Program Publications
Program Publications
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The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
| Title | Authors | Journal | PubMedID | Publication Date |
|---|---|---|---|---|
| The origins and functional effects of postzygotic mutations throughout the human life span. | Rockweiler, Nicole B; Ramu, Avinash; Nagirnaja, Liina; Wong, Wing H; Noordam, Michiel J; Drubin, Casey W; Huang, Ni; Miller, Brian; Todres, Ellen Z; Vigh-Conrad, Katinka A; Zito, Antonino; Small, Kerrin S; Ardlie, Kristin G; Cohen, Barak A; Conrad, Donald F | Science (New York, N.Y.) | 37053313 | 2023 Apr 14 |
| The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. | Rozowsky, Joel; Gao, Jiahao; Borsari, Beatrice; Yang, Yucheng T; Galeev, Timur; Gürsoy, Gamze; Epstein, Charles B; Xiong, Kun; Xu, Jinrui; Li, Tianxiao; Liu, Jason; Yu, Keyang; Berthel, Ana; Chen, Zhanlin; Navarro, Fabio; Sun, Maxwell S; Wright, James; Chang, Justin; Cameron, Christopher J F; Shoresh, Noam; Gaskell, Elizabeth; Drenkow, Jorg; Adrian, Jessika; Aganezov, Sergey; Aguet, François; Balderrama-Gutierrez, Gabriela; Banskota, Samridhi; Corona, Guillermo Barreto; Chee, Sora; Chhetri, Surya B; Cortez Martins, Gabriel Conte; Danyko, Cassidy; Davis, Carrie A; Farid, Daniel; Farrell, Nina P; Gabdank, Idan; Gofin, Yoel; Gorkin, David U; Gu, Mengting; Hecht, Vivian; Hitz, Benjamin C; Issner, Robbyn; Jiang, Yunzhe; Kirsche, Melanie; Kong, Xiangmeng; Lam, Bonita R; Li, Shantao; Li, Bian; Li, Xiqi; Lin, Khine Zin; Luo, Ruibang; Mackiewicz, Mark; Meng, Ran; Moore, Jill E; Mudge, Jonathan; Nelson, Nicholas; Nusbaum, Chad; Popov, Ioann; Pratt, Henry E; Qiu, Yunjiang; Ramakrishnan, Srividya; Raymond, Joe; Salichos, Leonidas; Scavelli, Alexandra; Schreiber, Jacob M; Sedlazeck, Fritz J; See, Lei Hoon; Sherman, Rachel M; Shi, Xu; Shi, Minyi; Sloan, Cricket Alicia; Strattan, J Seth; Tan, Zhen; Tanaka, Forrest Y; Vlasova, Anna; Wang, Jun; Werner, Jonathan; Williams, Brian; Xu, Min; Yan, Chengfei; Yu, Lu; Zaleski, Christopher; Zhang, Jing; Ardlie, Kristin; Cherry, J Michael; Mendenhall, Eric M; Noble, William S; Weng, Zhiping; Levine, Morgan E; Dobin, Alexander; Wold, Barbara; Mortazavi, Ali; Ren, Bing; Gillis, Jesse; Myers, Richard M; Snyder, Michael P; Choudhary, Jyoti; Milosavljevic, Aleksandar; Schatz, Michael C; Bernstein, Bradley E; Guigó, Roderic; Gingeras, Thomas R; Gerstein, Mark | Cell | 37001506 | 2023 Mar 30 |
| Hypotheses on a tree: new error rates and testing strategies. | Bogomolov, Marina; Peterson, Christine B; Benjamini, Yoav; Sabatti, Chiara | Biometrika | 36825068 | 2021 Sep |
| Day-night and seasonal variation of human gene expression across tissues. | Wucher, Valentin; Sodaei, Reza; Amador, Raziel; Irimia, Manuel; Guigó, Roderic | PLoS biology | 36745672 | 2023 Feb |
| DNA methylation QTL mapping across diverse human tissues provides molecular links between genetic variation and complex traits. | Oliva, Meritxell; Demanelis, Kathryn; Lu, Yihao; Chernoff, Meytal; Jasmine, Farzana; Ahsan, Habibul; Kibriya, Muhammad G; Chen, Lin S; Pierce, Brandon L | Nature genetics | 36510025 | 2022 Dec 12 |
| Leveraging pleiotropy for joint analysis of genome-wide association studies with per trait interpretations. | Taraszka, Kodi; Zaitlen, Noah; Eskin, Eleazar | PLoS genetics | 36342933 | 2022 Nov |
| The landscape of hervRNAs transcribed from human endogenous retroviruses across human body sites. | She, Jianqi; Du, Minghao; Xu, Zhanzhan; Jin, Yueqi; Li, Yu; Zhang, Daoning; Tao, Changyu; Chen, Jian; Wang, Jiadong; Yang, Ence | Genome biology | 36329469 | 2022 Nov 03 |
| RNA editing underlies genetic risk of common inflammatory diseases. | Li, Qin; Gloudemans, Michael J; Geisinger, Jonathan M; Fan, Boming; Aguet, François; Sun, Tao; Ramaswami, Gokul; Li, Yang I; Ma, Jin-Biao; Pritchard, Jonathan K; Montgomery, Stephen B; Li, Jin Billy | Nature | 35922514 | 2022 08 |
| Identification of human mitochondrial RNA cleavage sites and candidate RNA processing factors. | Carbajosa, Guillermo; Ali, Aminah T; Hodgkinson, Alan | BMC biology | 35869520 | 2022 07 22 |
| Estimating and accounting for unobserved covariates in high-dimensional correlated data. | McKennan, Chris; Nicolae, Dan | Journal of the American Statistical Association | 35615339 | 2022 |
| A comprehensive atlas of fetal splicing patterns in the brain of adult myotonic dystrophy type 1 patients. | Degener, Max J F; van Cruchten, Remco T P; Otero, Brittney A; Wang, Eric T; Wansink, Derick G; 't Hoen, Peter A C | NAR genomics and bioinformatics | 35274098 | 2022 Mar |
| Mitochondrial-nuclear epistasis underlying phenotypic variation in breast cancer pathology. | Bushel, Pierre R; Ward, James; Burkholder, Adam; Li, Jianying; Anchang, Benedict | Scientific reports | 35082309 | 2022 01 26 |
| A de novo paradigm for male infertility. | Oud, M S; Smits, R M; Smith, H E; Mastrorosa, F K; Holt, G S; Houston, B J; de Vries, P F; Alobaidi, B K S; Batty, L E; Ismail, H; Greenwood, J; Sheth, H; Mikulasova, A; Astuti, G D N; Gilissen, C; McEleny, K; Turner, H; Coxhead, J; Cockell, S; Braat, D D | Nature communications | 35013161 | 2022 Jan 10 |
| Mitochondrial-nuclear cross-talk in the human brain is modulated by cell type and perturbed in neurodegenerative disease. | Fairbrother-Browne, Aine; Ali, Aminah T; Reynolds, Regina H; Garcia-Ruiz, Sonia; Zhang, David; Chen, Zhongbo; Ryten, Mina; Hodgkinson, Alan | Communications biology | 34737414 | 2021 Nov 04 |
| Identifying causal variants by fine mapping across multiple studies. | LaPierre, Nathan; Taraszka, Kodi; Huang, Helen; He, Rosemary; Hormozdiari, Farhad; Eskin, Eleazar | PLoS genetics | 34543273 | 2021 Sep |
| Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression. | Võsa, Urmo; Claringbould, Annique; Westra, Harm-Jan; Bonder, Marc Jan; Deelen, Patrick; Zeng, Biao; Kirsten, Holger; Saha, Ashis; Kreuzhuber, Roman; Yazar, Seyhan; Brugge, Harm; Oelen, Roy; de Vries, Dylan H; van der Wijst, Monique G P; Kasela, Silva; Per | Nature genetics | 34475573 | 2021 09 |
| Systematic evaluation of transcriptomics-based deconvolution methods and references using thousands of clinical samples. | Nadel, Brian B; Oliva, Meritxell; Shou, Benjamin L; Mitchell, Keith; Ma, Feiyang; Montoya, Dennis J; Mouton, Alice; Kim-Hellmuth, Sarah; Stranger, Barbara E; Pellegrini, Matteo; Mangul, Serghei | Briefings in bioinformatics | 34346485 | 2021 11 05 |
| Mapping the miRNA-mRNA Interactome in Human Hepatocytes and Identification of Functional mirSNPs in Pharmacogenes. | Powell, Nicholas R; Zhao, Harrison; Ipe, Joseph; Liu, Yunlong; Skaar, Todd C | Clinical pharmacology and therapeutics | 34314509 | 2021 10 |
| Genetic drivers of m6A methylation in human brain, lung, heart and muscle. | Xiong, Xushen; Hou, Lei; Park, Yongjin P; Molinie, Benoit; GTEx Consortium; Gregory, Richard I; Kellis, Manolis | Nature genetics | 34211177 | 2021 Jul 01 |
| AdaTiSS: a novel data-Adaptive robust method for identifying Tissue Specificity Scores. | Wang, Meng; Jiang, Lihua; Snyder, Michael P | Bioinformatics (Oxford, England) | 34146104 | 2021 Dec 07 |
| Feasibility of predicting allele specific expression from DNA sequencing using machine learning. | Zhang, Zhenhua; van Dijk, Freerk; de Klein, Niek; van Gijn, Mariëlle E; Franke, Lude H; Sinke, Richard J; Swertz, Morris A; van der Velde, K Joeri | Scientific reports | 34012022 | 2021 May 19 |
| Population-scale tissue transcriptomics maps long non-coding RNAs to complex disease. | de Goede, Olivia M; Nachun, Daniel C; Ferraro, Nicole M; Gloudemans, Michael J; Rao, Abhiram S; Smail, Craig; Eulalio, Tiffany Y; Aguet, François; Ng, Bernard; Xu, Jishu; Barbeira, Alvaro N; Castel, Stephane E; Kim-Hellmuth, Sarah; Park, YoSon; Scott, Alexandra J; Strober, Benjamin J; GTEx Consortium; Brown, Christopher D; Wen, Xiaoquan; Hall, Ira M; Battle, Alexis; Lappalainen, Tuuli; Im, Hae Kyung; Ardlie, Kristin G; Mostafavi, Sara; Quertermous, Thomas; Kirkegaard, Karla; Montgomery, Stephen B | Cell | 33864768 | 2021 05 13 |
| Day-night and seasonal variation of human gene expression across tissues. | Wucher, Valentin; Sodaei, Reza; Amador, Raziel; Irimia, Manuel; Guigó, Roderic | bioRxiv : the preprint server for biology | 33688644 | 2021 Mar 01 |
| Regulatory genomic circuitry of human disease loci by integrative epigenomics. | Boix, Carles A; James, Benjamin T; Park, Yongjin P; Meuleman, Wouter; Kellis, Manolis | Nature | 33536621 | 2021 02 |
| Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome. | Garrido-Martín, Diego; Borsari, Beatrice; Calvo, Miquel; Reverter, Ferran; Guigó, Roderic | Nature communications | 33526779 | 2021 02 01 |
| Exploiting the GTEx resources to decipher the mechanisms at GWAS loci. | Barbeira, Alvaro N; Bonazzola, Rodrigo; Gamazon, Eric R; Liang, Yanyu; Park, YoSon; Kim-Hellmuth, Sarah; Wang, Gao; Jiang, Zhuoxun; Zhou, Dan; Hormozdiari, Farhad; Liu, Boxiang; Rao, Abhiram; Hamel, Andrew R; Pividori, Milton D; Aguet, François; GTEx GWAS | Genome biology | 33499903 | 2021 01 26 |
| Alterations observed in the interferon α and β signaling pathway in MDD patients are marginally influenced by cis-acting alleles. | Magri, Chiara; Giacopuzzi, Edoardo; Sacco, Chiara; Bocchio-Chiavetto, Luisella; Minelli, Alessandra; Gennarelli, Massimo | Scientific reports | 33436853 | 2021 01 12 |
| Sex-dimorphic genetic effects and novel loci for fasting glucose and insulin variability. | Lagou, Vasiliki; Mägi, Reedik; Hottenga, Jouke- Jan; Grallert, Harald; Perry, John R B; Bouatia-Naji, Nabila; Marullo, Letizia; Rybin, Denis; Jansen, Rick; Min, Josine L; Dimas, Antigone S; Ulrich, Anna; Zudina, Liudmila; Gådin, Jesper R; Jiang, Longda; Faggian, Alessia; Bonnefond, Amélie; Fadista, Joao; Stathopoulou, Maria G; Isaacs, Aaron; Willems, Sara M; Navarro, Pau; Tanaka, Toshiko; Jackson, Anne U; Montasser, May E; O'Connell, Jeff R; Bielak, Lawrence F; Webster, Rebecca J; Saxena, Richa; Stafford, Jeanette M; Pourcain, Beate St; Timpson, Nicholas J; Salo, Perttu; Shin, So-Youn; Amin, Najaf; Smith, Albert V; Li, Guo; Verweij, Niek; Goel, Anuj; Ford, Ian; Johnson, Paul C D; Johnson, Toby; Kapur, Karen; Thorleifsson, Gudmar; Strawbridge, Rona J; Rasmussen-Torvik, Laura J; Esko, Tõnu; Mihailov, Evelin; Fall, Tove; Fraser, Ross M; Mahajan, Anubha; Kanoni, Stavroula; Giedraitis, Vilmantas; Kleber, Marcus E; Silbernagel, Günther; Meyer, Julia; Müller-Nurasyid, Martina; Ganna, Andrea; Sarin, Antti-Pekka; Yengo, Loic; Shungin, Dmitry; Luan, Jian'an; Horikoshi, Momoko; An, Ping; Sanna, Serena; Boettcher, Yvonne; Rayner, N William; Nolte, Ilja M; Zemunik, Tatijana; Iperen, Erik van; Kovacs, Peter; Hastie, Nicholas D; Wild, Sarah H; McLachlan, Stela; Campbell, Susan; Polasek, Ozren; Carlson, Olga; Egan, Josephine; Kiess, Wieland; Willemsen, Gonneke; Kuusisto, Johanna; Laakso, Markku; Dimitriou, Maria; Hicks, Andrew A; Rauramaa, Rainer; Bandinelli, Stefania; Thorand, Barbara; Liu, Yongmei; Miljkovic, Iva; Lind, Lars; Doney, Alex; Perola, Markus; Hingorani, Aroon; Kivimaki, Mika; Kumari, Meena; Bennett, Amanda J; Groves, Christopher J; Herder, Christian; Koistinen, Heikki A; Kinnunen, Leena; Faire, Ulf de; Bakker, Stephan J L; Uusitupa, Matti; Palmer, Colin N A; Jukema, J Wouter; Sattar, Naveed; Pouta, Anneli; Snieder, Harold; Boerwinkle, Eric; Pankow, James S; Magnusson, Patrik K; Krus, Ulrika; Scapoli, Chiara; de Geus, Eco J C N; Blüher, Matthias; Wolffenbuttel, Bruce H R; Province, Michael A; Abecasis, Goncalo R; Meigs, James B; Hovingh, G Kees; Lindström, Jaana; Wilson, James F; Wright, Alan F; Dedoussis, George V; Bornstein, Stefan R; Schwarz, Peter E H; Tönjes, Anke; Winkelmann, Bernhard R; Boehm, Bernhard O; März, Winfried; Metspalu, Andres; Price, Jackie F; Deloukas, Panos; Körner, Antje; Lakka, Timo A; Keinanen-Kiukaanniemi, Sirkka M; Saaristo, Timo E; Bergman, Richard N; Tuomilehto, Jaakko; Wareham, Nicholas J; Langenberg, Claudia; Männistö, Satu; Franks, Paul W; Hayward, Caroline; Vitart, Veronique; Kaprio, Jaakko; Visvikis-Siest, Sophie; Balkau, Beverley; Altshuler, David; Rudan, Igor; Stumvoll, Michael; Campbell, Harry; van Duijn, Cornelia M; Gieger, Christian; Illig, Thomas; Ferrucci, Luigi; Pedersen, Nancy L; Pramstaller, Peter P; Boehnke, Michael; Frayling, Timothy M; Shuldiner, Alan R; Peyser, Patricia A; Kardia, Sharon L R; Palmer, Lyle J; Penninx, Brenda W; Meneton, Pierre; Harris, Tamara B; Navis, Gerjan; Harst, Pim van der; Smith, George Davey; Forouhi, Nita G; Loos, Ruth J F; Salomaa, Veikko; Soranzo, Nicole; Boomsma, Dorret I; Groop, Leif; Tuomi, Tiinamaija; Hofman, Albert; Munroe, Patricia B; Gudnason, Vilmundur; Siscovick, David S; Watkins, Hugh; Lecoeur, Cecile; Vollenweider, Peter; Franco-Cereceda, Anders; Eriksson, Per; Jarvelin, Marjo-Riitta; Stefansson, Kari; Hamsten, Anders; Nicholson, George; Karpe, Fredrik; Dermitzakis, Emmanouil T; Lindgren, Cecilia M; McCarthy, Mark I; Froguel, Philippe; Kaakinen, Marika A; Lyssenko, Valeriya; Watanabe, Richard M; Ingelsson, Erik; Florez, Jose C; Dupuis, Josée; Barroso, Inês; Morris, Andrew P; Prokopenko, Inga; Meta-Analyses of Glucose and Insulin-related traits Consortium (MAGIC) | Nature communications | 33402679 | 2021 01 05 |
| RobNorm: model-based robust normalization method for labeled quantitative mass spectrometry proteomics data. | Wang, Meng; Jiang, Lihua; Jian, Ruiqi; Chan, Joanne Y; Liu, Qing; Snyder, Michael P; Tang, Hua | Bioinformatics (Oxford, England) | 33098413 | 2021 May 05 |
| Robust Huber-LASSO for improved prediction of protein, metabolite and gene expression levels relying on individual genotype data. | Deutelmoser, Heike; Scherer, Dominique; Brenner, Hermann; Waldenberger, Melanie; INTERVAL study; Suhre, Karsten; Kastenmüller, Gabi; Lorenzo Bermejo, Justo | Briefings in bioinformatics | 33063116 | 2021 Jul 20 |
| Pleiotropic Locus 15q24.1 Reveals a Gender-Specific Association with Neovascular but Not Atrophic Age-Related Macular Degeneration (AMD). | Kiel, Christina; Strunz, Tobias; International Amd Genomics Consortium Project Manager Susan Blanton Iamdgc; Grassmann, Felix; Weber, Bernhard H F | Cells. | 33050031 | 2020 10 08; |
| Genetic variant effects on gene expression in human pancreatic islets and their implications for T2D. | Viñuela, Ana; Varshney, Arushi; van de Bunt, Martijn; Prasad, Rashmi B; Asplund, Olof; Bennett, Amanda; Boehnke, Michael; Brown, Andrew A; Erdos, Michael R; Fadista, João; Hansson, Ola; Hatem, Gad; Howald, Cédric; Iyengar, Apoorva K; Johnson, Paul; Krus, | Nature communications. | 32999275 | 2020 09 30; |
| Fine-mapping and QTL tissue-sharing information improves the reliability of causal gene identification. | Barbeira, Alvaro N; Melia, Owen J; Liang, Yanyu; Bonazzola, Rodrigo; Wang, Gao; Wheeler, Heather E; Aguet, François; Ardlie, Kristin G; Wen, Xiaoquan; Im, Hae K | Genetic epidemiology. | 32964524 | 2020 Sep 10; |
| PhenomeXcan: Mapping the genome to the phenome through the transcriptome. | Pividori, Milton; Rajagopal, Padma S; Barbeira, Alvaro; Liang, Yanyu; Melia, Owen; Bastarache, Lisa; Park, YoSon; Consortium, GTEx; Wen, Xiaoquan; Im, Hae K | Science advances | 32917697 | 2020 09 |
| A Quantitative Proteome Map of the Human Body. | Jiang, Lihua; Wang, Meng; Lin, Shin; Jian, Ruiqi; Li, Xiao; Chan, Joanne; Dong, Guanlan; Fang, Huaying; Robinson, Aaron E; GTEx Consortium; Snyder, Michael P | Cell. | 32916130 | 2020 Oct 01; |
| Genome-wide association study identifies novel single nucleotide polymorphisms having age-specific effect on prostate-specific antigen levels. | Li, Weiqiang; Bicak, Mesude; Sjoberg, Daniel D; Vertosick, Emily; Dahlin, Anders; Melander, Olle; Ulmert, David; Lilja, Hans; Klein, Robert J | The Prostate. | 32914890 | 2020 Dec; |
| The GTEx Consortium atlas of genetic regulatory effects across human tissues. | GTEx Consortium | Science (New York, N.Y.). | 32913098 | 2020 09 11; |
| Cell type-specific genetic regulation of gene expression across human tissues. | Kim-Hellmuth, Sarah; Aguet, François; Oliva, Meritxell; Muñoz-Aguirre, Manuel; Kasela, Silva; Wucher, Valentin; Castel, Stephane E; Hamel, Andrew R; Viñuela, Ana; Roberts, Amy L; Mangul, Serghei; Wen, Xiaoquan; Wang, Gao; Barbeira, Alvaro N; Garrido-Martí | Science (New York, N.Y.). | 32913075 | 2020 09 11; |
| Determinants of telomere length across human tissues. | Demanelis, Kathryn; Jasmine, Farzana; Chen, Lin S; Chernoff, Meytal; Tong, Lin; Delgado, Dayana; Zhang, Chenan; Shinkle, Justin; Sabarinathan, Mekala; Lin, Hannah; Ramirez, Eduardo; Oliva, Meritxell; Kim-Hellmuth, Sarah; Stranger, Barbara E; Lai, Tsung-Po | Science (New York, N.Y.). | 32913074 | 2020 09 11; |
| Transcriptomic signatures across human tissues identify functional rare genetic variation. | Ferraro, Nicole M; Strober, Benjamin J; Einson, Jonah; Abell, Nathan S; Aguet, Francois; Barbeira, Alvaro N; Brandt, Margot; Bucan, Maja; Castel, Stephane E; Davis, Joe R; Greenwald, Emily; Hess, Gaelen T; Hilliard, Austin T; Kember, Rachel L; Kotis, Benc | Science (New York, N.Y.). | 32913073 | 2020 09 11; |
| The impact of sex on gene expression across human tissues. | Oliva, Meritxell; Muñoz-Aguirre, Manuel; Kim-Hellmuth, Sarah; Wucher, Valentin; Gewirtz, Ariel D H; Cotter, Daniel J; Parsana, Princy; Kasela, Silva; Balliu, Brunilda; Viñuela, Ana; Castel, Stephane E; Mohammadi, Pejman; Aguet, François; Zou, Yuxin; Khram | Science (New York, N.Y.). | 32913072 | 2020 09 11; |
| A vast resource of allelic expression data spanning human tissues. | Castel, Stephane E; Aguet, François; Mohammadi, Pejman; GTEx Consortium; Ardlie, Kristin G; Lappalainen, Tuuli | Genome biology. | 32912332 | 2020 Sep 11; |
| Metalign: efficient alignment-based metagenomic profiling via containment min hash. | LaPierre, Nathan; Alser, Mohammed; Eskin, Eleazar; Koslicki, David; Mangul, Serghei | Genome biology. | 32912225 | 2020 09 10; |
| Low Baseline Pulmonary Levels of Cytotoxic Lymphocytes as a Predisposing Risk Factor for Severe COVID-19. | Duijf, Pascal H G | mSystems. | 32873611 | 2020 Sep 01; |
| Mutation of CFAP57, a protein required for the asymmetric targeting of a subset of inner dynein arms in Chlamydomonas, causes primary ciliary dyskinesia. | Bustamante-Marin, Ximena M; Horani, Amjad; Stoyanova, Mihaela; Charng, Wu-Lin; Bottier, Mathieu; Sears, Patrick R; Yin, Wei-Ning; Daniels, Leigh Anne; Bowen, Hailey; Conrad, Donald F; Knowles, Michael R; Ostrowski, Lawrence E; Zariwala, Maimoona A; Dutche | PLoS genetics. | 32764743 | 2020 08; |
| A limited set of transcriptional programs define major cell types. | Breschi, Alessandra; Muñoz-Aguirre, Manuel; Wucher, Valentin; Davis, Carrie A; Garrido-Martín, Diego; Djebali, Sarah; Gillis, Jesse; Pervouchine, Dmitri D; Vlasova, Anna; Dobin, Alexander; Zaleski, Chris; Drenkow, Jorg; Danyko, Cassidy; Scavelli, Alexandr | Genome research. | 32759341 | 2020 Jul; |
| DCAF1 regulates Treg senescence via the ROS axis during immunological aging. | Guo, Zengli; Wang, Gang; Wu, Bing; Chou, Wei-Chun; Cheng, Liang; Zhou, Chenlin; Lou, Jitong; Wu, Di; Su, Lishan; Zheng, Junnian; Ting, Jenny P-Y; Wan, Yisong Y | The Journal of clinical investigation. | 32730228 | 2020 Nov 02; |
| An enhanced machine learning tool for cis-eQTL mapping with regularization and confounder adjustments. | Yan, Kang K; Zhao, Hongyu; Wu, Joseph T; Pang, Herbert | Genetic epidemiology | 32700329 | 2020 Nov |
| Sparse multi-output Gaussian processes for online medical time series prediction. | Cheng, Li-Fang; Dumitrascu, Bianca; Darnell, Gregory; Chivers, Corey; Draugelis, Michael; Li, Kai; Engelhardt, Barbara E | BMC medical informatics and decision making. | 32641134 | 2020 Jul 08; |
| Baseline pulmonary levels of CD8+ T cells and NK cells inversely correlate with expression of the SARS-CoV-2 entry receptor ACE2. | Duijf, Pascal H G | bioRxiv : the preprint server for biology. | 32511391 | 2020 May 05; |
| Analysis of Genetically Regulated Gene Expression Identifies a Prefrontal PTSD Gene, SNRNP35, Specific to Military Cohorts. | Huckins, Laura M; Chatzinakos, Chris; Breen, Michael S; Hartmann, Jakob; Klengel, Torsten; da Silva Almeida, Ana C; Dobbyn, Amanda; Girdhar, Kiran; Hoffman, Gabriel E; Klengel, Claudia; Logue, Mark W; Lori, Adriana; Maihofer, Adam X; Morrison, Filomene G; | Cell reports. | 32492425 | 2020 Jun 02; |
| Genetic Determinants of Reduced Arsenic Metabolism Efficiency in the 10q24.32 Region Are Associated With Reduced AS3MT Expression in Multiple Human Tissue Types. | Chernoff, Meytal; Tong, Lin; Demanelis, Kathryn; Vander Griend, Donald; Ahsan, Habib; Pierce, Brandon L | Toxicological sciences : an official journal of the Society of Toxicology | 32433756 | 2020 08 01 |
| Analysis of mitochondrial m1A/G RNA modification reveals links to nuclear genetic variants and associated disease processes. | Ali, Aminah Tasnim; Idaghdour, Youssef; Hodgkinson, Alan | Communications biology | 32221480 | 2020 03 27 |
| A TESTING BASED APPROACH TO THE DISCOVERY OF DIFFERENTIALLY CORRELATED VARIABLE SETS. | Bodwin, By Kelly; Zhang, Kai; Nobel, Andrew | The annals of applied statistics. | 31871518 | 2018 Jun; |
| Community Extraction in Multilayer Networks with Heterogeneous Community Structure. | Wilson, James D; Palowitch, John; Bhamidi, Shankar; Nobel, Andrew B | Journal of machine learning research : JMLR. | 31871433 | 2017; |
| Leveraging allelic imbalance to refine fine-mapping for eQTL studies. | Zou, Jennifer; Hormozdiari, Farhad; Jew, Brandon; Castel, Stephane E; Lappalainen, Tuuli; Ernst, Jason; Sul, Jae Hoon; Eskin, Eleazar | PLoS genetics. | 31834882 | 2019 12; |
| Identification of genetic variants in CFAP221 as a cause of primary ciliary dyskinesia. | Bustamante-Marin, Ximena M; Shapiro, Adam; Sears, Patrick R; Charng, Wu-Lin; Conrad, Donald F; Leigh, Margaret W; Knowles, Michael R; Ostrowski, Lawrence E; Zariwala, Maimoona A | Journal of human genetics. | 31636325 | 2020 Jan; |
| Rare mutations in the complement regulatory gene CSMD1 are associated with male and female infertility. | Lee, Arthur S; Rusch, Jannette; Lima, Ana C; Usmani, Abul; Huang, Ni; Lepamets, Maarja; Vigh-Conrad, Katinka A; Worthington, Ronald E; Mägi, Reedik; Wu, Xiaobo; Aston, Kenneth I; Atkinson, John P; Carrell, Douglas T; Hess, Rex A; O'Bryan, Moira K; Conrad, Donald F | Nature communications. | 31604923 | 2019 Oct 11; |
| Genetically Increased Telomere Length and Aging-Related Traits in the U.K. Biobank. | Demanelis, Kathryn; Tong, Lin; Pierce, Brandon L | The journals of gerontology. Series A, Biological sciences and medical sciences | 31603979 | 2021 01 01 |
| Inferred divergent gene regulation in archaic hominins reveals potential phenotypic differences. | Colbran, Laura L; Gamazon, Eric R; Zhou, Dan; Evans, Patrick; Cox, Nancy J; Capra, John A | Nature ecology & evolution. | 31591491 | 2019 Oct 07; |
| Joint profiling of DNA methylation and chromatin architecture in single cells. | Li, Guoqiang; Liu, Yaping; Zhang, Yanxiao; Kubo, Naoki; Yu, Miao; Fang, Rongxin; Kellis, Manolis; Ren, Bing | Nature methods. | 31384045 | 2019 Oct; |
| Identifying causal variants and genes using functional genomics in specialized cell types and contexts. | Liu, Boxiang; Montgomery, Stephen B | Human genetics. | 31317254 | 2020 Jan; |
| Selection-adjusted inference: an application to confidence intervals for cis-eQTL effect sizes. | Panigrahi, Snigdha; Zhu, Junjie; Sabatti, Chiara | Biostatistics (Oxford, England) | 31301173 | 2021 01 28 |
| Unified single-cell analysis of testis gene regulation and pathology in five mouse strains. | Jung, Min; Wells, Daniel; Rusch, Jannette; Ahmad, Suhaira; Marchini, Jonathan; Myers, Simon R; Conrad, Donald F | eLife. | 31237565 | 2019 Jun 25; |
| Challenges and recommendations to improve the installability and archival stability of omics computational tools. | Mangul, Serghei; Mosqueiro, Thiago; Abdill, Richard J; Duong, Dat; Mitchell, Keith; Sarwal, Varuni; Hill, Brian; Brito, Jaqueline; Littman, Russell Jared; Statz, Benjamin; Lam, Angela Ka-Mei; Dayama, Gargi; Grieneisen, Laura; Martin, Lana S; Flint, Jonathan; Eskin, Eleazar; Blekhman, Ran | PLoS biology. | 31220077 | 2019 06; |
| MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples. | LaPierre, Nathan; Mangul, Serghei; Alser, Mohammed; Mandric, Igor; Wu, Nicholas C; Koslicki, David; Eskin, Eleazar | BMC genomics. | 31167634 | 2019 Jun 06; |
| Genetic analyses of human fetal retinal pigment epithelium gene expression suggest ocular disease mechanisms. | Liu, Boxiang; Calton, Melissa A; Abell, Nathan S; Benchorin, Gillie; Gloudemans, Michael J; Chen, Ming; Hu, Jane; Li, Xin; Balliu, Brunilda; Bok, Dean; Montgomery, Stephen B; Vollrath, Douglas | Communications biology. | 31123710 | 2019; |
| On Using Local Ancestry to Characterize the Genetic Architecture of Human Traits: Genetic Regulation of Gene Expression in Multiethnic or Admixed Populations. | Zhong, Yizhen; Perera, Minoli A; Gamazon, Eric R | American journal of human genetics. | 31104770 | 2019 Jun 06; |
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| DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements. | Mercer, Tim R; Edwards, Stacey L; Clark, Michael B; Neph, Shane J; Wang, Hao; Stergachis, Andrew B; John, Sam; Sandstrom, Richard; Li, Guoliang; Sandhu, Kuljeet S; Ruan, Yijun; Nielsen, Lars K; Mattick, John S; Stamatoyannopoulos, John A | Nature genetics | 23793028 | 2013 Aug |
| A genome-wide integrative study of microRNAs in human liver. | Gamazon, Eric R; Innocenti, Federico; Wei, Rongrong; Wang, Libo; Zhang, Min; Mirkov, Snezana; Ramirez, Jacqueline; Huang, R Stephanie; Cox, Nancy J; Ratain, Mark J; Liu, Wanqing | BMC genomics | 23758991 | 2013 |
| Integrative genomics: quantifying significance of phenotype-genotype relationships from multiple sources of high-throughput data. | Gamazon, Eric R; Huang, R Stephanie; Dolan, M Eileen; Cox, Nancy J; Im, Hae Kyung | Frontiers in genetics. | 23755062 | 2012; |
| Validation of Monte Carlo estimates of three-class ideal observer operating points for normal data. | Edwards, Darrin C | Academic radiology | 23747155 | 2013 Jul |
| JOINT AND INDIVIDUAL VARIATION EXPLAINED (JIVE) FOR INTEGRATED ANALYSIS OF MULTIPLE DATA TYPES. | Lock, Eric F; Hoadley, Katherine A; Marron, J S; Nobel, Andrew B | The annals of applied statistics | 23745156 | 2013 Mar 1 |
| The Genotype-Tissue Expression (GTEx) project. | Lonsdale J, Thomas J, Salvatore M, Phillips R, Lo E, Shad S, Hasz R, Walters G, Garcia F, Young N, Foster B, Moser M, Karasik E, Gillard B, Ramsey K, Sullivan S, Bridge J, Magazine H, Syron J, Fleming J, Siminoff L, Traino H, et al. | Nat Genet | 23715323 | 2013 May 29 |
| A statistical framework for joint eQTL analysis in multiple tissues. | Flutre, Timothee; Wen, Xiaoquan; Pritchard, Jonathan; Stephens, Matthew | PLoS genetics | 23671422 | 2013 May |
| eQTL Mapping Using RNA-seq Data. | Sun, Wei; Hu, Yijuan | Statistics in biosciences | 23667399 | 2013 May 1 |
| Marbled inflation from population structure in gene-based association studies with rare variants. | Liu, Qianying; Nicolae, Dan L; Chen, Lin S | Genetic epidemiology | 23468125 | 2013 Apr |
| Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes. | Ferreira, Pedro G; Patalano, Solenn; Chauhan, Ritika; Ffrench-Constant, Richard; Gabaldón, Toni; Guigó, Roderic; Sumner, Seirian | Genome biology. | 23442883 | 2013; |
| Network models of genome-wide association studies uncover the topological centrality of protein interactions in complex diseases. | Lee, Younghee; Li, Haiquan; Li, Jianrong; Rebman, Ellen; Achour, Ikbel; Regan, Kelly E; Gamazon, Eric R; Chen, James L; Yang, Xinan Holly; Cox, Nancy J; Lussier, Yves A | Journal of the American Medical Informatics Association : JAMIA | 23355459 | 2013 Jul-Aug |
| Modeling causality for pairs of phenotypes in system genetics. | Neto, Elias Chaibub; Broman, Aimee T; Keller, Mark P; Attie, Alan D; Zhang, Bin; Zhu, Jun; Yandell, Brian S | Genetics | 23288936 | 2013 Mar |
| Trans-population analysis of genetic mechanisms of ethnic disparities in neuroblastoma survival. | Gamazon, Eric R; Pinto, Navin; Konkashbaev, Anuar; Im, Hae Kyung; Diskin, Sharon J; London, Wendy B; Maris, John M; Dolan, M Eileen; Cox, Nancy J; Cohn, Susan L | Journal of the National Cancer Institute | 23243203 | 2013 Feb 20 |
| Integrative analysis of a cross-loci regulation network identifies App as a gene regulating insulin secretion from pancreatic islets. | Tu, Zhidong; Keller, Mark P; Zhang, Chunsheng; Rabaglia, Mary E; Greenawalt, Danielle M; Yang, Xia; Wang, I-Ming; Dai, Hongyue; Bruss, Matthew D; Lum, Pek Y; Zhou, Yun-Ping; Kemp, Daniel M; Kendziorski, Christina; Yandell, Brian S; Attie, Alan D; Schadt, Eric E; Zhu, Jun | PLoS genetics | 23236292 | 2012 |
| Controls of nucleosome positioning in the human genome. | Gaffney, Daniel J; McVicker, Graham; Pai, Athma A; Fondufe-Mittendorf, Yvonne N; Lewellen, Noah; Michelini, Katelyn; Widom, Jonathan; Gilad, Yoav; Pritchard, Jonathan K | PLoS genetics | 23166509 | 2012 |
| An exponential combination procedure for set-based association tests in sequencing studies. | Chen, Lin S; Hsu, Li; Gamazon, Eric R; Cox, Nancy J; Nicolae, Dan L | American journal of human genetics | 23159251 | 2012 Dec 7 |
| Variants affecting exon skipping contribute to complex traits. | Lee, Younghee; Gamazon, Eric R; Rebman, Ellen; Lee, Yeunsook; Lee, Sanghyuk; Dolan, M Eileen; Cox, Nancy J; Lussier, Yves A | PLoS genetics | 23133393 | 2012 |
| The GEM mapper: fast, accurate and versatile alignment by filtration. | Marco-Sola, Santiago; Sammeth, Michael; Guigo, Roderic; Ribeca, Paolo | Nature methods | 23103880 | 2012 Dec |
| Sex-biased genetic effects on gene regulation in humans. | Dimas, Antigone S; Nica, Alexandra C; Montgomery, Stephen B; Stranger, Barbara E; Raj, Towfique; Buil, Alfonso; Giger, Thomas; Lappalainen, Tuuli; Gutierrez-Arcelus, Maria; MuTHER Consortium; McCarthy, Mark I; Dermitzakis, Emmanouil T | Genome research | 22960374 | 2012 Dec |
| Genetic risk factors for type 2 diabetes: a trans-regulatory genetic architecture? | Elbein, Steven C; Gamazon, Eric R; Das, Swapan K; Rasouli, Neda; Kern, Philip A; Cox, Nancy J | American journal of human genetics | 22958899 | 2012 Sep 7 |
| Mapping cis- and trans-regulatory effects across multiple tissues in twins. | Grundberg, Elin; Small, Kerrin S; Hedman, Åsa K; Nica, Alexandra C; Buil, Alfonso; Keildson, Sarah; Bell, Jordana T; Yang, Tsun-Po; Meduri, Eshwar; Barrett, Amy; Nisbett, James; Sekowska, Magdalena; Wilk, Alicja; Shin, So-Youn; Glass, Daniel; Travers, Mary; Min, Josine L; Ring, Sue; Ho, Karen; Thorleifsson, Gudmar; Kong, Augustine; Thorsteindottir, Unnur; Ainali, Chrysanthi; Dimas, Antigone S; Hassanali, Neelam; Ingle, Catherine; Knowles, David; Krestyaninova, Maria; Lowe, Christopher E; Di Meglio, Paola; Montgomery, Stephen B; Parts, Leopold; Potter, Simon; Surdulescu, Gabriela; Tsaprouni, Loukia; Tsoka, Sophia; Bataille, Veronique; Durbin, Richard; Nestle, Frank O; O'Rahilly, Stephen; Soranzo, Nicole; Lindgren, Cecilia M; Zondervan, Krina T; Ahmadi, Kourosh R; Schadt, Eric E; Stefansson, Kari; Smith, George Davey; McCarthy, Mark I; Deloukas, Panos; Dermitzakis, Emmanouil T; Spector, Tim D; Multiple Tissue Human Expression Resource (MuTHER) Consortium | Nature genetics. | 22941192 | 2012 Oct; |
| Quantile-based permutation thresholds for quantitative trait loci hotspots. | Neto, Elias Chaibub; Keller, Mark P; Broman, Andrew F; Attie, Alan D; Jansen, Ritsert C; Broman, Karl W; Yandell, Brian S | Genetics | 22661325 | 2012 Aug |
| Reprioritizing genetic associations in hit regions using LASSO-based resample model averaging. | Valdar, William; Sabourin, Jeremy; Nobel, Andrew; Holmes, Christopher C | Genetic epidemiology | 22549815 | 2012 Jul |
| Matrix eQTL: ultra fast eQTL analysis via large matrix operations. | Shabalin, Andrey A | Bioinformatics (Oxford, England) | 22492648 | 2012 May 15 |
| On sharing quantitative trait GWAS results in an era of multiple-omics data and the limits of genomic privacy. | Im, Hae Kyung; Gamazon, Eric R; Nicolae, Dan L; Cox, Nancy J | American journal of human genetics | 22463877 | 2012 Apr 6 |
| Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data. | Veyrieras, Jean-Baptiste; Gaffney, Daniel J; Pickrell, Joseph K; Gilad, Yoav; Stephens, Matthew; Pritchard, Jonathan K | PloS one | 22359548 | 2012 |
| DNaseýýýI sensitivity QTLs are a major determinant of human expression variation. | Degner, Jacob F; Pai, Athma A; Pique-Regi, Roger; Veyrieras, Jean-Baptiste; Gaffney, Daniel J; Pickrell, Joseph K; De Leon, Sherryl; Michelini, Katelyn; Lewellen, Noah; Crawford, Gregory E; Stephens, Matthew; Gilad, Yoav; Pritchard, Jonathan K | Nature | 22307276 | 2012 Feb 16 |
| Computational tools for discovery and interpretation of expression quantitative trait loci. | Wright, Fred A; Shabalin, Andrey A; Rusyn, Ivan | Pharmacogenomics | 22304583 | 2012 Feb |
| Dissecting the regulatory architecture of gene expression QTLs. | Gaffney, Daniel J; Veyrieras, Jean-Baptiste; Degner, Jacob F; Pique-Regi, Roger; Pai, Athma A; Crawford, Gregory E; Stephens, Matthew; Gilad, Yoav; Pritchard, Jonathan K | Genome biology | 22293038 | 2012 |
| Enrichment of cis-regulatory gene expression SNPs and methylation quantitative trait loci among bipolar disorder susceptibility variants. | Gamazon, E R; Badner, J A; Cheng, L; Zhang, C; Zhang, D; Cox, N J; Gershon, E S; Kelsoe, J R; Greenwood, T A; Nievergelt, C M; Chen, C; McKinney, R; Shilling, P D; Schork, N J; Smith, E N; Bloss, C S; Nurnberger, J I; Edenberg, H J; Foroud, T; Koller, D L | Molecular psychiatry | 22212596 | 2013 Mar |
| seeQTL: a searchable database for human eQTLs. | Xia, Kai; Shabalin, Andrey A; Huang, Shunping; Madar, Vered; Zhou, Yi-Hui; Wang, Wei; Zou, Fei; Sun, Wei; Sullivan, Patrick F; Wright, Fred A | Bioinformatics (Oxford, England) | 22171328 | 2012 Feb 1 |
| Estimation of alternative splicing variability in human populations. | Gonzalez-Porta, Mar; Calvo, Miquel; Sammeth, Michael; Guigo, Roderic | Genome research | 22113879 | 2012 Mar |
| Rare and common regulatory variation in population-scale sequenced human genomes. | Montgomery, Stephen B; Lappalainen, Tuuli; Gutierrez-Arcelus, Maria; Dermitzakis, Emmanouil T | PLoS genetics | 21811411 | 2011 Jul |
| Phosphorylation of Spo0A by the histidine kinase KinD requires the lipoprotein med in Bacillus subtilis. | Banse, Allison V; Hobbs, Errett C; Losick, Richard | Journal of bacteriology | 21622736 | 2011 Aug |
| Copy number polymorphisms and anticancer pharmacogenomics. | Gamazon, Eric R; Huang, R Stephanie; Dolan, M Eileen; Cox, Nancy J | Genome biology | 21609475 | 2011 |
| Identification of an imprinted master trans regulator at the KLF14 locus related to multiple metabolic phenotypes. | Small, Kerrin S; Hedman, Asa K; Grundberg, Elin; Nica, Alexandra C; Thorleifsson, Gudmar; Kong, Augustine; Thorsteindottir, Unnur; Shin, So-Youn; Richards, Hannah B; GIANT Consortium; MAGIC Investigators; DIAGRAM Consortium; Soranzo, Nicole; Ahmadi, Kourosh R; Lindgren, Cecilia M; Stefansson, Kari; Dermitzakis, Emmanouil T; Deloukas, Panos; Spector, Timothy D; McCarthy, Mark I; MuTHER Consortium | Nature genetics | 21572415 | 2011 Jun |
| A study of CNVs as trait-associated polymorphisms and as expression quantitative trait loci. | Gamazon, Eric R; Nicolae, Dan L; Cox, Nancy J | PLoS genetics | 21304891 | 2011 |
| DiNAMIC: a method to identify recurrent DNA copy number aberrations in tumors. | Walter, Vonn; Nobel, Andrew B; Wright, Fred A | Bioinformatics (Oxford, England) | 21183584 | 2011 Mar 1 |
| Heading down the wrong pathway: on the influence of correlation within gene sets. | Gatti, Daniel M; Barry, William T; Nobel, Andrew B; Rusyn, Ivan; Wright, Fred A | BMC genomics | 20955544 | 2010 |
| Toxicogenetics: population-based testing of drug and chemical safety in mouse models. | Rusyn, Ivan; Gatti, Daniel M; Wiltshire, Timothy; Wilshire, Timothy; Kleeberger, Steven R; Threadgill, David W | Pharmacogenomics | 20704464 | 2010 Aug |
| Quantification of population structure using correlated SNPs by shrinkage principal components. | Zou, Fei; Lee, Seunggeun; Knowles, Michael R; Wright, Fred A | Human heredity. | 20413978 | 2010; |
