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Items: 1 to 50 of 63

1.

Gene Regulation Shifts Shed Light on Fungal Adaption in Plant Biomass Decomposers.

Zhang J, Silverstein KAT, Castaño JD, Figueroa M, Schilling JS.

mBio. 2019 Nov 19;10(6). pii: e02176-19. doi: 10.1128/mBio.02176-19.

2.

Emergence of the Ug99 lineage of the wheat stem rust pathogen through somatic hybridisation.

Li F, Upadhyaya NM, Sperschneider J, Matny O, Nguyen-Phuc H, Mago R, Raley C, Miller ME, Silverstein KAT, Henningsen E, Hirsch CD, Visser B, Pretorius ZA, Steffenson BJ, Schwessinger B, Dodds PN, Figueroa M.

Nat Commun. 2019 Nov 7;10(1):5068. doi: 10.1038/s41467-019-12927-7.

3.

Nodule-specific PLAT domain proteins are expanded in the Medicago lineage and required for nodulation.

Trujillo DI, Silverstein KAT, Young ND.

New Phytol. 2019 May;222(3):1538-1550. doi: 10.1111/nph.15697. Epub 2019 Feb 27.

PMID:
30664233
4.

Expression of Adipocyte/Macrophage Fatty Acid-Binding Protein in Tumor-Associated Macrophages Promotes Breast Cancer Progression.

Hao J, Yan F, Zhang Y, Triplett A, Zhang Y, Schultz DA, Sun Y, Zeng J, Silverstein KAT, Zheng Q, Bernlohr DA, Cleary MP, Egilmez NK, Sauter E, Liu S, Suttles J, Li B.

Cancer Res. 2018 May 1;78(9):2343-2355. doi: 10.1158/0008-5472.CAN-17-2465. Epub 2018 Feb 6.

5.

ODG: Omics database generator - a tool for generating, querying, and analyzing multi-omics comparative databases to facilitate biological understanding.

Guhlin J, Silverstein KAT, Zhou P, Tiffin P, Young ND.

BMC Bioinformatics. 2017 Aug 10;18(1):367. doi: 10.1186/s12859-017-1777-7.

6.

Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula.

Moll KM, Zhou P, Ramaraj T, Fajardo D, Devitt NP, Sadowsky MJ, Stupar RM, Tiffin P, Miller JR, Young ND, Silverstein KAT, Mudge J.

BMC Genomics. 2017 Aug 4;18(1):578. doi: 10.1186/s12864-017-3971-4.

7.

Hybrid assembly with long and short reads improves discovery of gene family expansions.

Miller JR, Zhou P, Mudge J, Gurtowski J, Lee H, Ramaraj T, Walenz BP, Liu J, Stupar RM, Denny R, Song L, Singh N, Maron LG, McCouch SR, McCombie WR, Schatz MC, Tiffin P, Young ND, Silverstein KAT.

BMC Genomics. 2017 Jul 19;18(1):541. doi: 10.1186/s12864-017-3927-8.

8.

Androgen Receptor Variant AR-V9 Is Coexpressed with AR-V7 in Prostate Cancer Metastases and Predicts Abiraterone Resistance.

Kohli M, Ho Y, Hillman DW, Van Etten JL, Henzler C, Yang R, Sperger JM, Li Y, Tseng E, Hon T, Clark T, Tan W, Carlson RE, Wang L, Sicotte H, Thai H, Jimenez R, Huang H, Vedell PT, Eckloff BW, Quevedo JF, Pitot HC, Costello BA, Jen J, Wieben ED, Silverstein KAT, Lang JM, Wang L, Dehm SM.

Clin Cancer Res. 2017 Aug 15;23(16):4704-4715. doi: 10.1158/1078-0432.CCR-17-0017. Epub 2017 May 4.

9.

Antagonism of B cell enhancer networks by STAT5 drives leukemia and poor patient survival.

Katerndahl CDS, Heltemes-Harris LM, Willette MJL, Henzler CM, Frietze S, Yang R, Schjerven H, Silverstein KAT, Ramsey LB, Hubbard G, Wells AD, Kuiper RP, Scheijen B, van Leeuwen FN, Müschen M, Kornblau SM, Farrar MA.

Nat Immunol. 2017 Jun;18(6):694-704. doi: 10.1038/ni.3716. Epub 2017 Apr 3.

10.

Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes.

Zhou P, Silverstein KA, Ramaraj T, Guhlin J, Denny R, Liu J, Farmer AD, Steele KP, Stupar RM, Miller JR, Tiffin P, Mudge J, Young ND.

BMC Genomics. 2017 Mar 27;18(1):261. doi: 10.1186/s12864-017-3654-1.

11.

CNV-RF Is a Random Forest-Based Copy Number Variation Detection Method Using Next-Generation Sequencing.

Onsongo G, Baughn LB, Bower M, Henzler C, Schomaker M, Silverstein KA, Thyagarajan B.

J Mol Diagn. 2016 Nov;18(6):872-881. doi: 10.1016/j.jmoldx.2016.07.001. Epub 2016 Sep 3.

12.

Augmenting Chinese hamster genome assembly by identifying regions of high confidence.

Vishwanathan N, Bandyopadhyay AA, Fu HY, Sharma M, Johnson KC, Mudge J, Ramaraj T, Onsongo G, Silverstein KA, Jacob NM, Le H, Karypis G, Hu WS.

Biotechnol J. 2016 Sep;11(9):1151-7. doi: 10.1002/biot.201500455. Epub 2016 Jul 19.

PMID:
27374913
13.

Insertional Mutagenesis Identifies a STAT3/Arid1b/β-catenin Pathway Driving Neurofibroma Initiation.

Wu J, Keng VW, Patmore DM, Kendall JJ, Patel AV, Jousma E, Jessen WJ, Choi K, Tschida BR, Silverstein KA, Fan D, Schwartz EB, Fuchs JR, Zou Y, Kim MO, Dombi E, Levy DE, Huang G, Cancelas JA, Stemmer-Rachamimov AO, Spinner RJ, Largaespada DA, Ratner N.

Cell Rep. 2016 Mar 1;14(8):1979-90. doi: 10.1016/j.celrep.2016.01.074. Epub 2016 Feb 18.

14.

Exploring structural variants in environmentally sensitive gene families.

Young ND, Zhou P, Silverstein KA.

Curr Opin Plant Biol. 2016 Apr;30:19-24. doi: 10.1016/j.pbi.2015.12.012. Epub 2016 Feb 8. Review.

PMID:
26855303
15.

ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly.

Yang R, Nelson AC, Henzler C, Thyagarajan B, Silverstein KA.

Genome Med. 2015 Dec 7;7:127. doi: 10.1186/s13073-015-0251-2.

16.

Cross platform analysis of methylation, miRNA and stem cell gene expression data in germ cell tumors highlights characteristic differences by tumor histology.

Poynter JN, Bestrashniy JR, Silverstein KA, Hooten AJ, Lees C, Ross JA, Tolar J.

BMC Cancer. 2015 Oct 23;15:769. doi: 10.1186/s12885-015-1796-6.

17.

Clonal Dissemination of Enterobacter cloacae Harboring blaKPC-3 in the Upper Midwestern United States.

Hargreaves ML, Shaw KM, Dobbins G, Snippes Vagnone PM, Harper JE, Boxrud D, Lynfield R, Aziz M, Price LB, Silverstein KA, Danzeisen JL, Youmans B, Case K, Sreevatsan S, Johnson TJ.

Antimicrob Agents Chemother. 2015 Dec;59(12):7723-34. doi: 10.1128/AAC.01291-15. Epub 2015 Oct 5.

18.

Transposon Mutagenesis Screen Identifies Potential Lung Cancer Drivers and CUL3 as a Tumor Suppressor.

Dorr C, Janik C, Weg M, Been RA, Bader J, Kang R, Ng B, Foran L, Landman SR, O'Sullivan MG, Steinbach M, Sarver AL, Silverstein KA, Largaespada DA, Starr TK.

Mol Cancer Res. 2015 Aug;13(8):1238-47. doi: 10.1158/1541-7786.MCR-14-0674-T. Epub 2015 May 20.

19.

Clinical validation of targeted next-generation sequencing for inherited disorders.

Yohe S, Hauge A, Bunjer K, Kemmer T, Bower M, Schomaker M, Onsongo G, Wilson J, Erdmann J, Zhou Y, Deshpande A, Spears MD, Beckman K, Silverstein KA, Thyagarajan B.

Arch Pathol Lab Med. 2015 Feb;139(2):204-10. doi: 10.5858/arpa.2013-0625-OA.

PMID:
25611102
20.

Genomic characterization of the LEED..PEEDs, a gene family unique to the medicago lineage.

Trujillo DI, Silverstein KA, Young ND.

G3 (Bethesda). 2014 Aug 25;4(10):2003-12. doi: 10.1534/g3.114.011874.

21.

Implementation of Cloud based next generation sequencing data analysis in a clinical laboratory.

Onsongo G, Erdmann J, Spears MD, Chilton J, Beckman KB, Hauge A, Yohe S, Schomaker M, Bower M, Silverstein KA, Thyagarajan B.

BMC Res Notes. 2014 May 23;7:314. doi: 10.1186/1756-0500-7-314.

22.

Central cell-derived peptides regulate early embryo patterning in flowering plants.

Costa LM, Marshall E, Tesfaye M, Silverstein KA, Mori M, Umetsu Y, Otterbach SL, Papareddy R, Dickinson HG, Boutiller K, VandenBosch KA, Ohki S, Gutierrez-Marcos JF.

Science. 2014 Apr 11;344(6180):168-72. doi: 10.1126/science.1243005.

23.

Fatty acid-binding protein E-FABP restricts tumor growth by promoting IFN-β responses in tumor-associated macrophages.

Zhang Y, Sun Y, Rao E, Yan F, Li Q, Zhang Y, Silverstein KA, Liu S, Sauter E, Cleary MP, Li B.

Cancer Res. 2014 Jun 1;74(11):2986-98. doi: 10.1158/0008-5472.CAN-13-2689. Epub 2014 Apr 8.

24.

Patterns of divergence of a large family of nodule cysteine-rich peptides in accessions of Medicago truncatula.

Nallu S, Silverstein KA, Zhou P, Young ND, Vandenbosch KA.

Plant J. 2014 May;78(4):697-705. doi: 10.1111/tpj.12506. Epub 2014 Apr 23.

25.

SHEAR: sample heterogeneity estimation and assembly by reference.

Landman SR, Hwang TH, Silverstein KA, Li Y, Dehm SM, Steinbach M, Kumar V.

BMC Genomics. 2014 Jan 29;15:84. doi: 10.1186/1471-2164-15-84.

26.

Polymorphisms within the Telomerase Reverse Transcriptase gene (TERT) in four breeds of dogs selected for difference in lifespan and cancer susceptibility.

McAloney CA, Silverstein KA, Modiano JF, Bagchi A.

BMC Vet Res. 2014 Jan 14;10:20. doi: 10.1186/1746-6148-10-20.

27.

Detecting small plant peptides using SPADA (Small Peptide Alignment Discovery Application).

Zhou P, Silverstein KA, Gao L, Walton JD, Nallu S, Guhlin J, Young ND.

BMC Bioinformatics. 2013 Nov 20;14:335. doi: 10.1186/1471-2105-14-335.

28.

TALEN-engineered AR gene rearrangements reveal endocrine uncoupling of androgen receptor in prostate cancer.

Nyquist MD, Li Y, Hwang TH, Manlove LS, Vessella RL, Silverstein KA, Voytas DF, Dehm SM.

Proc Natl Acad Sci U S A. 2013 Oct 22;110(43):17492-7. doi: 10.1073/pnas.1308587110. Epub 2013 Oct 7.

29.

MMuFLR: missense mutation and frameshift location reporter.

Rathe SK, Johnson JE, Silverstein KA, Erdmann JJ, Watson AL, Popescu FE, Ohlfest JR, Largaespada DA.

Bioinformatics. 2013 Sep 15;29(18):2353-4. doi: 10.1093/bioinformatics/btt385. Epub 2013 Jul 3.

30.

Large-scale integrative network-based analysis identifies common pathways disrupted by copy number alterations across cancers.

Hwang TH, Atluri G, Kuang R, Kumar V, Starr T, Silverstein KA, Haverty PM, Zhang Z, Liu J.

BMC Genomics. 2013 Jul 3;14:440. doi: 10.1186/1471-2164-14-440.

31.

Regulatory patterns of a large family of defensin-like genes expressed in nodules of Medicago truncatula.

Nallu S, Silverstein KA, Samac DA, Bucciarelli B, Vance CP, VandenBosch KA.

PLoS One. 2013;8(4):e60355. doi: 10.1371/journal.pone.0060355. Epub 2013 Apr 1.

32.

Spatio-temporal expression patterns of Arabidopsis thaliana and Medicago truncatula defensin-like genes.

Tesfaye M, Silverstein KA, Nallu S, Wang L, Botanga CJ, Gomez SK, Costa LM, Harrison MJ, Samac DA, Glazebrook J, Katagiri F, Gutierrez-Marcos JF, Vandenbosch KA.

PLoS One. 2013;8(3):e58992. doi: 10.1371/journal.pone.0058992. Epub 2013 Mar 18.

33.

Case-parent analysis of variation in pubertal hormone genes and pediatric osteosarcoma: a Children's Oncology Group (COG) study.

Musselman JR, Bergemann TL, Ross JA, Sklar C, Silverstein KA, Langer EK, Savage SA, Nagarajan R, Krailo M, Malkin D, Spector LG.

Int J Mol Epidemiol Genet. 2012;3(4):286-93. Epub 2012 Nov 15.

34.

Androgen receptor splice variants mediate enzalutamide resistance in castration-resistant prostate cancer cell lines.

Li Y, Chan SC, Brand LJ, Hwang TH, Silverstein KA, Dehm SM.

Cancer Res. 2013 Jan 15;73(2):483-9. doi: 10.1158/0008-5472.CAN-12-3630. Epub 2012 Nov 1.

35.

Sex bias occurrence of hepatocellular carcinoma in Poly7 molecular subclass is associated with EGFR.

Keng VW, Sia D, Sarver AL, Tschida BR, Fan D, Alsinet C, Solé M, Lee WL, Kuka TP, Moriarity BS, Villanueva A, Dupuy AJ, Riordan JD, Bell JB, Silverstein KA, Llovet JM, Largaespada DA.

Hepatology. 2013 Jan;57(1):120-30. doi: 10.1002/hep.26004. Epub 2012 Oct 19.

36.

TAPDANCE: an automated tool to identify and annotate transposon insertion CISs and associations between CISs from next generation sequence data.

Sarver AL, Erdman J, Starr T, Largaespada DA, Silverstein KA.

BMC Bioinformatics. 2012 Jun 29;13:154. doi: 10.1186/1471-2105-13-154.

37.

The deubiquitinase USP9X suppresses pancreatic ductal adenocarcinoma.

Pérez-Mancera PA, Rust AG, van der Weyden L, Kristiansen G, Li A, Sarver AL, Silverstein KA, Grützmann R, Aust D, Rümmele P, Knösel T, Herd C, Stemple DL, Kettleborough R, Brosnan JA, Li A, Morgan R, Knight S, Yu J, Stegeman S, Collier LS, ten Hoeve JJ, de Ridder J, Klein AP, Goggins M, Hruban RH, Chang DK, Biankin AV, Grimmond SM; Australian Pancreatic Cancer Genome Initiative, Wessels LF, Wood SA, Iacobuzio-Donahue CA, Pilarsky C, Largaespada DA, Adams DJ, Tuveson DA.

Nature. 2012 Apr 29;486(7402):266-70. doi: 10.1038/nature11114. Erratum in: Nature. 2013 Feb 21;494(7437):390. Scarlett, Christopher J [added]; Kaplan, Warren [added]; Scarpa, Aldo [added], Das, Amithabad [corrected to Das, Amitabha].

38.

Phosphorylated and sumoylation-deficient progesterone receptors drive proliferative gene signatures during breast cancer progression.

Knutson TP, Daniel AR, Fan D, Silverstein KA, Covington KR, Fuqua SA, Lange CA.

Breast Cancer Res. 2012 Jun 14;14(3):R95.

39.

A Sleeping Beauty mutagenesis screen reveals a tumor suppressor role for Ncoa2/Src-2 in liver cancer.

O'Donnell KA, Keng VW, York B, Reineke EL, Seo D, Fan D, Silverstein KA, Schrum CT, Xie WR, Mularoni L, Wheelan SJ, Torbenson MS, O'Malley BW, Largaespada DA, Boeke JD.

Proc Natl Acad Sci U S A. 2012 May 22;109(21):E1377-86. doi: 10.1073/pnas.1115433109. Epub 2012 May 3.

40.

Identification and characterization of the defensin-like gene family of grapevine.

Giacomelli L, Nanni V, Lenzi L, Zhuang J, Dalla Serra M, Banfield MJ, Town CD, Silverstein KA, Baraldi E, Moser C.

Mol Plant Microbe Interact. 2012 Aug;25(8):1118-31. doi: 10.1094/MPMI-12-11-0323.

41.

An insertional mutagenesis screen identifies genes that cooperate with Mll-AF9 in a murine leukemogenesis model.

Bergerson RJ, Collier LS, Sarver AL, Been RA, Lugthart S, Diers MD, Zuber J, Rappaport AR, Nixon MJ, Silverstein KA, Fan D, Lamblin AF, Wolff L, Kersey JH, Delwel R, Lowe SW, O'Sullivan MG, Kogan SC, Adams DJ, Largaespada DA.

Blood. 2012 May 10;119(19):4512-23. doi: 10.1182/blood-2010-04-281428. Epub 2012 Mar 16.

42.

AR intragenic deletions linked to androgen receptor splice variant expression and activity in models of prostate cancer progression.

Li Y, Hwang TH, Oseth LA, Hauge A, Vessella RL, Schmechel SC, Hirsch B, Beckman KB, Silverstein KA, Dehm SM.

Oncogene. 2012 Nov 8;31(45):4759-67. doi: 10.1038/onc.2011.637. Epub 2012 Jan 23.

43.

New methods for finding common insertion sites and co-occurring common insertion sites in transposon- and virus-based genetic screens.

Bergemann TL, Starr TK, Yu H, Steinbach M, Erdmann J, Chen Y, Cormier RT, Largaespada DA, Silverstein KA.

Nucleic Acids Res. 2012 May;40(9):3822-33. doi: 10.1093/nar/gkr1295. Epub 2012 Jan 12.

44.

The Medicago genome provides insight into the evolution of rhizobial symbioses.

Young ND, Debellé F, Oldroyd GE, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KF, Gouzy J, Schoof H, Van de Peer Y, Proost S, Cook DR, Meyers BC, Spannagl M, Cheung F, De Mita S, Krishnakumar V, Gundlach H, Zhou S, Mudge J, Bharti AK, Murray JD, Naoumkina MA, Rosen B, Silverstein KA, Tang H, Rombauts S, Zhao PX, Zhou P, Barbe V, Bardou P, Bechner M, Bellec A, Berger A, Bergès H, Bidwell S, Bisseling T, Choisne N, Couloux A, Denny R, Deshpande S, Dai X, Doyle JJ, Dudez AM, Farmer AD, Fouteau S, Franken C, Gibelin C, Gish J, Goldstein S, González AJ, Green PJ, Hallab A, Hartog M, Hua A, Humphray SJ, Jeong DH, Jing Y, Jöcker A, Kenton SM, Kim DJ, Klee K, Lai H, Lang C, Lin S, Macmil SL, Magdelenat G, Matthews L, McCorrison J, Monaghan EL, Mun JH, Najar FZ, Nicholson C, Noirot C, O'Bleness M, Paule CR, Poulain J, Prion F, Qin B, Qu C, Retzel EF, Riddle C, Sallet E, Samain S, Samson N, Sanders I, Saurat O, Scarpelli C, Schiex T, Segurens B, Severin AJ, Sherrier DJ, Shi R, Sims S, Singer SR, Sinharoy S, Sterck L, Viollet A, Wang BB, Wang K, Wang M, Wang X, Warfsmann J, Weissenbach J, White DD, White JD, Wiley GB, Wincker P, Xing Y, Yang L, Yao Z, Ying F, Zhai J, Zhou L, Zuber A, Dénarié J, Dixon RA, May GD, Schwartz DC, Rogers J, Quétier F, Town CD, Roe BA.

Nature. 2011 Nov 16;480(7378):520-4. doi: 10.1038/nature10625.

45.

Human colon cancer profiles show differential microRNA expression depending on mismatch repair status and are characteristic of undifferentiated proliferative states.

Sarver AL, French AJ, Borralho PM, Thayanithy V, Oberg AL, Silverstein KA, Morlan BW, Riska SM, Boardman LA, Cunningham JM, Subramanian S, Wang L, Smyrk TC, Rodrigues CM, Thibodeau SN, Steer CJ.

BMC Cancer. 2009 Nov 18;9:401. doi: 10.1186/1471-2407-9-401.

46.

Evaluation of a new high-dimensional miRNA profiling platform.

Cunningham JM, Oberg AL, Borralho PM, Kren BT, French AJ, Wang L, Bot BM, Morlan BW, Silverstein KA, Staggs R, Zeng Y, Lamblin AF, Hilker CA, Fan JB, Steer CJ, Thibodeau SN.

BMC Med Genomics. 2009 Aug 27;2:57. doi: 10.1186/1755-8794-2-57.

47.

Evolution of pathogenicity and sexual reproduction in eight Candida genomes.

Butler G, Rasmussen MD, Lin MF, Santos MA, Sakthikumar S, Munro CA, Rheinbay E, Grabherr M, Forche A, Reedy JL, Agrafioti I, Arnaud MB, Bates S, Brown AJ, Brunke S, Costanzo MC, Fitzpatrick DA, de Groot PW, Harris D, Hoyer LL, Hube B, Klis FM, Kodira C, Lennard N, Logue ME, Martin R, Neiman AM, Nikolaou E, Quail MA, Quinn J, Santos MC, Schmitzberger FF, Sherlock G, Shah P, Silverstein KA, Skrzypek MS, Soll D, Staggs R, Stansfield I, Stumpf MP, Sudbery PE, Srikantha T, Zeng Q, Berman J, Berriman M, Heitman J, Gow NA, Lorenz MC, Birren BW, Kellis M, Cuomo CA.

Nature. 2009 Jun 4;459(7247):657-62. doi: 10.1038/nature08064.

48.

A transposon-based genetic screen in mice identifies genes altered in colorectal cancer.

Starr TK, Allaei R, Silverstein KA, Staggs RA, Sarver AL, Bergemann TL, Gupta M, O'Sullivan MG, Matise I, Dupuy AJ, Collier LS, Powers S, Oberg AL, Asmann YW, Thibodeau SN, Tessarollo L, Copeland NG, Jenkins NA, Cormier RT, Largaespada DA.

Science. 2009 Mar 27;323(5922):1747-50. doi: 10.1126/science.1163040. Epub 2009 Feb 26.

49.

A conditional transposon-based insertional mutagenesis screen for genes associated with mouse hepatocellular carcinoma.

Keng VW, Villanueva A, Chiang DY, Dupuy AJ, Ryan BJ, Matise I, Silverstein KA, Sarver A, Starr TK, Akagi K, Tessarollo L, Collier LS, Powers S, Lowe SW, Jenkins NA, Copeland NG, Llovet JM, Largaespada DA.

Nat Biotechnol. 2009 Mar;27(3):264-74. doi: 10.1038/nbt.1526. Epub 2009 Feb 22.

50.

Expression of endogenous antimicrobial peptides in normal canine skin.

Wingate KV, Torres SM, Silverstein KA, Hendrickson JA, Rutherford MS.

Vet Dermatol. 2009 Feb;20(1):19-26. doi: 10.1111/j.1365-3164.2008.00707.x. Epub 2008 Nov 14.

PMID:
19037917

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