Departmental Publications 2016

Evolution of Osteocrin as an activity-regulated factor in the primate brain. Ataman B, Boulting GL, Harmin DA, Yang MG, Baker-Salisbury M, Yap EL, Malik AN, Mei K, Rubin AA, Spiegel I, Durresi E, Sharma N, Hu LS, Pletikos M, Griffith EC, Partlow JN, Stevens CR, Adli M, Chahrour M, Sestan N, Walsh CA, Berezovskii VK, Livingstone MS, Greenberg ME. Nature. 2016 Nov 10;539(7628):242-247. doi: 10.1038/nature20111. PMID: 27830782

Expression of lncRNAs in Low-Grade Gliomas and Glioblastoma Multiforme: An In Silico Analysis. Reon BJ, Anaya J, Zhang Y, Mandell J, Purow B, Abounader R, Dutta A. PLoS Med. 2016 Dec 6;13(12):e1002192. doi: 10.1371/journal.pmed.1002192. PMID: 27923049

The Current Revolution in Cryo-EM. Egelman EH. Biophys J. 2016 Mar 8;110(5):1008-12. doi: 10.1016/j.bpj.2016.02.001. Review. No abstract available.  PMID: 26958874

Biophysical Journal Special Issue: Focus on Cryo-EM. Egelman EH, Engel A. Biophys J. 2016 Feb 23;110(4):E01. doi: 10.1016/j.bpj.2016.01.025. No abstract available.  PMID: 26910436

Query-seeded iterative sequence similarity searching improves selectivity 5-20-fold. Pearson WR, Li W, Lopez R. Nucleic Acids Res. 2016 Dec 6. pii: gkw1207. PMID: 27923999  

Finding Protein and Nucleotide Similarities with FASTA. Pearson WR. Curr Protoc Bioinformatics. 2016 Mar 24;53:3.9.1-25. doi: 10.1002/0471250953.bi0309s53. PMID: 27010337

Tgif1 and Tgif2 repress expression of the RabGAP, Evi5l. Anderson AE, Taniguchi K, Hao Y, Melhuish TA, Shah A, Turner SD, Sutherland AE, Wotton D. Mol Cell Biol. 2016 Dec 12. pii: MCB.00527-16. PMID: 27956704

Genetic and Molecular Analyses indicate independent effects of TGIFs on Nodal and Gli3 in neural tube patterning. Taniguchi K, Anderson AE, Melhuish TA, Carlton AL, Manukyan A, Sutherland AE, Wotton D. Eur J Hum Genet. 2016 Dec 7. doi: 10.1038/ejhg.2016.164. PMID: 27924807

In Vitro Assay to Study Histone Ubiquitination During Transcriptional Regulation. Tushir-Singh J, Bhatnagar S. Methods Mol Biol. 2017;1507:235-244. PMID: 27832544

Combinatorial drug screening and molecular profiling reveal diverse mechanisms of intrinsic and adaptive resistance to BRAF inhibition in V600E BRAF mutant melanomas. Roller DG, Capaldo B, Bekiranov S, Mackey AJ, Conaway MR, Petricoin EF, Gioeli D, Weber MJ. Oncotarget. 2016 Jan 19;7(3):2734-53. doi: 10.18632/oncotarget.6548. PMID: 26673621

CRISPR-Cas9-AID base editor is a powerful gain-of-function screening tool. Kuscu C, Adli M. Nat Methods. 2016 Nov 29;13(12):983-984. doi: 10.1038/nmeth.4076. No abstract available. PMID: 27898061

Evolution of Osteocrin as an activity-regulated factor in the primate brain. Ataman B, Boulting GL, Harmin DA, Yang MG, Baker-Salisbury M, Yap EL, Malik AN, Mei K, Rubin AA, Spiegel I, Durresi E, Sharma N, Hu LS, Pletikos M, Griffith EC, Partlow JN, Stevens CR, Adli M, Chahrour M, Sestan N, Walsh CA, Berezovskii VK, Livingstone MS, Greenberg ME. Nature. 2016 Nov 9;539(7628):242-247. doi: 10.1038/nature20111. PMID: 27830782

Two subunits of human ORC are dispensable for DNA replication and proliferation. Shibata E, Kiran M, Shibata Y, Singh S, Kiran S, Dutta A. Elife. 2016 Dec 1;5. pii: e19084. doi: 10.7554/eLife.19084. PMID: 27906128  

Creating Patient-Specific Neural Cells for the In Vitro Study of Brain Disorders. Brennand KJ, Marchetto MC, Benvenisty N, Brüstle O, Ebert A, Izpisua Belmonte JC, Kaykas A, Lancaster MA, Livesey FJ, McConnell MJ, McKay RD, Morrow EM, Muotri AR, Panchision DM, Rubin LL, Sawa A, Soldner F, Song H, Studer L, Temple S, Vaccarino FM, Wu J, Vanderhaeghen P, Gage FH, Jaenisch R. Stem Cell Reports. 2015 Dec 8;5(6):933-45. doi: 10.1016/j.stemcr.2015.10.011. PMID: 26610635

Cryo-EM Structure of Caspase-8 Tandem DED Filament Reveals Assembly and Regulation Mechanisms of the Death-Inducing Signaling Complex. Fu TM, Li Y, Lu A, Li Z, Vajjhala PR, Cruz AC, Srivastava DB, DiMaio F, Penczek PA, Siegel RM, Stacey KJ, Egelman EH, Wu H. Mol Cell. 2016 Oct 20;64(2):236-250. doi: 10.1016/j.molcel.2016.09.009. PMID: 27746017

Bacterial flagellar capping proteins adopt diverse oligomeric states. Postel S, Deredge D, Bonsor DA, Yu X, Diederichs K, Helmsing S, Vromen A, Friedler A, Hust M, Egelman EH, Beckett D, Wintrode PL, Sundberg EJ. Elife. 2016 Sep 24;5. pii: e18857. doi: 10.7554/eLife.18857. PMID: 27664419

Structure of the Neisseria meningitidis Type IV pilus. Kolappan S, Coureuil M, Yu X, Nassif X, Egelman EH, Craig L. Nat Commun. 2016 Oct 4;7:13015. doi: 10.1038/ncomms13015. PMID: 27698424  

Structure of the Bacterial Sex F Pilus Reveals an Assembly of a Stoichiometric Protein-Phospholipid Complex. Costa TR, Ilangovan A, Ukleja M, Redzej A, Santini JM, Smith TK, Egelman EH, Waksman G. Cell. 2016 Sep 8;166(6):1436-1444.e10. doi: 10.1016/j.cell.2016.08.025. PMID: 27610568

A Pro-metastatic tRNA Pathway. Kuscu C, Dutta A. Cell. 2016 Jun 2;165(6):1314-5. doi: 10.1016/j.cell.2016.05.066. PMID: 27259143

Efficacy of Hybrid Tetrahydrobenzo[d]thiazole Based Aryl Piperazines D-264 and D-301 at D₂ and D₃ Receptors. Zhen J, Antonio T, Jacob JC, Grandy DK, Reith ME, Dutta AK, Selley DE. Neurochem Res. 2016 Feb;41(1-2):328-39. doi: 10.1007/s11064-015-1808-6.

HJURP interaction with the condensin II complex during G1 promotes CENP-A deposition. Barnhart-Dailey MC, Trivedi P, Stukenberg PT, Foltz DR. Mol Biol Cell. 2016 Nov 2. pii: mbc.E15-12-0843. PMID: 27807043

A Centromere-Signaling Network Underlies the Coordination among Mitotic Events. Trivedi P, Stukenberg PT. Trends Biochem Sci. 2016 Feb;41(2):160-74. doi: 10.1016/j.tibs.2015.11.002. Review. PMID: 26705896

Connecting the microtubule attachment status of each kinetochore to cell cycle arrest through the spindle assembly checkpoint. Stukenberg PT, Burke DJ. Chromosoma. 2015 Dec;124(4):463-80. doi: 10.1007/s00412-015-0515-z. Epub 2015 Apr 28. Review. PMID: 25917595

Bacterial flagellar capping proteins adopt diverse oligomeric states. Postel S, Deredge D, Bonsor DA, Yu X, Diederichs K, Helmsing S, Vromen A, Friedler A, Hust M, Egelman EH, Beckett D, Wintrode PL, Sundberg EJ. Elife. 2016 Sep 24;5. pii: e18857. doi: 10.7554/eLife.18857. PMID: 27664419

Structure of the Bacterial Sex F Pilus Reveals an Assembly of a Stoichiometric Protein-Phospholipid Complex. Costa TR, Ilangovan A, Ukleja M, Redzej A, Santini JM, Smith TK, Egelman EH, Waksman G. Cell. 2016 Sep 8;166(6):1436-1444.e10. doi: 10.1016/j.cell.2016.08.025. PMID: 27610568

Nuclear RNA-seq of single neurons reveals molecular signatures of activation. Lacar B, Linker SB, Jaeger BN, Krishnaswami S, Barron J, Kelder M, Parylak S, Paquola A, Venepally P, Novotny M, O’Connor C, Fitzpatrick C, Erwin J, Hsu JY, Husband D, McConnell MJ, Lasken R, Gage FH. Nat Commun. 2016 Apr 19;7:11022. doi: 10.1038/ncomms11022. PMID: 27090946

Preventing the Androgen Receptor N/C Interaction Delays Disease Onset in a Mouse Model of SBMA. Zboray L, Pluciennik A, Curtis D, Liu Y, Berman-Booty LD, Orr C, Kesler CT, Berger T, Gioeli D, Paschal BM, Merry DE. Cell Rep. 2015 Dec 15;13(10):2312-23. doi: 10.1016/j.celrep.2015.11.019. Epub 2015 Dec 7. PMID: 26673324

Dutta A. Curr Biol. 2015 Dec 7;25(23):R1112-4. No abstract available.  PMID: 27027134

Biological Processes Discovered by High-Throughput Sequencing. Reon BJ, Dutta A. Am J Pathol. 2016 Apr;186(4):722-32. doi: 10.1016/j.ajpath.2015.10.033. Epub 2016 Jan 30. Review. PMID: 26828742

Protein Function Prediction: Problems and Pitfalls. Pearson WR. Curr Protoc Bioinformatics. 2015 Sep 3;51:4.12.1-8. doi: 10.1002/0471250953.bi0412s51. Review. PMID: 26334923

Centromeres of a Different CAL-ibre. Zasadzińska E, Foltz DR. Dev Cell. 2016 Apr 18;37(2):105-6. doi: 10.1016/j.devcel.2016.04.006. PMID: 27093076

Archaeal flagellin combines a bacterial type IV pilin domain with an Ig-like domain. Braun T, Vos MR, Kalisman N, Sherman NE, Rachel R, Wirth R, Schröder GF, Egelman EH. Proc Natl Acad Sci U S A. 2016 Aug 30. pii: 201607756. PMID: 27578865

Resolution advances in cryo-EM enable application to drug discovery. Subramaniam S, Earl LA, Falconieri V, Milne JL, Egelman EH. Curr Opin Struct Biol. 2016 Aug 20;41:194-202. doi: 10.1016/j.sbi.2016.07.009. PMID: 27552081

Compstatin Cp40 blocks hematin-mediated deposition of C3b fragments on erythrocytes: Implications for treatment of malarial anemia. Lindorfer MA, Cook EM, Reis ES, Ricklin D, Risitano AM, Lambris JD, Taylor RP. Clin Immunol. 2016 Aug 18;171:32-35. doi: 10.1016/j.clim.2016.08.017. PMID: 27546448

Real-time analysis of the detailed sequence of cellular events in mAb-mediated complement-dependent cytotoxicity of B-cell lines and of chronic lymphocytic leukemia B-cells. Lindorfer MA, Cook EM, Tupitza JC, Zent CS, Burack R, de Jong RN, Beurskens FJ, Schuurman J, Parren PW, Taylor RP. Mol Immunol. 2016 Feb;70:13-23. doi: 10.1016/j.molimm.2015.12.007. Epub 2015 Dec 12. PMID: 26690706

Major histocompatibility complex class I molecules protect motor neurons from astrocyte-induced toxicity in amyotrophic lateral sclerosis. Song S, Miranda CJ, Braun L, Meyer K, Frakes AE, Ferraiuolo L, Likhite S, Bevan AK, Foust KD, McConnell MJ, Walker CM, Kaspar BK. Nat Med. 2016 Apr;22(4):397-403. doi: 10.1038/nm.4052. Epub 2016 Feb 29. PMID: 26928464

Transcription factors GAF and HSF act at distinct regulatory steps to modulate stress-induced gene activation. Duarte FM, Fuda NJ, Mahat DB, Core LJ, Guertin MJ, Lis JT. Genes Dev. 2016 Aug 4. PMID: 27492368

Selecting the Right Similarity-Scoring Matrix. Pearson WR. Curr Protoc Bioinformatics. 2013;43:3.5.1-9. doi: 10.1002/0471250953.bi0305s43. PMID: 24509512

Small Molecule Inhibitor of CBFβ-RUNX Binding for RUNX Transcription Factor Driven Cancers. Illendula A, Gilmour J, Grembecka J, Tirumala VS, Boulton A, Kuntimaddi A, Schmidt C, Wang L, Pulikkan JA, Zong H, Parlak M, Kuscu C, Pickin A, Zhou Y, Gao Y, Mishra L, Adli M, Castilla LH, Rajewski RA, Janes KA, Guzman ML, Bonifer C, Bushweller JH. EBioMedicine. 2016 Jun;8:117-31. doi: 10.1016/j.ebiom.2016.04.032. Epub 2016 Apr 29. PMID: 27428424

Antibodies That Efficiently Form Hexamers upon Antigen Binding Can Induce Complement-Dependent Cytotoxicity under Complement-Limiting Conditions. Cook EM, Lindorfer MA, van der Horst H, Oostindie S, Beurskens FJ, Schuurman J, Zent CS, Burack R, Parren PW, Taylor RP. J Immunol. 2016 Jul 29. pii: 1600648. PMID: 27474078

The Impact of dUTPase on Ribonucleotide Reductase-Induced Genome Instability in Cancer Cells. Chen CW, Tsao N, Huang LY, Yen Y, Liu X, Lehman C, Wang YH, Tseng MC, Chen YJ, Ho YC, Chen CF, Chang ZF. Cell Rep. 2016 Jul 20. pii: S2211-1247(16)30863-4. doi: 10.1016/j.celrep.2016.06.094.  PMID: 27452458

Licensing of Centromeric Chromatin Assembly through the Mis18α-Mis18β Heterotetramer. Nardi IK, Zasadzińska E, Stellfox ME, Knippler CM, Foltz DR. Mol Cell. 2016 Mar 3;61(5):774-87. doi: 10.1016/j.molcel.2016.02.014. PMID: 26942680

The Xenopus ORFeome: A resource that enables functional genomics. Grant IM, Balcha D, Hao T, Shen Y, Trivedi P, Patrushev I, Fortriede JD, Karpinka JB, Liu L, Zorn AM, Stukenberg PT, Hill DE, Gilchrist MJ. Dev Biol. 2015 Dec 15;408(2):345-57. doi: 10.1016/j.ydbio.2015.09.004. Epub 2015 Sep 29. PMID: 26391338

Structural basis for recognition and remodeling of the TBP:DNA:NC2 complex by Mot1. Butryn A, Schuller JM, Stoehr G, Runge-Wollmann P, Förster F, Auble DT, Hopfner KP. Elife. 2015 Aug 10;4. doi: 10.7554/eLife.07432. PMID: 26258880

Actin polymerization is stimulated by actin cross-linking protein palladin. Gurung R, Yadav R, Brungardt JG, Orlova A, Egelman EH, Beck MR. Biochem J. 2016 Feb 15;473(4):383-96. doi: 10.1042/BJ20151050. Epub 2015 Nov 25. PMID: 26607837

Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons. Krishnaswami SR, Grindberg RV, Novotny M, Venepally P, Lacar B, Bhutani K, Linker SB, Pham S, Erwin JA, Miller JA, Hodge R, McCarthy JK, Kelder M, McCorrison J, Aevermann BD, Fuertes FD, Scheuermann RH, Lee J, Lein ES, Schork N, McConnell MJ, Gage FH, Lasken RS. Nat Protoc. 2016 Mar;11(3):499-524. doi: 10.1038/nprot.2016.015. Epub 2016 Feb 18. PMID: 26890679

Echocardiographic Ischemic Memory Imaging Through Complement-Mediated Vascular Adhesion of Phosphatidylserine-Containing Microbubbles. Mott B, Packwood W, Xie A, Belcik JT, Taylor RP, Zhao Y, Davidson BP, Lindner JR. JACC Cardiovasc Imaging. 2016 Jun 10. pii: S1936-878X(16)30244-3. doi: 10.1016/j.jcmg.2015.11.031. PMID: 27318722

Molecular Mechanism of Mot1, a TATA-Binding Protein (TBP)-DNA Dissociating Enzyme. Viswanathan R, True JD, Auble DT. J Biol Chem. 2016 Jun 2. pii: jbc.M116.730366. PMID: 27255709

The Mot1 ATPase and Spt16 Histone Chaperone Co-Regulate Transcription through Preinitiation Complex Assembly and Nucleosome Organization. True JD, Muldoon JJ, Carver MN, Poorey K, Shetty SJ, Bekiranov S, Auble DT.J Biol Chem. 2016 May 16. pii: jbc.M116.735134. PMID: 27226635

Differential Binding Partners of the Mis18α/β YIPPEE Domains Regulate Mis18 Complex Recruitment to Centromeres. Stellfox ME, Nardi IK, Knippler CM, Foltz DR. Cell Rep. 2016 May 25. pii: S2211-1247(16)30557-5. doi: 10.1016/j.celrep.2016.05.004. PMID: 27239045

Classical Genetics with Saccharomyces cerevisiae. Amberg DC, Burke DJ. Cold Spring Harb Protoc. 2016 May 2;2016(5):pdb.top077628. doi: 10.1101/pdb.top077628. PMID: 27140921

Cas9-chromatin binding information enables more accurate CRISPR off-target prediction. Singh R, Kuscu C, Quinlan A, Qi Y, Adli M. Nucleic Acids Res. 2015 Oct 15;43(18):e118. doi: 10.1093/nar/gkv575. Epub 2015 Jun 1. PMID: 26032770

Structure of a Chaperone-Usher Pilus Reveals the Molecular Basis of Rod Uncoiling. Hospenthal MK, Redzej A, Dodson K, Ukleja M, Frenz B, Rodrigues C, Hultgren SJ, DiMaio F, Egelman EH, Waksman G. Cell. 2016 Jan 14;164(1-2):269-78. doi: 10.1016/j.cell.2015.11.049. Epub 2015 Dec 24. PMID: 26724865

Assembly-driven activation of the AIM2 foreign-dsDNA sensor provides a polymerization template for downstream ASC. Morrone SR, Matyszewski M, Yu X, Delannoy M, Egelman EH, Sohn J. Nat Commun. 2015 Jul 22;6:7827. doi: 10.1038/ncomms8827. PMID: 26197926

Biogenesis and Function of Transfer RNA-Related Fragments (tRFs). Kumar P, Kuscu C, Dutta A. Trends Biochem Sci. 2016 Jun 1. pii: S0968-0004(16)30032-9. doi: 10.1016/j.tibs.2016.05.004. Review. PMID: 27263052

A Pro-metastatic tRNA Pathway. Kuscu C, Dutta A. Cell. 2016 Jun 2;165(6):1314-5. doi: 10.1016/j.cell.2016.05.066. PMID: 27259143

Tgif1 and Tgif2 Regulate Axial Patterning in Mouse. Melhuish TA, Taniguchi K, Wotton D. PLoS One. 2016 May 17;11(5):e0155837. doi: 10.1371/journal.pone.0155837. eCollection 2016. PMID: 27187787

A CREB1-TGFβ2 self-sustaining loop in glioblastoma. Wotton D. Cancer Discov. 2014 Oct;4(10):1123-5. doi: 10.1158/2159-8290.CD-14-0861. PMID: 25274684  

The Mot1 ATPase and Spt16 Histone Chaperone Co-Regulate Transcription through Preinitiation Complex Assembly and Nucleosome Organization. True JD, Muldoon JJ, Carver MN, Poorey K, Shetty SJ, Bekiranov S, Auble DT. J Biol Chem. 2016 May 16. pii: jbc.M116.735134. PMID: 27226635

Activation of the pluripotency factor OCT4 in smooth muscle cells is atheroprotective. Cherepanova OA, Gomez D, Shankman LS, Swiatlowska P, Williams J, Sarmento OF, Alencar GF, Hess DL, Bevard MH, Greene ES, Murgai M, Turner SD, Geng YJ, Bekiranov S, Connelly JJ, Tomilin A, Owens GK. Nat Med. 2016 May 16. doi: 10.1038/nm.4109.  PMID: 27183216

Systems Analysis of Adaptive Responses to MAP Kinase Pathway Blockade in BRAF Mutant Melanoma. Capaldo BJ, Roller D, Axelrod MJ, Koeppel AF, Petricoin EF, Slingluff CL Jr, Weber MJ, Mackey AJ, Gioeli D, Bekiranov S. PLoS One. 2015 Sep 25;10(9):e0138210. doi: 10.1371/journal.pone.0138210. eCollection 2015. PMID: 26405815

MCM8-9 complex promotes resection of double-strand break ends by MRE11-RAD50-NBS1 complex. Lee KY, Im JS, Shibata E, Park J, Handa N, Kowalczykowski SC, Dutta A. Nat Commun. 2015 Jul 28;6:7744. doi: 10.1038/ncomms8744. PMID: 26215093  

Nuclear RNA-seq of single neurons reveals molecular signatures of activation. Lacar B, Linker SB, Jaeger BN, Krishnaswami S, Barron J, Kelder M, Parylak S, Paquola A, Venepally P, Novotny M, O’Connor C, Fitzpatrick C, Erwin J, Hsu JY, Husband D, McConnell MJ, Lasken R, Gage FH. Nat Commun. 2016 Apr 19;7:11022. doi: 10.1038/ncomms11022. PMID: 27090946

RNA Polymerase I and Fob1 contributions to transcriptional silencing at the yeast rDNA locus. Buck SW, Maqani N, Matecic M, Hontz RD, Fine RD, Li M, Smith JS. Nucleic Acids Res. 2016 Apr 8. pii: gkw212. PMID: 27060141  

Centromeres of a Different CAL-ibre. Zasadzińska E, Foltz DR. Dev Cell. 2016 Apr 18;37(2):105-6. doi: 10.1016/j.devcel.2016.04.006. PMID: 27093076

Ethanolamine Signaling Promotes Salmonella Niche Recognition and Adaptation during Infection. Anderson CJ, Clark DE, Adli M, Kendall MM. PLoS Pathog. 2015 Nov 13;11(11):e1005278. doi: 10.1371/journal.ppat.1005278. eCollection 2015 Nov. Erratum in: PLoS Pathog. 2015 Dec;11(12):e1005365.  PMID: 26565973

Harbom LJ, Chronister WD, McConnell MJ. Single neuron transcriptome analysis can reveal more than cell type classification: Does it matter if every neuron is unique? Bioessays. 2016 Feb;38(2):157-61. doi: 10.1002/bies.201500097. Epub 2016 Jan 8. PubMed PMID: 26749010.

Lacar, B, Linker, S.B., Jaeger, B.N., Krishnaswami, S., Barron, J., Kelder, M.S., Parylak, S., Paquola, A., Venepally, P., Novotny, M., O’Connor, C., Fitzpatrick, C., Erwin, J., Hsu, J.Y., Husband, D. McConnell, M.J., Lasken, R. and F.H. Gage. (2016). Nuclear RNA-seq of Single Neurons Reveals Signatures of Activation. Nature Communications, in press.

Song S, Miranda CJ, Braun L, Meyer K, Frakes AE, Ferraiuolo L, Likhite S, Bevan AK, Foust KD, McConnell MJ, Walker CM, Kaspar BK. Major histocompatibility complex class I molecules protect motor neurons from astrocyte-induced toxicity in amyotrophic lateral sclerosis. Nat Med. 2016 Feb 29;PubMed PMID: 26928464.

Krishnaswami SR, Grindberg RV, Novotny M, Venepally P, Lacar B, Bhutani K, Linker SB, Pham S, Erwin JA, Miller JA, Hodge R, McCarthy JK, Kelder M, McCorrison J, Aevermann BD, Fuertes FD, Scheuermann RH, Lee J, Lein ES, Schork N, McConnell MJ, Gage FH, Lasken RS. Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons. Nat Protoc. 2016 Mar;11(3):499-524. PubMed PMID: 26890679.

Sharlow, E., Leimgruber, S., Lira, A., McConnell, MJ, Norambuena, A., Bloom, G., Epperly, M., Greenberger, J., Lazo, J.S.  A small molecule screen exposes mTOR signaling pathway involvement in radiation-induced apoptosis.  ACS Chem Biol.  2016.  Mar 14 (Epub). PubMed PMID: 26938669

The human SKA complex drives the metaphase-anaphase cell cycle transition by recruiting protein phosphatase 1 to kinetochores. Sivakumar S, Janczyk PŁ, Qu Q, Brautigam CA, Stukenberg PT, Yu H, Gorbsky GJ. Elife. 2016 Mar 16;5. pii: e12902. doi: 10.7554/eLife.12902. PMID: 26981768

Production of Extrachromosomal MicroDNAs Is Linked to Mismatch Repair Pathways and Transcriptional Activity. Dillon LW, Kumar P, Shibata Y, Wang YH, Willcox S, Griffith JD, Pommier Y, Takeda S, Dutta A. Cell Rep. 2015 Jun 23;11(11):1749-59. doi: 10.1016/j.celrep.2015.05.020. Epub 2015 Jun 4. PMID: 26051933

The lncRNA DRAIC/PCAT29 Locus Constitutes a Tumor-Suppressive Nexus. Sakurai K, Reon BJ, Anaya J, Dutta A. Mol Cancer Res. 2015 May;13(5):828-38. doi: 10.1158/1541-7786.MCR-15-0016-T. Epub 2015 Feb 20. PMID: 25700553

The Current Revolution in Cryo-EM. Egelman EH. Biophys J. 2016 Mar 8;110(5):1008-12. doi: 10.1016/j.bpj.2016.02.001. Review. No abstract available.  PMID: 26958874

CK2α’ Drives Lung Cancer Metastasis by Targeting BRMS1 Nuclear Export and Degradation. Liu Y, Amin EB, Mayo MW, Chudgar NP, Bucciarelli PR, Kadota K, Adusumilli PS, Jones DR. Cancer Res. 2016 Mar 15. pii: canres.2888.2015. PMID: 26980766

Finding Protein and Nucleotide Similarities with FASTA. Pearson WR. Curr Protoc Bioinformatics. 2016 Mar 24;53:3.9.1-3.9.25. doi: 10.1002/0471250953.bi0309s53. PMID: 27010337

Cytotoxic mechanisms of immunotherapy: Harnessing complement in the action of anti-tumor monoclonal antibodies. Taylor RP, Lindorfer MA. Semin Immunol. 2016 Mar 18. pii: S1044-5323(16)00010-5. doi: 10.1016/j.smim.2016.03.003. Review. PMID: 27009480

Production of Extrachromosomal MicroDNAs Is Linked to Mismatch Repair Pathways and Transcriptional Activity. Dillon LW, Kumar P, Shibata Y, Wang YH, Willcox S, Griffith JD, Pommier Y, Takeda S, Dutta A. Cell Rep. 2015 Jun 23;11(11):1749-59. doi: 10.1016/j.celrep.2015.05.020. Epub 2015 Jun 4. PMID: 26051933

DNA Replication Dynamics of the GGGGCC Repeat of the C9orf72 Gene. Thys RG, Wang YH. J Biol Chem. 2015 Nov 27;290(48):28953-62. doi: 10.1074/jbc.M115.660324. Epub 2015 Oct 13. PMID: 26463209

Licensing of Centromeric Chromatin Assembly through the Mis18α-Mis18β Heterotetramer. Nardi IK, Zasadzińska E, Stellfox ME, Knippler CM, Foltz DR. Mol Cell. 2016 Mar 3;61(5):774-87. doi: 10.1016/j.molcel.2016.02.014. PMID: 26942680

Formaldehyde crosslinking: a tool for the study of chromatin complexes. Hoffman EA, Frey BL, Smith LM, Auble DT. J Biol Chem. 2015 Oct 30;290(44):26404-11. doi: 10.1074/jbc.R115.651679. Epub 2015 Sep 9. Review. PMID: 26354429

Degree of recruitment of DOT1L to MLL-AF9 defines level of H3K79 Di- and tri-methylation on target genes and transformation potential. Kuntimaddi A, Achille NJ, Thorpe J, Lokken AA, Singh R, Hemenway CS, Adli M, Zeleznik-Le NJ, Bushweller JH. Cell Rep. 2015 May 5;11(5):808-20. doi: 10.1016/j.celrep.2015.04.004. Epub 2015 Apr 23. PMID: 25921540

Biological Processes Discovered by High-Throughput Sequencing. Reon BJ, Dutta A. Am J Pathol. 2016 Jan 29. pii: S0002-9440(16)00006-7. doi: 10.1016/j.ajpath.2015.10.033. Review. PMID: 26828742

Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons. Krishnaswami SR, Grindberg RV, Novotny M, Venepally P, Lacar B, Bhutani K, Linker SB, Pham S, Erwin JA, Miller JA, Hodge R, McCarthy JK, Kelder M, McCorrison J, Aevermann BD, Fuertes FD, Scheuermann RH, Lee J, Lein ES, Schork N, McConnell MJ, Gage FH, Lasken RS. Nat Protoc. 2016 Mar;11(3):499-524. doi: 10.1038/nprot.2016.015. Epub 2016 Feb 18. PMID: 26890679

Major histocompatibility complex class I molecules protect motor neurons from astrocyte-induced toxicity in amyotrophic lateral sclerosis. Song S, Miranda CJ, Braun L, Meyer K, Frakes AE, Ferraiuolo L, Likhite S, Bevan AK, Foust KD, McConnell MJ, Walker CM, Kaspar BK. Nat Med. 2016 Feb 29. doi: 10.1038/nm.4052. PMID: 26928464

Biophysical Journal Special Issue: Focus on Cryo-EM. Egelman EH, Engel A. Biophys J. 2016 Feb 23;110(4):E01. doi: 10.1016/j.bpj.2016.01.025. No abstract available. PMID: 26910436

Structure and assembly of the mouse ASC inflammasome by combined NMR spectroscopy and cryo-electron microscopy. Sborgi L, Ravotti F, Dandey VP, Dick MS, Mazur A, Reckel S, Chami M, Scherer S, Huber M, Böckmann A, Egelman EH, Stahlberg H, Broz P, Meier BH, Hiller S. Proc Natl Acad Sci U S A. 2015 Oct 27;112(43):13237-42. doi: 10.1073/pnas.1507579112. Epub 2015 Oct 13. PMID: 26464513

Most partial domains in proteins are alignment and annotation artifacts. Triant DA, Pearson WR. Genome Biol. 2015 May 15;16:99. doi: 10.1186/s13059-015-0656-7. PMID: 25976240

Epigenetic States of nephron progenitors and epithelial differentiation. Adli M, Parlak M, Li Y, El-Dahr SS. J Cell Biochem. 2015 Jun;116(6):893-902. doi: 10.1002/jcb.25048. Review. PMID: 25560433

Structure of a Chaperone-Usher Pilus Reveals the Molecular Basis of Rod Uncoiling. Hospenthal MK, Redzej A, Dodson K, Ukleja M, Frenz B, Rodrigues C, Hultgren SJ, DiMaio F, Egelman EH, Waksman G. Cell. 2016 Jan 14;164(1-2):269-78. doi: 10.1016/j.cell.2015.11.049. Epub 2015 Dec 24. PMID: 26724865

Single neuron transcriptome analysis can reveal more than cell type classification: Does it matter if every neuron is unique? Harbom LJ, Chronister WD, McConnell MJ. Bioessays. 2016 Feb;38(2):157-61. doi: 10.1002/bies.201500097. Epub 2016 Jan 8. PMID: 26749010

The distinct functions of CENP-C and CENP-T/W in centromere propagation and function in Xenopus egg extracts. Krizaic I, Williams SJ, Sánchez P, Rodríguez-Corsino M, Stukenberg PT, Losada A. Nucleus. 2015;6(2):133-43. doi: 10.1080/19491034.2014.1003509. Epub 2015 Jan 8. PMID: 25569378