NIBR
POSTDOCTORAL PROGRAM

Publications

A key guiding principle for our program is that postdoctoral scholars publish their work in highly-respected journals. Our postdocs publish extensively in the biomedical sciences, chemistry, and computational sciences. A few selected publications, with our postdocs as the lead authors, are highlighted here.

Click here for all NIBR publications.

  • 2017
  • 2016
  • 2015
  • 2014
  • 2013
  • 2012
  • 2011
  • 2010 - 2008

Inverting conventional chemoselectivity in Pd-catalyzed amine arylations with multiply halogenated pyridines.
Keylor MH, Niemeyer ZL, Sigman MS, Tan KL.
J Am Chem Soc. 2017 Aug 9;139(31):10613-10616.

Reverse translation of adverse event reports paves the way for de-risking preclinical off-targets.
Maciejewski M, Lounkine E, Whitebread S, Farmer P, DuMouchel W, Shoichet BK, Urban L.
Elife. 2017 Aug 8;6. pii: e25818.

Indoleacrylic Acid Produced by Commensal Peptostreptococcus Species Suppresses Inflammation. 
Wlodarska M, Luo C, Kolde R, d'Hennezel E, Annand JW, Heim CE, Krastel P, Schmitt EK, Omar AS, Creasey EA, Garner AL, Mohammadi S, O'Connell DJ, Abubucker S, Arthur TD, Franzosa EA, Huttenhower C, Murphy LO, Haiser HJ, Vlamakis H, Porter JA, Xavier RJ.
Cell Host Microbe. 2017 Jul 12;22(1):25-37.

The SIAH E3 ubiquitin ligases promote Wnt/β-catenin signaling through mediating Wnt-induced Axin degradation.
Ji L, Jiang B, Jiang X, Charlat O, Chen A, Mickanin C, Bauer A, Xu W, Yan X, Cong F.
Genes Dev. 2017 May 1;31(9):904-915.

A multi-scale convolutional neural network for phenotyping high-content cellular images.
Godinez WJ, Hossain I, Lazic SE, Davies JW, Zhang X.
Bioinformatics. 2017 Feb 15. doi: 10.1093/bioinformatics/btx069.

Structure-kinetic relationships of passive membrane permeation from multiscale modeling.
Dickson CJ, Hornak V, Pearlstein RA, Duca JS.
J Am Chem Soc. 2017 Jan 11;139(1):442-452.

Genetic ablation of AXL does not protect human neural progenitor cells and cerebral organoids from Zika virus infection.
Wells MF*, Salick MR*, Wiskow O, Ho DJ, Worringer KA, Ihry RJ, Kommineni S, Bilican B, Klim JR, Hill EJ, Kane LT, Ye C, Kaykas A, Eggan K.
Cell Stem Cell. 2016 Dec 1;19(6):703-708.
*Co-first authors

Accessing drug metabolites via transition-metal catalyzed C-H oxidation: The liver as synthetic inspiration.
Genovino J, Sames D, Hamann LG, Touré BB.
Angew Chem Int Ed Engl. 2016 Nov 7;55(46):14218-14238. Review.

CRISPR screens provide a comprehensive assessment of cancer vulnerabilities but generate false-positive hits for highly amplified genomic regions. 
Munoz DM, Cassiani PJ, Li L, Billy E, Korn JM, Jones MD, Golji J, Ruddy DA, Yu K, McAllister G, DeWeck A, Abramowski D, Wan J, Shirley MD, Neshat SY, Rakiec D, de Beaumont R, Weber O, Kauffmann A, McDonald ER, Keen N, Hofmann F, Sellers WR, Schmelzle T, Stegmeier F, Schlabach MR. 
Cancer Discov. 2016 Aug;6(8):900-13.

The RSPO-LGR4/5-ZNRF3/RNF43 module controls liver zonation and size.  
Planas-Paz L, Orsini V, Boulter L, Calabrese D, Pikiolek M, Nigsch F, Xie Y, Roma G, Donovan A, Marti P, Beckmann N, Dill MT, Carbone W, Bergling S, Isken A, Mueller M, Kinzel B, Yang Y, Mao X, Nicholson TB, Zamponi R, Capodieci P, Valdez R, Rivera D, Loew A, Ukomadu C, Terracciano LM, Bouwmeester T, Cong F, Heim MH, Forbes SJ, Ruffner H, Tchorz JS. 
Nat Cell Biol. 2016 May;18(5):467-79.

Big Data from Pharmaceutical Patents: A Computational Analysis of Medicinal Chemists' Bread and Butter.  
Schneider N, Lowe DM, Sayle RA, Tarselli MA, Landrum GA.
J Med Chem. 2016 May 12;59(9):4385-402. doi: 10.1021/acs.jmedchem.6b00153. Epub 2016 Apr 8.

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans.
Vatanen T*, Kostic AD*, d'Hennezel E*, Siljander H, Franzosa EA, Yassour M, Kolde R, Vlamakis H, Arthur TD, Hämäläinen AM, Peet A, Tillmann V, Uibo R, Mokurov S, Dorshakova N, Ilonen J, Virtanen SM, Szabo SJ, Porter JA, Lähdesmäki H, Huttenhower C, Gevers D, Cullen TW, Knip M; DIABIMMUNE Study Group, Xavier RJ.
Cell. 2016 May 5;165(4):842-53. doi: 10.1016/j.cell.2016.04.007. Epub 2016 Apr 28. *Co-first authors​

CLK2 inhibition ameliorates autistic features associated with SHANK3 deficiency. 
Bidinosti M, Botta P, Krüttner S, Proenca CC, Stoehr N, Bernhard M, Fruh I, Mueller M, Bonenfant D, Voshol H, Carbone W, Neal SJ, McTighe SM, Roma G, Dolmetsch RE, Porter J, Caroni P, Bouwmeester T, Lüthi A, Galimberti I. 
Science. 2016 Mar 11;351(6278):1199-203

Dark chemical matter as a promising starting point for drug lead discovery.
Wassermann AM, Lounkine E, Hoepfner D, Le Goff G, King FJ, Studer C, Peltier JM, Grippo ML, Prindle V, Tao J, Schuffenhauer A, Wallace IM, Chen S, Krastel P, Cobos-Correa A, Parker CN, Davies JW, Glick M. 
Nat Chem Biol. 2015 Oct 19. doi: 10.1038/nchembio.1936.

Small-molecule inhibitors: bULKing up mTOR inhibition.(Review) 
Goodwin JM, Murphy LO. 
Nat Chem Biol. 2015 Sep 17;11(10):758-760. doi: 10.1038/nchembio.1909.

A Long Non-coding RNA, LncMyoD, Regulates Skeletal Muscle Differentiation by Blocking IMP2-Mediated mRNA Translation. 
Gong C, Li Z, Ramanujan K, Clay I, Zhang Y, Lemire-Brachat S, Glass DJ. 
Dev Cell. 2015 Jul 1. S1534-5807(15)00325-1.

ATP citrate lyase improves mitochondrial function in skeletal muscle. 
Das S, Morvan F, Jourde B, Meier V, Kahle P, Brebbia P, Toussaint G, Glass DJ, Fornaro M. 
Cell Metab. 2015 Jun 2;21(6):868-76. doi: 10.1016/j.cmet.2015.05.006

Studying clonal dynamics in response to cancer therapy using high-complexity barcoding.
Bhang HE, Ruddy DA, Krishnamurthy Radhakrishna V, Caushi JX, Zhao R, Hims MM, Singh AP, Kao I, Rakiec D, Shaw P, Balak M, Raza A, Ackley E, Keen N, Schlabach MR, Palmer M, Leary RJ, Chiang DY, Sellers WR, Michor F, Cooke VG, Korn JM, Stegmeier F.
Nat Med. 2015 May:21(5):440-8

Dishevelled Promotes Wnt Receptor Degradation through Recruitment of ZNRF3/RNF43 E3 Ubiquitin Ligases. 
Jiang X, Charlat O, Zamponi R, Yang Y, Cong F. 
Mol Cell. 2015 Apr 15. pii: S1097-2765(15)00180-X. doi: 10.1016/j.molcel.2015.03.015.

Late-stage C-H functionalization of complex alkaloids and drug molecules via intermolecular rhodium-carbenoid insertion.
He J, Hamann LG, Davies HM, Beckwith RE.
Nat Commun. 2015 Jan 12;6:5943. doi: 10.1038/ncomms6943.

Cessation of CCL2 inhibition accelerates breast cancer metastasis by promoting angiogenesis.
Bonapace L, Coissieux MM, Wyckoff J, Mertz KD, Varga Z, Junt T, Bentires-Alj M.
Nature. 2014 Nov 6;515(7525):130-3

Selective VPS34 inhibitor blocks autophagy and uncovers a role for NCOA4 in ferritin degradation and iron homeostasis in vivo.
Dowdle WE, Nyfeler B, Nagel J, Elling RA, Liu S, Triantafellow E, Menon S, Wang Z, Honda A, Pardee G, Cantwell J, Luu C, Cornella-Taracido I, Harrington E, Fekkes P, Lei H, Fang Q, Digan ME, Burdick D, Powers AF, Helliwell SB, D'Aquin S, Bastien J, Wang H, Wiederschain D, Kuerth J, Bergman P, Schwalb D, Thomas J, Ugwonali S, Harbinski F, Tallarico J, Wilson CJ, Myer VE, Porter JA, Bussiere DE, Finan PM, Labow MA, Mao X, Hamann LG, Manning BD, Valdez RA, Nicholson T, Schirle M, Knapp MS, Keaney EP, Murphy LO.
Nat Cell Biol. 2014 Nov;16(11):1069-79.

Transneuronal propagation of mutant huntingtin contributes to non-cell autonomous pathology in neurons.
Pecho-Vrieseling E, Rieker C, Fuchs S, Bleckmann D, Esposito MS, Botta P, Goldstein C, Bernhard M, Galimberti I, Müller M, Lüthi A, Arber S, Bouwmeester T, van der Putten H, Di Giorgio FP.
Nat Neurosci. 2014 Jul 13. doi: 10.1038/nn.3761.

DNA sequencing and CRISPR-Cas9 gene editing for target validation in mammalian cells.
Smurnyy Y, Cai M, Wu H, McWhinnie E, Tallarico JA, Yang Y, Feng Y.
Nat Chem Biol. 2014 Jun 15. doi: 10.1038/nchembio.1550.

Asymmetric palladium-catalyzed directed intermolecular fluoroarylation of styrenes.
Talbot EP, Fernandes Tde A, McKenna JM, Toste FD.
J Am Chem Soc. 2014 Mar 19;136(11):4101-4.

Pharmacological and genomic profiling identifies NF-κB-targeted treatment strategies for mantle cell lymphoma.
Rahal R, Frick M, Romero R, Korn JM, Kridel R, Chan FC, Meissner B, Bhang HE, Ruddy D, Kauffmann A, Farsidjani A, Derti A, Rakiec D, Naylor T, Pfister E, Kovats S, Kim S, Dietze K, Dörken B, Steidl C, Tzankov A, Hummel M, Monahan J, Morrissey MP, Fritsch C, Sellers WR, Cooke VG, Gascoyne RD, Lenz G, Stegmeier F.
Nat Med. 2014 Jan;20(1):87-92

Complementation of biotransformations with chemical C-H oxidation: copper-catalyzed oxidation of tertiary amines in complex pharmaceuticals.
Genovino J, Lütz S, Sames D, Touré BB.
J Am Chem Soc. 2013 Aug 21;135(33):12346-52.

Identification of NUB1 as a suppressor of mutant Huntingtin toxicity via enhanced protein clearance.
Lu B, Al-Ramahi I, Valencia A, Wang Q, Berenshteyn F, Yang H, Gallego-Flores T, Ichcho S, Lacoste A, Hild M, Difiglia M, Botas J, Palacino J.
Nat Neurosci. 2013 May;16(5):562-70.

RAF Inhibitors Activate the MAPK Pathway by Relieving Inhibitory Autophosphorylation.

Holderfield M, Merritt H, Chan J, Wallroth M, Tandeske L, Zhai H, Tellew J, Hardy S, Hekmat-Nejad M, Stuart DD, McCormick F, Nagel TE.
Cancer Cell. 2013 May 13;23(5):594-602.

A Unique Herpesviral Transcriptional Program in KSHV-Infected Lymphatic Endothelial Cells Leads to mTORC1 Activation and Rapamycin Sensitivity.
Chang HH, Ganem D.

Cell Host Microbe. 2013 Apr 17;13(4):429-40.

Modelling vemurafenib resistance in melanoma reveals a strategy to forestall drug resistance.
Das Thakur M, Salangsang F, Landman AS, Sellers WR, Pryer NK, Levesque MP, Dummer R, McMahon M, Stuart DD.

Nature. 2013 Feb 14;494(7436):251-5.

An HMGA2-IGF2BP2 axis regulates myoblast proliferation and myogenesis.
Li Z, Gilbert JA, Zhang Y, Zhang M, Qiu Q, Ramanujan K, Shavlakadze T, Eash JK, Scaramozza A, Goddeeris MM, Kirsch DG, Campbell KP, Brack AS, Glass DJ.

Dev Cell. 2012 Dec 11;23(6):1176-88.

Inside the mind of a medicinal chemist: the role of human bias in compound prioritization during drug discovery.
Kutchukian PS, Vasilyeva NY, Xu J, Lindvall MK, Dillon MP, Glick M, Coley JD, Brooijmans N.
PLoS One. 2012;7(11):e48476.

Rethinking molecular similarity: comparing compounds on the basis of biological activity.
Petrone PM, Simms B, Nigsch F, Lounkine E, Kutchukian P, Cornett A, Deng Z, Davies JW, Jenkins JL, Glick M.

ACS Chem Biol. 2012 Aug 17;7(8):1399-409.

Large-scale prediction and testing of drug activity on side-effect targets.
Lounkine E, Keiser MJ, Whitebread S, Mikhailov D, Hamon J, Jenkins JL, Lavan P, Weber E, Doak AK, Côté S, Shoichet BK, Urban L.

Nature. 2012 Jun 10;486(7403):361-7.

ZNRF3 promotes Wnt receptor turnover in an R-spondin-sensitive manner.
Hao HX, Xie Y, Zhang Y, Charlat O, Oster E, Avello M, Lei H, Mickanin C, Liu D, Ruffner H, Mao X, Ma Q, Zamponi R, Bouwmeester T, Finan PM, Kirschner MW, Porter JA, Serluca FC, Cong F.

Nature. 2012 Apr 29;485(7397):195-200.

The SCF-Fbxo40 Complex Induces IRS1 Ubiquitination in Skeletal Muscle, Limiting IGF1 Signaling.
Shi J, Luo L, Eash J, Ibebunjo C, Glass DJ.

Dev Cell. 2011 Nov 15;21(5):835-47.

Human cytomegalovirus escapes a naturally occurring neutralizing antibody by incorporating it into assembling virions.
Manley K, Anderson J, Yang F, Szustakowski J, Oakeley EJ, Compton T, Feire AL.

Cell Host Microbe. 2011 Sep 15;10(3):197-209.

RNF146 is a poly(ADP-ribose)-directed E3 ligase that regulates axin degradation and Wnt signalling
Zhang Y, Liu S, Mickanin C, Feng Y, Charlat O, Michaud GA, Schirle M, Shi X, Hild M, Bauer A, Myer VE, Finan PM, Porter JA, Huang SM, Cong F.

Nat Cell Biol. 2011 May;13(5):623-9.

Continuous flow coupling and decarboxylation reactions promoted by copper tubing.
Zhang Y, Jamison TF, Patel S, Mainolfi N.

Org Lett. 2011 Jan 21;13(2):280-3.

Safe and Reliable Synthesis of Diazoketones and Quinoxalines in a Continuous Flow Reactor

Martin LJ, Marzinzik AL, Ley SV, Baxendale IR.

Org Lett. 2011 Jan 21;13(2):320-3.

Automated NMR resonance assignment of large proteins for protein-ligand interaction studies.
Gossert AD, Hiller S, Fernández C.
J Am Chem Soc. 2011 Jan 19;133(2):210-3.

Loss of the tumor suppressor Snf5 leads to aberrant activation of the Hedgehog-Gli pathway.
Jagani Z, Mora-Blanco EL, Sansam CG, McKenna ES, Wilson B, Chen D, Klekota J, Tamayo P, Nguyen PT, Tolstorukov M, Park PJ, Cho YJ, Hsiao K, Buonamici S, Pomeroy SL, Mesirov JP, Ruffner H, Bouwmeester T, Luchansky SJ, Murtie J, Kelleher JF, Warmuth M, Sellers WR, Roberts CW, Dorsch M.

Nat Med. 2010 Dec;16(12):1429-33.

KDM1B is a histone H3K4 demethylase required to establish maternal genomic imprints.
Ciccone DN, Su H, Hevi S, Gay F, Lei H, Bajko J, Xu G, Li E, Chen T.

Nature. 2009 Sep 17;461(7262):415-8.

Persistent signaling induced by FTY720-phosphate is mediated by internalized S1P1 receptors.
Mullershausen F, Zecri F, Cetin C, Billich A, Guerini D, Seuwen K.

Nat Chem Biol. 2009 Jun;5(6):428-34.

Mapping adverse drug reactions in chemical space.
Scheiber J, Jenkins JL, Sukuru SC, Bender A, Mikhailov D, Milik M, Azzaoui K, Whitebread S, Hamon J, Urban L, Glick M, Davies JW.
J Med Chem. 2009 May 14;52(9):3103-7.

The lysine demethylase LSD1 (KDM1) is required for maintenance of global DNA methylation.
Wang J, Hevi S, Kurash JK, Lei H, Gay F, Bajko J, Su H, Sun W, Chang H, Xu G, Gaudet F, Li E, Chen T.

Nat Genet. 2009 Jan;41(1):125-9.

The Duffy antigen receptor for chemokines transports chemokines and supports their promigratory activity.
Pruenster M, Mudde L, Bombosi P, Dimitrova S, Zsak M, Middleton J, Richmond A, Graham GJ, Segerer S, Nibbs RJ, Rot A.

Nat Immunol. 2009 Jan;10(1):101-8.

Triggering the succinate receptor GPR91 on dendritic cells enhances immunity.
Rubic, T. Lametschwandtner G, Jost S, Hinteregger S, Kund J, Carballido-Perrig N, Schwarzler C, Junt T, Voshol H, Meingassner JG, Mao X, Werner G, Rot A, Carballido JM.

Nat Immunol. 2008 Nov;9(11):1261-9.

Methylation of p53 by Set7/9 Mediates p53 Acetylation and Activity In Vivo.
Kurash, JK, Lei, H, Shen, Q, Marston, WL, Granda, BW, Fan, H, Wall, D, Li, E, and Gaudet, F.

Mol. Cell. 2008 Feb 15;29(3):392-400.

Integrating high-content screening and ligand-target prediction to identify mechanism of action.
Young DW, Bender A, Hoyt J, McWhinnie E, Chirn GW, Tao CY, Tallarico JA, Labow M, Jenkins JL, Mitchison TJ, Feng Y.
Nat Chem Biol. 2008 Jan;4(1):59-68.

Featured Publication

Planas NCBThe RSPO-LGR4/5-ZNRF3/RNF43 module controls liver zonation and size.
Planas-Paz L, Orsini V, Boulter L, Calabrese D, Pikiolek M, Nigsch F, Xie Y, Roma G, Donovan A, Marti P, Beckmann N, Dill MT, Carbone W, Bergling S, Isken A, Mueller M, Kinzel B, Yang Y, Mao X, Nicholson TB, Zamponi R, Capodieci P, Valdez R, Rivera D, Loew A, Ukomadu C, Terracciano LM, Bouwmeester T, Cong F, Heim MH, Forbes SJ, Ruffner H, Tchorz JS.
Nat Cell Biol. 2016 May;18(5):467-79.