2018 Computational Sciences Publications

1Q – 2018

1.         Wang X, Philip VM, Ananda G, White CC, Malhotra A, Michalski PJ, Karuturi KRM, Chintalapudi SR, Acklin C, Sasner M, Bennett DA, De Jager PL, Howell GR, Carter GW. A Bayesian Framework for Generalized Linear Mixed Modeling Identifies New Candidate Loci for Late-Onset Alzheimer's Disease. Genetics. 2018;209(1):51-64. Epub 2018/03/07. doi: 10.1534/genetics.117.300673. PubMed PMID: 29507048; PMCID: PMC5937180.

2.         Raghupathy N, Choi K, Vincent MJ, Beane GL, Sheppard KS, Munger SC, Korstanje R, Pardo-Manual de Villena F, Churchill GA. Hierarchical analysis of RNA-seq reads improves the accuracy of allele-specific expression. Bioinformatics (Oxford, England). 2018;34(13):2177-84. Epub 2018/02/15. doi: 10.1093/bioinformatics/bty078. PubMed PMID: 29444201; PMCID: PMC6022640.

3.         Pullagura SRN, Buaas B, Gray N, Krening LC, Srivastava A, Braun RE. Functional Redundancy of DICER Cofactors TARBP2 and PRKRA During Murine Embryogenesis Does Not Involve miRNA Biogenesis. Genetics. 2018;208(4):1513-22. Epub 2018/02/23. doi: 10.1534/genetics.118.300791. PubMed PMID: 29467169; PMCID: PMC5887145.

4.         Chae YK, Anker JF, Bais P, Namburi S, Giles FJ, Chuang JH. Mutations in DNA repair genes are associated with increased neo-antigen load and activated T cell infiltration in lung adenocarcinoma. Oncotarget. 2018;9(8):7949-60. Epub 2018/03/01. doi: 10.18632/oncotarget.23742. PubMed PMID: 29487705; PMCID: PMC5814272.

5.         Becker T, Lee WP, Leone J, Zhu Q, Zhang C, Liu S, Sargent J, Shanker K, Mil-Homens A, Cerveira E, Ryan M, Cha J, Navarro FCP, Galeev T, Gerstein M, Mills RE, Shin DG, Lee C, Malhotra A. FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods. Genome biology. 2018;19(1):38. Epub 2018/03/22. doi: 10.1186/s13059-018-1404-6. PubMed PMID: 29559002; PMCID: PMC5859555.

6.         Parker CC, Dickson PE, Philip VM, Thomas M, Chesler EJ. Systems Genetic Analysis in GeneNetwork.org. Current protocols in neuroscience. 2017;79:8.39.1-8..20. Epub 2017/04/12. doi: 10.1002/cpns.23. PubMed PMID: 28398643; PMCID: PMC5548442.

2Q-2018

1.        Yuan JT, Gatti DM, Philip VM, Kasparek S, Kreuzman AM, Mansky B, Sharif K, Taterra D, Taylor WM, Thomas M, Ward JO, Holmes A, Chesler EJ, Parker CC. Genome-wide association for testis weight in the diversity outbred mouse population. Mammalian genome : official journal of the International Mammalian Genome Society. 2018;29(5-6):310-24. Epub 2018/04/25. doi: 10.1007/s00335-018-9745-8. PubMed PMID: 29691636.

2.       Abrams D, Kumar P, Karuturi KM, George J. A computational method to aid the design and analysis of single cell RNA-seq experiments for cell type identification. bioRxiv. 2018:247114. doi: 10.1101/247114

3.      Flynn WF, Namburi S, Paisie CA, Reddi HV, Li S, Karuturi RKM, George J. Pan-cancer machine learning predictors of primary site of origin and molecular subtype. bioRxiv. 2018:333914. doi: 10.1101/333914.

4.      Kim H, Kumar P, Menghi F, Noorbakhsh J, Cerveira E, Ryan M, Zhu Q, Ananda G, George J, Chen H, Mockus S, Zhang C, Yang Y, Keck J, Karuturi RKM, Bult CJ, Lee C, Liu ET, Chuang JH. Evolution of an intratumoral ecology susceptible to successive treatment in breast cancer xenografts. 2bioRxiv. 018:249797. doi: 10.1101/249797.

3Q - 2018

1.     Guo J, Wilken S, Jimenez V, Choi CJ, Ansong C, Dannebaum R, Sudek L, Milner DS, Bachy C, Reistetter EN, Elrod VA, Klimov D, Purvine SO, Wei CL, Kunde-Ramamoorthy G, Richards TA, Goodenough U, Smith RD, Callister SJ, Worden AZ. Specialized proteomic responses and an ancient photoprotection mechanism sustain marine green algal growth during phosphate limitation. Nature microbiology. 2018;3(7):781-90. Epub 2018/06/28. doi: 10.1038/s41564-018-0178-7. PubMed PMID: 29946165.

2.     Presa M, Racine JJ, Dwyer JR, Lamont DJ, Ratiu JJ, Sarsani VK, Chen YG, Geurts A, Schmitz I, Stearns T, Allocco J, Chapman HD, Serreze DV. A Hypermorphic Nfkbid Allele Contributes to Impaired Thymic Deletion of Autoreactive Diabetogenic CD8(+) T Cells in NOD Mice. Journal of immunology (Baltimore, Md : 1950). 2018;201(7):1907-17. Epub 2018/08/22. doi: 10.4049/jimmunol.1800465. PubMed PMID: 30127089; PMCID: PMC6143397

3.     Linn SC, Mustonen AM, Silva KA, Kennedy VE, Sundberg BA, Bechtold LS, Alghamdi S, Hoehndorf R, Schofield PN, Sundberg JP. Nail abnormalities identified in an ageing study of 30 inbred mouse strains. Experimental dermatology. 2018. Epub 2018/08/04. doi: 10.1111/exd.13759. PubMed PMID: 30074290; PMCID: PMC6360140.

4.     Wilson JJ, Chow KH, Labrie NJ, Branca JA, Sproule TJ, Perkins BRA, Wolf EE, Costa M, Stafford G, Rosales C, Mills KD, Roopenian DC, Hasham MG. Enhancing the efficacy of glycolytic blockade in cancer cells via RAD51 inhibition. Cancer biology & therapy. 2018:1-14. Epub 2018/09/06. doi: 10.1080/15384047.2018.1507666. PubMed PMID: 30183475; PMCID: PMC6343731. 5. Costa, M. W., Bais, P. et al. (2018). "Metformin Intervention Prevents Cardiac Dysfunction in a Murine Model of Adult Congenital Heart Disease." bioRxiv.

5.     Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez O, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Kong X, Hormozdiari F, Lee D, Wenger AM, Hastie A, Antaki D, Audano P, Brand H, Cantsilieris S, Cao H, Cerveira E, Chen C, Chen X, Chin C-S, Chong Z, Chuang NT, Lambert CC, Church DM, Clarke L, Farrell A, Flores J, Galeev T, Gorkin D, Gujral M, Guryev V, Haynes Heaton W, Korlach J, Kumar S, Kwon JY, Lee JE, Lee J, Lee W-P, Lee SP, Li S, Marks P, Viaud-Martinez K, Meiers S, Munson KM, Navarro F, Nelson BJ, Nodzak C, Noor A, Kyriazopoulou-Panagiotopoulou S, Pang A, Qiu Y, Rosanio G, Ryan M, Stutz A, Spierings DCJ, Ward A, Welch AE, Xiao M, Xu W, Zhang C, Zhu Q, Zheng-Bradley X, Lowy E, Yakneen S, McCarroll S, Jun G, Ding L, Koh CL, Ren B, Flicek P, Chen K, Gerstein MB, Kwok P-Y, Lansdorp PM, Marth G, Sebat J, Shi X, Bashir A, Ye K, Devine SE, Talkowski M, Mills RE, Marschall T, Korbel JO, Eichler EE, Lee C. Multi-platform discovery of haplotype-resolved structural variation in human genomes. bioRxiv. 2018:193144. doi: 10.1101/193144.

6.    Panahi M, Papanikolaou A, Torabi A, Zhang JG, Khan H, Vazir A, Hasham MG, Cleland JGF, Rosenthal NA, Harding SE, Sattler S. Immunomodulatory interventions in myocardial infarction and heart failure: a systematic review of clinical trials and meta-analysis of IL-1 inhibition. Cardiovascular research. 2018;114(11):1445-61. Epub 2018/07/17. doi: 10.1093/cvr/cvy145. PubMed PMID: 30010800; PMCID: PMC6106100.

7.   Woo XY, Srivastava A, Graber JH, Yadav V, Sarsani VK, Simons A, Beane G, Grubb S, Ananda G, Liu R, Stafford G, Chuang JH, Airhart SD, Karuturi RKM, George J, Bult CJ. Bioinformatics workflows for genomic analysis of tumors from Patient Derived Xenografts (PDX): challenges and guidelines. bioRxiv. 2018:414946. doi: 10.1101/414946.

 4Q - 2018

1.         Wilmanns JC, Pandey R, Hon O, Chandran A, Schilling JM, Forte E, Wu Q, Cagnone G, Bais P, Philip V, Coleman D, Kocalis H, Archer SK, Pearson JT, Ramialison M, Heineke J, Patel HH, Rosenthal NA, Furtado MB, Costa MW. Metformin intervention prevents cardiac dysfunction in a murine model of adult congenital heart disease. Molecular metabolism. 2019;20:102-14. Epub 2018/11/30. doi: 10.1016/j.molmet.2018.11.002. PubMed PMID: 30482476; PMCID: PMC6358551.

2.         Srivastava A, Kumar Sarsani V, Fiddes I, Sheehan SM, Seger RL, Barter ME, Neptune-Bear S, Lindqvist C, Korstanje R. Genome assembly and gene expression in the American black bear provides new insights into the renal response to hibernation. DNA research : an international journal for rapid publication of reports on genes and genomes. 2019;26(1):37-44. Epub 2018/11/06. doi: 10.1093/dnares/dsy036. PubMed PMID: 30395234; PMCID: PMC6379037.

3.         Kohler S, Carmody L, Vasilevsky N, Jacobsen JOB, Danis D, Gourdine JP, Gargano M, Harris NL, Matentzoglu N, McMurry JA, Osumi-Sutherland D, Cipriani V, Balhoff JP, Conlin T, Blau H, Baynam G, Palmer R, Gratian D, Dawkins H, Segal M, Jansen AC, Muaz A, Chang WH, Bergerson J, Laulederkind SJF, Yuksel Z, Beltran S, Freeman AF, Sergouniotis PI, Durkin D, Storm AL, Hanauer M, Brudno M, Bello SM, Sincan M, Rageth K, Wheeler MT, Oegema R, Lourghi H, Della Rocca MG, Thompson R, Castellanos F, Priest J, Cunningham-Rundles C, Hegde A, Lovering RC, Hajek C, Olry A, Notarangelo L, Similuk M, Zhang XA, Gomez-Andres D, Lochmuller H, Dollfus H, Rosenzweig S, Marwaha S, Rath A, Sullivan K, Smith C, Milner JD, Leroux D, Boerkoel CF, Klion A, Carter MC, Groza T, Smedley D, Haendel MA, Mungall C, Robinson PN. Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. Nucleic acids research. 2019;47(D1):D1018-d27. Epub 2018/11/27. doi: 10.1093/nar/gky1105. PubMed PMID: 30476213; PMCID: PMC6324074.

4.         Tuttle AH, Philip VM, Chesler EJ, Mogil JS. Comparing phenotypic variation between inbred and outbred mice. Nature methods. 2018;15(12):994-6. Epub 2018/12/07. doi: 10.1038/s41592-018-0224-7. PubMed PMID: 30504873.

5.         Thompson MJ, Chwialkowska K, Rubbi L, Lusis AJ, Davis RC, Srivastava A, Korstanje R, Churchill GA, Horvath S, Pellegrini M. A multi-tissue full lifespan epigenetic clock for mice. Aging. 2018;10(10):2832-54. Epub 2018/10/24. doi: 10.18632/aging.101590. PubMed PMID: 30348905; PMCID: PMC6224226.

6.         Lee D, Cheng A, Lawlor N, Bolisetty M, Ucar D. Detection of correlated hidden factors from single cell transcriptomes using Iteratively Adjusted-SVA (IA-SVA). Scientific reports. 2018;8(1):17040. Epub 2018/11/20. doi: 10.1038/s41598-018-35365-9. PubMed PMID: 30451954; PMCID: PMC6242813.

7.         Kleftogiannis D, Ashoor H, Bajic VB. TELS: A Novel Computational Framework for Identifying Motif Signatures of Transcribed Enhancers. Genomics, proteomics & bioinformatics. 2018;16(5):332-41. Epub 2018/12/24. doi: 10.1016/j.gpb.2018.05.003. PubMed PMID: 30578915; PMCID: PMC6364045.

8.         Kim H, Kumar P, Menghi F, Noorbakhsh J, Cerveira E, Ryan M, Zhu Q, Ananda G, George J, Chen HC, Mockus S, Zhang C, Yang Y, Keck J, Karuturi RKM, Bult CJ, Lee C, Liu ET, Chuang JH. High-resolution deconstruction of evolution induced by chemotherapy treatments in breast cancer xenografts. Scientific reports. 2018;8(1):17937. Epub 2018/12/19. doi: 10.1038/s41598-018-36184-8. PubMed PMID: 30560892; PMCID: PMC6298990.

9.         Garrett AM, Khalil A, Walton DO, Burgess RW. DSCAM promotes self-avoidance in the developing mouse retina by masking the functions of cadherin superfamily members. Proceedings of the National Academy of Sciences of the United States of America. 2018;115(43):E10216-e24. Epub 2018/10/10. doi: 10.1073/pnas.1809430115. PubMed PMID: 30297418; PMCID: PMC6205498.

10.       Arjunan P, Meghil MM, Pi W, Xu J, Lang L, El-Awady A, Sullivan W, Rajendran M, Rabelo MS, Wang T, Tawfik OK, Kunde-Ramamoorthy G, Singh N, Muthusamy T, Susin C, Teng Y, Arce RM, Cutler CW. Oral Pathobiont Activates Anti-Apoptotic Pathway, Promoting both Immune Suppression and Oncogenic Cell Proliferation. Scientific reports. 2018;8(1):16607. Epub 2018/11/11. doi: 10.1038/s41598-018-35126-8. PubMed PMID: 30413788; PMCID: PMC6226501.

11.      Dominguez PM, Ghamlouch H, Rosikiewicz W, Kumar P, Beguelin W, Fontan L, Rivas MA, Pawlikowska P, Armand M, Mouly E, Torres-Martin M, Doane AS, Calvo Fernandez MT, Durant M, Della-Valle V, Teater M, Cimmino L, Droin N, Tadros S, Motanagh S, Shih AH, Rubin MA, Tam W, Aifantis I, Levine RL, Elemento O, Inghirami G, Green MR, Figueroa ME, Bernard OA, Aoufouchi S, Li S, Shaknovich R, Melnick AM. TET2 Deficiency Causes Germinal Center Hyperplasia, Impairs Plasma Cell Differentiation, and Promotes B-cell Lymphomagenesis. Cancer discovery. 2018;8(12):1632-53. Epub 2018/10/03. doi: 10.1158/2159-8290.Cd-18-0657. PubMed PMID: 30274972; PMCID: PMC6279514.

12.     Kesarwani AK, Malhotra A, Srivastava A, Ananda G, Ashoor H, Kumar P, Kesharwani RK, Sarsani VK, Li Y, George J, Karuturi RKM. Genome Informatics. In: Ranganathan S, Gribskov M, Nakai K, Schönbach C, editors. Encyclopedia of Bioinformatics and Computational Biology. Oxford: Academic Press; 2019. p. 178-94.

13.     Srivastava A, George J, Karuturi RKM. Transcriptome Analysis. In: Ranganathan S, Gribskov M, Nakai K, Schönbach C, editors. Encyclopedia of Bioinformatics and Computational Biology. Oxford: Academic Press; 2019. p. 792-805.