Bruce Conklin, MD

Bio

Honors and Awards

Publications

• SARS-CoV-2 infection of human iPSC-derived cardiac cells reflects cytopathic features in hearts of patients with COVID-19. Perez-Bermejo JA, Kang S, Rockwood SJ, Simoneau CR, Joy DA, Silva AC, Ramadoss GN, Flanigan WR, Fozouni P, Li H, Chen PY, Nakamura K, Whitman JD, Hanson PJ, McManus BM, Ott M, Conklin BR, McDevitt TC. Sci Transl Med. 2021 Mar 15.
• BRD2 inhibition blocks SARS-CoV-2 infection in vitro by reducing transcription of the host cell receptor ACE2. Tian R, Samelson AJ, Rezelj VV, Chen M, Ramadoss GN, Guo X, Kain AM, Tran QD, Lim SA, Lui I, Nunez J, Rockwood SJ, Liu N, Carlson-Stevermer J, Oki J, Maures T, Holden K, Weissman JS, Wells JA, Conklin B, Vignuzzi M, Kampmann M. bioRxiv. 2021 Jan 19.
• Investigating Zeta Globin Gene Expression to Develop a Potential Therapy for Alpha Thalassemia Major. Georgia L. Gregory, Beeke Wienert, Marisa Schwab, Billie Rachael Lianoglou, Roger P. Hollis, Donald B. Kohn, Bruce R. Conklin, Tippi C. MacKenzie. Blood. 2020 Nov 5; 136(Supplement 1):3-4.
• SARS-CoV-2 infection of human iPSC-derived cardiac cells predicts novel cytopathic features in hearts of COVID-19 patients. Pérez-Bermejo JA, Kang S, Rockwood SJ, Simoneau CR, Joy DA, Ramadoss GN, Silva AC, Flanigan WR, Li H, Nakamura K, Whitman JD, Ott M, Conklin BR, McDevitt TC. bioRxiv. 2020 Sep 12.
• Rapid, precise quantification of large DNA excisions and inversions by ddPCR. Watry HL, Feliciano CM, Gjoni K, Takahashi G, Miyaoka Y, Conklin BR, Judge LM. Sci Rep. 2020 09 10; 10(1):14896.
• Critical Roles of Translation Initiation and RNA Uridylation in Endogenous Retroviral Expression and Neural Differentiation in Pluripotent Stem Cells. Takahashi K, Jeong D, Wang S, Narita M, Jin X, Iwasaki M, Perli SD, Conklin BR, Yamanaka S. Cell Rep. 2020 06 02; 31(9):107715.
• Timed inhibition of CDC7 increases CRISPR-Cas9 mediated templated repair. Wienert B, Nguyen DN, Guenther A, Feng SJ, Locke MN, Wyman SK, Shin J, Kazane KR, Gregory GL, Carter MAM, Wright F, Conklin BR, Marson A, Richardson CD, Corn JE. Nat Commun. 2020 04 30; 11(1):2109.
• CRISPR off-target detection with DISCOVER-seq. Wienert B, Wyman SK, Yeh CD, Conklin BR, Corn JE. Nat Protoc. 2020 05; 15(5):1775-1799.
• Cardiac Microtissues: Maladaptive Contractility of 3D Human Cardiac Microtissues to Mechanical Nonuniformity (Adv. Healthcare Mater. 8/2020). Chenyan Wang, Sangmo Koo, Minok Park, Zacharias Vangelatos, Plansky Hoang, Bruce R. Conklin, Costas P. Grigoropoulos, Kevin E. Healy, Zhen Ma. Advanced Healthcare Materials. 2020 Apr 1; 9(8):2070024.
• Maladaptive Contractility of 3D Human Cardiac Microtissues to Mechanical Nonuniformity. Wang C, Koo S, Park M, Vangelatos Z, Hoang P, Conklin BR, Grigoropoulos CP, Healy KE, Ma Z. Adv Healthc Mater. 2020 04; 9(8):e1901373.
• Automated Design of Pluripotent Stem Cell Self-Organization. Libby ARG, Briers D, Haghighi I, Joy DA, Conklin BR, Belta C, McDevitt TC. Cell Syst. 2019 11 27; 9(5):483-495.e10.
• AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design. Keough KC, Lyalina S, Olvera MP, Whalen S, Conklin BR, Pollard KS. Genome Biol. 2019 08 15; 20(1):167.
• Abstract 934: Physical and Genetic Interaction Analyses in Human Pluripotent Stem Cell-Derived Cardiomyocytes to Study Protein Quality Control Disease in the Heart. Juan A Perez-Bermejo, Luke M Judge, Kenneth Wu, Christina L Jensen, Robyn M Kaake, Danielle Swaney, Po-Lin So, Nevan J Krogan, Bruce R Conklin. Circulation Research. 2019 Aug 2; 125(Suppl_1).
• Phenotype-Based High-Throughput Classification of Long QT Syndrome Subtypes Using Human Induced Pluripotent Stem Cells. Yoshinaga D, Baba S, Makiyama T, Shibata H, Hirata T, Akagi K, Matsuda K, Kohjitani H, Wuriyanghai Y, Umeda K, Yamamoto Y, Conklin BR, Horie M, Takita J, Heike T. Stem Cell Reports. 2019 08 13; 13(2):394-404.
• Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes. Song M, Yang X, Ren X, Maliskova L, Li B, Jones IR, Wang C, Jacob F, Wu K, Traglia M, Tam TW, Jamieson K, Lu SY, Ming GL, Li Y, Yao J, Weiss LA, Dixon JR, Judge LM, Conklin BR, Song H, Gan L, Shen Y. Nat Genet. 2019 08; 51(8):1252-1262.
• A NOVEL ROLE FOR THE FTD-CAUSING PROTEIN PROGRANULIN IN APOPTOSIS SIGNALING. Claire Clelland, J. Iker Etchegaray, Lay Kodama, Faten Sayed, Aradhana Sachdev, Yaqiao Li, David Le, Lihong Zhan, Yungui Zhou, Duc Duong, Nicholas T. Seyfried, Thomas G. Kukar, Li Xuan Tan, Aparna Lakkaraju, Bruce Conklin, Li Gan. Alzheimer's & Dementia. 2019 Jul 1; 15(7):p1509.
• Unbiased detection of CRISPR off-targets in vivo using DISCOVER-Seq. Wienert B, Wyman SK, Richardson CD, Yeh CD, Akcakaya P, Porritt MJ, Morlock M, Vu JT, Kazane KR, Watry HL, Judge LM, Conklin BR, Maresca M, Corn JE. Science. 2019 04 19; 364(6437):286-289.
• On the road to a gene drive in mammals. Conklin BR. Nature. 2019 02; 566(7742):43-45.
• MESP1 knock-down in human iPSC attenuates early vascular progenitor cell differentiation after completed primitive streak specification. Eskildsen TV, Ayoubi S, Thomassen M, Burton M, Mandegar MA, Conklin BR, Jensen CH, Andersen DC, Sheikh SP. Dev Biol. 2019 01 01; 445(1):1-7.
• Spatiotemporal mosaic self-patterning of pluripotent stem cells using CRISPR interference. Libby AR, Joy DA, So PL, Mandegar MA, Muncie JM, Mendoza-Camacho FN, Weaver VM, Conklin BR, McDevitt TC. Elife. 2018 10 09; 7.
• Contractile deficits in engineered cardiac microtissues as a result of MYBPC3 deficiency and mechanical overload. Ma Z, Huebsch N, Koo S, Mandegar MA, Siemons B, Boggess S, Conklin BR, Grigoropoulos CP, Healy KE. Nat Biomed Eng. 2018 12; 2(12):955-967.
• Quantitatively characterizing drug-induced arrhythmic contractile motions of human stem cell-derived cardiomyocytes. Hoang P, Huebsch N, Bang SH, Siemons BA, Conklin BR, Healy KE, Ma Z, Jacquir S. Biotechnol Bioeng. 2018 08; 115(8):1958-1970.
• Quantitatively Characterizing Drug-Induced Arrhythmic Contractile Motions of Human Stem Cell-Derived Cardiomyocytes. Plansky Hoang, Nathaniel Huebsch, Shin Hyuk Bang, Brian A. Siemons, Bruce R. Conklin, Kevin E. Healy, Zhen Ma, Sabir Jacquir. Biotechnology and Bioengineering. 2018 Apr 12.
• Generation of spatial-patterned early-developing cardiac organoids using human pluripotent stem cells. Hoang P, Wang J, Conklin BR, Healy KE, Ma Z. Nat Protoc. 2018 04; 13(4):723-737.
• Detection and Quantification of HDR and NHEJ Induced by Genome Editing at Endogenous Gene Loci Using Droplet Digital PCR. Miyaoka Y, Mayerl SJ, Chan AH, Conklin BR. Methods Mol Biol. 2018; 1768:349-362.
• TMOD-09. HUMAN PLURIPOTENT STEM CELL-BASED MODELS OF NEUROBLASTOMA. Miller Huang, Tina Zheng, Jeffrey Guo, Colin Sperring, Matthew Miller, Lauren McHenry, Qiqi Zhen, Branden Moriarity, Marianne Bronner, Bruce Conklin, David Largaespada, John Maris, Katherine Matthay, William Weiss. Neuro-Oncology. 2017 Nov 6; 19(suppl_6):vi256-vi256.
• A BAG3 chaperone complex maintains cardiomyocyte function during proteotoxic stress. Judge LM, Perez-Bermejo JA, Truong A, Ribeiro AJ, Yoo JC, Jensen CL, Mandegar MA, Huebsch N, Kaake RM, So PL, Srivastava D, Pruitt BL, Krogan NJ, Conklin BR. JCI Insight. 2017 Jul 20; 2(14).
• Multi-Imaging Method to Assay the Contractile Mechanical Output of Micropatterned Human iPSC-Derived Cardiac Myocytes. Ribeiro AJS, Schwab O, Mandegar MA, Ang YS, Conklin BR, Srivastava D, Pruitt BL. Circ Res. 2017 May 12; 120(10):1572-1583.
• CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells. Liu SJ, Horlbeck MA, Cho SW, Birk HS, Malatesta M, He D, Attenello FJ, Villalta JE, Cho MY, Chen Y, Mandegar MA, Olvera MP, Gilbert LA, Conklin BR, Chang HY, Weissman JS, Lim DA. Science. 2017 01 06; 355(6320).
• Engineered human pluripotent-stem-cell-derived intestinal tissues with a functional enteric nervous system. Workman MJ, Mahe MM, Trisno S, Poling HM, Watson CL, Sundaram N, Chang CF, Schiesser J, Aubert P, Stanley EG, Elefanty AG, Miyaoka Y, Mandegar MA, Conklin BR, Neunlist M, Brugmann SA, Helmrath MA, Wells JM. Nat Med. 2017 01; 23(1):49-59.
• GENT-49. SYSTEMATIC IDENTIFICATION OF ESSENTIAL LONG NON-CODING RNA GENES IN GLIOBLASTOMA. Siyuan Liu, Max Horlbeck, Seung Woo Cho, Harjus Birk, Martina Malatesta, Daniel He, Jacqueline Villalta, Min Cho, Yuwen Chen, Mohammad Mandegar, Michael Olvera, Bruce Conklin, Howard Chang, Jonathan Weissman, Daniel Lim. Neuro-Oncology. 2016 Nov 1; 18(suppl_6):vi84-vi85.
• BMP-SMAD-ID promotes reprogramming to pluripotency by inhibiting p16/INK4A-dependent senescence. Hayashi Y, Hsiao EC, Sami S, Lancero M, Schlieve CR, Nguyen T, Yano K, Nagahashi A, Ikeya M, Matsumoto Y, Nishimura K, Fukuda A, Hisatake K, Tomoda K, Asaka I, Toguchida J, Conklin BR, Yamanaka S. Proc Natl Acad Sci U S A. 2016 11 15; 113(46):13057-13062.
• Organs-on-a-chip – Microphysiological platforms as in vitro models of cardiac and adipose tissue. P. Loskill, A. Mathur, B.R. Conklin, A. Stahl, L.P. Lee, K.E. Healy. Toxicology Letters. 2016 Sep 1; 258:s153.
• Detecting Single-Nucleotide Substitutions Induced by Genome Editing. Miyaoka Y, Chan AH, Conklin BR. Cold Spring Harb Protoc. 2016 08 01; 2016(8).
• Using Digital Polymerase Chain Reaction to Detect Single-Nucleotide Substitutions Induced by Genome Editing. Miyaoka Y, Chan AH, Conklin BR. Cold Spring Harb Protoc. 2016 08 01; 2016(8).
• Ligand-binding domains of nuclear receptors facilitate tight control of split CRISPR activity. Nguyen DP, Miyaoka Y, Gilbert LA, Mayerl SJ, Lee BH, Weissman JS, Conklin BR, Wells JA. Nat Commun. 2016 07 01; 7:12009.
• Miniaturized iPS-Cell-Derived Cardiac Muscles for Physiologically Relevant Drug Response Analyses. Huebsch N, Loskill P, Deveshwar N, Spencer CI, Judge LM, Mandegar MA, Fox CB, Mohamed TM, Ma Z, Mathur A, Sheehan AM, Truong A, Saxton M, Yoo J, Srivastava D, Desai TA, So PL, Healy KE, Conklin BR. Sci Rep. 2016 Apr 20; 6:24726.
• Systematic quantification of HDR and NHEJ reveals effects of locus, nuclease, and cell type on genome-editing. Miyaoka Y, Berman JR, Cooper SB, Mayerl SJ, Chan AH, Zhang B, Karlin-Neumann GA, Conklin BR. Sci Rep. 2016 Mar 31; 6:23549.
• CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs. Mandegar MA, Huebsch N, Frolov EB, Shin E, Truong A, Olvera MP, Chan AH, Miyaoka Y, Holmes K, Spencer CI, Judge LM, Gordon DE, Eskildsen TV, Villalta JE, Horlbeck MA, Gilbert LA, Krogan NJ, Sheikh SP, Weissman JS, Qi LS, So PL, Conklin BR. Cell Stem Cell. 2016 Apr 07; 18(4):541-53.
• Generating trunk neural crest from human pluripotent stem cells. Huang M, Miller ML, McHenry LK, Zheng T, Zhen Q, Ilkhanizadeh S, Conklin BR, Bronner ME, Weiss WA. Sci Rep. 2016 Jan 27; 6:19727.
• Efficient CRISPR/Cas9-Based Genome Engineering in Human Pluripotent Stem Cells. Kime C, Mandegar MA, Srivastava D, Yamanaka S, Conklin BR, Rand TA. Curr Protoc Hum Genet. 2016 Jan 01; 88:21.4.1-21.4.23.
• Self-organizing human cardiac microchambers mediated by geometric confinement. Ma Z, Wang J, Loskill P, Huebsch N, Koo S, Svedlund FL, Marks NC, Hua EW, Grigoropoulos CP, Conklin BR, Healy KE. Nat Commun. 2015 Jul 14; 6:7413.
• Dysregulation of locus coeruleus development in congenital central hypoventilation syndrome. Nobuta H, Cilio MR, Danhaive O, Tsai HH, Tupal S, Chang SM, Murnen A, Kreitzer F, Bravo V, Czeisler C, Gokozan HN, Gygli P, Bush S, Weese-Mayer DE, Conklin B, Yee SP, Huang EJ, Gray PA, Rowitch D, Otero JJ. Acta Neuropathol. 2015 Aug; 130(2):171-83.
• Loss of Gi G-Protein-Coupled Receptor Signaling in Osteoblasts Accelerates Bone Fracture Healing. Wang L, Hsiao EC, Lieu S, Scott M, O'Carroll D, Urrutia A, Conklin BR, Colnot C, Nissenson RA. J Bone Miner Res. 2015 Oct; 30(10):1896-904.
• Structure-based discovery of NANOG variant with enhanced properties to promote self-renewal and reprogramming of pluripotent stem cells. Hayashi Y, Caboni L, Das D, Yumoto F, Clayton T, Deller MC, Nguyen P, Farr CL, Chiu HJ, Miller MD, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Tomoda K, Conklin BR, Wilson IA, Yamanaka S, Fletterick RJ. Proc Natl Acad Sci U S A. 2015 Apr 14; 112(15):4666-71.
• A non-invasive platform for functional characterization of stem-cell-derived cardiomyocytes with applications in cardiotoxicity testing. Maddah M, Heidmann JD, Mandegar MA, Walker CD, Bolouki S, Conklin BR, Loewke KE. Stem Cell Reports. 2015 Apr 14; 4(4):621-31.
• Human iPSC-based cardiac microphysiological system for drug screening applications. Mathur A, Loskill P, Shao K, Huebsch N, Hong S, Marcus SG, Marks N, Mandegar M, Conklin BR, Lee LP, Healy KE. Sci Rep. 2015 Mar 09; 5:8883.
• Assessing the osteoblast transcriptome in a model of enhanced bone formation due to constitutive Gs-G protein signaling in osteoblasts. Wattanachanya L, Wang L, Millard SM, Lu WD, O'Carroll D, Hsiao EC, Conklin BR, Nissenson RA. Exp Cell Res. 2015 May 01; 333(2):289-302.
• Gai/o-coupled receptor signaling restricts pancreatic ß-cell expansion. Berger M, Scheel DW, Macias H, Miyatsuka T, Kim H, Hoang P, Ku GM, Honig G, Liou A, Tang Y, Regard JB, Sharifnia P, Yu L, Wang J, Coughlin SR, Conklin BR, Deneris ES, Tecott LH, German MS. Proc Natl Acad Sci U S A. 2015 Mar 03; 112(9):2888-93.
• Astrocytic adenosine receptor A2A and Gs-coupled signaling regulate memory. Orr AG, Hsiao EC, Wang MM, Ho K, Kim DH, Wang X, Guo W, Kang J, Yu GQ, Adame A, Devidze N, Dubal DB, Masliah E, Conklin BR, Mucke L. Nat Neurosci. 2015 Mar; 18(3):423-34.
• Automated Video-Based Analysis of Contractility and Calcium Flux in Human-Induced Pluripotent Stem Cell-Derived Cardiomyocytes Cultured over Different Spatial Scales. Huebsch N, Loskill P, Mandegar MA, Marks NC, Sheehan AS, Ma Z, Mathur A, Nguyen TN, Yoo JC, Judge LM, Spencer CI, Chukka AC, Russell CR, So PL, Conklin BR, Healy KE. Tissue Eng Part C Methods. 2015 May; 21(5):467-79.
• Classifying the Electrophysiological Effects of Chronotropic Drugs on Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes using Voltage Sensitive Dyes and Supervised Machine Learning. Christopher M. Heylman, Rupsa Datta, Bruce R. Conklin, Steven C. George, Enrico Gratton. Biophysical Journal. 2015 Jan 1; 108(2):110a.
• Calcium transients closely reflect prolonged action potentials in iPSC models of inherited cardiac arrhythmia. Spencer CI, Baba S, Nakamura K, Hua EA, Sears MA, Fu CC, Zhang J, Balijepalli S, Tomoda K, Hayashi Y, Lizarraga P, Wojciak J, Scheinman MM, Aalto-Setälä K, Makielski JC, January CT, Healy KE, Kamp TJ, Yamanaka S, Conklin BR. Stem Cell Reports. 2014 Aug 12; 3(2):269-81.
• Synthetic control of mammalian-cell motility by engineering chemotaxis to an orthogonal bioinert chemical signal. Park JS, Rhau B, Hermann A, McNally KA, Zhou C, Gong D, Weiner OD, Conklin BR, Onuffer J, Lim WA. Proc Natl Acad Sci U S A. 2014 Apr 22; 111(16):5896-901.
• Isolation of single-base genome-edited human iPS cells without antibiotic selection. Miyaoka Y, Chan AH, Judge LM, Yoo J, Huang M, Nguyen TD, Lizarraga PP, So PL, Conklin BR. Nat Methods. 2014 Mar; 11(3):291-3.
• Human induced pluripotent stem cell-based microphysiological tissue models of myocardium and liver for drug development. Mathur A, Loskill P, Hong S, Lee J, Marcus SG, Dumont L, Conklin BR, Willenbring H, Lee LP, Healy KE. Stem Cell Res Ther. 2013; 4 Suppl 1:S14.
• Induced pluripotent stem cells from patients with human fibrodysplasia ossificans progressiva show increased mineralization and cartilage formation. Matsumoto Y, Hayashi Y, Schlieve CR, Ikeya M, Kim H, Nguyen TD, Sami S, Baba S, Barruet E, Nasu A, Asaka I, Otsuka T, Yamanaka S, Conklin BR, Toguchida J, Hsiao EC. Orphanet J Rare Dis. 2013 Dec 09; 8:190.
• Three-dimensional filamentous human diseased cardiac tissue model. Ma Z, Koo S, Finnegan MA, Loskill P, Huebsch N, Marks NC, Conklin BR, Grigoropoulos CP, Healy KE. Biomaterials. 2014 Feb; 35(5):1367-77.
• The C-terminus of the long AKAP13 isoform (AKAP-Lbc) is critical for development of compensatory cardiac hypertrophy. Taglieri DM, Johnson KR, Burmeister BT, Monasky MM, Spindler MJ, DeSantiago J, Banach K, Conklin BR, Carnegie GK. J Mol Cell Cardiol. 2014 Jan; 66:27-40.
• Sculpting genomes with a hammer and chisel. Conklin BR. Nat Methods. 2013 Sep; 10(9):839-40.
• A robust method to derive functional neural crest cells from human pluripotent stem cells. Kreitzer FR, Salomonis N, Sheehan A, Huang M, Park JS, Spindler MJ, Lizarraga P, Weiss WA, So PL, Conklin BR. Am J Stem Cells. 2013; 2(2):119-31.
• AKAP13 Rho-GEF and PKD-binding domain deficient mice develop normally but have an abnormal response to ß-adrenergic-induced cardiac hypertrophy. Spindler MJ, Burmeister BT, Huang Y, Hsiao EC, Salomonis N, Scott MJ, Srivastava D, Carnegie GK, Conklin BR. PLoS One. 2013; 8(4):e62705.
• Structure of a novel winged-helix like domain from human NFRKB protein. Kumar A, Möcklinghoff S, Yumoto F, Jaroszewski L, Farr CL, Grzechnik A, Nguyen P, Weichenberger CX, Chiu HJ, Klock HE, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Conklin BR, Fletterick RJ, Wilson IA. PLoS One. 2012; 7(9):e43761.
• Derivation conditions impact X-inactivation status in female human induced pluripotent stem cells. Tomoda K, Takahashi K, Leung K, Okada A, Narita M, Yamada NA, Eilertson KE, Tsang P, Baba S, White MP, Sami S, Srivastava D, Conklin BR, Panning B, Yamanaka S. Cell Stem Cell. 2012 Jul 06; 11(1):91-9.
• GO-Elite: a flexible solution for pathway and ontology over-representation. Zambon AC, Gaj S, Ho I, Hanspers K, Vranizan K, Evelo CT, Conklin BR, Pico AR, Salomonis N. Bioinformatics. 2012 Aug 15; 28(16):2209-10.
• WikiPathways: building research communities on biological pathways. Kelder T, van Iersel MP, Hanspers K, Kutmon M, Conklin BR, Evelo CT, Pico AR. Nucleic Acids Res. 2012 Jan; 40(Database issue):D1301-7.
• Model for long QT syndrome type 2 using human iPS cells demonstrates arrhythmogenic characteristics in cell culture. Lahti AL, Kujala VJ, Chapman H, Koivisto AP, Pekkanen-Mattila M, Kerkelä E, Hyttinen J, Kontula K, Swan H, Conklin BR, Yamanaka S, Silvennoinen O, Aalto-Setälä K. Dis Model Mech. 2012 Mar; 5(2):220-30.
• Mineral composition is altered by osteoblast expression of an engineered G(s)-coupled receptor. Kazakia GJ, Speer D, Shanbhag S, Majumdar S, Conklin BR, Nissenson RA, Hsiao EC. Calcif Tissue Int. 2011 Jul; 89(1):10-20.
• Blockade of receptor-activated G(i) signaling in osteoblasts in vivo leads to site-specific increases in cortical and cancellous bone formation. Millard SM, Louie AM, Wattanachanya L, Wronski TJ, Conklin BR, Nissenson RA. J Bone Miner Res. 2011 Apr; 26(4):822-32.
• Constitutive Gs activation using a single-construct tetracycline-inducible expression system in embryonic stem cells and mice. Hsiao EC, Nguyen TD, Ng JK, Scott MJ, Chang WC, Zahed H, Conklin BR. Stem Cell Res Ther. 2011 Mar 04; 2(2):11.
• Finding the right questions: exploratory pathway analysis to enhance biological discovery in large datasets. Kelder T, Conklin BR, Evelo CT, Pico AR. PLoS Biol. 2010 Aug 31; 8(8).
• Stem cell pluripotency: alternative modes of transcription regulation. Salomonis N, Conklin BR. . 2010 Aug 15; 9(16):3133-4.
• Reporter-based isolation of induced pluripotent stem cell- and embryonic stem cell-derived cardiac progenitors reveals limited gene expression variance. van Laake LW, Qian L, Cheng P, Huang Y, Hsiao EC, Conklin BR, Srivastava D. Circ Res. 2010 Aug 06; 107(3):340-7.
• AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. Emig D, Salomonis N, Baumbach J, Lengauer T, Conklin BR, Albrecht M. Nucleic Acids Res. 2010 Jul; 38(Web Server issue):W755-62.
• Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation. Salomonis N, Schlieve CR, Pereira L, Wahlquist C, Colas A, Zambon AC, Vranizan K, Spindler MJ, Pico AR, Cline MS, Clark TA, Williams A, Blume JE, Samal E, Mercola M, Merrill BJ, Conklin BR. Proc Natl Acad Sci U S A. 2010 Jun 08; 107(23):10514-9.
• Gs G protein-coupled receptor signaling in osteoblasts elicits age-dependent effects on bone formation. Hsiao EC, Boudignon BM, Halloran BP, Nissenson RA, Conklin BR. J Bone Miner Res. 2010 Mar; 25(3):584-93.
• Ligand-mediated activation of an engineered gs g protein-coupled receptor in osteoblasts increases trabecular bone formation. Hsiao EC, Millard SM, Louie A, Huang Y, Conklin BR, Nissenson RA. Mol Endocrinol. 2010 Mar; 24(3):621-31.
• Cloning mice and men: prohibiting the use of iPS cells for human reproductive cloning. Lo B, Parham L, Alvarez-Buylla A, Cedars M, Conklin B, Fisher S, Gates E, Giudice L, Halme DG, Hershon W, Kriegstein A, Kwok PY, Wagner R. Cell Stem Cell. 2010 Jan 08; 6(1):16-20.
• The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. van Iersel MP, Pico AR, Kelder T, Gao J, Ho I, Hanspers K, Conklin BR, Evelo CT. BMC Bioinformatics. 2010 Jan 04; 11:5.
• G(i)-coupled GPCR signaling controls the formation and organization of human pluripotent colonies. Nakamura K, Salomonis N, Tomoda K, Yamanaka S, Conklin BR. PLoS One. 2009 Nov 10; 4(11):e7780.
• Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors. Salomonis N, Nelson B, Vranizan K, Pico AR, Hanspers K, Kuchinsky A, Ta L, Mercola M, Conklin BR. PLoS Comput Biol. 2009 Nov; 5(11):e1000553.
• Consent: criteria should be drawn up for tissue donors. Lo B, Conklin BR. Nature. 2009 Oct 01; 461(7264):593.
• Journal club. A geneticist wonders why we need to sleep. Conklin BR. Nature. 2009 Oct 01; 461(7264):573.
• Mining biological pathways using WikiPathways web services. Kelder T, Pico AR, Hanspers K, van Iersel MP, Evelo C, Conklin BR. PLoS One. 2009 Jul 30; 4(7):e6447.
• AKAP10 (I646V) functional polymorphism predicts heart rate and heart rate variability in apparently healthy, middle-aged European-Americans. Neumann SA, Tingley WG, Conklin BR, Shrader CJ, Peet E, Muldoon MF, Jennings JR, Ferrell RE, Manuck SB. Psychophysiology. 2009 May; 46(3):466-72.
• Endogenous Gi signaling in osteoblasts participates in sexually dimorphic regulation of cancellous bone structure. S. Millard, A. Louie, C. Manalac, W. Lu, N. Cotte, T.J. Wronski, B. Conklin, R.A. Nissenson. Bone. 2009 May 1; 44:s153.
• Lentiviral vectors and protocols for creation of stable hESC lines for fluorescent tracking and drug resistance selection of cardiomyocytes. Kita-Matsuo H, Barcova M, Prigozhina N, Salomonis N, Wei K, Jacot JG, Nelson B, Spiering S, Haverslag R, Kim C, Talantova M, Bajpai R, Calzolari D, Terskikh A, McCulloch AD, Price JH, Conklin BR, Chen HS, Mercola M. PLoS One. 2009; 4(4):e5046.
• Obtaining consent for future research with induced pluripotent cells: opportunities and challenges. Aalto-Setälä K, Conklin BR, Lo B. PLoS Biol. 2009 Feb 24; 7(2):e42.
• SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system. Pico AR, Smirnov IV, Chang JS, Yeh RF, Wiemels JL, Wiencke JK, Tihan T, Conklin BR, Wrensch M. Nucleic Acids Res. 2009 Jan; 37(Database issue):D803-9.
• Presenting and exploring biological pathways with PathVisio. van Iersel MP, Kelder T, Pico AR, Hanspers K, Coort S, Conklin BR, Evelo C. BMC Bioinformatics. 2008 Sep 25; 9:399.
• Engineering GPCR signaling pathways with RASSLs. Conklin BR, Hsiao EC, Claeysen S, Dumuis A, Srinivasan S, Forsayeth JR, Guettier JM, Chang WC, Pei Y, McCarthy KD, Nissenson RA, Wess J, Bockaert J, Roth BL. Nat Methods. 2008 Aug; 5(8):673-8.
• WikiPathways: pathway editing for the people. Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. PLoS Biol. 2008 Jul 22; 6(7):e184.
• Marking embryonic stem cells with a 2A self-cleaving peptide: a NKX2-5 emerald GFP BAC reporter. Hsiao EC, Yoshinaga Y, Nguyen TD, Musone SL, Kim JE, Swinton P, Espineda I, Manalac C, deJong PJ, Conklin BR. PLoS One. 2008 Jul 02; 3(7):e2532.
• An Introduction to Pathway Analysis with GenMAPP. Kristina Hanspers, Alexander R. Pico, Nathan Salomonis, Alexander C. Zambon, Karen Vranizan, Steven C. Lawlor, Kam D. Dahlquist, Scott W. Doniger, Bruce R. Conklin. NCI Nature Pathway Interaction Database. 2008 Apr 8.
• MicroRNA regulation of cell lineages in mouse and human embryonic stem cells. Ivey KN, Muth A, Arnold J, King FW, Yeh RF, Fish JE, Hsiao EC, Schwartz RJ, Conklin BR, Bernstein HS, Srivastava D. Cell Stem Cell. 2008 Mar 06; 2(3):219-29.
• Comparative analysis of wild-type and cAMP-deathless S49 lymphoma cells identifies genes and pathways of cAMP/PKA-promoted apoptosis. Lingzhi Zhang, Alexander C Zambon, Karen Vranizan, Kanishka Pothula, Bruce R Conklin, Paul A Insel. The FASEB Journal. 2008 Mar 1; 22:648.13-648.13.
• Osteoblast expression of an engineered Gs-coupled receptor dramatically increases bone mass. Hsiao EC, Boudignon BM, Chang WC, Bencsik M, Peng J, Nguyen TD, Manalac C, Halloran BP, Conklin BR, Nissenson RA. Proc Natl Acad Sci U S A. 2008 Jan 29; 105(4):1209-14.
• Modifying ligand-induced and constitutive signaling of the human 5-HT4 receptor. Chang WC, Ng JK, Nguyen T, Pellissier L, Claeysen S, Hsiao EC, Conklin BR. PLoS One. 2007 Dec 19; 2(12):e1317.
• Conditional expression of a Gi-coupled receptor in osteoblasts results in trabecular osteopenia. Peng J, Bencsik M, Louie A, Lu W, Millard S, Nguyen P, Burghardt A, Majumdar S, Wronski TJ, Halloran B, Conklin BR, Nissenson RA. Endocrinology. 2008 Mar; 149(3):1329-37.
• Gene expression signatures of cAMP/protein kinase A (PKA)-promoted, mitochondrial-dependent apoptosis. Comparative analysis of wild-type and cAMP-deathless S49 lymphoma cells. Zhang L, Zambon AC, Vranizan K, Pothula K, Conklin BR, Insel PA. J Biol Chem. 2008 Feb 15; 283(7):4304-13.
• Engineering the melanocortin-4 receptor to control constitutive and ligand-mediated G(S) signaling in vivo. Srinivasan S, Santiago P, Lubrano C, Vaisse C, Conklin BR. PLoS One. 2007 Aug 01; 2(7):e668.
• Modeling insertional mutagenesis using gene length and expression in murine embryonic stem cells. Nord AS, Vranizan K, Tingley W, Zambon AC, Hanspers K, Fong LG, Hu Y, Bacchetti P, Ferrin TE, Babbitt PC, Doniger SW, Skarnes WC, Young SG, Conklin BR. PLoS One. 2007 Jul 18; 2(7):e617.
• GenMAPP 2: new features and resources for pathway analysis. Salomonis N, Hanspers K, Zambon AC, Vranizan K, Lawlor SC, Dahlquist KD, Doniger SW, Stuart J, Conklin BR, Pico AR. BMC Bioinformatics. 2007 Jun 24; 8:217.
• Canonical Wnt signaling is a positive regulator of mammalian cardiac progenitors. Kwon C, Arnold J, Hsiao EC, Taketo MM, Conklin BR, Srivastava D. Proc Natl Acad Sci U S A. 2007 Jun 26; 104(26):10894-9.
• Interfacing silicon nanowires with mammalian cells. Kim W, Ng JK, Kunitake ME, Conklin BR, Yang P. J Am Chem Soc. 2007 Jun 13; 129(23):7228-9.
• Gene-trapped mouse embryonic stem cell-derived cardiac myocytes and human genetics implicate AKAP10 in heart rhythm regulation. Tingley WG, Pawlikowska L, Zaroff JG, Kim T, Nguyen T, Young SG, Vranizan K, Kwok PY, Whooley MA, Conklin BR. Proc Natl Acad Sci U S A. 2007 May 15; 104(20):8461-6.
• New tools to build synthetic hormonal pathways. Conklin BR. Proc Natl Acad Sci U S A. 2007 Mar 20; 104(12):4777-8.
• Development of hydrocephalus in mice expressing the G(i)-coupled GPCR Ro1 RASSL receptor in astrocytes. Sweger EJ, Casper KB, Scearce-Levie K, Conklin BR, McCarthy KD. J Neurosci. 2007 Feb 28; 27(9):2309-17.
• Integration of biological networks and gene expression data using Cytoscape. Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD. Nat Protoc. 2007; 2(10):2366-82.
• mGluR2 acts through inhibitory Galpha subunits to regulate transmission and long-term plasticity at hippocampal mossy fiber-CA3 synapses. Nicholls RE, Zhang XL, Bailey CP, Conklin BR, Kandel ER, Stanton PK. Proc Natl Acad Sci U S A. 2006 Apr 18; 103(16):6380-5.
• A Series of RASSLs Activated by a Single Agonist. Peter Chang, Edward Hsiao, Alex C Zambon, Bruce R Conklin. The FASEB Journal. 2006 Mar 1; 20(4):a249-a249.
• The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse. Nord AS, Chang PJ, Conklin BR, Cox AV, Harper CA, Hicks GG, Huang CC, Johns SJ, Kawamoto M, Liu S, Meng EC, Morris JH, Rossant J, Ruiz P, Skarnes WC, Soriano P, Stanford WL, Stryke D, von Melchner H, Wurst W, Yamamura K, Young SG, Babbitt PC, Ferrin TE. Nucleic Acids Res. 2006 Jan 01; 34(Database issue):D642-8.
• Sustained preconditioning induced by cardiac transgenesis with the tetracycline transactivator. Turnbull L, Zhou HZ, Swigart PM, Turcato S, Karliner JS, Conklin BR, Simpson PC, Baker AJ. . 2006 Mar; 290(3):H1103-9.
• Gene expression patterns define key transcriptional events in cell-cycle regulation by cAMP and protein kinase A. Zambon AC, Zhang L, Minovitsky S, Kanter JR, Prabhakar S, Salomonis N, Vranizan K, Dubchak I, Conklin BR, Insel PA. Proc Natl Acad Sci U S A. 2005 Jun 14; 102(24):8561-6.
• Cardiac transgenesis with the tetracycline transactivator changes myocardial function and gene expression. McCloskey DT, Turnbull L, Swigart PM, Zambon AC, Turcato S, Joho S, Grossman W, Conklin BR, Simpson PC, Baker AJ. Physiol Genomics. 2005 Jun 16; 22(1):118-26.
• Engineered G protein coupled receptors reveal independent regulation of internalization, desensitization and acute signaling. Scearce-Levie K, Lieberman MD, Elliott HH, Conklin BR. BMC Biol. 2005 Feb 11; 3:3.
• Identifying genetic networks underlying myometrial transition to labor. Salomonis N, Cotte N, Zambon AC, Pollard KS, Vranizan K, Doniger SW, Dolganov G, Conklin BR. Genome Biol. 2005; 6(2):R12.
• Constitutive activity of the melanocortin-4 receptor is maintained by its N-terminal domain and plays a role in energy homeostasis in humans. Srinivasan S, Lubrano-Berthelier C, Govaerts C, Picard F, Santiago P, Conklin BR, Vaisse C. J Clin Invest. 2004 Oct; 114(8):1158-64.
• A public gene trap resource for mouse functional genomics. Skarnes WC, von Melchner H, Wurst W, Hicks G, Nord AS, Cox T, Young SG, Ruiz P, Soriano P, Tessier-Lavigne M, Conklin BR, Stanford WL, Rossant J. Nat Genet. 2004 Jun; 36(6):543-4.
• Time- and exercise-dependent gene regulation in human skeletal muscle. Zambon AC, McDearmon EL, Salomonis N, Vranizan KM, Johansen KL, Adey D, Takahashi JS, Schambelan M, Conklin BR. Genome Biol. 2003; 4(10):R61.
• Engineering the melanocortin-4 receptor to control G(s) signaling in vivo. Srinivasan S, Vaisse C, Conklin BR. Ann N Y Acad Sci. 2003 Jun; 994:225-32.
• MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Doniger SW, Salomonis N, Dahlquist KD, Vranizan K, Lawlor SC, Conklin BR. Genome Biol. 2003; 4(1):R7.
• Regression approaches for microarray data analysis. Segal MR, Dahlquist KD, Conklin BR. J Comput Biol. 2003; 10(6):961-80.
• GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Dahlquist KD, Salomonis N, Vranizan K, Lawlor SC, Conklin BR. Nat Genet. 2002 May; 31(1):19-20.
• Tools for dissecting signaling pathways in vivo: receptors activated solely by synthetic ligands. Scearce-Levie K, Coward P, Redfern CH, Conklin BR. Methods Enzymol. 2002; 343:232-48.
• Engineering receptors activated solely by synthetic ligands (RASSLs). Scearce-Levie K, Coward P, Redfern CH, Conklin BR. Trends Pharmacol Sci. 2001 Aug; 22(8):414-20.
• Abnormal contraction caused by expression of G(i)-coupled receptor in transgenic model of dilated cardiomyopathy. Baker AJ, Redfern CH, Harwood MD, Simpson PC, Conklin BR. . 2001 Apr; 280(4):H1653-9.
• Tetracycline-inducible system for photoreceptor-specific gene expression. Chang MA, Horner JW, Conklin BR, DePinho RA, Bok D, Zack DJ. Invest Ophthalmol Vis Sci. 2000 Dec; 41(13):4281-7.
• Conditional expression of a Gi-coupled receptor causes ventricular conduction delay and a lethal cardiomyopathy. Redfern CH, Degtyarev MY, Kwa AT, Salomonis N, Cotte N, Nanevicz T, Fidelman N, Desai K, Vranizan K, Lee EK, Coward P, Shah N, Warrington JA, Fishman GI, Bernstein D, Baker AJ, Conklin BR. Proc Natl Acad Sci U S A. 2000 Apr 25; 97(9):4826-31.
• A critical period of vulnerability to hyperactive Gq signaling revealed by inducible and heart-specific expression of Gq* in transgenic mice. Nathalie Cotte, Charles H. Redfern, Peter Mikus, Nathan Salomonis, Michael Y. Degtyarev, Peter S. Coward, Andrew Kwa, Tetsuo Shioi, Nila Shah, Tim McKinsey, Eric Olson, Seigo Izumo, Janet Warrington, Anthony J. Baker, Bruce R. Conklin. Journal of Cardiac Failure. 1999 Sep 1; 5(3):12.
• Genomic analysis of an inducible and reversible model of dilated cardiomyopathy. Charles H. Redfern, Michael Y. Degtyarev, Kavin Desai, Andrew Kwa, Glenn I. Fishman, Daniel Bernstein, Anthony J. Baker, Bruce R. Conklin. Journal of Cardiac Failure. 1999 Sep 1; 5(3):14.
• Chimeric G proteins allow a high-throughput signaling assay of Gi-coupled receptors. Coward P, Chan SD, Wada HG, Humphries GM, Conklin BR. Anal Biochem. 1999 Jun 01; 270(2):242-8.
• Conditional expression and signaling of a specifically designed Gi-coupled receptor in transgenic mice. Redfern CH, Coward P, Degtyarev MY, Lee EK, Kwa AT, Hennighausen L, Bujard H, Fishman GI, Conklin BR. Nat Biotechnol. 1999 Feb; 17(2):165-9.
• Controlling signaling with a specifically designed Gi-coupled receptor. Coward P, Wada HG, Falk MS, Chan SD, Meng F, Akil H, Conklin BR. Proc Natl Acad Sci U S A. 1998 Jan 06; 95(1):352-7.
• The N-terminal extension of Galphaq is critical for constraining the selectivity of receptor coupling. Kostenis E, Degtyarev MY, Conklin BR, Wess J. J Biol Chem. 1997 Aug 01; 272(31):19107-10.
• Molecular basis of receptor/G protein coupling selectivity studied by coexpression of wild type and mutant m2 muscarinic receptors with mutant G alpha(q) subunits. Kostenis E, Conklin BR, Wess J. Biochemistry. 1997 Feb 11; 36(6):1487-95.
• Interactions of muscarinic receptors with the heterotrimeric G proteins Gq and G12: transduction of proliferative signals. Burstein ES, Bräuner-Osborne H, Spalding TA, Conklin BR, Brann MR. J Neurochem. 1997 Feb; 68(2):525-33.
• Carboxyl-terminal mutations of Gq alpha and Gs alpha that alter the fidelity of receptor activation. Conklin BR, Herzmark P, Ishida S, Voyno-Yasenetskaya TA, Sun Y, Farfel Z, Bourne HR. Mol Pharmacol. 1996 Oct; 50(4):885-90.
• Molecular mechanisms involved in muscarinic acetylcholine receptor-mediated G protein activation studied by insertion mutagenesis. Liu J, Blin N, Conklin BR, Wess J. J Biol Chem. 1996 Mar 15; 271(11):6172-8.
• Identification of a receptor/G-protein contact site critical for signaling specificity and G-protein activation. Liu J, Conklin BR, Blin N, Yun J, Wess J. Proc Natl Acad Sci U S A. 1995 Dec 05; 92(25):11642-6.
• Coupling of the alpha 2A-adrenergic receptor to multiple G-proteins. A simple approach for estimating receptor-G-protein coupling efficiency in a transient expression system. Chabre O, Conklin BR, Brandon S, Bourne HR, Limbird LE. J Biol Chem. 1994 Feb 25; 269(8):5730-4.
• G alpha 13 stimulates Na-H exchange. Voyno-Yasenetskaya T, Conklin BR, Gilbert RL, Hooley R, Bourne HR, Barber DL. J Biol Chem. 1994 Feb 18; 269(7):4721-4.
• Homeostatic signals. Marriage of the flytrap and the serpent. Conklin BR, Bourne HR. Nature. 1994 Jan 06; 367(6458):22.
• Mouse coat colour reconsidered. Conklin BR, Bourne HR. Nature. 1993 Jul 08; 364(6433):110.
• Type II adenylylcyclase integrates coincident signals from Gs, Gi, and Gq. Lustig KD, Conklin BR, Herzmark P, Taussig R, Bourne HR. J Biol Chem. 1993 Jul 05; 268(19):13900-5.
• Structural elements of G alpha subunits that interact with G beta gamma, receptors, and effectors. Conklin BR, Bourne HR. Cell. 1993 May 21; 73(4):631-41.
• Substitution of three amino acids switches receptor specificity of Gq alpha to that of Gi alpha. Conklin BR, Farfel Z, Lustig KD, Julius D, Bourne HR. Nature. 1993 May 20; 363(6426):274-6.
• A recombinant calcitonin receptor independently stimulates 3',5'-cyclic adenosine monophosphate and Ca2+/inositol phosphate signaling pathways. Chabre O, Conklin BR, Lin HY, Lodish HF, Wilson E, Ives HE, Catanzariti L, Hemmings BA, Bourne HR. Mol Endocrinol. 1992 Apr; 6(4):551-6.
• Hormonal stimulation of adenylyl cyclase through Gi-protein beta gamma subunits. Federman AD, Conklin BR, Schrader KA, Reed RR, Bourne HR. Nature. 1992 Mar 12; 356(6365):159-61.
• Gz-mediated hormonal inhibition of cyclic AMP accumulation. Wong YH, Conklin BR, Bourne HR. Science. 1992 Jan 17; 255(5042):339-42.
• Recombinant Gq alpha. Mutational activation and coupling to receptors and phospholipase C. Conklin BR, Chabre O, Wong YH, Federman AD, Bourne HR. J Biol Chem. 1992 Jan 05; 267(1):31-4.
• Detection of coincident signals by G proteins and adenylyl cyclase. Bourne HR, Lustig KD, Wong YH, Conklin BR. Cold Spring Harb Symp Quant Biol. 1992; 57:145-8.
• Carbachol-induced reverse transformation of Chinese hamster ovary cells transfected with and expressing the m5 muscarinic acetylcholine receptor. Felder CC, Ma AL, Conklin BR. FEBS Lett. 1989 Mar 13; 245(1-2):75-9.
• Stimulation of arachidonic acid release and inhibition of mitogenesis by cloned genes for muscarinic receptor subtypes stably expressed in A9 L cells. Conklin BR, Brann MR, Buckley NJ, Ma AL, Bonner TI, Axelrod J. Proc Natl Acad Sci U S A. 1988 Nov; 85(22):8698-702.
• Distinct bradykinin receptors mediate stimulation of prostaglandin synthesis by endothelial cells and fibroblasts. Conklin BR, Burch RM, Steranka LR, Axelrod J. J Pharmacol Exp Ther. 1988 Feb; 244(2):646-9.

More Publications

Contact