Kateryna Makova, Ph.D. - Related publications

Biology Pennsylvania State University, State College, PA, United States 
Molecular evolution, comparative genomics
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50 most relevant papers in past 60 days:
Year Citation  Score
2020 Yan Y, Li Z, Li Y, Wu Z, Yang R. Correlated evolution of large DNA fragments in the 3D genome of Arabidopsis thaliana. Molecular Biology and Evolution. PMID 32044988 DOI: 10.1093/molbev/msaa031   
2020 Khan A, Asaf S, Khan AL, Shehzad T, Al-Rawahi A, Al-Harrasi A. Comparative Chloroplast Genomics of Endangered Species: Insights into Hotspot Divergence, Repetitive Sequence Variation, and Phylogeny. Plants (Basel, Switzerland). 9. PMID 32033491 DOI: 10.3390/plants9020199   
2020 Sherman RM, Salzberg SL. Pan-genomics in the human genome era. Nature Reviews. Genetics. PMID 32034321 DOI: 10.1038/s41576-020-0210-7   
2020 Shen F, Kidd JM. Rapid, Paralog-Sensitive CNV Analysis of 2457 Human Genomes Using QuicK-mer2. Genes. 11. PMID 32013076 DOI: 10.3390/genes11020141   
2020 Juan L, Wang Y, Jiang J, Yang Q, Jiang Q, Wang Y. PGsim: A Comprehensive and Highly Customizable Personal Genome Simulator. Frontiers in Bioengineering and Biotechnology. 8: 28. PMID 32047747 DOI: 10.3389/fbioe.2020.00028   
2020 Pascoal S, Risse JE, Zhang X, Blaxter M, Cezard T, Challis RJ, Gharbi K, Hunt J, Kumar S, Langan E, Liu X, Rayner JG, Ritchie MG, Snoek BL, Trivedi U, et al. Field cricket genome reveals the footprint of recent, abrupt adaptation in the wild. Evolution Letters. 4: 19-33. PMID 32055408 DOI: 10.1002/evl3.148   
2020 Mosquera Orgueira A, Rodríguez Antelo B, Díaz Arias JÁ, Díaz Varela N, Alonso Vence N, González Pérez MS, Bello López JL. Novel Mutation Hotspots within Non-Coding Regulatory Regions of the Chronic Lymphocytic Leukemia Genome. Scientific Reports. 10: 2407. PMID 32051441 DOI: 10.1038/s41598-020-59243-5   
2020 Naumenko AN, Karagodin DA, Yurchenko AA, Moskaev AV, Martin OI, Baricheva EM, Sharakhov IV, Gordeev MI, Sharakhova MV. Chromosome and Genome Divergence between the Cryptic Eurasian Malaria Vector-Species and . Genes. 11. PMID 32033356 DOI: 10.3390/genes11020165   
2020 Louha S, Ray DA, Winker K, Glenn TC. A High-Quality Genome Assembly of the North American Song Sparrow, . G3 (Bethesda, Md.). PMID 32075855 DOI: 10.1534/g3.119.400929   
2020 Borys SM, Younger ST. Identification of functional regulatory elements in the human genome using pooled CRISPR screens. Bmc Genomics. 21: 107. PMID 32005150 DOI: 10.1186/s12864-020-6497-0   
2020 Adrion JR, Galloway JG, Kern AD. Predicting the landscape of recombination using deep learning. Molecular Biology and Evolution. PMID 32077950 DOI: 10.1093/molbev/msaa038   
2020 Ely B. Recombination and gene loss occur simultaneously during bacterial horizontal gene transfer. Plos One. 15: e0227987. PMID 31990919 DOI: 10.1371/journal.pone.0227987   
2020 Tekedar HC, Blom J, Kalindamar S, Nho S, Karsi A, Lawrence ML. Comparative genomics of the fish pathogens 93-146 and C07-087. Microbial Genomics. 6. PMID 32108566 DOI: 10.1099/mgen.0.000322   
2020 Tekedar HC, Blom J, Kalindamar S, Nho S, Karsi A, Lawrence ML. Comparative genomics of the fish pathogens 93-146 and C07-087. Microbial Genomics. 6. PMID 32108566 DOI: 10.1099/mgen.0.000322   
2020 , Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, ... , ... , et al. Genomic basis for RNA alterations in cancer. Nature. 578: 129-136. PMID 32025019 DOI: 10.1038/s41586-020-1970-0   
2020 O'Neill K, Brocks D, Hammell MG. Mobile genomics: tools and techniques for tackling transposons. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 375: 20190345. PMID 32075565 DOI: 10.1098/rstb.2019.0345   
2020 Joly-Lopez Z, Platts AE, Gulko B, Choi JY, Groen SC, Zhong X, Siepel A, Purugganan MD. An inferred fitness consequence map of the rice genome. Nature Plants. PMID 32042156 DOI: 10.1038/s41477-019-0589-3   
2020 Loh JW, Ha H, Lin T, Sun N, Burns KH, Xing J. Integrated Mobile Element Scanning (ME-Scan) method for identifying multiple types of polymorphic mobile element insertions. Mobile Dna. 11: 12. PMID 32110248 DOI: 10.1186/s13100-020-00207-x   
2020 Huang S, Ge X, Cano A, Salazar BGM, Deng Y. Comparative analysis of chloroplast genomes for five species (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution. Peerj. 8: e8450. PMID 32071806 DOI: 10.7717/peerj.8450   
2020 Liu H, Jian L, Xu J, Zhang Q, Zhang M, Jin M, Peng Y, Yan J, Han B, Liu J, Gao F, Liu X, Huang L, Wei W, Ding Y, et al. High-Throughput CRISPR/Cas9 Mutagenesis Streamlines Trait Gene Identification in Maize. The Plant Cell. PMID 32102844 DOI: 10.1105/tpc.19.00934   
2020 Corbett-Detig R, Russell S, Nielsen R, Losos J. Phenotypic convergence is not mirrored at the protein level in a lizard adaptive radiation. Molecular Biology and Evolution. PMID 32027369 DOI: 10.1093/molbev/msaa028   
2020 Singh U, Syrkin Wurtele E. How new genes are born. Elife. 9. PMID 32072921 DOI: 10.7554/eLife.55136   
2020 McKerrow W, Tang Z, Steranka JP, Payer LM, Boeke JD, Keefe D, Fenyö D, Burns KH, Liu C. Human transposon insertion profiling by sequencing (TIPseq) to map LINE-1 insertions in single cells. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 375: 20190335. PMID 32075555 DOI: 10.1098/rstb.2019.0335   
2020 Suzuki T, Tsukumo Y, Furihata C, Naito M, Kohara A. Preparation of the standard cell lines for reference mutations in cancer gene-panels by genome editing in HEK 293 T/17 cells. Genes and Environment : the Official Journal of the Japanese Environmental Mutagen Society. 42: 8. PMID 32071619 DOI: 10.1186/s41021-020-0147-2   
2020 Hovhannisyan H, Hafez A, Llorens C, Gabaldón T. CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies. Bioinformatics (Oxford, England). 36: 925-927. PMID 31392323 DOI: 10.1093/bioinformatics/btz626   
2020 De Luca C, Race V, Keldermans L, Bauters M, Van Esch H. Challenges in molecular diagnosis of X-linked Intellectual disability. British Medical Bulletin. PMID 32043524 DOI: 10.1093/bmb/ldz039   
2020 Brandis G, Hughes D. The SNAP hypothesis: Chromosomal rearrangements could emerge from positive Selection during Niche Adaptation. Plos Genetics. 16: e1008615. PMID 32130223 DOI: 10.1371/journal.pgen.1008615   
2020 Sun X, Ding Y, Orr MC, Zhang F. Streamlining universal single-copy ortholog and ultraconserved element design: a case study in Collembola. Molecular Ecology Resources. PMID 32065730 DOI: 10.1111/1755-0998.13146   
2020 Rosa BA, Mihindukulasuriya K, Hallsworth-Pepin K, Wollam A, Martin J, Snowden C, Dunne WM, Weinstock GM, Burnham CA, Mitreva M. Improving Characterization of Understudied Human Microbiomes Using Targeted Phylogenetics. Msystems. 5. PMID 32098835 DOI: 10.1128/mSystems.00096-20   
2020 Pengelly RJ, Ward D, Hunt D, Mattocks C, Ennis S. Comparison of Mendeliome exome capture kits for use in clinical diagnostics. Scientific Reports. 10: 3235. PMID 32094380 DOI: 10.1038/s41598-020-60215-y   
2020 Goubert C, Thomas J, Payer LM, Kidd JM, Feusier J, Watkins WS, Burns KH, Jorde LB, Feschotte C. TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data. Nucleic Acids Research. PMID 32067044 DOI: 10.1093/nar/gkaa074   
2020 Boquete MT, Wagemaker NCAM, Vergeer P, Mounger J, Richards CL. Epigenetic Approaches in Non-Model Plants. Methods in Molecular Biology (Clifton, N.J.). 2093: 203-215. PMID 32088898 DOI: 10.1007/978-1-0716-0179-2_14   
2020 Beaulaurier J, Luo E, Eppley JM, Den Uyl P, Dai X, Burger A, Turner DJ, Pendleton M, Juul S, Harrington E, DeLong EF. Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities. Genome Research. PMID 32075851 DOI: 10.1101/gr.251686.119   
2020 Zhao Y, Long L, Wan J, Biliya S, Brady SC, Lee D, Ojemakinde A, Andersen EC, Vannberg FO, Lu H, McGrath PT. A spontaneous complex structural variant in rcan-1 increases exploratory behavior and laboratory fitness of Caenorhabditis elegans. Plos Genetics. 16: e1008606. PMID 32092052 DOI: 10.1371/journal.pgen.1008606   
2020 Kabadi A, McDonnell E, Frank CL, Drowley L. Applications of Functional Genomics for Drug Discovery. Slas Discovery : Advancing Life Sciences R & D. 2472555220902092. PMID 32026742 DOI: 10.1177/2472555220902092   
2020 Barbanti A, Torrado H, Macpherson E, Bargelloni L, Franch R, Carreras C, Pascual M. Helping decision making for reliable and cost-effective 2b-RAD sequencing and genotyping analyses in non-model species. Molecular Ecology Resources. PMID 32061018 DOI: 10.1111/1755-0998.13144   
2020 Harris RA, Raveendran M, Worley KC, Rogers J. Unusual sequence characteristics of human chromosome 19 are conserved across 11 nonhuman primates. Bmc Evolutionary Biology. 20: 33. PMID 32106815 DOI: 10.1186/s12862-020-1595-9   
2020 Lin HN, Hsu WL. GSAlign: an efficient sequence alignment tool for intra-species genomes. Bmc Genomics. 21: 182. PMID 32093618 DOI: 10.1186/s12864-020-6569-1   
2020 Rizwan M, Liang P, Ali H, Li Z, Nie H, Ahmed Saqib HS, Fiaz S, Niu Q, Su S. Population genomics of honey bees reveals a selection signature indispensable for royal jelly production. Molecular and Cellular Probes. 101542. PMID 32105702 DOI: 10.1016/j.mcp.2020.101542   
2020 Avdeyev P, Alexeev N, Rong Y, Alekseyev MA. A Unified ILP Framework for Core Ancestral Genome Reconstruction Problems. Bioinformatics (Oxford, England). PMID 32058559 DOI: 10.1093/bioinformatics/btaa100   
2020 Pillai S, Maksemous N, Lam AK. Genome Sequencing in Esophageal Squamous Cell Carcinoma. Methods in Molecular Biology (Clifton, N.J.). 2129: 217-240. PMID 32056181 DOI: 10.1007/978-1-0716-0377-2_17   
2020 Wang J, Street NR, Park EJ, Liu J, Ingvarsson PK. Evidence for widespread selection in shaping the genomic landscape during speciation of Populus. Molecular Ecology. PMID 32068935 DOI: 10.1111/mec.15388   
2020 Wilson J, Staley JM, Wyckoff GJ. Extinction of chromosomes due to specialization is a universal occurrence. Scientific Reports. 10: 2170. PMID 32034231 DOI: 10.1038/s41598-020-58997-2   
2020 Szczerba H, Komoń-Janczara E, Krawczyk M, Dudziak K, Nowak A, Kuzdraliński A, Waśko A, Targoński Z. Genome analysis of a wild rumen bacterium Enterobacter aerogenes LU2 - a novel bio-based succinic acid producer. Scientific Reports. 10: 1986. PMID 32029880 DOI: 10.1038/s41598-020-58929-0   
2020 Sundaram V, Wysocka J. Transposable elements as a potent source of diverse -regulatory sequences in mammalian genomes. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 375: 20190347. PMID 32075564 DOI: 10.1098/rstb.2019.0347   
2020 Zhu Y, Lu J, Zhao J, Zhang X, Yu HH, Velkov T, Li J. Complete genome sequence and genome-scale metabolic modelling of Acinetobacter baumannii type strain ATCC 19606. International Journal of Medical Microbiology : Ijmm. 151412. PMID 32081464 DOI: 10.1016/j.ijmm.2020.151412   
2020 Park I, Song JH, Yang S, Moon BC. Comparative Analysis of Chloroplast Genomes and Molecular Marker Development for the Identification of Authentic Cimicifugae Rhizoma. Plants (Basel, Switzerland). 9. PMID 32012666 DOI: 10.3390/plants9020157   
2020 Maggiolini FAM, Mercuri L, Antonacci F, Anaclerio F, Calabrese FM, Lorusso N, L'Abbate A, Sorensen M, Giannuzzi G, Eichler EE, Catacchio CR, Ventura M. Evolutionary Dynamics of the POTE Gene Family in Human and Nonhuman Primates. Genes. 11. PMID 32085667 DOI: 10.3390/genes11020213   
2020 Yang S, Cao X, Yu W, Li S, Zhou YJ. Efficient targeted mutation of genomic essential genes in yeast Saccharomyces cerevisiae. Applied Microbiology and Biotechnology. PMID 32043190 DOI: 10.1007/s00253-020-10405-5   
2020 Yin Y, Yang T, Liu H, Huang Z, Zhang Y, Song Y, Wang W, Guang X, Sahu SK, Kristiansen K. The draft genome of mandrill (Mandrillus sphinx): An Old World monkey. Scientific Reports. 10: 2431. PMID 32051450 DOI: 10.1038/s41598-020-59110-3