Millard and Muriel Jacobs Genetics and Genomics Laboratory
Publications
The following publications report experiments and analyses performed at, or facilitated by, the Millard and Muriel Jacobs Genetics and Genomics Laboratory.

  • Laso-Perez R, Wu F, Cremiere A, Speth DR, Magyar JS, Zhao K, Krupovic M, Orphan VJ. Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome. Nat Microbiol. 2023 Feb;8(2):231-245.

  • Hutchins EJ, Gandhi S, Chacon J, Piacentino M, Bronner ME. RNA-binding protein Elavl1/HuR is required for maintenance of cranial neural crest specification. Elife. 2022 Oct 3;11:e63600.

  • Zhou W, Gao F, Romero-Wolf M, Jo S, Rothenberg EV. Single-cell deletion analyses show control of pro-T cell developmental speed and pathways by Tcf7, Spi1, Gata3, Bcl11a, Erg, and Bcl11b. Sci Immunol. 2022 May 20;7(71):eabm1920.

  • Wu F, Speth DR, Philosof A, Cremiere A, Narayanan A, Barco RA, Connon SA, Amend JP, Antoshechkin IA, Orphan VJ. Unique mobile elements and scalable gene flow at the prokaryote-eukaryote boundary revealed by circularized Asgard archaea genomes. Nat Microbiol. 2022 Feb;7(2):200-212.

  • Wittmann, B.J., Johnston, K.E., Almhjell, P.J., Arnold, F.H. evSeq: Cost-Effective Amplicon Sequencing of Every Variant in a Protein Library. ACS Synthetic Biology. 11, 1313-1324 (2022).

  • Williams RM, Lukoseviciute M, Sauka-Spengler T, Bronner ME. Single-cell atlas of early chick development reveals gradual segregation of neural crest lineage from the neural plate border during neurulation. Elife. 2022 Jan 28;11:e74464.

  • Bruckner A, Badroos JM, Learsch RW, Yousefelahiyeh M, Kitchen SA, Parker J. Evolutionary assembly of cooperating cell types in an animal chemical defense system. Cell. 2021 Dec 9;184(25):6138-6156.e28.

  • Chen P, Luo Y, Aravin AA. RDC complex executes a dynamic piRNA program during Drosophila spermatogenesis to safeguard male fertility. PLoS Genet. 2021 Sep 2;17(9):e1009591.

  • Li M, Yang T, Bui M, Gamez S, Wise T, Kandul NP, Liu J, Alcantara L, Lee H, Edula JR, Raban R, Zhan Y, Wang Y, DeBeaubien N, Chen J, Sanchez C HM, Bennett JB, Antoshechkin I, Montell C, Marshall JM, Akbari OS. Suppressing mosquito populations with precision guided sterile males. Nat Commun. 2021 Sep 10;12(1):5374.

  • Hosokawa H, Koizumi M, Masuhara K, Romero-Wolf M, Tanaka T, Nakayama T, Rothenberg EV. Stage-specific action of Runx1 and GATA3 controls silencing of PU.1 expression in mouse pro-T cells. J Exp Med. 2021 Aug 2;218(8):e20202648.

  • Chen P, Kotov AA, Godneeva BK, Bazylev SS, Olenina LV, Aravin AA. piRNA-mediated gene regulation and adaptation to sex-specific transposon expression in D. melanogaster male germline. Genes Dev. 2021 Jun;35(11-12):914-935.

  • Hutchins EJ, Piacentino ML, Bronner ME. Transcriptomic Identification of Draxin-Responsive Targets During Cranial Neural Crest EMT. Front Physiol. 2021 Feb 3;12:624037.

  • Shin B, Hosokawa H, Romero-Wolf M, Zhou W, Masuhara K, Tobin VR, Levanon D, Groner Y, Rothenberg EV. Runx1 and Runx3 drive progenitor to T-lineage transcriptome conversion in mouse T cell commitment via dynamic genomic site switching. Proc Natl Acad Sci U S A. 2021 Jan 26;118(4):e2019655118.

  • Ho MCW, Quintero-Cadena P, Sternberg PW. Genome-wide discovery of active regulatory elements and transcription factor footprints in Caenorhabditis elegans using DNase-seq. Genome Res. 2017 Oct 26.

  • Rogers AK, Situ K, Perkins EM, Toth KF. (2017) Zucchini-dependent piRNA processing is triggered by recruitment to the cytoplasmic processing machinery. Genes Dev. 2017 Sep 15;31(18):1858-1869.

  • Angeles-Albores D, Leighton DHW, Tsou T, Khaw TH, Antoshechkin I, Sternberg PW. The Caenorhabditis elegans Female-Like State: Decoupling the Transcriptomic Effects of Aging and Sperm Status. G3 (Bethesda). 2017 Sep 7;7(9):2969-2977.

  • Li F, He B, Ma X, Yu S, Bhave RR, Lentz SR, Tan K, Guzman ML, Zhao C, Xue HH. Prostaglandin E1 and Its Analog Misoprostol Inhibit Human CML Stem Cell Self-Renewal via EP4 Receptor Activation and Repression of AP-1. Cell Stem Cell. 2017 Sep 7;21(3):359-373.e5.

  • Shan Q, Zeng Z, Xing S, Li F, Hartwig SM, Gullicksrud JA, Kurup SP, Van Braeckel-Budimir N, Su Y, Martin MD, Varga SM, Taniuchi I, Harty JT, Peng W, Badovinac VP, Xue HH. The transcription factor Runx3 guards cytotoxic CD8+ effector T cells against deviation towards follicular helper T cell lineage. Nat Immunol. 2017 Aug;18(8):931-939.

  • Gullicksrud JA, Li F, Xing S, Zeng Z, Peng W, Badovinac VP, Harty JT, Xue HH. Differential Requirements for Tcf1 Long Isoforms in CD8+ and CD4+ T Cell Responses to Acute Viral Infection. J Immunol. 2017 Aug 1;199(3):911-919.

  • William J. R. Longabaugh, Weihua Zeng, Jingli A. Zhang, Hiroyuki Hosokawa, Camden S. Jansen, Long Li, Maile Romero-Wolf, Pentao Liu, Hao Yuan Kueh, Ali Mortazavi, and Ellen V. Rothenberg. Bcl11b and combinatorial resolution of cell fate in the T-cell gene regulatory network. Proc Natl Acad Sci U S A. 2017 Jun 6;114(23):5800-5807.

  • Seet CS, He C, Bethune MT, Li S, Chick B, Gschweng EH, Zhu Y, Kim K, Kohn DB, Baltimore D, Crooks GM, Montel-Hagen A. Generation of mature T cells from human hematopoietic stem and progenitor cells in artificial thymic organoids. Nat Methods. 2017 May;14(5):521-530.

  • Kurmis AA, Yang F, Welch TR, Nickols NG, Dervan PB. A Pyrrole-Imidazole Polyamide is Active against Enzalutamide-Resistant Prostate Cancer. (2017) Cancer Research. 77, 2207-2212.

  • Basta DW, Bergkessel M, Newman DK. 2017. Identification of fitness determinants during energy-limited growth arrest in Pseudomonas aeruginosa. mBio 8:e01170-17.

  • Xu Z, Xing S, Shan Q, Gullicksrud JA, Bair TB, Du Y, Liu C, Xue HH. Cutting Edge: β-Catenin-Interacting Tcf1 Isoforms Are Essential for Thymocyte Survival but Dispensable for Thymic Maturation Transitions. J Immunol. 2017 May 1;198(9):3404-3409.

  • Shin CS, Mishra P, Watrous JD, Carelli V, D'Aurelio M, Jain M, Chan DC. The glutamate/cystine xCT antiporter antagonizes glutamine metabolism and reduces nutrient flexibility. Nature Communications. 2017;8:15074

  • Xiu Y, Xue WY, Lambertz A, Leidinger M, Gibson-Corley K, Zhao C. Constitutive Activation of NIK Impairs the Self-Renewal of Hematopoietic Stem/Progenitor Cells and Induces Bone Marrow Failure. Stem Cells. 2017 Mar;35(3):777-786.

  • He B, Xing S, Chen C, Gao P, Teng L, Shan Q, Gullicksrud JA, Martin MD, Yu S, Harty JT, Badovinac VP, Tan K, Xue HH. CD8+ T Cells Utilize Highly Dynamic Enhancer Repertoires and Regulatory Circuitry in Response to Infections. Immunity. 2016 Dec 20;45(6):1341-1354.

  • Chen CK, Blanco M, Jackson C, Aznauryan E, Ollikainen N, Surka C, Chow A, Cerase A, McDonel P, Guttman M. Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing. Science. 2016 Oct 28;354(6311):468-472. PMID: 27492478

  • Shikuma NJ, Antoshechkin I, Medeiros JM, Pilhofer M, Newman DK. Stepwise metamorphosis of the tubeworm Hydroides elegans is mediated by a bacterial inducer and MAPK signaling. Proc Natl Acad Sci U S A. 2016 Sep 6;113(36):10097-102.

  • Kueh HY, Yui MA, Ng KK, Pease SS, Zhang JA, Damle SS, Freedman G, Siu S, Bernstein ID, Elowitz MB, Rothenberg EV. Asynchronous combinatorial action of four regulatory factors activates Bcl11b for T cell commitment. Nat Immunol. 2016 Aug;17(8):956-65.

  • Y. Chen, E. Stuwe, Y. Luo, M. Ninova, A. Le Thomas, E. Rozhavskaya, S. Li, S. Vempati, J. Laver, D. Patel, C. Smibert, H. Lipshitz, K. Fejes Toth and A. Aravin. Cutoff suppresses RNA polymerase II termination to ensure expression of piRNA precursors. Mol Cell. 2016 Jul 7;63(1):97-109.

  • Xing S, Li F, Zeng Z, Zhao Y, Yu S, Shan Q, Li Y, Phillips FC, Maina PK, Qi HH, Liu C, Zhu J, Pope RM, Musselman CA, Zeng C, Peng W, Xue HH. Tcf1 and Lef1 transcription factors establish CD8(+) T cell identity through intrinsic HDAC activity. Nat Immunol. 2016 Jun;17(6):695-703.

  • Szablowski JO, Raskatov JA, Dervan PB. An HRE-binding Py-Im polyamide impairs hypoxic signaling in tumors. Mol Cancer Ther. 2016 Apr;15(4):608-17.

  • J. Hur, Y. Luo, S. Moon, M. Ninova, G. Marinov, Y. Chung and A. Aravin. Splicing-independent loading of TREX on nascent RNA is required for efficient expression of dual-strand piRNA clusters in Drosophila. Genes Dev. 2016 Apr 1;30(7):840-55.

  • Rudgalvyte M, Peltonen J, Lakso M, Nass R, Wong G. RNA-Seq reveals acute manganese exposure increases endoplasmic reticulum related and lipocalin mRNAs in Caenorhabditis elegans. J Biochem Mol Toxicol. 2016 Feb;30(2):97-105.

  • Babin BM, Bergkessel M, Sweredoski MJ, Moradian A, Hess S, Newman DK, Tirrell DA. SutA is a bacterial transcription factor expressed during slow growth in Pseudomonas aeruginosa. Proc Natl Acad Sci U S A. 2016 Feb 2;113(5):E597-605.

  • Hargrove AE, Martinez TF, Hare AA, Kurmis AA, Phillips JW, Sud S, Pienta KJ, Dervan PB. Tumor Repression of VCaP Xenografts by a Pyrrole-Imidazole Polyamide. PLoS One. 2015 Nov 16;10(11):e0143161.

  • Costa KC, Bergkessel M, Saunders S, Korlach J, Newman DK. Enzymatic Degradation of Phenazines Can Generate Energy and Protect Sensitive Organisms from Toxicity. MBio. 2015 Oct 27;6(6):e01520-15.

  • Lin Y, Sohn CH, Dalal CK, Cai L, Elowitz MB. Combinatorial gene regulation by modulation of relative pulse timing. Nature. 2015 Nov 5;527(7576):54-8.

  • Choi YS, Gullicksrud JA, Xing S, Zeng Z, Shan Q, Li F, Love PE, Peng W, Xue HH, Crotty S. LEF-1 and TCF-1 orchestrate T(FH) differentiation by regulating differentiation circuits upstream of the transcriptional repressor Bcl6. Nat Immunol. 2015 Sep;16(9):980-90.

  • S. Manakov, D. Pezic, G. Marinov, W. Pastor, R. Sachidanandam and A. Aravin. MIWI2 and MILI have differential effects on piRNA biogenesis and DNA methylation. Cell Rep. 2015 Aug 25;12(8):1234-43.

  • Kreamer NN, Costa F, Newman DK. The ferrous iron-responsive BqsRS two-component system activates genes that promote cationic stress tolerance. MBio. 2015 Feb 24;6(2):e02549.

  • Yihan Lin, Chang Ho Sohn, Chiraj K. Dalal, Long Cai & Michael B. Elowitz, Combinatorial gene regulation by modulation of relative pulse timing. Nature 527, 54-58 (05 November 2015).

  • Dillman AR, Macchietto M, Porter CF, Rogers A, Williams B, Antoshechkin I, Lee MM, Goodwin Z, Lu X, Lewis EE, Goodrich-Blair H, Stock SP, Adams BJ, Sternberg PW, Mortazavi A. Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks. Genome Biol. 2015 Sep 21;16(1):200.

  • Mehta A, Mann M, Zhao JL, Marinov GK, Majumdar D, Garcia-Flores Y, Du X, Erikci E, Chowdhury K, Baltimore D. The microRNA-212/132 cluster regulates B cell development by targeting Sox4. J Exp Med. 2015 Sep 14. pii: jem.20150489.

  • Manakov SA, Pezic D, Marinov GK, Pastor WA, Sachidanandam R, Aravin AA. MIWI2 and MILI Have Differential Effects on piRNA Biogenesis and DNA Methylation. Cell Rep. 2015 Aug 25;12(8):1234-43. doi: 10.1016/j.celrep.2015.07.036.

  • Webster A, Li S, Hur JK, Wachsmuth M, Bois JS, Perkins EM, Patel DJ, Aravin AA. Aub and Ago3 Are Recruited to Nuage through Two Mechanisms to Form a Ping-Pong Complex Assembled by Krimper. Mol Cell. 2015 Aug 20;59(4):564-75. doi: 10.1016/j.molcel.2015.07.017.

  • Mehta A, Zhao JL, Sinha N, Marinov GK, Mann M, Kowalczyk MS, Galimidi RP, Du X, Erikci E, Regev A, Chowdhury K, Baltimore D. The MicroRNA-132 and MicroRNA-212 Cluster Regulates Hematopoietic Stem Cell Maintenance and Survival with Age by Buffering FOXO3 Expression. Immunity. 2015 Jun 16;42(6):1021-32. doi: 10.1016/j.immuni.2015.05.017.

  • McHugh CA, Chen CK, Chow A, Surka CF, Tran C, McDonel P, Pandya-Jones A, Blanco M, Burghard C, Moradian A, Sweredoski MJ, Shishkin AA, Su J, Lander ES, Hess S, Plath K, Guttman M. The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature. 2015 May 14;521(7551):232-6. doi: 10.1038/nature14443.

  • Schwarz EM, Hu Y, Antoshechkin I, Miller MM, Sternberg PW, Aroian RV. The genome and transcriptome of the zoonotic hookworm Ancylostoma ceylanicum identify infection-specific gene families. Nat Genet. 2015 Apr;47(4):416-22. doi: 10.1038/ng.3237.

  • Champhekar A, Damle SS, Freedman G, Carotta S, Nutt SL, Rothenberg EV. Regulation of early T-lineage gene expression and developmental progression by the progenitor cell transcription factor PU.1. Genes Dev. 2015 Apr 15;29(8):832-48. doi: 10.1101/gad.259879.115.

  • Shishkin AA, Giannoukos G, Kucukural A, Ciulla D, Busby M, Surka C, Chen J, Bhattacharyya RP, Rudy RF, Patel MM, Novod N, Hung DT, Gnirke A, Garber M, Guttman M, Livny J. Simultaneous generation of many RNA-seq libraries in a single reaction. Nat Methods. 2015 Apr;12(4):323-5. doi: 10.1038/nmeth.3313.

  • Smalley MD, Marinov GK, Bertani LE, DeSalvo G. Genome Sequence of Magnetospirillum magnetotacticum Strain MS-1. Genome Announc. 2015 Apr 2;3(2). pii: e00233-15. doi: 10.1128/genomeA.00233-15.

  • Pulsipher A, Griffin ME, Stone SE, Hsieh-Wilson LC. Long-lived engineering of glycans to direct stem cell fate. Angew Chem Int Ed Engl. 2015 Jan 26;54(5):1466-70. doi: 10.1002/anie.201409258.

  • Kim DH, Marinov GK, Pepke S, Singer ZS, He P, Williams B, Schroth GP, Elowitz MB, Wold BJ. Single-cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming. Cell Stem Cell. 2015 Jan 8;16(1):88-101. doi: 10.1016/j.stem.2014.11.005.

  • Matho MH, de Val N, Miller GM, Brown J, Schlossman A, Meng X, Crotty S, Peters B, Xiang Y, Hsieh-Wilson LC, Ward AB, Zajonc DM. Murine anti-vaccinia virus D8 antibodies target different epitopes and differ in their ability to block D8 binding to CS-E. PLoS Pathog. 2014 Dec 4;10(12):e1004495. doi: 10.1371/journal.ppat.1004495. eCollection 2014.

  • Abelin AC, Marinov GK, Williams BA, McCue K, Wold BJ. A ratiometric-based measure of gene co-expression. BMC Bioinformatics. 2014 Nov 20;15:331. doi: 10.1186/1471-2105-15-331.

  • Scripture-Adams DD, Damle SS, Li L, Elihu KJ, Qin S, Arias AM, Butler RR 3rd, Champhekar A, Zhang JA, Rothenberg EV. GATA-3 Dose-Dependent Checkpoints in Early T Cell Commitment. J Immunol. 2014 Oct 1;193(7):3470-91.

  • Le Thomas A, Marinov GK, Aravin AA. A transgenerational process defines piRNA biogenesis in Drosophila virilis. Cell Rep. 2014 Sep 25;8(6):1617-23. doi: 10.1016/j.celrep.2014.08.013.

  • Le Thomas A, Stuwe E, Li S, Du J, Marinov G, Rozhkov N, Chen YC, Luo Y, Sachidanandam R, Toth KF, Patel D, Aravin AA. Transgenerationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing. Genes Dev. 2014 Aug 1;28(15):1667-80. doi: 10.1101/gad.245514.114.

  • Ma L, Kim J, Hatzenpichler R, Karymov MA, Hubert N, Hanan IM, Chang EB, Ismagilov RF. Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project's Most Wanted taxa. Proc Natl Acad Sci U S A. 2014 Jul 8;111(27):9768-73. doi: 10.1073/pnas.1404753111.

  • Pezic D, Manakov SA, Sachidanandam R, Aravin AA. piRNA pathway targets active LINE1 elements to establish the repressive H3K9me3 mark in germ cells. Genes Dev. 2014 Jul 1;28(13):1410-28. doi: 10.1101/gad.240895.114.

  • Gasper WC, Marinov GK, Pauli-Behn F, Scott MT, Newberry K, DeSalvo G, Ou S, Myers RM, Vielmetter J, Wold BJ. Fully automated high-throughput chromatin immunoprecipitation for ChIP-seq: identifying ChIP-quality p300 monoclonal antibodies. Sci Rep. 2014 Jun 12;4:5152. doi: 10.1038/srep05152.

  • Barsi JC, Tu Q, Davidson EH. General approach for in vivo recovery of cell type-specific effector gene sets. Genome Res. 2014 May;24(5):860-8.

  • Tan FE, Elowitz MB. Brf1 posttranscriptionally regulates pluripotency and differentiation responses downstream of Erk MAP kinase. Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):E1740-8.

  • Marinov GK, Williams BA, McCue K, Schroth GP, Gertz J, Myers RM, Wold BJ. From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing. Genome Res. 2014 Mar;24(3):496-510. doi: 10.1101/gr.161034.113.

  • Kang JS, Meier JL, Dervan PB. Design of sequence-specific DNA binding molecules for DNA methyltransferase inhibition. J Am Chem Soc. 2014 Mar 5;136(9):3687-94.

  • Aarnio V, Heikkinen L, Peltonen J, Goldsteins G, Lakso M, Wong G. Transcriptional profiling reveals differential expression of a neuropeptide-like protein and pseudogenes in aryl hydrocarbon receptor-1 mutant Caenorhabditis elegans. Comp Biochem Physiol Part D Genomics Proteomics. 2014 Mar;9:40-8. doi: 10.1016/j.cbd.2013.12.001. Epub 2014 Jan 2.

  • Simões-Costa M, Tan-Cabugao J, Antoshechkin I, Sauka-Spengler T, Bronner ME. Transcriptome analysis reveals novel players in the cranial neural crest gene regulatory network. Genome Res. 2014 Feb;24(2):281-90.

  • Matson EG, Rosenthal AZ, Zhang X, Leadbetter JR. Genome-Wide Effects of Selenium and Translational Uncoupling on Transcription in the Termite Gut Symbiont Treponema primitia. 12 November 2013 mBio vol. 4 no. 6 e00869-13.

  • Beverley M. Henley, Brian A. Williams, Rahul Srinivasan, Bruce N. Cohen, Cheng Xiao, Elisha D.W. Mackey, Barbara J. Wold, Henry A. Lester, Transcriptional regulation by nicotine in dopaminergic neurons. Biochemical Pharmacology, Volume 86, Issue 8, 15 October 2013, Pages 1074-1083.

  • Adam Z. Rosenthal, Xinning Zhang, Kaitlyn S. Lucey, Elizabeth A. Ottesen, Vikas Trivedi, Harry M. T. Choi, Niles A. Pierce, and Jared R. Leadbetter. Localizing transcripts to single cells suggests an important role of uncultured deltaproteobacteria in the termite gut hydrogen economy. PNAS October 1, 2013 vol. 110 no. 40 16163-16168

  • EM Schwarz, PK Korhonen, BE Campbell, ND Young, AR Jex, A Jabbar, RS Hall, A Mondal, AC Howe, J Pell, A Hofmann, PR Boag, X-Q Zhu, TR Gregory, A Loukas, BA Williams, I Antoshechkin, CT Brown, PW Sternberg and RB Gasser. The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus. Genome Biology August 28 2013, 14:R89.

  • H Chiu, HT Schwartz, I Antoshechkin, and PW Sternberg. Transgene-free genome editing in Caenorhabditis elegans using CRISPR Cas. Genetics. August 26, 2013.

  • OS Akbari, I Antoshechkin, BA Hay, PM Ferree. Transcriptome profiling of Nasonia vitripennis testis reveals novel transcripts expressed from the selfish B chromosome, Paternal Sex Ratio. G3 July 26, 2013.

  • OS Akbari, I Antoshechkin, H Amrhein, B Williams, R Diloreto, J Sandler and BA Hay. The Developmental Transcriptome of the Mosquito Aedes aegypti, an invasive species and major arbovirus vector. G3 July 5, 2013.

  • Brown JM, Xia J, Zhuang B, Cho KS, Rogers CJ, Gama CI, Rawat M, Tully SE, Uetani N, Mason DE, Tremblay ML, Peters EC, Habuchi O, Chen DF, Hsieh-Wilson LC. A sulfated carbohydrate epitope inhibits axon regeneration after injury. Proc Natl Acad Sci U S A. 2012 Mar 27;109(13):4768-73.

  • Zhang JA, Mortazavi A, Williams BA, Wold BJ, Rothenberg EV. Dynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity. Cell. 2012 Apr 13;149(2):467-82.

  • W. Huang, P. Perez-Garcia, A. Pokhilko, A. J. Millar, I. Antoshechkin, J. L. Riechmann, P. Mas. Mapping the Core of the Arabidopsis Circadian Clock Defines the Network Structure of the Oscillator. Science 6 April 2012: Vol. 336 no. 6077 pp. 75-79.

  • Rosenthal AZ, Matson EG, Eldar A, Leadbetter JR. RNA-seq reveals cooperative metabolic interactions between two termite-gut spirochete species in co-culture. ISME J. 2011 Jul;5(7):1133-42.

  • Tai PW, Fisher-Aylor KI, Himeda CL, Smith CL, Mackenzie AP, Helterline DL, Angello JC, Welikson RE, Wold BJ, Hauschka SD. Differentiation and fiber type-specific activity of a muscle creatine kinase intronic enhancer. Skelet Muscle. 2011 Jul 7;1:25.

  • Chen S, Beeby M, Murphy GE, Leadbetter JR, Hendrixson DR, Briegel A, Li Z, Shi J, Tocheva EI, Müller A, Dobro MJ, Jensen GJ. Structural diversity of bacterial flagellar motors. EMBO J. 2011 Jun 14;30(14):2972-81

  • Rogers CJ, Clark PM, Tully SE, Abrol R, Garcia KC, Goddard WA 3rd, Hsieh-Wilson LC. Elucidating glycosaminoglycan-protein-protein interactions using carbohydrate microarray and computational approaches. Proc Natl Acad Sci U S A. 2011 Jun 14;108(24):9747-52.

  • Budd ME, Antoshechkin IA, Reis C, Wold BJ, Campbell JL. Inviability of a DNA2 deletion mutant is due to the DNA damage checkpoint. Cell Cycle. 2011 May 15;10(10):1690-8.

  • Ozdemir A, Fisher-Aylor KI, Pepke S, Samanta M, Dunipace L, McCue K, Zeng L, Ogawa N, Wold BJ, Stathopoulos A. High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation. Genome Res. 2011 Apr;21(4):566-77.

  • Ali Mortazavi, Erich M. Schwarz, Brian Williams, Lorian Schaeffer, Igor Antoshechkin, Barbara J. Wold and Paul W. Sternberg. Scaffolding a Caenorhabditis nematode genome with RNA-seq. Genome Research. 2010 Dec;20(12):1740-7.

  • Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010 May;28(5):511-5.

  • Chow J, Mazmanian SK. A pathobiont of the microbiota balances host colonization and intestinal inflammation. Cell Host Microbe. 2010 Apr 22;7(4):265-76.

  • Chen H, Vermulst M, Wang YE, Chomyn A, Prolla TA, McCaffery JM, Chan DC. Mitochondrial fusion is required for mtDNA stability in skeletal muscle and tolerance of mtDNA mutations. Cell. 2010 Apr 16;141(2):280-9.

  • Kaufmann K, Wellmer F, Muino JM, Ferrier T, Wuest SE, Kumar V, Serrano-Mislata A, Madueno F, Krajewski P, Meyerowitz EM, Angenent GC, Riechmann JL. Orchestration of floral initiation by APETALA1. Science. 2010 Apr 2;328(5974):85-9.

  • Sugimoto K, Jiao Y, Meyerowitz EM. Arabidopsis regeneration from multiple tissues occurs via a root development pathway. Dev Cell. 2010 Mar 16;18(3):463-71.

  • Nam J, Dong P, Tarpine R, Istrail S, Davidson EH. Functional cis-regulatory genomics for systems biology. Proc Natl Acad Sci U S A. 2010 Feb 23;107(8):3930-5.

  • Brian M. Zid, Aric N. Rogers, Subhash D. Katewa, Misha A. Vargas, Marysia C. Kolipinski, Tony Au Lu, Seymour Benzer and Pankaj Kapahi. (2009) 4E-BP Extends Lifespan upon Dietary Restriction by Enhancing Mitochondrial Activity in Drosophila. Cell, 139(1):149-160.

  • Katy A. Muzikar, Nicholas G. Nickols, Peter B. Dervan. (2009) Repression of DNA-binding dependent glucocorticoid receptor-mediated gene expression. Proc. Natl. Acad. Sci. USA, 106:16598-16603.

  • Baugh LR, Demodena J, Sternberg PW. (2009) RNA Pol II accumulates at promoters of growth genes during developmental arrest. Science, 324(5923):92-4.

  • Hassibi, A., Vikalo, H., Riechmann, J.L. and Hassibi, B. Real-time microarray detection. Nucleic Acids Res. 2009 Nov;37(20):e132.

  • Yuling Jiao, Jose Luis Riechmann and Elliot M. Meyerowitz (2008) Transcriptome-Wide Analysis of Uncapped mRNAs in Arabidopsis Reveals Regulation of mRNA Degradation. The Plant Cell, 20:2571-2585.

  • Wang, L., Dankert, H., Perona, P. and Anderson, D.J. (2008) A common genetic target for environmental and heritable influences on aggressiveness in Drosophila. Proc. Natl. Acad. Sci. USA 105(15):5657-5663.

  • O'Connell, R.M., Rao, D.S., Chaudhuri, A.A., Boldin, M.P., Taganov, K.D., Nicoll, J., Paquette, R.L. and Baltimore, D. (2008) Sustained expression of microRNA-155 in hematopoietic stem cells causes a myeloproliferative disorder. J. Exp. Med. 205(3):585-594.

  • Alves-Ferreira, M., Wellmer, F., Banhara, A., Kumar, V., Riechmann, J.L. and Meyerowitz, E.M. (2007) Global expression profiling applied to the analysis of Arabidopsis stamen development. Plant Physiol. 145(3):747-762.

  • Kannangara, R., Branigan, C., Liu, Y., Penfield, T., Rao, V., Mouille, G., Hofte, H., Pauly, M., Riechmann, J.L. and Broun, P. (2007) Transcription factor WIN1/SHN1 regulates cutin biosynthesis in Arabidopsis. Plant Cell 19(3):1278-1294.

  • Sieber P, Wellmer F, Gheyselinck J, Riechmann JL, Meyerowitz EM (2007). Redundancy and specialization among plant microRNAs: Role of the MIR164 family in developmental robustness. Development 134, 1051-1060.

  • O'Connell, R.M., Taganov, K.D., Boldin, M.P., Cheng, G. and Baltimore, D. (2007) MicroRNA-155 is induced during the macrophage inflammatory response. Proc. Natl. Acad. Sci. USA 104(5):1604-1609.

  • Shipp, E.L. and Hsieh-Wilson, L.C. (2007) Profiling the sulfation specificities of glycosaminoglycan interactions with growth factors and chemotactic proteins using microarrays. Chem. Biol. 14(2):195-208.

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