation. Journal of Virology. 81: 2980-94. PMID 17202210 DOI: 10.1128/Jvi.02339-06 |
0.361 |
|
| 2006 |
Chia N, Bundschuh R. A practical approach to significance assessment in alignment with gaps. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 13: 429-41. PMID 16597250 DOI: 10.1089/Cmb.2006.13.429 |
0.519 |
|
| 2006 |
Bundschuh R, Gerland U. Dynamics of intramolecular recognition: Base-pairing in DNA/RNA near and far from equilibrium European Physical Journal E. 19: 319-329. PMID 16520899 DOI: 10.1140/Epje/I2005-10061-3 |
0.352 |
|
| 2006 |
Guttal V, Bundschuh R. Model for folding and aggregation in RNA secondary structures. Physical Review Letters. 96: 018105. PMID 16486525 DOI: 10.1103/Physrevlett.96.018105 |
0.368 |
|
| 2005 |
Liu T, Bundschuh R. Quantification of the differences between quenched and annealed averaging for RNA secondary structures. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 72: 061905. PMID 16485972 DOI: 10.1103/Physreve.72.061905 |
0.361 |
|
| 2005 |
Bundschuh R, Gerland U. Coupled dynamics of RNA folding and nanopore translocation. Physical Review Letters. 95: 208104. PMID 16384104 DOI: 10.1103/Physrevlett.95.208104 |
0.364 |
|
| 2005 |
Chia N, Bundschuh R. Numerical method for accessing the universal scaling function for a multiparticle discrete time asymmetric exclusion process. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 72: 051102. PMID 16383588 DOI: 10.1103/Physreve.72.051102 |
0.506 |
|
| 2005 |
Liu T, Bundschuh R. Model for codon position bias in RNA editing. Physical Review Letters. 95: 088101. PMID 16196905 DOI: 10.1103/Physrevlett.95.088101 |
0.378 |
|
| 2005 |
Gott JM, Parimi N, Bundschuh R. Discovery of new genes and deletion editing in Physarum mitochondria enabled by a novel algorithm for finding edited mRNAs. Nucleic Acids Research. 33: 5063-72. PMID 16147990 DOI: 10.1093/Nar/Gki820 |
0.38 |
|
| 2005 |
Layton DM, Bundschuh R. A statistical analysis of RNA folding algorithms through thermodynamic parameter perturbation Nucleic Acids Research. 33: 519-524. DOI: 10.1093/Nar/Gkh983 |
0.317 |
|
| 2004 |
Gerland U, Bundschuh R, Hwa T. Translocation of structured polynucleotides through nanopores. Physical Biology. 1: 19-26. PMID 16204818 DOI: 10.1088/1478-3967/1/1/002 |
0.567 |
|
| 2004 |
Chia N, Bundschuh R. Finite width model sequence comparison. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 70: 021906. PMID 15447514 DOI: 10.1103/Physreve.70.021906 |
0.559 |
|
| 2004 |
Liu T, Bundschuh R. Analytical description of finite size effects for RNA secondary structures. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 69: 061912. PMID 15244622 DOI: 10.1103/Physreve.69.061912 |
0.399 |
|
| 2004 |
Bundschuh R. Computational prediction of RNA editing sites Bioinformatics. 20: 3214-3220. PMID 15231535 DOI: 10.1093/Bioinformatics/Bth387 |
0.391 |
|
| 2004 |
Gerland U, Bundschuh R, Hwa T. Translocation of structured polynucleotides through nanopores Physical Biology. 1: 19-26. DOI: 10.1088/1478-3967/1/1/002 |
0.46 |
|
| 2004 |
Li Y, Lauria M, Bundschuh R. Using hybrid alignment for iterative sequence database searches Concurrency Computation Practice and Experience. 16: 841-853. DOI: 10.1002/Cpe.809 |
0.332 |
|
| 2003 |
Gerland U, Bundschuh R, Hwa T. Mechanically probing the folding pathway of single RNA molecules Biophysical Journal. 84: 2831-2840. PMID 12719217 DOI: 10.1016/S0006-3495(03)70012-5 |
0.599 |
|
| 2002 |
Yu YK, Bundschuh R, Hwa T. Hybrid alignment: High-performance with universal statistics Bioinformatics. 18: 864-872. PMID 12075022 DOI: 10.1093/Bioinformatics/18.6.864 |
0.557 |
|
| 2002 |
Bundschuh R. Rapid significance estimation in local sequence alignment with gaps. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 9: 243-60. PMID 12015880 DOI: 10.1089/10665270252935449 |
0.316 |
|
| 2002 |
Bundschuh R, Hwa T. Statistical mechanics of secondary structures formed by random RNA sequences. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 65: 031903. PMID 11909105 DOI: 10.1103/Physreve.65.031903 |
0.6 |
|
| 2002 |
Bundschuh R, Hwa T. Phrases of the secondary structures of RNA sequences Europhysics Letters. 59: 903-909. DOI: 10.1209/Epl/I2002-00128-3 |
0.609 |
|
| 2002 |
Bundschuh R. Asymmetric exclusion process and extremal statistics of random sequences Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 65. DOI: 10.1103/Physreve.65.031911 |
0.31 |
|
| 2001 |
Gerland U, Bundschuh R, Hwa T. Force-induced denaturation of RNA. Biophysical Journal. 81: 1324-32. PMID 11509348 DOI: 10.1016/S0006-3495(01)75789-X |
0.596 |
|
| 2001 |
Altschul SF, Bundschuh R, Olsen R, Hwa T. The estimation of statistical parameters for local alignment score distributions. Nucleic Acids Research. 29: 351-61. PMID 11139604 DOI: 10.1093/Nar/29.2.351 |
0.537 |
|
| 2000 |
Bundschuh R, Hwa T. An analytic study of the phase transition line in local sequence alignment with gaps Discrete Applied Mathematics. 104: 113-142. DOI: 10.1016/S0166-218X(00)00188-8 |
0.551 |
|
| 2000 |
Bundschuh R, Lässig M, Lipowsky R. Semi-flexible polymers with attractive interactions. European Physical Journal E. 3: 295-306. DOI: 10.1007/S101890070022 |
0.463 |
|
| 1999 |
Olsen R, Bundschuh R, Hwa T. Rapid assessment of extremal statistics for gapped local alignment. Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 211-22. PMID 10786304 |
0.521 |
|
| 1999 |
Bundschuh R, Hwa T. RNA secondary structure formation: A solvable model of heteropolymer folding Physical Review Letters. 83: 1479-1482. DOI: 10.1103/Physrevlett.83.1479 |
0.611 |
|
| 1999 |
Bundschuh R, Hwa T. Analytic study of the phase transition line in local sequence alignment with gaps Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 70-76. |
0.495 |
|
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