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Publication TitleAuthorsJournalPublication DatePage NoPubMedID
CCR7-dependent trafficking of RORýýýýý ILCs creates a unique microenvironment within mucosal draining lymph nodes.Mackley, Emma C; Houston, Stephanie; Marriott, Clare L; Halford, Emily E; Lucas, Beth; Cerovic, Vuk; Filbey, Kara J; Maizels, Rick M; Hepworth, Matthew R; Sonnenberg, Gregory F; Milling, Simon; Withers, David RNature communications.2015;25575242
Validation of in vivo 2D displacements from spiral cine DENSE at 3T.Wehner, Gregory J; Suever, Jonathan D; Haggerty, Christopher M; Jing, Linyuan; Powell, David K; Hamlet, Sean M; Grabau, Jonathan D; Mojsejenko, Walter Dimitri; Zhong, Xiaodong; Epstein, Frederick H; Fornwalt, Brandon KJournal of cardiovascular magnetic resonance : official journal of the Society for Cardiovascular Magnetic Resonance.2015;25634468
Identification and selective expansion of functionally superior T cells expressing chimeric antigen receptors.Chang, ZeNan L; Silver, Pamela A; Chen, Yvonne YJournal of translational medicine.2015;25990251
Caspase-8 scaffolding function and MLKL regulate NLRP3 inflammasome activation downstream of TLR3.Kang, Seokwon; Fernandes-Alnemri, Teresa; Rogers, Corey; Mayes, Lindsey; Wang, Ying; Dillon, Christopher; Roback, Linda; Kaiser, William; Oberst, Andrew; Sagara, Junji; Fitzgerald, Katherine A; Green, Douglas R; Zhang, Jianke; Mocarski, Edward S; Alnemri, Emad SNature communications.2015;26104484
Optical coherence contrast imaging using gold nanorods in living mice eyes.de la Zerda, Adam; Prabhulkar, Shradha; Perez, Victor L; Ruggeri, Marco; Paranjape, Amit S; Habte, Frezghi; Gambhir, Sanjiv S; Awdeh, Richard MClinical & experimental ophthalmology.2015 May;358-6624533647
The cluster graphical lasso for improved estimation of Gaussian graphical models.Tan, Kean Ming; Witten, Daniela; Shojaie, AliComputational statistics & data analysis.2015 May;23-3625642008
Cost savings associated with expanded hospice use in Medicare.Powers, Brian W; Makar, Maggie; Jain, Sachin H; Cutler, David M; Obermeyer, ZiadJournal of palliative medicine.2015 May;400-125806563
Necroptosis: The Trojan horse in cell autonomous antiviral host defense.Mocarski, Edward S; Guo, Hongyan; Kaiser, William JVirology.2015 May;160-625819165
Immune tolerance. Group 3 innate lymphoid cells mediate intestinal selection of commensal bacteria-specific CD4? T cells.Hepworth, Matthew R; Fung, Thomas C; Masur, Samuel H; Kelsen, Judith R; McConnell, Fiona M; Dubrot, Juan; Withers, David R; Hugues, Stephanie; Farrar, Michael A; Reith, Walter; Eberl, Gérard; Baldassano, Robert N; Laufer, Terri M; Elson, Charles O; Sonnenberg, Gregory FScience (New York, N.Y.).2015 May 29;1031-525908663
Lineage-Specific Viral Hijacking of Non-canonical E3 Ubiquitin Ligase Cofactors in the Evolution of Vif Anti-APOBEC3 Activity.Kane, Joshua R; Stanley, David J; Hultquist, Judd F; Johnson, Jeffrey R; Mietrach, Nicole; Binning, Jennifer M; Jónsson, Stefán R; Barelier, Sarah; Newton, Billy W; Johnson, Tasha L; Franks-Skiba, Kathleen E; Li, Ming; Brown, William L; Gunnarsson, Hörður I; Adalbjornsdóttir, Adalbjorg; Fraser, James S; Harris, Reuben S; Andrésdóttir, Valgerður; Gross, John D; Krogan, Nevan JCell reports.2015 May 26;1236-5025981045
The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3.McHugh, Colleen A; Chen, Chun-Kan; Chow, Amy; Surka, Christine F; Tran, Christina; McDonel, Patrick; Pandya-Jones, Amy; Blanco, Mario; Burghard, Christina; Moradian, Annie; Sweredoski, Michael J; Shishkin, Alexander A; Su, Julia; Lander, Eric S; Hess, Sonja; Plath, Kathrin; Guttman, MitchellNature.2015 May 14;232-625915022
Suppression of RIP3-dependent necroptosis by human cytomegalovirus.Omoto, Shinya; Guo, Hongyan; Talekar, Ganesh R; Roback, Linda; Kaiser, William J; Mocarski, Edward SThe Journal of biological chemistry.2015 May 1;11635-4825778401
Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics.Yaung, Stephanie J; Deng, Luxue; Li, Ning; Braff, Jonathan L; Church, George M; Bry, Lynn; Wang, Harris H; Gerber, Georg KMolecular systems biology.2015 Mar;26148351
Group 2 innate lymphoid cells promote beiging of white adipose tissue and limit obesity.Brestoff, Jonathan R; Kim, Brian S; Saenz, Steven A; Stine, Rachel R; Monticelli, Laurel A; Sonnenberg, Gregory F; Thome, Joseph J; Farber, Donna L; Lutfy, Kabirullah; Seale, Patrick; Artis, DavidNature.2015 Mar 12;242-625533952
Manipulation of apoptosis and necroptosis signaling by herpesviruses.Guo, Hongyan; Kaiser, William J; Mocarski, Edward SMedical microbiology and immunology.2015 Jun;439-4825828583
Physician Characteristics Strongly Predict Patient Enrollment In Hospice.Obermeyer, Ziad; Powers, Brian W; Makar, Maggie; Keating, Nancy L; Cutler, David MHealth affairs (Project Hope).2015 Jun;993-100026056205
Innate lymphoid cells in the initiation, regulation and resolution of inflammation.Sonnenberg, Gregory F; Artis, DavidNature medicine.2015 Jul;698-70826121198
Proton Pump Inhibitors Alter Specific Taxa in the Human Gastrointestinal Microbiome: A Crossover Trial.Freedberg, Daniel E; Toussaint, Nora C; Chen, Sway P; Ratner, Adam J; Whittier, Susan; Wang, Timothy C; Wang, Harris H; Abrams, Julian AGastroenterology.2015 Jul 8;26164495
One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites.Fischer, Marcus; Shoichet, Brian K; Fraser, James SChembiochem : a European journal of chemical biology.2015 Jul 27;1560-426032594
Negative Epistasis and Evolvability in TEM-1 *-Lactamase-The Thin Line between an Enzyme's Conformational Freedom and Disorder.Dellus-Gur, Eynat; Elias, Mikael; Caselli, Emilia; Prati, Fabio; Salverda, Merijn L M; de Visser, J Arjan G M; Fraser, James S; Tawfik, Dan SJournal of molecular biology.2015 Jul 17;2396-40926004540
Aging and brain rejuvenation as systemic events.Bouchard, Jill; Villeda, Saul AJournal of neurochemistry.2015 Jan;25327899
A chemical rescue screen identifies a Plasmodium falciparum apicoplast inhibitor targeting MEP isoprenoid precursor biosynthesis.Wu, Wesley; Herrera, Zachary; Ebert, Danny; Baska, Katie; Cho, Seok H; DeRisi, Joseph L; Yeh, EllenAntimicrobial agents and chemotherapy.2015 Jan;356-6425367906
Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics.Yaung, Stephanie J; Deng, Luxue; Li, Ning; Braff, Jonathan L; Church, George M; Bry, Lynn; Wang, Harris H; Gerber, Georg KMolecular systems biology.2015 Jan;25762151
Pathway Graphical Lasso.Grechkin, Maxim; Fazel, Maryam; Witten, Daniela; Lee, Su-InProceedings of the ... AAAI Conference on Artificial Intelligence. AAAI Conference on Artificial Intelligence.2015 Jan;2617-262326167394
Subclonal mutations in SETBP1 confer a poor prognosis in juvenile myelomonocytic leukemia.Stieglitz, Elliot; Troup, Camille B; Gelston, Laura C; Haliburton, John; Chow, Eric D; Yu, Kristie B; Akutagawa, Jon; Taylor-Weiner, Amaro N; Liu, Y Lucy; Wang, Yong-Dong; Beckman, Kyle; Emanuel, Peter D; Braun, Benjamin S; Abate, Adam; Gerbing, Robert B; Alonzo, Todd A; Loh, Mignon LBlood.2015 Jan 15;516-2425395418
Keep on moving: discovering and perturbing the conformational dynamics of enzymes.Bhabha, Gira; Biel, Justin T; Fraser, James SAccounts of chemical research.2015 Feb 17;423-3025539415
A strategy for tissue self-organization that is robust to cellular heterogeneity and plasticity.Cerchiari, Alec E; Garbe, James C; Jee, Noel Y; Todhunter, Michael E; Broaders, Kyle E; Peehl, Donna M; Desai, Tejal A; LaBarge, Mark A; Thomson, Matthew; Gartner, Zev JProceedings of the National Academy of Sciences of the United States of America.2015 Feb 17;2287-9225633040
Herpes simplex virus suppresses necroptosis in human cells.Guo, Hongyan; Omoto, Shinya; Harris, Philip A; Finger, Joshua N; Bertin, John; Gough, Peter J; Kaiser, William J; Mocarski, Edward SCell host & microbe.2015 Feb 11;243-5125674983
Caspase-8 as an Effector and Regulator of NLRP3 Inflammasome Signaling.Antonopoulos, Christina; Russo, Hana M; El Sanadi, Caroline; Martin, Bradley N; Li, Xiaoxia; Kaiser, William J; Mocarski, Edward S; Dubyak, George RThe Journal of biological chemistry.2015 Aug 14;20167-8426100631
Simultaneous generation of many RNA-seq libraries in a single reaction.Shishkin, Alexander A; Giannoukos, Georgia; Kucukural, Alper; Ciulla, Dawn; Busby, Michele; Surka, Christine; Chen, Jenny; Bhattacharyya, Roby P; Rudy, Robert F; Patel, Milesh M; Novod, Nathaniel; Hung, Deborah T; Gnirke, Andreas; Garber, Manuel; Guttman, Mitchell; Livny, JonathanNature methods.2015 Apr;323-525730492
Integrative, dynamic structural biology at atomic resolution--it's about time.van den Bedem, Henry; Fraser, James SNature methods.2015 Apr;307-1825825836
The Diversity of Meningococcal Carriage Across the African Meningitis Belt and the Impact of Vaccination With a Group A Meningococcal Conjugate Vaccine.MenAfriCar consortiumThe Journal of infectious diseases.2015 Apr 9;25858956
Sparse Biclustering of Transposable Data.Tan, Kean Ming; Witten, Daniela MJournal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America.2014;985-100825364221
Simplified post processing of cine DENSE cardiovascular magnetic resonance for quantification of cardiac mechanics.Suever, Jonathan D; Wehner, Gregory J; Haggerty, Christopher M; Jing, Linyuan; Hamlet, Sean M; Binkley, Cassi M; Kramer, Sage P; Mattingly, Andrea C; Powell, David K; Bilchick, Kenneth C; Epstein, Frederick H; Fornwalt, Brandon KJournal of cardiovascular magnetic resonance : official journal of the Society for Cardiovascular Magnetic Resonance.2014;25430079
TNFR1-dependent cell death drives inflammation in Sharpin-deficient mice.Rickard, James A; Anderton, Holly; Etemadi, Nima; Nachbur, Ueli; Darding, Maurice; Peltzer, Nieves; Lalaoui, Najoua; Lawlor, Kate E; Vanyai, Hannah; Hall, Cathrine; Bankovacki, Aleks; Gangoda, Lahiru; Wong, Wendy Wei-Lynn; Corbin, Jason; Huang, Chunzi; Mocarski, Edward S; Murphy, James M; Alexander, Warren S; Voss, Anne K; Vaux, David L; Kaiser, William J; Walczak, Henning; Silke, JohneLife.2014;25443632
Environmental statistics and optimal regulation.Sivak, David A; Thomson, MattPLoS computational biology.2014 Sep;e100382625254493
RNA-RNA interactions enable specific targeting of noncoding RNAs to nascent Pre-mRNAs and chromatin sites.Engreitz, Jesse M; Sirokman, Klara; McDonel, Patrick; Shishkin, Alexander A; Surka, Christine; Russell, Pamela; Grossman, Sharon R; Chow, Amy Y; Guttman, Mitchell; Lander, Eric SCell.2014 Sep 25;188-9925259926
Learning Graphical Models With Hubs.Tan, Kean Ming; London, Palma; Mohan, Karthik; Lee, Su-In; Fazel, Maryam; Witten, DanielaJournal of machine learning research : JMLR.2014 Oct;3297-333125620891
Discovery and characterization of gut microbiota decarboxylases that can produce the neurotransmitter tryptamine.Williams, Brianna B; Van Benschoten, Andrew H; Cimermancic, Peter; Donia, Mohamed S; Zimmermann, Michael; Taketani, Mao; Ishihara, Atsushi; Kashyap, Purna C; Fraser, James S; Fischbach, Michael ACell host & microbe.2014 Oct 8;495-50325263219
Characterizing immune repertoires by high throughput sequencing: strategies and applications.Calis, Jorg J A; Rosenberg, Brad RTrends in immunology.2014 Oct 8;581-59025306219
Long noncoding RNAs: an emerging link between gene regulation and nuclear organization.Quinodoz, Sofia; Guttman, MitchellTrends in cell biology.2014 Nov;651-6325441720
RIP3 induces apoptosis independent of pronecrotic kinase activity.Mandal, Pratyusha; Berger, Scott B; Pillay, Sirika; Moriwaki, Kenta; Huang, Chunzi; Guo, Hongyan; Lich, John D; Finger, Joshua; Kasparcova, Viera; Votta, Bart; Ouellette, Michael; King, Bryan W; Wisnoski, David; Lakdawala, Ami S; DeMartino, Michael P; Casillas, Linda N; Haile, Pamela A; Sehon, Clark A; Marquis, Robert W; Upton, Jason; Daley-Bauer, Lisa P; Roback, Linda; Ramia, Nancy; Dovey, Cole M; Carette, Jan E; Chan, Francis Ka-Ming; Bertin, John; Gough, Peter J; Mocarski, Edward S; Kaiser, William JMolecular cell.2014 Nov 20;481-9525459880
Association between the Medicare hospice benefit and health care utilization and costs for patients with poor-prognosis cancer.Obermeyer, Ziad; Makar, Maggie; Abujaber, Samer; Dominici, Francesca; Block, Susan; Cutler, David MJAMA.2014 Nov 12;1888-9625387186
Prediction of resistance development against drug combinations by collateral responses to component drugs.Munck, Christian; Gumpert, Heidi K; Wallin, Annika I Nilsson; Wang, Harris H; Sommer, Morten O AScience translational medicine.2014 Nov 12;262ra15625391482
Transfer of noncoding DNA drives regulatory rewiring in bacteria.Oren, Yaara; Smith, Mark B; Johns, Nathan I; Kaplan Zeevi, Millie; Biran, Dvora; Ron, Eliora Z; Corander, Jukka; Wang, Harris H; Alm, Eric J; Pupko, TalProceedings of the National Academy of Sciences of the United States of America.2014 Nov 11;16112-725313052
The genomic landscape of polymorphic human nuclear mitochondrial insertions.Dayama, Gargi; Emery, Sarah B; Kidd, Jeffrey M; Mills, Ryan ENucleic acids research.2014 Nov 10;12640-925348406
Caspase-8 and RIP kinases regulate bacteria-induced innate immune responses and cell death.Weng, Dan; Marty-Roix, Robyn; Ganesan, Sandhya; Proulx, Megan K; Vladimer, Gregory I; Kaiser, William J; Mocarski, Edward S; Pouliot, Kimberly; Chan, Francis Ka-Ming; Kelliher, Michelle A; Harris, Phillip A; Bertin, John; Gough, Peter J; Shayakhmetov, Dmitry M; Goguen, Jon D; Fitzgerald, Katherine A; Silverman, Neal; Lien, EgilProceedings of the National Academy of Sciences of the United States of America.2014 May 20;7391-624799678
Young blood reverses age-related impairments in cognitive function and synaptic plasticity in mice.Villeda, Saul A; Plambeck, Kristopher E; Middeldorp, Jinte; Castellano, Joseph M; Mosher, Kira I; Luo, Jian; Smith, Lucas K; Bieri, Gregor; Lin, Karin; Berdnik, Daniela; Wabl, Rafael; Udeochu, Joe; Wheatley, Elizabeth G; Zou, Bende; Simmons, Danielle A; Xie, Xinmin S; Longo, Frank M; Wyss-Coray, TonyNature medicine.2014 Jun;659-6324793238
Therapeutic implications of activation of the host gene (Dleu2) promoter for miR-15a/16-1 in chronic lymphocytic leukemia.Kasar, S; Underbayev, C; Yuan, Y; Hanlon, M; Aly, S; Khan, H; Chang, V; Batish, M; Gavrilova, T; Badiane, F; Degheidy, H; Marti, G; Raveche, EOncogene.2014 Jun 19;3307-1523995789
Node-Based Learning of Multiple Gaussian Graphical Models.Mohan, Karthik; London, Palma; Fazel, Maryam; Witten, Daniela; Lee, Su-InJournal of machine learning research : JMLR.2014 Jan 1;445-48825309137
Germline signals deploy NHR-49 to modulate fatty-acid *-oxidation and desaturation in somatic tissues of C. elegans.Ratnappan, Ramesh; Amrit, Francis R G; Chen, Shaw-Wen; Gill, Hasreet; Holden, Kyle; Ward, Jordan; Yamamoto, Keith R; Olsen, Carissa P; Ghazi, ArjumandPLoS genetics.2014 Dec;e100482925474470
Cause-specific risk of hospital admission related to extreme heat in older adults.Bobb, Jennifer F; Obermeyer, Ziad; Wang, Yun; Dominici, FrancescaJAMA.2014 Dec 24-31;2659-6725536257
Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering.Wall, Michael E; Van Benschoten, Andrew H; Sauter, Nicholas K; Adams, Paul D; Fraser, James S; Terwilliger, Thomas CProceedings of the National Academy of Sciences of the United States of America.2014 Dec 16;17887-9225453071
Transcriptome sequencing from diverse human populations reveals differentiated regulatory architecture.Martin, Alicia R; Costa, Helio A; Lappalainen, Tuuli; Henn, Brenna M; Kidd, Jeffrey M; Yee, Muh-Ching; Grubert, Fabian; Cann, Howard M; Snyder, Michael; Montgomery, Stephen B; Bustamante, Carlos DPLoS genetics.2014 Aug;e100454925121757
Emerging Roles of Alternative Pre-mRNA Splicing Regulation in Neuronal Development and Function.Norris, Adam D; Calarco, John AFrontiers in neuroscience.2012;22936897
Structured Learning of Gaussian Graphical Models.Mohan, Karthik; Chung, Michael Jae-Yoon; Han, Seungyeop; Witten, Daniela; Lee, Su-In; Fazel, MaryamAdvances in neural information processing systems.2012;629-63725360066
Programming cells by multiplex genome engineering and accelerated evolution.Wang, Harris H; Isaacs, Farren J; Carr, Peter A; Sun, Zachary Z; Xu, George; Forest, Craig R; Church, George MNature.2009 Aug 13;894-819633652
Regulation of intestinal health and disease by innate lymphoid cells.Sonnenberg, Gregory FInternational immunology2014 Sep501-50724821261
E pluribus unum, no more: from one crystal, many conformations.Woldeyes, Rahel A; Sivak, David A; Fraser, James SCurrent opinion in structural biology2014 Aug 856-6225113271
Quantification of left ventricular volumes, mass, and ejection fraction using cine displacement encoding with stimulated echoes (DENSE) MRI.Haggerty, Christopher M; Kramer, Sage P; Skrinjar, Oskar; Binkley, Cassi M; Powell, David K; Mattingly, Andrea C; Epstein, Frederick H; Fornwalt, Brandon KJournal of magnetic resonance imaging : JMRI2014 Aug398-40624923710
Patients with repaired tetralogy of Fallot suffer from intra- and inter-ventricular cardiac dyssynchrony: a cardiac magnetic resonance study.Jing, Linyuan; Haggerty, Christopher M; Suever, Jonathan D; Alhadad, Sudad; Prakash, Ashwin; Cecchin, Frank; Skrinjar, Oskar; Geva, Tal; Powell, Andrew J; Fornwalt, Brandon KEuropean heart journal cardiovascular Imaging2014 Jul 4NULL24996664
MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering.Bonde, Mads T; Klausen, Michael S; Anderson, Mads V; Wallin, Annika I N; Wang, Harris H; Sommer, Morten O ANucleic acids research2014 JulW408-1524838561
The transcription factor Foxp1 is a critical negative regulator of the differentiation of follicular helper T cells.Wang, Haikun; Geng, Jianlin; Wen, Xiaomin; Bi, Enguang; Kossenkov, Andrew V; Wolf, Amaya I; Tas, Jeroen; Choi, Youn Soo; Takata, Hiroshi; Day, Timothy J; Chang, Li-Yuan; Sprout, Stephanie L; Becker, Emily K; Willen, Jessica; Tian, Lifeng; Wang, Xinxin; XiNature immunology2014 Jul667-7524859450
Anatomical localization of commensal bacteria in immune cell homeostasis and disease.Fung, Thomas C; Artis, David; Sonnenberg, Gregory FImmunological reviews2014 Jul35-4924942680
Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery.Fischer, Marcus; Coleman, Ryan G; Fraser, James S; Shoichet, Brian KNature chemistry2014 Jul575-8324950326
Long-term effects of the 2003 ACGME resident duty hour reform on hospital mortality.Jena, Anupam B; Prasad, Vinay; Romley, John AMayo Clinic proceedings2014 Jul1023-524996240
Inferring clonal composition from multiple sections of a breast cancer.Zare, Habil; Wang, Junfeng; Hu, Alex; Weber, Kris; Smith, Josh; Nickerson, Debbie; Song, ChaoZhong; Witten, Daniela; Blau, C Anthony; Noble, William StaffordPLoS computational biology2014 Jule100370325010360
Direct Mutagenesis of Thousands of Genomic Targets Using Microarray-Derived Oligonucleotides.Bonde, Mads T; Kosuri, Sriram; Genee, Hans J; Sarup-Lytzen, Kira; Church, George M; Sommer, Morten O A; Wang, Harris HACS synthetic biology2014 Jun 20NULL24856730
Crystal Cryocooling Distorts Conformational Heterogeneity in a Model Michaelis Complex of DHFR.Keedy, Daniel A; van den Bedem, Henry; Sivak, David A; Petsko, Gregory A; Ringe, Dagmar; Wilson, Mark A; Fraser, James SStructure (London, England : 1993)2014 Jun 10899-91024882744
A Pair of RNA-Binding Proteins Controls Networks of Splicing Events Contributing to Specialization of Neural Cell Types.Norris, Adam D; Gao, Shangbang; Norris, Megan L; Ray, Debashish; Ramani, Arun K; Fraser, Andrew G; Morris, Quaid; Hughes, Timothy R; Zhen, Mei; Calarco, John AMolecular cell2014 Jun 4NULL24910101
The Declining Demand for Hospital Care as a Rationale for Duty Hour Reform.Jena, Anupam B; DePasse, Jacqueline W; Prasad, VinayJournal of general internal medicine2014 May 28NULL24866469
RIP1 suppresses innate immune necrotic as well as apoptotic cell death during mammalian parturition.Kaiser, William J; Daley-Bauer, Lisa P; Thapa, Roshan J; Mandal, Pratyusha; Berger, Scott B; Huang, Chunzi; Sundararajan, Aarthi; Guo, Hongyan; Roback, Linda; Speck, Samuel H; Bertin, John; Gough, Peter J; Balachandran, Siddharth; Mocarski, Edward SProceedings of the National Academy of Sciences of the United States of America2014 May 277753-824821786
Syntrophic exchange in synthetic microbial communities.Mee, Michael T; Collins, James J; Church, George M; Wang, Harris HProceedings of the National Academy of Sciences of the United States of America2014 May 20E2149-5624778240
Combinatorial therapy discovery using mixed integer linear programming.Pang, Kaifang; Wan, Ying-Wooi; Choi, William T; Donehower, Lawrence A; Sun, Jingchun; Pant, Dhruv; Liu, ZhandongBioinformatics (Oxford, England)2014 May 151456-6324463180
Cutting Edge: RIP1 Kinase Activity Is Dispensable for Normal Development but Is a Key Regulator of Inflammation in SHARPIN-Deficient Mice.Berger, Scott B; Kasparcova, Viera; Hoffman, Sandy; Swift, Barb; Dare, Lauren; Schaeffer, Michelle; Capriotti, Carol; Cook, Michael; Finger, Joshua; Hughes-Earle, Angela; Harris, Philip A; Kaiser, William J; Mocarski, Edward S; Bertin, John; Gough, Peter Journal of immunology (Baltimore, Md. : 1950)2014 May 12NULL24821972
A versatile framework for microbial engineering using synthetic non-coding RNAs.Qi, Lei S; Arkin, Adam PNature reviews. Microbiology2014 May341-5424736794
Medical professional liability risk among US cardiologists.Mangalmurti, Sandeep; Seabury, Seth A; Chandra, Amitabh; Lakdawalla, Darius; Oetgen, William J; Jena, Anupam BAmerican heart journal2014 May690-624766979
A versatile framework for microbial engineering using synthetic non-coding RNAs.Qi, Lei S; Arkin, Adam PNature reviews. Microbiology2014 May341-5424847554
Clonal and cellular dynamics in germinal centers.Victora, Gabriel D; Mesin, LukaCurrent opinion in immunology2014 Mar 2690-9624681449
Prion-like polymerization underlies signal transduction in antiviral immune defense and inflammasome activation.Cai, Xin; Chen, Jueqi; Xu, Hui; Liu, Siqi; Jiang, Qiu-Xing; Halfmann, Randal; Chen, Zhijian JCell2014 Mar 131207-2224630723
True grit: programmed necrosis in antiviral host defense, inflammation, and immunogenicity.Mocarski, Edward S; Kaiser, William J; Livingston-Rosanoff, Devon; Upton, Jason W; Daley-Bauer, Lisa PJournal of immunology (Baltimore, Md. : 1950)2014 Mar 12019-2624563506
Regulation of the adaptive immune system by innate lymphoid cells.Hepworth, Matthew R; Sonnenberg, Gregory FCurrent opinion in immunology2014 Mar 175-8224594491
Graph Estimation with Joint Additive Models.Voorman, Arend; Shojaie, Ali; Witten, DanielaBiometrika2014 Mar 185-10125013234
A general framework for estimating the relative pathogenicity of human genetic variants.Kircher, Martin; Witten, Daniela M; Jain, Preti; O'Roak, Brian J; Cooper, Gregory M; Shendure, JayNature genetics2014 Mar310-524487276
The joint graphical lasso for inverse covariance estimation across multiple classes.Danaher, Patrick; Wang, Pei; Witten, Daniela MJournal of the Royal Statistical Society. Series B, Statistical methodology2014 Mar373-39724817823
The Cluster Elastic Net for High-Dimensional Regression With Unknown Variable Grouping.Witten, Daniela M; Shojaie, Ali; Zhang, FanTechnometrics : a journal of statistics for the physical, chemical, and engineering sciences2014 Feb 20112-12224817772
Diffuse x-ray scattering to model protein motions.Wall, Michael E; Adams, Paul D; Fraser, James S; Sauter, Nicholas KStructure (London, England : 1993)2014 Feb 4182-424507780
Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR.Fenwick, R Bryn; van den Bedem, Henry; Fraser, James S; Wright, Peter EProceedings of the National Academy of Sciences of the United States of America2014 Jan 28E445-5424474795
Does the Declining Lethality of Gunshot Injuries Mask a Rising Epidemic of Gun Violence in the United States?Jena, Anupam B; Sun, Eric C; Prasad, VinayJournal of general internal medicine2014 Jan 23NULL24452421
Protein structural ensembles are revealed by redefining X-ray electron density noise.Lang, P Therese; Holton, James M; Fraser, James S; Alber, TomProceedings of the National Academy of Sciences of the United States of America2014 Jan 7237-4224363322
Careful use of science to advance the debate on the UK Cancer Drugs Fund.Lakdawalla, Darius N; Jena, Anupam B; Doctor, Jason NJAMA : the journal of the American Medical Association2014 Jan 125-624381964
Animal reservoir, natural and socioeconomic variations and the transmission of hemorrhagic fever with renal syndrome in Chenzhou, China, 2006-2010.Xiao, Hong; Tian, Huai-Yu; Gao, Li-Dong; Liu, Hai-Ning; Duan, Liang-Song; Basta, Nicole; Cazelles, Bernard; Li, Xiu-Jun; Lin, Xiao-Ling; Wu, Hong-Wei; Chen, Bi-Yun; Yang, Hui-Suo; Xu, Bing; Grenfell, BryanPLoS neglected tropical diseases2014 Jane261524421910
Opioid prescribing by multiple providers in Medicare: retrospective observational study of insurance claims.Jena, Anupam B; Goldman, Dana; Weaver, Lesley; Karaca-Mandic, PinarBMJ (Clinical research ed.)2014g139324553363
Fusion FISH imaging: single-molecule detection of gene fusion transcripts in situ.Markey, Fatu Badiane; Ruezinsky, William; Tyagi, Sanjay; Batish, MonaPloS one2014e9348824675777
Porphyrin-phospholipid liposomes permeabilized by near-infrared light.Carter, Kevin A; Shao, Shuai; Hoopes, Matthew I; Luo, Dandan; Ahsan, Bilal; Grigoryants, Vladimir M; Song, Wentao; Huang, Haoyuan; Zhang, Guojian; Pandey, Ravindra K; Geng, Jumin; Pfeifer, Blaine A; Scholes, Charles P; Ortega, Joaquin; Karttunen, Mikko; LNature communications2014354624699423
Exome capture from saliva produces high quality genomic and metagenomic data.Kidd, Jeffrey M; Sharpton, Thomas J; Bobo, Dean; Norman, Paul J; Martin, Alicia R; Carpenter, Meredith L; Sikora, Martin; Gignoux, Christopher R; Nemat-Gorgani, Neda; Adams, Alexandra; Guadalupe, Moraima; Guo, Xiaosen; Feng, Qiang; Li, Yingrui; Liu, Xiao;BMC genomics201426224708091
Alternative splicing regulates vesicular trafficking genes in cardiomyocytes during postnatal heart development.Giudice, Jimena; Xia, Zheng; Wang, Eric T; Scavuzzo, Marissa A; Ward, Amanda J; Kalsotra, Auinash; Wang, Wei; Wehrens, Xander H T; Burge, Christopher B; Li, Wei; Cooper, Thomas ANature communications2014360324752171
Recent progress in engineering human-associated microbiomes.Yaung, Stephanie J; Church, George M; Wang, Harris HMethods in molecular biology (Clifton, N.J.)201425-Mar24838875
Efficient Genome Engineering of Toxoplasma gondii Using CRISPR/Cas9.Sidik, Saima M; Hackett, Caroline G; Tran, Fanny; Westwood, Nicholas J; Lourido, SebastianPloS one2014e10045024971596
Mortality among high-risk patients with acute myocardial infarction admitted to U.S. Teaching-Intensive Hospitals in July: a retrospective observational study.Jena, Anupam B; Sun, Eric C; Romley, John ACirculation2013 Dec 242754-6324152859
Imaging the glycosylation state of cell surface glycoproteins by two-photon fluorescence lifetime imaging microscopy.Belardi, Brian; de la Zerda, Adam; Spiciarich, David R; Maund, Sophia L; Peehl, Donna M; Bertozzi, Carolyn RAngewandte Chemie (International ed. in English)2013 Dec 2314045-924259491
Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system.Chen, Baohui; Gilbert, Luke A; Cimini, Beth A; Schnitzbauer, Joerg; Zhang, Wei; Li, Gene-Wei; Park, Jason; Blackburn, Elizabeth H; Weissman, Jonathan S; Qi, Lei S; Huang, BoCell2013 Dec 191479-9124360272
Histone deacetylase 3 coordinates commensal-bacteria-dependent intestinal homeostasis.Alenghat, Theresa; Osborne, Lisa C; Saenz, Steven A; Kobuley, Dmytro; Ziegler, Carly G K; Mullican, Shannon E; Choi, Inchan; Grunberg, Stephanie; Sinha, Rohini; Wynosky-Dolfi, Meghan; Snyder, Annelise; Giacomin, Paul R; Joyce, Karen L; Hoang, Tram B; BewtNature2013 Dec 5153-724185009
Distinct and overlapping sarcoma subtypes initiated from muscle stem and progenitor cells.Blum, Jordan M; Ano, Leonor; Li, Zhizhong; Van Mater, David; Bennett, Brian D; Sachdeva, Mohit; Lagutina, Irina; Zhang, Minsi; Mito, Jeffrey K; Dodd, Leslie G; Cardona, Diana M; Dodd, Rebecca D; Williams, Nerissa; Ma, Yan; Lepper, Christoph; Linardic, CorCell reports2013 Nov 27933-4024239359
Pd-Porphyrin-Cross-Linked Implantable Hydrogels with Oxygen-Responsive Phosphorescence.Huang, Haoyuan; Song, Wentao; Chen, Guanying; Reynard, Justin M; Ohulchanskyy, Tymish Y; Prasad, Paras N; Bright, Frank V; Lovell, Jonathan FAdvanced healthcare materials2013 Nov 20NULL24259519
Yeast Oligo-Mediated Genome Engineering (YOGE).Dicarlo, James E; Conley, Andrew J; Penttila, Merja; Jantti, Jussi; Wang, Harris H; Church, George MACS synthetic biology2013 Nov 18NULL24160921
Myf5-positive satellite cells contribute to Pax7-dependent long-term maintenance of adult muscle stem cells.Gunther, Stefan; Kim, Johnny; Kostin, Sawa; Lepper, Christoph; Fan, Chen-Ming; Braun, ThomasCell stem cell2013 Nov 7590-60123933088
Proapoptotic chemotherapeutic drugs induce noncanonical processing and release of IL-1* via caspase-8 in dendritic cells.Antonopoulos, Christina; El Sanadi, Caroline; Kaiser, William J; Mocarski, Edward S; Dubyak, George RJournal of immunology (Baltimore, Md. : 1950)2013 Nov 14789-80324078693
Apaf1 apoptotic function critically limits Sonic hedgehog signaling during craniofacial development.Long, A B; Kaiser, W J; Mocarski, E S; Caspary, TCell death and differentiation2013 Nov1510-2023892366
Heritable custom genomic modifications in Caenorhabditis elegans via a CRISPR-Cas9 system.Tzur, Yonatan B; Friedland, Ari E; Nadarajan, Saravanapriah; Church, George M; Calarco, John A; Colaiacovo, Monica PGenetics2013 Nov1181-523979579
CRISPR interference (CRISPRi) for sequence-specific control of gene expression.Larson, Matthew H; Gilbert, Luke A; Wang, Xiaowo; Lim, Wendell A; Weissman, Jonathan S; Qi, Lei SNature protocols2013 Nov2180-9624136345
Editorial: New tricks for innate lymphoid cells.Sonnenberg, Gregory FJournal of leukocyte biology2013 Nov862-424179147
Toll-like receptor 3-mediated necrosis via TRIF, RIP3, and MLKL.Kaiser, William J; Sridharan, Haripriya; Huang, Chunzi; Mandal, Pratyusha; Upton, Jason W; Gough, Peter J; Sehon, Clark A; Marquis, Robert W; Bertin, John; Mocarski, Edward SThe Journal of biological chemistry2013 Oct 2531268-7924019532
Genomically recoded organisms expand biological functions.Lajoie, Marc J; Rovner, Alexis J; Goodman, Daniel B; Aerni, Hans-Rudolf; Haimovich, Adrian D; Kuznetsov, Gleb; Mercer, Jaron A; Wang, Harris H; Carr, Peter A; Mosberg, Joshua A; Rohland, Nadin; Schultz, Peter G; Jacobson, Joseph M; Rinehart, Jesse; ChurchScience (New York, N.Y.)2013 Oct 18357-6024136966
From Structure to Systems: High-Resolution, Quantitative Genetic Analysis of RNA Polymerase II.Braberg, Hannes; Jin, Huiyan; Moehle, Erica A; Chan, Yujia A; Wang, Shuyi; Shales, Michael; Benschop, Joris J; Morris, John H; Qiu, Chenxi; Hu, Fuqu; Tang, Leung K; Fraser, James S; Holstege, Frank C P; Hieter, Philip; Guthrie, Christine; Kaplan, Craig D;Cell2013 Aug 15775-8823932120
T follicular helper cell dynamics in germinal centers.Shulman, Ziv; Gitlin, Alexander D; Targ, Sasha; Jankovic, Mila; Pasqual, Giulia; Nussenzweig, Michel C; Victora, Gabriel DScience (New York, N.Y.)2013 Aug 9673-723887872
Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females.Poznik, G David; Henn, Brenna M; Yee, Muh-Ching; Sliwerska, Elzbieta; Euskirchen, Ghia M; Lin, Alice A; Snyder, Michael; Quintana-Murci, Lluis; Kidd, Jeffrey M; Underhill, Peter A; Bustamante, Carlos DScience (New York, N.Y.)2013 Aug 2562-523908239
Meningococcal carriage in the African meningitis belt.MenAfriCar Consortium; Ali, Oumer; Aseffa, Abraham; Bedru, Ahmed; Lemma, Tsehaynesh; Moti, Tesfaye; Workhu, Alemayehu; Guebre Xabher, Haimanot; Yamuah, Lawrence; Boukary, Rahamatou Moustapha; Collard, Jean-Marc; Dano, Ibrahim Dan; Habiboulaye, Ibrahim; IsTropical medicine & international health : TM & IH2013 Aug968-7823682910
Heritable genome editing in C. elegans via a CRISPR-Cas9 system.Friedland, Ari E; Tzur, Yonatan B; Esvelt, Kevin M; Colaiacovo, Monica P; Church, George M; Calarco, John ANature methods2013 Aug741-323817069
Automated identification of functional dynamic contact networks from X-ray crystallography.van den Bedem, Henry; Bhabha, Gira; Yang, Kun; Wright, Peter E; Fraser, James SNature methods2013 Aug896-90223913260
The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome.Engreitz, Jesse M; Pandya-Jones, Amy; McDonel, Patrick; Shishkin, Alexander; Sirokman, Klara; Surka, Christine; Kadri, Sabah; Xing, Jeffrey; Goren, Alon; Lander, Eric S; Plath, Kathrin; Guttman, MitchellScience (New York, N.Y.)2013 Jul 4NULL23828888
Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins.Guttman, Mitchell; Russell, Pamela; Ingolia, Nicholas T; Weissman, Jonathan S; Lander, Eric SCell2013 Jul 3240-5123810193
Innate lymphoid cells regulate CD4+ T-cell responses to intestinal commensal bacteria.Hepworth, Matthew R; Monticelli, Laurel A; Fung, Thomas C; Ziegler, Carly G K; Grunberg, Stephanie; Sinha, Rohini; Mantegazza, Adriana R; Ma, Hak-Ling; Crawford, Alison; Angelosanto, Jill M; Wherry, E John; Koni, Pandelakis A; Bushman, Frederic D; Elson, Nature2013 Jun 6113-723698371
Viral modulation of programmed necrosis.Kaiser, William J; Upton, Jason W; Mocarski, Edward SCurrent opinion in virology2013 Jun296-30623773332
T cell factor 1 is required for group 2 innate lymphoid cell generation.Yang, Qi; Monticelli, Laurel A; Saenz, Steven A; Chi, Anthony Wei-Shine; Sonnenberg, Gregory F; Tang, Jiangbo; De Obaldia, Maria Elena; Bailis, Will; Bryson, Jerrod L; Toscano, Kristin; Huang, Jian; Haczku, Angela; Pear, Warren S; Artis, David; Bhandoola,Immunity2013 Apr 18694-70423601684
Heritable remodeling of yeast multicellularity by an environmentally responsive prion.Holmes, Daniel L; Lancaster, Alex K; Lindquist, Susan; Halfmann, RandalCell2013 Mar 28153-6523540696
Priorities for research on meningococcal disease and the impact of serogroup A vaccination in the African meningitis belt.Dakar discussion group on priorities for research on epidemic meningococcal disease in Africa; Altmann, Danny; Aseffa, Abraham; Bash, Margaret; Basta, Nicole; Borrow, Ray; Broome, Claire; Caugant, Dominique; Clark, Tom; Collard, Jean-Marc; Djingarey, MamoVaccine2013 Mar 11453-723273967
Resistin-like molecule ýý promotes pathogenic Th17 cell responses and bacterial-induced intestinal inflammation.Osborne, Lisa C; Joyce, Karen L; Alenghat, Theresa; Sonnenberg, Gregory F; Giacomin, Paul R; Du, Yurong; Bergstrom, Kirk S; Vallance, Bruce A; Nair, Meera GJournal of immunology (Baltimore, Md. : 1950)2013 Mar 12292-30023355735
TSLP elicits IL-33-independent innate lymphoid cell responses to promote skin inflammation.Kim, Brian S; Siracusa, Mark C; Saenz, Steven A; Noti, Mario; Monticelli, Laurel A; Sonnenberg, Gregory F; Hepworth, Matthew R; Van Voorhees, Abby S; Comeau, Michael R; Artis, DavidScience translational medicine2013 Jan 30170ra1623363980
From systems to structure: bridging networks and mechanism.Fraser, James S; Gross, John D; Krogan, Nevan JMolecular cell2013 Jan 24222-3123352243
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Flexible backbone sampling methods to model and design protein alternative conformations.Ollikainen, Noah; Smith, Colin A; Fraser, James S; Kortemme, TanjaMethods in enzymology201361-8523422426
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Reproducibility of cine displacement encoding with stimulated echoes (DENSE) cardiovascular magnetic resonance for measuring left ventricular strains, torsion, and synchrony in mice.Haggerty, Christopher M; Kramer, Sage P; Binkley, Cassi M; Powell, David K; Mattingly, Andrea C; Charnigo, Richard; Epstein, Frederick H; Fornwalt, Brandon KJournal of cardiovascular magnetic resonance : official journal of the Society for Cardiovascular Magnetic Resonance20137123981339
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Obesity reduces left ventricular strains, torsion, and synchrony in mouse models: a cine displacement encoding with stimulated echoes (DENSE) cardiovascular magnetic resonance study.Kramer, Sage P; Powell, David K; Haggerty, Christopher M; Binkley, Cassi M; Mattingly, Andrea C; Cassis, Lisa A; Epstein, Frederick H; Fornwalt, Brandon KJournal of cardiovascular magnetic resonance : official journal of the Society for Cardiovascular Magnetic Resonance201310924380567
Innate lymphoid cell interactions with microbiota: implications for intestinal health and disease.Sonnenberg, Gregory F; Artis, DavidImmunity2012 Oct 19601-1023084357
The satellite cell builds its nest under Notch's guidance.Lepper, Christoph; Low, SiewHui; Partridge, Terence ACell stem cell2012 Oct 5443-423040471
Engineering ecosystems and synthetic ecologies.Mee, Michael T; Wang, Harris HMolecular bioSystems2012 Oct2470-8322722235
CheShift-2 resolves a local inconsistency between two X-ray crystal structures.Vila, Jorge A; Sue, Shih-Che; Fraser, James S; Scheraga, Harold A; Dyson, H JaneJournal of biomolecular NMR2012 Oct193-822945426
Prion formation by a yeast GLFG nucleoporin.Halfmann, Randal; Wright, Jessica R; Alberti, Simon; Lindquist, Susan; Rexach, MichaelPrion2012 Sep-Oct391-922561191
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Role of satellite cells versus myofibers in muscle hypertrophy induced by inhibition of the myostatin/activin signaling pathway.Lee, Se-Jin; Huynh, Thanh V; Lee, Yun-Sil; Sebald, Suzanne M; Wilcox-Adelman, Sarah A; Iwamori, Naoki; Lepper, Christoph; Matzuk, Martin M; Fan, Chen-MingProceedings of the National Academy of Sciences of the United States of America2012 Aug 28E2353-6022869749
Molecular signatures from omics data: from chaos to consensus.Sung, Jaeyun; Wang, Yuliang; Chandrasekaran, Sriram; Witten, Daniela M; Price, Nathan DBiotechnology journal2012 Aug946-5722528809
Systematic functional prioritization of protein posttranslational modifications.Beltrao, Pedro; Albanese, Veronique; Kenner, Lillian R; Swaney, Danielle L; Burlingame, Alma; Villen, Judit; Lim, Wendell A; Fraser, James S; Frydman, Judith; Krogan, Nevan JCell2012 Jul 20413-2522817900
Linking data and models: the importance of statistical analyses to inform models for the transmission dynamics of infections.Pitzer, Virginia E; Basta, Nicole EEpidemiology (Cambridge, Mass.)2012 Jul520-222659545
Global connectivity of prefrontal cortex predicts cognitive control and intelligence.Cole, Michael W; Yarkoni, Tal; Repovs, Grega; Anticevic, Alan; Braver, Todd SThe Journal of neuroscience : the official journal of the Society for Neuroscience2012 Jun 278988-9922745498
Genome-scale promoter engineering by coselection MAGE.Wang, Harris H; Kim, Hwangbeom; Cong, Le; Jeong, Jaehwan; Bang, Duhee; Church, George MNature methods2012 Jun591-322484848
On the assessment of statistical significance of three-dimensional colocalization of sets of genomic elements.Witten, Daniela M; Noble, William StaffordNucleic acids research2012 May3849-5522266657
Massively parallel functional dissection of mammalian enhancers in vivo.Patwardhan, Rupali P; Hiatt, Joseph B; Witten, Daniela M; Kim, Mee J; Smith, Robin P; May, Dalit; Lee, Choli; Andrie, Jennifer M; Lee, Su-In; Cooper, Gregory M; Ahituv, Nadav; Pennacchio, Len A; Shendure, JayNature biotechnology2012 Mar265-7022371081
Multiplexed in vivo His-tagging of enzyme pathways for in vitro single-pot multi-enzyme catalysis.Wang, Harris H; Huang, Po-Yi; Xu, George; Haas, Wilhelm; Marblestone, Adam; Li, Jun; Gygi, Steven; Forster, Anthony C; Jewett, Michael C; Church, George MACS synthetic biology2012 Feb 1643-5222737598
Improving lambda red genome engineering in Escherichia coli via rational removal of endogenous nucleases.Mosberg, Joshua A; Gregg, Christopher J; Lajoie, Marc J; Wang, Harris H; Church, George MPloS one2012e4463822957093
RIP3 mediates the embryonic lethality of caspase-8-deficient mice.Kaiser, William J; Upton, Jason W; Long, Alyssa B; Livingston-Rosanoff, Devon; Daley-Bauer, Lisa P; Hakem, Razqallah; Caspary, Tamara; Mocarski, Edward SNature2011 Mar 17368-7221368762


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