PAN_Publications

Oligo Synthesis (back to top)

Structural and Functional Analysis of a β2-Adrenergic Receptor Complex with GRK5.
Komolov KE, Du Y, Duc NM, Betz RM, Rodrigues JPGLM, Leib RD, Patra D, Skiniotis G, Adams CM, Dror RO, Chung KY, Kobilka BK, Benovic JL.
Cell, (2017), 169(3):407-421.e16.
Bassoon Controls Presynaptic Autophagy through Atg5.
Okerlund ND, Schneider K, Leal-Ortiz S, Montenegro-Venegas C, Kim SA, Garner LC, Gundelfinger ED, Reimer RJ, Garner CC.
Neuron, (2017), 93(4):897-913.e7.
Molecular definition of a metastatic lung cancer state reveals a targetable CD109–Janus kinase–Stat axis.
Chuang CH, Greenside PG, Rogers ZN, Brady JJ, Yang D, Ma RK, Caswell DR, Chiou SH, Winters AF, Grüner BM, Ramaswami G, Spencley AL, Kopecky KE, Sayles LC, Sweet-Cordero EA, Li JB, Kundaje A, Winslow MM.
Nat Med., (2017), 23(3):291-300.
Pseudouridine and N-6 methyladenosine modifications weaken PUF protein/RNA interactions.
Vaidyanathan PP, AlSadhan I, Merriman DK, Al-Hashimi HM, Herschlag D.
RNA, (2017), 23(5):611-618.
High-throughput precision measurement of subcellular localization in single cells.
Burns TJ, Frei AP, Gherardini PF, Bava FA, Batchelder JE, Yoshiyasu Y, Yu JM, Groziak AR, Kimmey SC, Gonzalez VD, Fantl WJ, Nolan GP.
Cytometry A., (2017), 91(2):180-189.
Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping.
Viviana I. Risca, Sarah K. Denny, Aaron F. Straight & William J. Greenleaf.
Nature, (2017), 541:237–241.
Tailored Nanoparticle Codelivery of antimiR-21 and antimiR-10b Augments Glioblastoma Cell Kill by Temozolomide: Toward a “Personalized” Anti-microRNA Therapy.
Jeyarama S. Ananta, Ramasamy Paulmurugan, and Tarik F. Massoud.
Mol. Pharmaceutics, (2016), 13(9):3164–3175.
Directed Chemical Evolution with an Outsized Genetic Code.
Krusemark CJ, Tilmans NP, Brown PO, Harbury PB.
PLoS One, (2016), 11(8):e0154765.
Engineering a microbial platform for de novo biosynthesis of diverse methylxanthines.
Maureen McKeague, Yen-Hsiang Wang, Aaron Cravens, Maung Nyan Win, Christina D. Smolke.
Metabolic Engineering, (2016), 38:191-203.
An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions.
Sengupta RN, Van Schie SN, Giambaşu G, Dai Q, Yesselman JD, York D, Piccirilli JA, Herschlag D.
RNA, (2016), 22(1):32-48.
An Arntl2-Driven Secretome Enables Lung Adenocarcinoma Metastatic Self-Sufficiency.
Brady JJ, Chuang CH, Greenside PG, Rogers ZN, Murray CW, Caswell DR, Hartmann U, Connolly AJ, Sweet-Cordero EA, Kundaje A, Winslow MM.
Cancer Cell, (2016), 29(5):697-710.
Mutant cycle analysis with modified saxitoxins reveals specific interactions critical to attaining high-affinity inhibition of hNaV1.7.
Thomas-Tran R, Du Bois J.
Proc Natl Acad Sci U S A, (2016), 113(21):5856-61.
Rational elicitation of cold-sensitive phenotypes.
Baliga C, Majhi S, Mondal K, Bhattacharjee A, VijayRaghavan K, Varadarajan R.
Proc Natl Acad Sci U S A, (2016), 113(18):E2506-15.
Supporting Role for GTPase Rab27a in Hepatitis C Virus RNA Replication through a Novel miR-122-Mediated Effect.
Chen TC, Hsieh CH, Sarnow P.
PLoS Pathog., (2015), 11(8):e1005116.
In silico investigation of FOXM1 binding and novel inhibitors in epithelial ovarian cancer.
Yi Chen, Eliza A. Ruben, Jayakumar Rajadas, Nelson N.H. Teng.
Bioorg Med Chem., (2015), 23(15):4576-82.
Complete biosynthesis of opioids in yeast.
Stephanie Galanie, Kate Thodey, Isis J. Trenchard, Maria Filsinger Interrante, Christina D. Smolke.
Science, (2015), aac9373.
Organocatalytic removal of formaldehyde adducts from RNA and DNA bases.
Saswata Karmakar, Emily M. Harcourt, David S. Hewings, Alexander F. Lovejoy, David M. Kurtz, Thomas Ehrenschwender, Luzi J. Barandun, Caroline Roost, Ash A. Alizadeh & Eric T. Kool.
Nature Chemistry, (2015), 7:752–758.
Capture, unfolding, and detection of individual tRNA molecules using a nanopore device.
Smith Andrew M, AbuShumays Robin L, Akeson Mark, Bernick David L.
Frontiers in Bioengineering and Biotechnology, (2015), 3:91.
Engineering strategies for the fermentative production of plant alkaloids in yeast.
Isis J. Trenchard, Christina D. Smolke.
Metabolic Engineering, (2015), 30:96-104.
Formulation of Anti-miR-21 and 4‑Hydroxytamoxifen Co-loaded Biodegradable Polymer Nanoparticles and Their Antiproliferative Effect on Breast Cancer Cells.
Rammohan Devulapally, Thillai V. Sekar, and Ramasamy Paulmurugan.
Mol. Pharmaceutics, (2015).
Synthetic feedback control using an RNAi-based gene-regulatory device.
Ryan J Bloom, Sally M Winkler and Christina D Smolke.
Journal of Biological Engineering, (2015), 9:5.
Elafin Reverses Pulmonary Hypertension via Caveolin-1 Dependent Bone Morphogenetic Protein Signaling.
Nickel NP, Spiekerkoetter E, Gu M, Li CG, Li H, Kaschwich M, Diebold I, Hennigs JK, Kim KY, Miyagawa K, Wang L, Cao A, Sa S, Jiang X, Stockstill RW, Nicolls MR, Zamanian RT, Bland RD, Rabinovitch M.
Am J Respir Crit Care Med., (2015).
Systematic Discovery of Xist RNA Binding Proteins.
Chu C, Zhang QC, da Rocha ST, Flynn RA, Bharadwaj M, Calabrese JM, Magnuson T, Heard E, Chang HY.
Cell, (2015), pii:S0092-8674(15)00312-8.
A system for multilocus chromosomal integration and transformation-free selection marker rescue.
Michael S. Siddiqui, Atri Choksi and Christina D. Smolke.
FEMS Yeast Research, (2014), 14(8):1171–1185.
Kinetic Mechanism at the Branchpoint between the DNA Synthesis and Editing Pathways in Individual DNA Polymerase Complexes.
Kate R. Lieberman, Joseph M. Dahl, and Hongyun Wang.
J. Am. Chem. Soc., (2014), 136(19):7117–7131.
Coupling isotachophoresis with affinity chromatography for rapid and selective purification with high column utilization, part 2: experimental study.
Shkolnikov V, Santiago JG.
Anal Chem., (2014), 86(13):6229-36.
Precise gene deletion and replacement using the CRISPR/Cas9 system in human cells.
Zheng Q, Cai X, Tan MH, Schaffert S, Arnold CP, Gong X, Chen CZ, Huang S.
Biotechniques, (2014), 57(3):115-24.
Protein-responsive ribozyme switches in eukaryotic cells.
Andrew B. Kennedy, James V. Vowles, Leo d'Espaux, and Christina D. Smolke.
Nucl. Acids Res., (2014).
A quantitative framework for the forward design of synthetic miRNA circuits.
Ryan J Bloom, Sally M Winkler & Christina D Smolke.
Nature Methods, (2014), 1548-7105.
Long noncoding RNA-mediated intrachromosomal interactions promote imprinting at the Kcnq1 locus.
He Zhang, Michael J. Zeitz, Hong Wang, Beibei Niu, Shengfang Ge, Wei Li, Jiuwei Cui, Guanjun Wang, Guanxiang Qian, Michael J. Higgins, Xianqun Fan, Andrew R. Hoffman, Ji-Fan Hu.
J. Cell Biol, (2014), 204:61-75.
Hard X-ray-induced optical luminescence via biomolecule-directed metal clusters.
Osakada Y, Pratx G, Sun C, Sakamoto M, Ahmad M, Volotskova O, Ong Q, Teranishi T, Harada Y, Xing L, Cui B.
Chem Commun (Camb), (2014), 50(27):3549-51.
Dynamics of Translocation and Substrate Binding in Individual Complexes Formed with Active Site Mutants of Φ29 DNA Polymerase.
Dahl JM, Wang H, Lazaro JM, Salas M, Lieberman KR.
J Biol Chem. (2014).
Microdroplet temperature calibration via thermal dissociation of quenched DNA oligomers.
Eric W. Hall and Gregory W. Faris.
Biomed. Opt. Express, (2014), 5:737-751.
Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes.
Jason D Buenrostro, Carlos L Araya, Lauren M Chircus, Curtis J Layton, Howard Y Chang, Michael P Snyder & William J Greenleaf.
Nature Biotechnology, (2014).
Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands.
Schreiber J, Zachary L. Wescoe ZL, Abu-Shumays R, Vivian JT, Baatar B, Karplus K, Akeson M.
Proc Natl Acad Sci USA, (2013), 110(47):18910-18915.

Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase.
Manrao EA, Derrington IM, Laszlo AH, Langford KW, Hopper MK, Gillgren N, Pavlenok M, Niederweis M, Gundlach JH.
Nature Biotechnology, (2012), 30:349-353.

Gene Expression/Bioanalyzer QC (back to top)

Exposure to Bacterial CpG DNA Protects from Airway Allergic Inflammation by Expanding Regulatory Lung Interstitial Macrophages.
Sabatel C, Radermecker C, Fievez L, Paulissen G, Chakarov S, Fernandes C, Olivier S, Toussaint M, Pirottin D, Xiao X, Quatresooz P, Sirard JC, Cataldo D, Gillet L, Bouabe H, Desmet CJ, Ginhoux F, Marichal T, Bureau F.
Immunity, (2017), 46(3):457-473.
Crebbp loss cooperates with Bcl2 over-expression to promote lymphoma in mice.
García-Ramírez I, Tadros S, González-Herrero I, Martín-Lorenzo A, Rodríguez-Hernández G, Moore D, Ruiz-Roca L, Blanco O, Alonso-López D, Rivas JL, Hartert K, Duval R, Klinkebiel D, Bast M, Vose J, Lunning M, Fu K, Greiner T, Rodrigues-Lima F, Jiménez R, Criado FJG, Cenador MBG, Brindle P, Vicente-Dueñas C, Alizadeh A, Sánchez-García I, Green MR.
Blood, (2017), 129(19):2645-2656.
Pharmacological rescue of diabetic skeletal stem cell niches.
Tevlin R, Seo EY, Marecic O, McArdle A, Tong X, Zimdahl B, Malkovskiy A, Sinha R, Gulati G, Li X, Wearda T, Morganti R, Lopez M, Ransom RC, Duldulao CR, Rodrigues M, Nguyen A, Januszyk M, Maan Z, Paik K, Yapa KS, Rajadas J, Wan DC, Gurtner GC, Snyder M, Beachy PA, Yang F, Goodman SB, Weissman IL, Chan CK, Longaker MT.
Sci Transl Med., (2017), 11;9(372).
A Quiescent Bcl11b High Stem Cell Population Is Required for Maintenance of the Mammary Gland.
Shang Cai, Tomer Kalisky, Debashis Sahoo, Piero Dalerba, Weiguo Feng, Yuan Lin, Dalong Qian, Angela Kong, Jeffrey Yu, Flora Wang, Elizabeth Y. Chen, Ferenc A. Scheeren, Angera H. Kuo, Shaheen S. Sikandar, Shigeo Hisamori, Linda J. van Weele, Diane Heiser, Sopheak Sim, Jessica Lam, Stephen Quake, Michael F. Clarke.
Cell Stem Cell, (2016), 20(2):247-260.e5.
Control of inflammation by stromal Hedgehog pathway activation restrains colitis.
Lee JJ, Rothenberg ME, Seeley ES, Zimdahl B, Kawano S, Lu WJ, Shin K, Sakata-Kato T, Chen JK, Diehn M, Clarke MF, Beachy PA.
Proc Natl Acad Sci U S A, (2016), 113(47):E7545-E7553.
Lung-resident eosinophils represent a distinct regulatory eosinophil subset.
Mesnil C, Raulier S, Paulissen G, Xiao X, Birrell MA, Pirottin D, Janss T, Starkl P, Ramery E, Henket M, Schleich FN, Radermecker M, Thielemans K, Gillet L, Thiry M, Belvisi MG, Louis R, Desmet C, Marichal T, Bureau F.
J Clin Invest., (2016), 126(9):3279-3295.
Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast.
Sandeep Venkataram, Barbara Dunn, Yuping Li, Atish Agarwala, Jessica Chang, Emily R. Ebel, Kerry Geiler-Samerotte, Lucas Hérissant, Jamie R. Blundell, Sasha F. Levy, Daniel S. Fisher, Gavin Sherlock, Dmitri A. Petrov.
Cell, (2016), 166(6):1585-1596.e22.
SGK1 regulation by miR-466g in cortical collecting duct cells.
Jacobs ME, Kathpalia PP, Chen Y, Thomas SV, Noonan EJ, Pao AC.
Am J Physiol Renal Physiol., (2016), 310(11):F1251-7.
Cyclooxygenase inhibition targets neurons to prevent early behavioural decline in Alzheimer’s disease model mice.
Woodling NS, Colas D, Wang Q, Minhas P, Panchal M, Liang X, Mhatre SD, Brown H, Ko N, Zagol-Ikapitte I, van der Hart M, Khroyan TV, Chuluun B, Priyam PG, Milne GL, Rassoulpour A, Boutaud O, Manning-Boğ AB, Heller HC, Andreasson KI.
Brain, (2016), 139(Pt 7):2063-81.
Localized JNK signaling regulates organ size during development.
Willsey HR, Zheng X, Carlos Pastor-Pareja J, Willsey AJ, Beachy PA, Xu T.
Elife, (2016), 5. pii: e11491.
Stable 5-Hydroxymethylcytosine (5hmC) Acquisition Marks Gene Activation During Chondrogenic Differentiation.
Taylor SE, Li YH, Smeriglio P, Rath M, Wong WH, Bhutani N.
J Bone Miner Res., (2016), 31(3):524-34.
CD93 Marks a Non-Quiescent Human Leukemia Stem Cell Population and Is Required for Development of MLL-Rearranged Acute Myeloid Leukemia.
Iwasaki M, Liedtke M, Gentles AJ, Cleary ML.
Cell Stem Cell, (2015), 17(4):412-21.
Microarray analysis of the in vivo response of microglia to Aβ peptides in mice with conditional deletion of the prostaglandin EP2 receptor.
Johansson JU, Woodling NS, Brown HD, Wang Q, Andreasson KI.
Genom Data, (2015), 5:268-271.
Comprehensive genomic profiles of small cell lung cancer.
George J, Lim JS, Jang SJ, Cun Y, Ozretić L, Kong G, Leenders F, Lu X, Fernández-Cuesta L, Bosco G, Müller C, Dahmen I, Jahchan NS, Park KS, Yang D, Karnezis AN, Vaka D, Torres A, Wang MS, Korbel JO, Menon R, Chun SM, Kim D, Wilkerson M, Hayes N, Engelmann D, Pützer B, Bos M, Michels S, Vlasic I, Seidel D, Pinther B, Schaub P, Becker C, Altmüller J, Yokota J, Kohno T, Iwakawa R, Tsuta K, Noguchi M, Muley T, Hoffmann H, Schnabel PA, Petersen I, Chen Y, Soltermann A, Tischler V, Choi CM, Kim YH, Massion PP, Zou Y, Jovanovic D, Kontic M, Wright GM, Russell PA, Solomon B, Koch I, Lindner M, Muscarella LA, la Torre A, Field JK, Jakopovic M, Knezevic J, Castaños-Vélez E, Roz L, Pastorino U, Brustugun OT, Lund-Iversen M, Thunnissen E, Köhler J, Schuler M, Botling J, Sandelin M, Sanchez-Cespedes M, Salvesen HB, Achter V, Lang U, Bogus M, Schneider PM, Zander T, Ansén S, Hallek M, Wolf J, Vingron M, Yatabe Y, Travis WD, Nürnberg P, Reinhardt C, Perner S, Heukamp L, Büttner R, Haas SA, Brambilla E, Peifer M, Sage J, Thomas RK.
Nature, (2015), 524(7563):47-53.
Generation and transcriptional programming of intestinal dendritic cells: essential role of retinoic acid.
R Zeng, M Bscheider, K Lahl, M Lee, and E C Butcher.
Mucosal Immunology, (2015).
Genome-wide mapping of DNA hydroxymethylation in osteoarthritic chondrocytes.
Taylor SE, Henry Li Y, Wong WH, Bhutani N.
Arthritis Rheumatol, (2015).
Early induction of a prechondrogenic population allows efficient generation of stable chondrocytes from human induced pluripotent stem cells.
Lee J, Taylor SE, Smeriglio P, Lai J, Maloney WJ, Yang F, Bhutani N.
FASEB J., (2015).
A Continuous Molecular Roadmap to iPSC Reprogramming through Progression Analysis of Single-Cell Mass Cytometry.
Eli R. Zunder, Ernesto Lujan, Yury Goltsev, Marius Wernig, Garry P. Nolan.
Cell Stem Cell, (2015), 16(3):323-337.
Tenofovir Disoproxil Fumarate: Toxicity, Toxicokinetics, and Toxicogenomics Analysis After 13 Weeks of Oral Administration in Mice.
Hanna H. Ng, Howard Stock, L. J Rausch, Deborah I. Bunin, Abraham Wang, Shirley Brill, Jason Gow and Jon C. Mirsalis.
Int J Toxicol., (2015), pii: 1091581814565669.
Identification and Specification of the Mouse Skeletal Stem Cell.
Charles K.F. Chan, Eun Young Seo, James Y. Chen, David Lo, Adrian McArdle, Rahul Sinha, Ruth Tevlin, Jun Seita, Justin Vincent-Tompkins, Taylor Wearda, Wan-Jin Lu, Kshemendra Senarath-Yapa, Michael T. Chung, Owen Marecic, Misha Tran, Kelley S. Yan, Rosalynd Upton, Graham G. Walmsley, Andrew S. Lee, Debashis Sahoo, Calvin J. Kuo, Irving L. Weissman, Michael T. Longaker.
Cell, (2015), 160(1-2):285-298.
Transcriptional programs of lymphoid tissue capillary and high endothelium reveal control mechanisms for lymphocyte homing.
Mike Lee, Helena Kiefel, Melissa D LaJevic, Matthew S Macauley, Hiroto Kawashima, Edward O'Hara, Junliang Pan, James C Paulson & Eugene C Butcher.
Nature Immunology, (2014), 15:982–995.
Global Transcriptional Profiling Reveals Distinct Functions of Thymic Stromal Subsets and Age-Related Changes during Thymic Involution.
Sanghee Ki, Daechan Park, Hilary J. Selden, Jun Seita, Haewon Chung, Jonghwan Kim, Vishwanath R. Iyer, Lauren I.R. Ehrlich.
Cell Reports, (2014), 9(1):402-415.
Prostaglandin signaling suppresses beneficial microglial function in Alzheimer’s disease models.
Jenny U. Johansson, Nathaniel S. Woodling, Qian Wang, Maharshi Panchal, Xibin Liang, Angel Trueba-Saiz, Holden D. Brown, Siddhita D. Mhatre, Taylor Loui, and Katrin I. Andreasson.
J Clin Invest., (2014).
Upregulation of CD11A on Hematopoietic Stem Cells Denotes the Loss of Long-Term Reconstitution Potential.
John W. Fathman, Nathaniel B. Fernhoff, Jun Seita, Connie Chao, Vanessa M. Scarfone, Irving L. Weissman, Matthew A. Inlay.
Stem Cell Reports, (2014), 3(5):707-715.
Suppression of Alzheimer-associated inflammation by microglial prostaglandin-E2 EP4 receptor signaling.
Woodling NS, Wang Q, Priyam PG, Larkin P, Shi J, Johansson JU, Zagol-Ikapitte I, Boutaud O, Andreasson KI.
J Neurosci., (2014), 34(17):5882-94.
An Integrated Cell Purification and Genomics Strategy Reveals Multiple Regulators of Pancreas Development.
Cecil M. Benitez, Kun Qu, Takuya Sugiyama, Philip T. Pauerstein, Yinghua Liu, Jennifer Tsai, Xueying Gu, Amar Ghodasara, H. Efsun Arda, Jiajing Zhang, Joseph D. Dekker, Haley O. Tucker, Howard Y. Chang, Seung K. Kim.
PLoS Genetics, (2014), 10(10):e1004645.
m6A RNA Modification Controls Cell Fate Transition in Mammalian Embryonic Stem Cells.
Pedro J. Batista, Benoit Molinie, Jinkai Wang, Kun Qu, Jiajing Zhang, Lingjie Li, Donna M. Bouley, Ernesto Lujan, Bahareh Haddad, Kaveh Daneshvar, Ava C. Carter, Ryan A. Flynn, Chan Zhou, Kok-Seong Lim, Peter Dedon, Marius Wernig, Alan C. Mullen, Yi Xing, Cosmas C. Giallourakis, Howard Y. Chang.
Cell Stem Cell, (2014).
Alveolar progenitor and stem cells in lung development, renewal and cancer.
Tushar J. Desai, Douglas G. Brownfield & Mark A. Krasnow.
Nature, (2014), 507:190–194.
A meta-analysis of lung cancer gene expression identifies PTK7 as a survival gene in lung adenocarcinoma.
Chen R, Khatri P, Mazur PK, Polin M, Zheng Y, Vaka D, Hoang CD, Shrager J, Xu Y, Vicent S, Butte AJ, Sweet-Cordero EA.
Cancer Res., (2014), 74(10):2892-902.
Toxoplasma Effector MAF1 Mediates Recruitment of Host Mitochondria and Impacts the Host Response.
Yaw Adomako-Ankomah, Anjali J. Shastri, Sarah E. Ewald, Moritz Treeck, Jon P. Boyle, John C. Boothroyd.
PLoS Biol, (2014), 12(4):e1001845.
mTORC1 controls the adaptive transition of quiescent stem cells from G0 to G(Alert).
Rodgers JT, King KY, Brett JO, Cromie MJ, Charville GW, Maguire KK, Brunson C, Mastey N, Liu L, Tsai CR, Goodell MA, Rando TA.
Nature, (2014), 510(7505):393-6.
Calcineurin Signaling Regulates Neural Induction through Antagonizing the BMP Pathway.
Cho A, Tang Y, Davila J, Deng S, Chen L, Miller E, Wernig M, Graef IA.
Neuron, (2014), 82(1):109-24.
Noninvasive in vivo monitoring of tissue-specific global gene expression in humans.
Winston Koh, Wenying Pan, Charles Gawad, H. Christina Fan, Geoffrey A. Kerchner, Tony Wyss-Coray, Yair J. Blumenfeld, Yasser Y. El-Sayed, and Stephen R. Quake.
PNAS, (2014).
Patient-derived xenografts of triple-negative breast cancer reproduce molecular features of patient tumors and respond to mTOR inhibition.
Zhang H, Cohen AL, Krishnakumar S, Wapnir IL, Veeriah S, Deng G, Coram MA, Piskun CM, Longacre TA, Herrler M, Frimannsson DO, Telli ML, Dirbas FM, Matin AC, Dairkee SH, Larijani B, Glinsky GV, Bild AH, Jeffrey SS.
Breast Cancer Res., (2014), 16(2):R36.
Males shorten the life span of C. elegans hermaphrodites via secreted compounds.
Maures T.J., Booth L.N., Benayoun B.A., Izrayelit Y., Schroeder F.C., Brunet A.
Science, (2014) , 343(6170):541-544.
Transcriptional response of Enterococcus faecalis to sunlight.
Sassoubre LM, Ramsey MM, Gilmore MS, Boehm AB.
J Photochem Photobiol B., (2014), 130:349-56.
Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency.
Yul W Yang, Ryan A Flynn, Yong Chen, Kun Qu, Bingbing Wan, Kevin C Wang, Ming Lei, Howard Y Chang.
ELife, (2014), 3:e02046.
Age-Related Modulation of the Effects of Obesity on Gene Expression Profiles of Mouse Bone Marrow and Epididymal Adipocytes.
Liu L.-F., Shen W.-J., Ueno M., Patel S., Azhar S., Kraemer F.B.
PLoS ONE, (2013), 8(8):e72367.
Hormonal Regulation of MicroRNA Expression in Steroid Producing Cells of the Ovary, Testis and Adrenal Gland.
Hu Z, Shen W-J, Cortez Y, Tang X, Liu L-F, et al.
PLoS ONE, (2013), 8(10):e78040.
The polyubiquitin gene Ubi-p63E is essential for male meiotic cell cycle progression and germ cell differentiation in Drosophila.
Lu C, Kim J, Fuller MT.
J Cell Sci, (2013), 126:e1.
Platelet-biased stem cells reside at the apex of the haematopoietic stem-cell hierarchy.
Alejandra Sanjuan-Pla, Iain C. Macaulay, Christina T. Jensen, Petter S. Woll, Tiago C. Luis, Adam Mead, Susan Moore, Cintia Carella, Sahoko Matsuoka, Tiphaine Bouriez Jones, Onima Chowdhury, Laura Stenson, Michael Lutteropp, Joanna C. A. Green, Raffaella Facchini, Hanane Boukarabila, Amit Grover, Adriana Gambardella, Supat Thongjuea, Joana Carrelha, Paul Tarrant, Deborah Atkinson, Sally-Ann Clark, Claus Nerlov & Sten Eirik W. Jacobsen.
Nature, (2013), 502(7470):232-236.
Targeted Disruption of Hotair Leads to Homeotic Transformation and Gene Derepression.
Lingjie Li, Bo Liu, Orly L. Wapinski, Miao-Chih Tsai, Kun Qu, Jiajing Zhang, Jeff C. Carlson, Meihong Lin, Fengqin Fang, Rajnish A. Gupta, Jill A. Helms, Howard Y. Chang.
Cell Reports, (2013), 5(1):3-12.
The human oviduct transcriptome reveals an anti-inflammatory, anti-angiogenic, secretory and matrix-stable environment during embryo transit.
A.P. Hess, S. Talbi, A.E. Hamilton, D.M. Baston-Buest, M. Nyegaard, J.C. Irwin, F. Barragan, J.S. Kruessel, A. Germeyer, L.C. Giudice.
Reproductive BioMedicine Online, (2013), 27(4):423-435.
Suppression of Inflammation with Conditional Deletion of the Prostaglandin E2 EP2 Receptor in Macrophages and Brain Microglia.
Jenny U. Johansson, Suraj Pradhan, Ludmila A. Lokteva, Nathaniel S. Woodling, Novie Ko, Holden D. Brown, Qian Wang, Christina Loh, Egle Cekanaviciute, Marion Buckwalter, Amy B. Manning-Boğ, and Katrin I. Andreasson.
The Journal of Neuroscience, (2013), 33(40):16016-16032.
Chromatin Modifications as Determinants of Muscle Stem Cell Quiescence and Chronological Aging.
Ling Liu, Tom H. Cheung, Gregory W. Charville, Bernadette Marie Ceniza Hurgo, Tripp Leavitt, Johnathan Shih, Anne Brunet, Thomas A. Rando.
Cell Reports, (2013), 4(1):189-204.
FLT3-ITDs Instruct a Myeloid Differentiation and Transformation Bias in Lymphomyeloid Multipotent Progenitors.
Adam J. Mead, Shabnam Kharazi, Deborah Atkinson, Iain Macaulay, Christian Pecquet, Stephen Loughran, Michael Lutteropp, Petter Woll, Onima Chowdhury, Sidinh Luc, Natalija Buza-Vidas, Helen Ferry, Sally-Ann Clark, Nicolas Goardon, Paresh Vyas, Stefan N. Constantinescu, Ewa Sitnicka, Claus Nerlov, Sten Eirik W. Jacobsen.
Cell Reports, (2013), 3(6):1766-1776.
Expansion of oligodendrocyte progenitor cells following SIRT1 inactivation in the adult brain.
Rafalski VA, Ho PP, Brett JO, Ucar D, Dugas JC, Pollina EA, Chow LM, Ibrahim A, Baker SJ, Barres BA, Steinman L, Brunet A. Nat
Cell Biol, (2013), 15(6):614-624.
Control of somatic tissue differentiation by the long non-coding RNA TINCR.
Markus Kretz, Zurab Siprashvili, Ci Chu, Dan E. Webster, Ashley Zehnder, Kun Qu, Carolyn S. Lee, Ross J. Flockhart, Abigail F. Groff, Jennifer Chow, Danielle Johnston, Grace E. Kim, Robert C. Spitale, Ryan A. Flynn, Grace X. Y. Zheng, Subhadra Aiyer, Arjun Raj, John L. Rinn, Howard Y. Chang, and Paul A. Khavari.
Nature, (2013), 493:231–235.
IQGAP1 scaffold-kinase interaction blockade selectively targets RAS-MAP kinase-driven tumors.
Katherine L Jameson, Pawel K Mazur, Ashley M Zehnder, Jiajing Zhang, Brian Zarnegar, Julien Sage, and Paul A Khavari.
Nature Medicine, (2013), 19:626–630.

Dicer is selectively important for the earliest stages of erythroid development.
Natalija Buza-Vidas, Valeriu B. Cismasiu, Susan Moore, Adam J. Mead, Petter S. Woll, Michael Lutteropp, Luca Melchiori, Sidinh Luc, Tiphaine Bouriez-Jones, Deborah Atkinson, Donal O'Carroll, Sten Eirik W. Jacobsen, and Claus Nerlov.
Blood, (2012), 120:2412-2416.
Gene Expression Commons: An Open Platform for Absolute Gene Expression Profiling.
Seita J, Sahoo D, Rossi DJ, Bhattacharya D, Serwold T, et al.
PLoS ONE, (2012), 7(7):e40321.
Mice lacking the β2 adrenergic receptor have a unique genetic profile before and after focal brain ischaemia.
Robin E White, Curtis Palm, Lijun Xu, Evelyn Ling, Mitchell Ginsburg, Bernie J Daigle, Ruquan Han, Andrew Patterson, Russ B Altman and Rona G Giffard.
ASN NEURO, (2012), 4(5).
Innate Immune Responses of Drosophila melanogaster Are Altered by Spaceflight.
Oana Marcu, Matthew P. Lera, Max E. Sanchez, Edina Levic, Laura A. Higgins, Alena Shmygelska, Thomas F. Fahlen, Helen Nichol, Sharmila Bhattacharya.
PLoS One, (2011), 6(1):e15361.

Real-Time PCR (back to top)

DNA Barcoding for Fractured Reservoir Analysis – An Initial Investigation.
Yuran ZHANG, Zhirui ZENG, Kewen LI, Roland N. HORNE.
Stanford University, (2017).
Potential biomarkers to follow the progression and treatment response of Huntington’s disease.
Disatnik MH, Joshi AU, Saw NL, Shamloo M, Leavitt BR, Qi X, Mochly-Rosen D.
J Exp Med., (2016), 213(12):2655-2669.
Replication initiator DnaA binds at the Caulobacter centromere and enables chromosome segregation.
Paola E. Mera, Virginia S. Kalogeraki, and Lucy Shapiro.
PNAS, (2014), 111(45):16100-16105.
Adaptive human CDKAL1 variants underlie hormonal response variations at the enteroinsular axis.
Chia Lin Chang, James J Cai, Shang Yu Huang, Po Jen Cheng, Ho Yen Chueh, Sheau Yu Teddy Hsu.
PLoS One, (2014), 15;9(9):e105410.
Identification of metabolic modifiers that underlie phenotypic variations in energy-balance regulation.
Chang CL, Cai JJ, Cheng PJ, Chueh HY, Hsu SY.
Diabetes, (2011), 60(3):726-734.

Pyrosequencing (back to top)

Zinc deficiency enhanced inflammatory response by increasing immune cell activation and inducing IL6 promoter demethylation.
Wong CP, Rinaldi NA, Ho E.
Mol Nutr Food Res., (2015).
Pyrosequencing: applicability for studying DNA damage-induced mutagenesis.
Irina G. Minko, Lauriel F.Earley, Kimberly E.Larlee, Ying-Chih Lin and R.Stephen Lloyd.
Environmental and Molecular Mutagenesis, (2014), 55(8):601–608.
Maternal bias and escape from X chromosome imprinting in the midgestation mouse placenta.
Elizabeth H. Finn, Cheryl L. Smith, Jesse Rodriguez, Arend Sidow, Julie C. Baker.
Developmental Biology, (2014), 390(1):80-92.
Investigation of HOXA9 promoter methylation as a biomarker to distinguish oral cancer patients at low risk of neck metastasis.
Uchida K, Veeramachaneni R, Huey B, Bhattacharya A, Schmidt BL, Albertson DG.
BMC Cancer, (2014), 14:353.
Effects of Sulforaphane and 3,3′-Diindolylmethane on Genome-Wide Promoter Methylation in Normal Prostate Epithelial Cells and Prostate Cancer Cell.
Carmen P. Wong, Anna Hsu, Alex Buchanan, Zoraya Palomera-Sanchez, Laura M. Beaver, E. Andres Houseman, David E. Williams, Roderick H. Dashwood, Emily Ho.
PLoS One, (2014), 9:e86787.
Coronary Heart Disease-Associated Variation in TCF21 Disrupts a miR-224 Binding Site and miRNA-Mediated Regulation.
Miller CL, Haas U, Diaz R, Leeper NJ, Kundu RK, et al.
PLoS Genet, (2014), 10(3):e1004263.
Epigenetic inactivation of endothelin-2 and endothelin-3 in colon cancer.
Wang, R., Löhr, C. V., Fischer, K., Dashwood, W. M., Greenwood, J. A., Ho, E., Williams, D. E., Ashktorab, H., Dashwood, M. R. and Dashwood, R. H.
Int. J. Cancer, (2013), 132:1004–1012.
Disease-Related Growth Factor and Embryonic Signaling Pathways Modulate an Enhancer of TCF21 Expression at the 6q23.2 Coronary Heart Disease Locus.
Clint L. Miller mail, D. Ryan Anderson, Ramendra K. Kundu, Azad Raiesdana, Sylvia T. Nürnberg, Roxanne Diaz, Karen Cheng, Nicholas J. Leeper, Chung-Hsing Chen, I-Shou Chang, Eric E. Schadt, Chao Agnes Hsiung, Themistocles L. Assimes, Thomas Quertermous.
PLoS Genetics, (2013), 9(7):e1003652.
DNA methylome signature in rheumatoid arthritis.
Nakano K, Whitaker JW, Boyle DL, et al.
Ann Rheum Dis, (2013), 72:110-117.

Next Generation Sequencing (back to top)

iSeq: A New Double-Barcode Method for Detecting Dynamic Genetic Interactions in Yeast.
Jaffe M, Sherlock G, Levy SF.
G3 (Bethesda), (2017), 7(1):143-153.
Cell cycle progression in Caulobacter requires a nucleoid-associated protein with high AT sequence recognition.
Ricci DP, Melfi MD, Lasker K, Dill DL, McAdams HH, Shapiro L.
Proc Natl Acad Sci U S A, (2016), 113(40):E5952-E5961.
A long noncoding RNA protects the heart from pathological hypertrophy.
Pei Han, Wei Li, Chiou-Hong Lin, Jin Yang, Ching Shang, Sylvia T. Nuernberg, Kevin Kai Jin, Weihong Xu, Chieh-Yu Lin, Chien-Jung Lin, Yiqin Xiong, Huan-Chieh Chien, Bin Zhou, Euan Ashley, Daniel Bernstein, Peng-Sheng Chen, Huei-Sheng Vincent Chen, Thomas Quertermous, and Ching-Pin Chang.
Nature, (2014), 514(7520):102-6.

DNA Sequencing (Sanger)/Fragment Analysis (back to top)

Rapid increase in genetic diversity in an endemic Patagonian tuco-tuco following a recent volcanic eruption.
Jeremy L. Hsu Sharon Kam Mauro N. Tammone Eileen A. Lacey Elizabeth A. Hadly.
J Mammal., (2017), gyx008.
De novo and rare mutations in the HSPA1L heat shock gene associated with inflammatory bowel disease.
Takahashi S, Andreoletti G, Chen R, Munehira Y, Batra A, Afzal NA, Beattie RM, Bernstein JA, Ennis S, Snyder M.
Genome Med., (2017), 9(1):8.
Association of AHSG with alopecia and mental retardation (APMR) syndrome.
Reza Sailani M, Jahanbani F, Nasiri J, Behnam M, Salehi M, Sedghi M, Hoseinzadeh M, Takahashi S, Zia A, Gruber J, Lynch JL, Lam D, Winkelmann J, Amirkiai S, Pang B, Rego S, Mazroui S, Bernstein JA, Snyder MP.
Hum Genet., (2017), 136(3):287-296.
Cabozantinib inhibits tumor growth and metastasis of a patient-derived xenograft model of papillary renal cell carcinoma with MET mutation.
Hongjuan Zhao, Rosalie Nolley, Andy M.W. Chan, Erinn B. Rankin & Donna M. Peehl.
Cancer Biology & Therapy, (2016), Vol. 0 , Iss. ja,0
Scaffold-mediated BMP-2 minicircle DNA delivery accelerated bonerepair in a mouse critical-size calvarial defect model.
Keeney M, Chung MT, Zielins ER, Paik KJ, McArdle A, Morrison SD, Ransom RC, Barbhaiya N, Atashroo D, Jacobson G, Zare RN, Longaker MT, Wan DC, Yang F.
J Biomed Mater Res A, (2016), 104(8):2099-107.
Short Hairpin RNA Silencing of PHD-2 Improves Neovascularization and Functional Outcomes in Diabetic Wounds and Ischemic Limbs.
Paik KJ, Maan ZN, Zielins ER, Duscher D, Whittam AJ, Morrison SD, Brett EA, Ransom RC, Hu MS, Wu JC, Gurtner GC, Longaker MT, Wan DC.
PLoS One, (2016), 11(3):e0150927.
Analytical and Clinical Validation of a Digital Sequencing Panel for Quantitative, Highly Accurate Evaluation of Cell-Free Circulating Tumor DNA.
Lanman RB, Mortimer SA, Zill OA, Sebisanovic D, Lopez R, Blau S, Collisson EA, Divers SG, Hoon DS, Kopetz ES, Lee J, Nikolinakos PG, Baca AM, Kermani BG, Eltoukhy H, Talasaz A.
PLoS One, (2015), 10(10):e0140712.
Using Unnatural Amino Acids to Probe the Energetics of Oxyanion Hole Hydrogen Bonds in the Ketosteroid Isomerase Active Site.
Aditya Natarajan , Jason P. Schwans , and Daniel Herschlag.
J. Am. Chem. Soc., (2014), 136(21):7643–7654.
Vitamin D Receptor Mutations in Patients with Hereditary 1,25-Dihydroxyvitamin D-Resistant Rickets.
Peter J. Malloya, Velibor Tasicb, Doris Tahac, Filiz Tütüncülerd, Goh Siok Yinge, Loke Kah Yine, Jining Wanga, David Feldman.
Molecular Genetics and Metabolism, (2014), 111(1):33-40.

Honey Bees Avoid Nectar Colonized by Three Bacterial Species, But Not by a Yeast Species, Isolated from the Bee Gut.
Ashley P. Good, Marie-Pierre L. Gauthier, Rachel L. Vannette, Tadashi Fukami.
PLoS ONE, (2014), 9(1):e86494.
Hands and Water as Vectors of Diarrheal Pathogens in Bagamoyo, Tanzania.
Mia Catharine Mattioli, Amy J. Pickering, Rebecca J. Gilsdorf, Jennifer Davis, and Alexandria B. Boehm.
Environmental Science & Technology, (2013), 47 (1):355-363.
Exome sequencing to identify de novo mutations in sporadic ALS trios.
Alessandra Chesi, Brett T Staahl, Ana Jovičić, Julien Couthouis, Maria Fasolino, Alya R Raphael, Tomohiro Yamazaki, Laura Elias, Meraida Polak, Crystal Kelly, Kelly L Williams, Jennifer A Fifita, Nicholas J Maragakis, Garth A Nicholson, Oliver D King, Robin Reed, Gerald R Crabtree, Ian P Blair, Jonathan D Glass, and Aaron D Gitler.
Nature Neuroscience, (2013), 16(7):851–855.
Enteral calcium infusion used successfully as treatment for a patient with hereditary vitamin D resistant rickets (HVDRR) without alopecia: a novel mutation.
Huang K, Malloy P, Feldman D, Pitukcheewanont P.
Gene, (2013), 512(2):554-559.
Structural Map of a MicroRNA-122: Hepatitis C Virus Complex.
Pang, Phillip S.; Pham, Edward A.; Elazar, Menashe; et al.
JOURNAL OF VIROLOGY, (2012), 86(2):1250-1254.
Influence of 17β-estradiol on gene expression of paracoccidioides during mycelia-to-yeast transition.
Shankar J., Wu T.D., Clemons K.V., Monteiro J.P., Mirels L.F., Stevens D.A.
PLoS ONE, (2011), 6(12):e28402.
A synthetic library of RNA control modules for predictable tuning of gene expression in yeast.
Babiskin AH, Smolke CD.
Mol Syst Biol, (2011), 7:471.
Simplified RNA secondary structure mapping by automation of SHAPE data analysis.
Pang PS, Elazar M, Pham EA, Glenn JS.
Nucleic Acids Res, (2011), 39(22):e151.
Hereditary 1,25-dihydroxyvitamin D-resistant rickets with alopecia resulting from a novel missense mutation in the DNA-binding domain of the vitamin D receptor.
Malloy PJ, Wang J, Srivastava T, Feldman D.
Mol Genet Metab, (2010), 99(1):72-79.
Hereditary vitamin D resistant rickets: identification of a novel splice site mutation in the vitamin D receptor gene and successful treatment with oral calcium therapy.
Ma NS, Malloy PJ, Pitukcheewanont P, Dreimane D, Geffner ME, Feldman D.
Bone, (2009), 45(4):743-746.
Phase variation and microevolution at homopolymeric tracts in Bordetella pertussis.
Gogol EB, Cummings CA, Burns RC, Relman DA.
BMC Genomics, (2007), 8:122.
Growth of a Dehalococcoides-like microorganism on vinyl chloride and cis-dichloroethene as electron acceptors as determined by competitive PCR.
Cupples AM, Spormann AM, McCarty PL.
Appl Environ Microbiol, (2003), 69(2):953-959.
A novel nonsense mutation in the ligand binding domain of the vitamin D receptor causes hereditary 1,25-dihydroxyvitamin D-resistant rickets.
Malloy PJ, Zhu W, Bouillon R, Feldman D.
Mol Genet Metab, (2002), 77(4):314-318.
Impaired transactivation of the glucocorticoid receptor cloned from the Guyanese squirrel monkey.
Patel PD, Lyons DM, Zhang Z, Ngo H, Schatzberg AF.
J Steroid Biochem Mol Biol, (2000), 72(3-4):115-123.
PDZK1 and GREB1 are estrogen-regulated genes expressed in hormone-responsive breast cancer.
Ghosh MG, Thompson DA, Weigel RJ.
Cancer Res, (2000), 60(22):6367-6375.

Peptide Synthesis (back to top)

Inhibitors of protein arginine deiminases and their efficacy in animal models of multiple sclerosis.
Sarswat A, Wasilewski E, Chakka SK, Bello AM, Caprariello AV, Muthuramu CM, Stys PK, Dunn SE, Kotra LP.
Bioorg Med Chem., (2017), 25(9):2643-2656.
Oral administration of the nitroxide radical TEMPOL exhibits immunomodulatory and therapeutic properties in multiple sclerosis models.
Neil S, Huh J, Baronas V, Li X, McFarland HF, Cherukuri M, Mitchell JB, Quandt JA.
Brain Behav Immun., (2017), 62:332-343.
PKC-ALDH2 Pathway Plays a Novel Role in Adipocyte Differentiation.
Yu YH, Liao PR, Guo CJ, Chen CH, Mochly-Rosen D, Chuang LM.
PLoS One, (2016), 11(8):e0161993.
A PWWP domain of histone-lysine N-methyltransferase NSD2 binds to dimethylated Lys36 of histone H3 and regulates NSD2 function at chromatin.
Sankaran SM, Wilkinson AW, Elias JE, Gozani O.
J Biol Chem., (2016), 291(16):8465-74.
Two cytochromes P450 catalyze S-heterocyclizations in cabbage phytoalexin biosynthesis.
Klein AP, Sattely ES.
Nat Chem Biol., (2015), 11(11):837-9.
Apela regulates fluid homeostasis by binding to the APJ receptor to activate Gi signaling.
Cheng Deng, Haidi Chen, Na Yang, Yi Feng, and Aaron J. W. Hsueh.
JBC, (2015).
Early Telomerase Inactivation Accelerates Aging Independently of Telomere Length.
Zhengwei Xie, Kyle A. Jay, Dana L. Smith, Yi Zhang, Zairan Liu, Jiashun Zheng, Ruilin Tian, Hao Li, Elizabeth H. Blackburn.
Cell, (2015), 60(5):928-939.
Tetramers reveal IL-17–secreting CD4+ T cells that are specific for U1-70 in lupus and mixed connective tissue disease.
Nicole H. Kattah, Evan W. Newell, Justin Ansel Jarrell, Alvina D. Chu, Jianming Xie, Michael G. Kattah, Ofir Goldberger, Jessica Ye, Eliza F. Chakravarty, Mark M. Davis, and Paul J. Utz.
PNAS, (2015), 112(10):3044-3049.
A Novel CMKLR1 Small Molecule Antagonist Suppresses CNS Autoimmune Inflammatory Disease.
Kareem L. Graham, Jian V. Zhang, Susanna Lewén, Thomas M. Burke, Ton Dang, Maria Zoudilova, Raymond A. Sobel, Eugene C. Butcher, Brian A. Zabel.
PLoS ONE, (2014), 9(12):e112925.
Optimal Attenuation of Experimental Autoimmune Encephalomyelitis by Intravenous Immunoglobulin Requires an Intact Interleukin-11 Receptor.
Carlyn A. Figueiredo, Paulina C. Drohomyrecky, Stephen D. S. McCarthy, Danila Leontyev, Xue-Zhong Ma, Donald R. Branch, Shannon E. Dunn.
PLoS ONE, (20140, 9(7):e101947.
CXCL11-dependent induction of FOXP3-negative regulatory T cells suppresses autoimmune encephalomyelitis.
Yaniv Zohar, Gizi Wildbaum, Rostislav Novak, Andrew L. Salzman, Marcus Thelen, Ronen Alon, Yiftah Barsheshet, Christopher L. Karp and Nathan Karin.
J Clin Invest., (2014), 124(5):2009–2022.
Antiviral drug ganciclovir is a potent inhibitor of microglial proliferation and neuroinflammation.
Zhaoqing Ding, Vidhu Mathur, Peggy P. Ho, Michelle L. James, Kurt M. Lucin, Aileen Hoehne, Haitham Alabsi, Sanjiv S. Gambhir, Lawrence Steinman, Jian Luo, Tony Wyss-Coray.
J. Exp. Med., (2014), 211:189-198.
Maternal immune stimulation during pregnancy shapes the immunological phenotype of offspring.
Mili Mandal, Robert Donnelly, Stella Elkabes, Pan Zhang, Dan Davinic, Brian T. David, Nicholas M. Ponzio.
Brain, Behavior, and Immunity, (2013), 33:33-45.
Molecular photoacoustic imaging of follicular thyroid carcinoma.
Levi, J., Kothapalli, S.-R., Bohndiek, S., Yoon, J.-K., Dragulescu-Andrasi, A., Nielsen, C., Tisma, A., Bodapati, S., Gowrishankar, G., Yan, X., Chan, C., Starcevic, D., Gambhir, S.S.
Clinical Cancer Research, (2013), 19(6):1494-1502.
Azetidine-2-carboxylic acid in the food chain.
Rubenstein E, McLaughlin T, Winant RC, Sanchez A, Eckart M, Krasinska KM, Chien A.
Phytochemistry, (2009), 70(1):100-104.
Structure-activity studies on high affinity NOP-active hexapeptides.
Judd AK, Tuttle DJ, Jones RW, Sanchez A, Polgar W, Berzetei-Gurske I, Toll L.
J Pept Res., (2004), 64(3):87-94.
N-terminal modifications leading to peptide ORL1 partial agonists and antagonists.
Judd AK, Kaushanskaya A, Tuttle DJ, Sanchez A, Khroyan T, Polgar W, Toll L.
J Pept Res., (2003), 62(5):191-198.

Mass Spectrometry (back to top)

Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells.
Lund PJ, Elias JE, Davis MM.
J Immunol., (2016), 197(8):3086-3098.
SIRT6 deacetylates H3K18ac at pericentric chromatin to prevent mitotic errors and cellular senescence.
Tasselli L, Xi Y, Zheng W, Tennen RI, Odrowaz Z, Simeoni F, Li W, Chua KF.
Nat Struct Mol Biol., (2016), 23(5):434-40.
Anti-citrullinated protein antibodies promote apoptosis of mature human Saos-2 osteoblasts via cell-surface binding to citrullinated heat shock protein 60.
Lu MC, Yu CL, Yu HC, Huang HB, Koo M, Lai NS.
Immunobiology, (2015), pii: S0171-2985(15)30038-3.
Pattern-based detection of anion pollutants in water with DNA polyfluorophores.
Hyukin Kwon, Wei Jiang and Eric T. Kool.
Chem. Sci., (2015), 6:2575-2583.
Structural and functional modularity of the orange carotenoid protein: distinct roles for the N- and C-terminal domains in cyanobacterial photoprotection.
Leverenz RL, Jallet D, Li MD, Mathies RA, Kirilovsky D, Kerfeld CA.
Plant Cell, (2014), 26(1):426-37.
99mTc-Labeled Cystine Knot Peptide Targeting Integrin αvβ6 for Tumor SPECT Imaging.
Xiaohua Zhu, Jinbo Li, Yeongjin Hong, Richard H. Kimura, Xiaowei Ma, Hongguang Liu, Chunxia Qin, Xiang Hu, Thomas R. Hayes, Paul Benny, Sanjiv Sam Gambhir, and Zhen Cheng.
Mol. Pharmaceutics, (2014), 11(4):1208–1217.
Multi-Site Functionalization of Protein Scaffolds for Bimetallic Nanoparticle Templating.
Kelly N. L. Huggins , Alia P. Schoen , Manickam Adhimoolam Arunagirinathan , and Sarah C. Heilshorn.
Advanced Functional Materials, (2014), 24(48):7737–7744.
A Bioengineered Peptide that Localizes to and Illuminates Medulloblastoma: A New Tool with Potential for Fluorescence-Guided Surgical Resection.
Shelley E. Ackerman , Christy M. Wilson , Suzana A. Kahn , James R. Kintzing , Darren A. Jindal , Samuel H. Cheshier , Gerald A. Grant , Jennifer R. Cochran.
Cureus, (2014), 6(9):e207.
Molecular Recognition of Methyl α-d-Mannopyranoside by Antifreeze (Glyco)Proteins.
Sen Wang, Xin Wen, Arthur L. DeVries, Yelena Bagdagulyan, Alexander Morita, James A. Golen, John G. Duman, and Arnold L. Rheingold.
J. Am. Chem. Soc., (2014), 136(25):8973–8981.
The initiation ketosynthase (FabH) is the sole rate-limiting enzyme of the fatty acid synthase of Synechococcus sp. PCC 7002.
James Kuo, Chaitan Khosla.
Metabolic Engineering, (2014), 22:60–68.
Engineering agatoxin, a cystine-knot Peptide from spider venom, as a molecular probe for in vivo tumor imaging.
Moore SJ, Leung CL, Norton HK, Cochran JR.
PloS One, (2013), 8:e60498.
Engineered knottin peptide enables noninvasive optical imaging of intracranial medulloblastoma.
Sarah J. Moore, Melanie G. Hayden Gephart, Jamie M. Bergen, YouRong S. Su, Helen Rayburn, Matthew P. Scott, and Jennifer R. Cochran.
PNAS, (2013), 110(36):14598-14603.
Genetically Encoded Multispectral Labeling of Proteins with Polyfluorophores on a DNA Backbone.
Vijay Singh, Shenliang Wang, and Eric T. Kool.
Journal of the American Chemical Society, (2013), 135(16):6184-6191.
Monodisperse, "highly" positively charged protein polymer drag-tags generated in an intein-mediated purification system used in free-solution electrophoretic separations of DNA.
Wang X, Albrecht JC, Lin JS, Barron AE.
Biomacromolecules, (2012), 13(1):117-123.
Diffusion of protein through the human cornea.
Charalel RA, Engberg K, Noolandi J, Cochran JR, Frank C, Ta CN.
Ophthalmic Res, (2012), 48(1):50-55.
Defective autoimmune regulator-dependent central tolerance to myelin protein zero is linked to autoimmune peripheral neuropathy.
Su MA, Davini D, Cheng P, Giang K, Fan U, DeVoss JJ, Johannes KP, Taylor L, Shum AK, Valenzise M, Meloni A, Bour-Jordan H, Anderson MS.
J Immunol, (2012), 188(10):4906-4912.
Regulation of chemerin chemoattractant and antibacterial activity by human cysteine cathepsins.
Kulig P, Kantyka T, Zabel BA, Banas M, Chyra A, Stefanska A, Tu H, Allen SJ, Handel TM, Kozik A, Potempa J, Butcher EC, Cichy J.
J Immunol, (2011), 187(3):1403-1410.
Structure of betaglycan zona pellucida (ZP)-C domain provides insights into ZP-mediated protein polymerization and TGF-beta binding.
Lin SJ, Hu Y, Zhu J, Woodruff TK, Jardetzky TS.
Proc Natl Acad Sci, (2011), 108(13):5232-5236.
In vitro reconstitution and steady-state analysis of the fatty acid synthase from Escherichia coli.
Xingye Yu, Tiangang Liu, Fayin Zhu, and Chaitan Khosla.
PNAS, (2011), 108(46):18643-18648.
Plasma carboxypeptidase B downregulates inflammatory responses in autoimmune arthritis.
Jason J. Song, Inyong Hwang, Kyung H. Cho, Michael A. Garcia, Arthur J. Kim, Tiffany H. Wang, Tamsin M. Lindstrom, Annette T. Lee, Toshihiko Nishimura, Lei Zhao, John Morser, Michael Nesheim, Stuart B. Goodman, David M. Lee, S. Louis Bridges Jr., Peter K. Gregersen, Lawrence L. Leung, William H. Robinson.
J Clin Invest., (2011), 121(9):3517–3527.
Tropomyosin is an interaction partner of the Drosophila coiled coil protein yuri gagarin.
Texada MJ, Simonette RA, Deery WJ, Beckingham KM.
Exp Cell Res., (2011), 317(4):474-487.
Phylogenomic analyses reveal the evolutionary origin of the inhibin alpha-subunit, a unique TGFbeta superfamily antagonist.
Zhu J, Braun EL, Kohno S, Antenos M, Xu EY, Cook RW, Lin SJ, Moore BC, Guillette LJ Jr, Jardetzky TS, Woodruff TK.
PLoS One, (2010), 5(3):e9457.
Engineered cystine-knot peptides that bind alpha(v)beta(3) integrin with antibody-like affinities.
Adam P. Silverman, Aron M. Levin, Jennifer L. Lahti, and Jennifer R. Cochran.
J Mol Biol, (2009), 385(4):1064–1075.
Kruppel-associated box domain-associated protein-1 as a latency regulator for Kaposi's sarcoma-associated herpesvirus and its modulation by the viral protein kinase.
Chang PC, Fitzgerald LD, Van Geelen A, Izumiya Y, Ellison TJ, Wang DH, Ann DK, Luciw PA, Kung HJ.
Cancer Res., (2009), 69(14):5681-5689.
Kinetics of protein substrate degradation by HslUV.
Kwon AR, Trame CB, McKay DB.
J Struct Biol, (2004), 146(1-2):141-147.
Functional expression and characterization of Schistosoma mansoni cathepsin B and its trans-activation by an endogenous asparaginyl endopeptidase.
Sajid M, McKerrow JH, Hansell E, Mathieu MA, Lucas KD, Hsieh I, Greenbaum D, Bogyo M, Salter JP, Lim KC, Franklin C, Kim JH, Caffrey CR.
Mol Biochem Parasitol, (2003), 131(1):65-75.

Protein Analytics - Mass Mapping/Edman Sequencing (back to top)

High-Efficiency “–1” and “–2” Ribosomal Frameshiftings Revealed by Force Spectroscopy.
Te-Wei Tsai, Haopeng Yang, Heng Yin, Shoujun Xu, and Yuhong Wang.
ACS Chemical Biology, (2017)
Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains.
Peter S. Shen, Joseph Park, Yidan Qin, Xueming Li, Krishna Parsawar, Matthew H. Larson, James Cox, Yifan Cheng, Alan M. Lambowitz, Jonathan S. Weissman, Onn Brandman, Adam Frost.
Science, (2015), 347(6217):75-78.
Organocatalytic removal of formaldehyde adducts from RNA and DNA bases.
Saswata Karmakar, Emily M. Harcourt, David S. Hewings, Florian Scherer, Alexander F. Lovejoy, David M. Kurtz, Thomas Ehrenschwender, Luzi J. Barandun, Caroline Roost, Ash A. Alizadeh & Eric T. Kool.
Nature Chemistry, (2015), 7:752–758.
A cell cycle and nutritional checkpoint controlling bacterial surface adhesion.
Fiebig A, Herrou J, Fumeaux C, Radhakrishnan SK, Viollier PH, Crosson S.
PLoS Genet., (2014), 10(1):e1004101.
Complexin inhibits spontaneous release and synchronizes Ca2+-triggered synaptic vesicle fusion by distinct mechanisms.
Lai Y, Diao J, Cipriano DJ, Zhang Y, Pfuetzner RA, Padolina MS, Brunger AT.
Elife, (2014), 3:e03756.
Structural and Functional Modularity of the Orange Carotenoid Protein: Distinct Roles for the N- and C-Terminal Domains in Cyanobacterial Photoprotection.
Ryan L. Leverenz, Denis Jallet, Ming-De Li, Richard A. Mathies, Diana Kirilovsky, and Cheryl A. Kerfeld.
The Plant Cell, (2014), 26(1):426-437.
Engineered knottin peptide enables noninvasive optical imaging of intracranial medulloblastoma.
Sarah J. Moore, Melanie G. Hayden Gephart, Jamie M. Bergen, YouRong S. Su, Helen Rayburn, Matthew P. Scott, and Jennifer R. Cochran.
PNAS 2013.
Engineering Agatoxin, a cystine-knot peptide from spider venom, as a molecular probe for in vivo tumor imaging.
Moore, S. J., Leung, C. L., Norton, H.K., and Cochran, J. R..
PLoS ONE, (2013), 8:e60498.
Defective Autoimmune Regulator-Dependent Central Tolerance to Myelin Protein Zero Is Linked to Autoimmune Peripheral Neuropathy.
Maureen A., Davini, Dan, Cheng, Philip, et al.
JOURNAL OF IMMUNOLOGY, (2012), 188(10):4906-4912.

Purification, characterization and cloning of tensilin, the collagen-fibril binding and tissue-stiffening factor from Cucumaria frondosa dermis.
Tipper JP, Lyons-Levy G, Atkinson MA, Trotter JA.
Matrix Biol., (2012), 21(8):625-635.
Comparative analysis of the XopD type III secretion (T3S) effector family in plant pathogenic bacteria.
Kim JG, Taylor KW, Mudgett MB.
Mol Plant Pathol., (2011), 12(8):715-730.
Crystal structures of TbCatB and rhodesain, potential chemotherapeutic targets and major cysteine proteases of Trypanosoma brucei.
Kerr I.D., Wu P., Marion-Tsukamaki R., Mackey Z.B., Brinen L.S.
PLoS Neglected Tropical Diseases, (2010), 4(6):e701.
Molecular characterization and antibody detection of a nitrogen-regulated cell-surface protein of the coccolithophore Emiliania Huxleyi (Prymnesiophyceae).
Landry, D. M., Kristiansen, S. and Palenik, B. P.
Journal of Phycology, (2009), 45(3):650–659.
Subunit Composition, Protein Interactions, and Structures of the Mammalian Brain sec6/8 Complex and Septin Filaments.
Hsu SC, Hazuka CD, Roth R, Foletti DL, Heuser J, Scheller RH.
Neuron, (1998), 20(6):1111-22.

Surface Plasmon Resonance (Biacore) (back to top)

A Localized Complex of Two Protein Oligomers Controls the Orientation of Cell Polarity.
Perez AM, Mann TH, Lasker K, Ahrens DG, Eckart MR, Shapiro L.
mBio., (2017), 8(1):e02238-16.
Small molecule inhibition of cAMP response element binding protein in human acute myeloid leukemia cells.
Mitton B, Chae HD, Hsu K, Dutta R, Aldana-Masangkay G, Ferrari R, Davis K, Tiu BC, Kaul A, Lacayo N, Dahl G, Xie F, Li BX, Breese MR, Landaw EM, Nolan G, Pellegrini M, Romanov S, Xiao X, Sakamoto KM.
Leukemia, (2016), 30(12):2302-2311.
Fragments of the V1/V2 domain of HIV-1 glycoprotein 120 engineered for improved binding to the broadly neutralizing PG9 antibody.
Javier F. Morales, Bin Yu, Gerardo Perez, Kathryn A. Mesa, David L. Alexander, Phillip W. Berman.
Molecular Immunology, (2016), 77:14-25.
A cell cycle kinase with tandem sensory PAS domains integrates cell fate cues.
Mann TH, Seth Childers W, Blair JA, Eckart MR, Shapiro L.
Nat Commun., (2016), 7:11454.
The Structural Basis of Substrate Recognition by the Eukaryotic Chaperonin TRiC/CCT.
Lukasz A. Joachimiak, Thomas Walzthoeni, Corey W. Liu, Ruedi Aebersold, Judith Frydman.
Cell, (2014), 159(5):1042–1055.
Type IV collagen is an activating ligand for the adhesion G protein-coupled receptor GPR126.
Paavola KJ, Sidik H, Zuchero JB, Eckart M, Talbot WS.
Sci Signal., (2014), 7(338):ra76.
Bacterial scaffold directs pole-specific centromere segregation.
Jerod L. Ptacin, Andreas Gahlmann, Grant R. Bowman, Adam M. Perez, Alexander R. S. von Diezmann, Michael R. Eckart, W. E. Moerner, and Lucy Shapiro.
PNAS, (2014).
Branched Signal Wiring of an Essential Bacterial Cell-Cycle Phosphotransfer Protein.
Blair, Jimmy A.; Xu, Qingping; Childers, W. Seth; Mathews, Irimpan I.; Kern, Justin W.; Eckart, Michael; Deacon, Ashley M.; Shapiro, Lucy.
Structure, (2013), 21(9):1590-1601.
ALIX is a Lys63-specific polyubiquitin binding protein that functions in retrovirus budding.
Dowlatshahi DP, Sandrin V, Vivona S, Shaler TA, Kaiser SE, Melandri F, Sundquist WI, Kopito RR.
Dev Cell, (2012), 23(6):1247-54.

A versatile cis-blocking and trans-activation strategy for ribozyme characterization.
Kennedy AB, Liang JC, Smolke CD.
Nucleic Acids Res., (2012), 41(2):e41.
Clinical Utility of Insulin-Like Growth Factor 1 and 2; Determination by High Resolution Mass Spectrometry.
Bystrom C., Sheng S., Zhang K., Caulfield M., Clarke N.J., Reitz R.
PLoS ONE, (2012), 7(9):e43457.
Niemann-Pick type C 1 function requires lumenal domain residues that mediate cholesterol-dependent NPC2 binding.
Deffieu MS, Pfeffer SR.
Proc Natl Acad Sci U S A, (2011), 108(47):18932-18936.
Antagonistic VEGF variants engineered to simultaneously bind to and inhibit VEGFR2 and αvβ3 integrin.
Niv Papo, Adam P. Silverman, Jennifer L. Lahti, and Jennifer R. Cochran.
PNAS, (2011), 108(34):14067-14072.
The cell-adhesion G protein-coupled receptor BAI3 is a high-affinity receptor for C1q-like proteins.
Bolliger MF, Martinelli DC, Südhof TC.
Proc Natl Acad Sci U S A, (2011), 108(6):2534-2539.
Antagonistic VEGF variants engineered to simultaneously bind to and inhibit VEGFR2 and alpha(v)beta(3) integrin.
Papo, Niv ; Silverman, Adam P. ; Lahti, Jennifer L.; et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, (2011), 108(34):14067-14072.
Quantification of protein interactions and solution transport using high-density GMR sensor arrays.
Richard S. Gaster, Liang Xu, Shu-Jen Han, Robert J. Wilson, Drew A. Hall, Sebastian J. Osterfeld, Heng Yu, and Shan X. Wang.
Nature Nanotechnology, (2011), 6:314–320.
A spindle-like apparatus guides bacterial chromosome segregation.
Jerod L. Ptacin, Steven F. Lee, Ethan C. Garner, Esteban Toro, Michael Eckart, Luis R. Comolli, W.E. Moerner, and Lucy Shapiro.
Nature Cell Biology, (2010), 12:791–798.
Highly parallel measurements of interaction kinetic constants with a microfabricated optomechanical device.
Bates, Steven R. and Quake, Stephen R.,
Applied Physics Letters, (2009), 95.
A polymeric protein anchors the chromosomal origin/ParB complex at a bacterial cell pole.
Bowman GR, Comolli LR, Zhu J, Eckart M, Koenig M, Downing KH, Moerner WE, Earnest T, Shapiro L.
Cell, (2008), 134(6):945-955.