Common Fund Data Ecosystem (CFDE)
Common Fund Data Ecosystem (CFDE)
Program Publications
Publications Search by Program
Search Results
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 |
|---|---|---|---|---|
| Lipidomic Analysis Reveals Differences in the Extent of Remyelination in the Brain and Spinal Cord. | De Silva Mohotti, Nishama; Kobayashi, Hiroko; Williams, Jenna M; Binjawadagi, Rashmi; Evertsen, Michel P; Christ, Ethan G; Hartley, Meredith D | Journal of proteome research | 38018851 | 2024 Aug 02 |
| Metabolic reprogramming by histone deacetylase inhibition preferentially targets NRF2-activated tumors. | Karagiannis, Dimitris; Wu, Warren; Li, Albert; Hayashi, Makiko; Chen, Xiao; Yip, Michaela; Mangipudy, Vaibhav; Xu, Xinjing; Sánchez-Rivera, Francisco J; Soto-Feliciano, Yadira M; Ye, Jiangbin; Papagiannakopoulos, Thales; Lu, Chao | Cell reports | 38165806 | 2024 Jan 23 |
| reguloGPT: Harnessing GPT for Knowledge Graph Construction of Molecular Regulatory Pathways. | Wu, Xidong; Zeng, Yiming; Das, Arun; Jo, Sumin; Zhang, Tinghe; Patel, Parth; Zhang, Jianqiu; Gao, Shou-Jiang; Pratt, Dexter; Chiu, Yu-Chiao; Huang, Yufei | bioRxiv : the preprint server for biology | 38313267 | 2024 Jan 30 |
| Exploring the interplay between running exercises, microbial diversity, and tryptophan metabolism along the microbiota-gut-brain axis. | Vazquez-Medina, Alejandra; Rodriguez-Trujillo, Nicole; Ayuso-Rodriguez, Kiara; Marini-Martinez, Fabiana; Angeli-Morales, Roberto; Caussade-Silvestrini, Gerardo; Godoy-Vitorino, Filipa; Chorna, Nataliya | Frontiers in microbiology | 38318337 | 2024 |
| Molecular Atlas of HER2+ Breast Cancer Cells Treated with Endogenous Ligands: Temporal Insights into Mechanisms of Trastuzumab Resistance. | Mukund, Kavitha; Alva-Ornelas, Jackelyn A; Maddox, Adam L; Murali, Divya; Veraksa, Darya; Saftics, Andras; Tomsic, Jerneja; Frankhouser, David; Razo, Meagan; Jovanovic-Talisman, Tijana; Seewaldt, Victoria L; Subramaniam, Shankar | Cancers | 38339304 | 2024 Jan 27 |
| shinyDeepDR: A user-friendly R Shiny app for predicting anti-cancer drug response using deep learning. | Wang, Li-Ju; Ning, Michael; Nayak, Tapsya; Kasper, Michael J; Monga, Satdarshan P; Huang, Yufei; Chen, Yidong; Chiu, Yu-Chiao | Patterns (New York, N.Y.) | 38370127 | 2024 Feb 09 |
| Less-is-more: selecting transcription factor binding regions informative for motif inference. | Xu, Jinrui; Gao, Jiahao; Ni, Pengyu; Gerstein, Mark | Nucleic acids research | 38214231 | 2024 Feb 28 |
| A nested case-control study of untargeted plasma metabolomics and lung cancer among never-smoking women within the prospective Shanghai Women's Health Study. | Rahman, Mohammad L; Shu, Xiao-Ou; Jones, Dean P; Hu, Wei; Ji, Bu-Tian; Blechter, Batel; Wong, Jason Y Y; Cai, Qiuyin; Yang, Gong; Gao, Yu-Tang; Zheng, Wei; Rothman, Nathaniel; Walker, Douglas; Lan, Qing | International journal of cancer | 38651675 | 2024 Aug 01 |
| Reproducible mass spectrometry data processing and compound annotation in MZmine 3. | Heuckeroth, Steffen; Damiani, Tito; Smirnov, Aleksandr; Mokshyna, Olena; Brungs, Corinna; Korf, Ansgar; Smith, Joshua David; Stincone, Paolo; Dreolin, Nicola; Nothias, Louis-Félix; Hyötyläinen, Tuulia; Orešič, Matej; Karst, Uwe; Dorrestein, Pieter C; Petras, Daniel; Du, Xiuxia; van der Hooft, Justin J J; Schmid, Robin; Pluskal, Tomáš | Nature protocols | 38769143 | 2024 Sep |
| Signature reversion of three disease-associated gene signatures prioritizes cancer drug repurposing candidates. | Fisher, Jennifer L; Wilk, Elizabeth J; Oza, Vishal H; Gary, Sam E; Howton, Timothy C; Flanary, Victoria L; Clark, Amanda D; Hjelmeland, Anita B; Lasseigne, Brittany N | FEBS open bio | 38531616 | 2024 May |
| An open source knowledge graph ecosystem for the life sciences. | Callahan, Tiffany J; Tripodi, Ignacio J; Stefanski, Adrianne L; Cappelletti, Luca; Taneja, Sanya B; Wyrwa, Jordan M; Casiraghi, Elena; Matentzoglu, Nicolas A; Reese, Justin; Silverstein, Jonathan C; Hoyt, Charles Tapley; Boyce, Richard D; Malec, Scott A; Unni, Deepak R; Joachimiak, Marcin P; Robinson, Peter N; Mungall, Christopher J; Cavalleri, Emanuele; Fontana, Tommaso; Valentini, Giorgio; Mesiti, Marco; Gillenwater, Lucas A; Santangelo, Brook; Vasilevsky, Nicole A; Hoehndorf, Robert; Bennett, Tellen D; Ryan, Patrick B; Hripcsak, George; Kahn, Michael G; Bada, Michael; Baumgartner Jr, William A; Hunter, Lawrence E | Scientific data | 38605048 | 2024 Apr 11 |
| Fetal growth delay caused by loss of non-canonical imprinting is resolved late in pregnancy and culminates in offspring overgrowth. | Oberin, Ruby; Petautschnig, Sigrid; Jarred, Ellen G; Qu, Zhipeng; Tsai, Tesha; Youngson, Neil A; Pulsoni, Gabrielle; Truong, Thi T; Fernando, Dilini; Bildsoe, Heidi; Blücher, Rheannon O; van den Buuse, Maarten; Gardner, David K; Sims, Natalie A; Adelson, David L; Western, Patrick S | eLife | 38813868 | 2024 May 30 |
| Characterization of aberrant splicing in pediatric central nervous system tumors reveals CLK1 as a candidate oncogenic dependency. | Naqvi, Ammar S; Corbett, Ryan J; Seghal, Priyanka; Conkrite, Karina L; Rathi, Komal S; Ennis, Brian M; Hayer, Katharina E; Zhang, Bo; Brown, Miguel A; Miller, Daniel P; Kraya, Adam A; Dybas, Joseph M; Geng, Zhuangzhuang; Blackden, Christopher; Arif, Shehbeel; Chroni, Antonia; Lahiri, Aditya; Hollawell, Madison L; Storm, Phillip B; Foster, Jessica B; Koptyra, Mateusz; Madsen, Peter J; Diskin, Sharon J; Thomas-Tikhonenko, Andrei; Resnick, Adam C; Rokita, Jo Lynne | bioRxiv : the preprint server for biology | 39149264 | 2024 Aug 22 |
| Fatty acid metabolism promotes TRPV4 activity in lung microvascular endothelial cells in pulmonary arterial hypertension. | Philip, Nicolas; Yun, Xin; Pi, Hongyang; Murray, Samuel; Hill, Zack; Fonticella, Jay; Perez, Preston; Zhang, Cissy; Pathmasiri, Wimal; Sumner, Susan; Servinsky, Laura; Jiang, Haiyang; Huetsch, John C; Oldham, William M; Visovatti, Scott; Leary, Peter J; Gharib, Sina A; Brittain, Evan; Simpson, Catherine E; Le, Anne; Shimoda, Larissa A; Suresh, Karthik | American journal of physiology. Lung cellular and molecular physiology | 38226418 | 2024 Mar 01 |
| Mondrian Abstraction and Language Model Embeddings for Differential Pathway Analysis. | Al Abir, Fuad; Chen, Jake Y | bioRxiv : the preprint server for biology | 38659966 | 2024 Aug 19 |
| FGFR inhibition blocks NF-ĸB-dependent glucose metabolism and confers metabolic vulnerabilities in cholangiocarcinoma. | Zhen, Yuanli; Liu, Kai; Shi, Lei; Shah, Simran; Xu, Qin; Ellis, Haley; Balasooriya, Eranga R; Kreuzer, Johannes; Morris, Robert; Baldwin, Albert S; Juric, Dejan; Haas, Wilhelm; Bardeesy, Nabeel | Nature communications | 38714664 | 2024 May 07 |
| Emerging delivery approaches for targeted pulmonary fibrosis treatment. | Diwan, Rimpy; Bhatt, Himanshu N; Beaven, Elfa; Nurunnabi, Md | Advanced drug delivery reviews | 38065244 | 2024 Jan |
| Liver fibrosis pathologies and potentials of RNA based therapeutics modalities. | Diwan, Rimpy; Gaytan, Samantha Lynn; Bhatt, Himanshu Narendrakumar; Pena-Zacarias, Jacqueline; Nurunnabi, Md | Drug delivery and translational research | 38446352 | 2024 Oct |
| Phosphate availability conditions caspofungin tolerance, capsule attachment and titan cell formation in Cryptococcus neoformans. | Qu, Xianya; Bhalla, Kabir; Horianopoulos, Linda C; Hu, Guanggan; Alcázar Magaña, Armando; Foster, Leonard J; Roque da Silva, Leandro Buffoni; Kretschmer, Matthias; Kronstad, James W | Frontiers in fungal biology | 39206133 | 2024 |
| Potentials of ionic liquids to overcome physical and biological barriers. | Beaven, Elfa; Kumar, Raj; An, Jeong Man; Mendoza, Hannia; Sutradhar, Sabuj Chandra; Choi, Wonho; Narayan, Mahesh; Lee, Yong-Kyu; Nurunnabi, Md | Advanced drug delivery reviews | 38104896 | 2024 Jan |
| Leptochelins A-C, Cytotoxic Metallophores Produced by Geographically Dispersed Leptothoe Strains of Marine Cyanobacteria. | Avalon, Nicole E; Reis, Mariana A; Thornburg, Christopher C; Williamson, R Thomas; Petras, Daniel; Aron, Allegra T; Neuhaus, George F; Al-Hindy, Momen; Mitrevska, Jana; Ferreira, Leonor; Morais, João; El Abiead, Yasin; Glukhov, Evgenia; Alexander, Kelsey L; Vulpanovici, F Alexandra; Bertin, Matthew J; Whitner, Syrena; Choi, Hyukjae; Spengler, Gabriella; Blinov, Kirill; Almohammadi, Ameen M; Shaala, Lamiaa A; Kew, William R; Paša-Tolić, Ljiljana; Youssef, Diaa T A; Dorrestein, Pieter C; Vasconcelos, Vitor; Gerwick, Lena; McPhail, Kerry L; Gerwick, William H | Journal of the American Chemical Society | 38918178 | 2024 Jul 10 |
| Loss of Pip4k2c confers liver-metastatic organotropism through insulin-dependent PI3K-AKT pathway activation. | Rogava, Meri; Aprati, Tyler J; Chi, Wei-Yu; Melms, Johannes C; Hug, Clemens; Davis, Stephanie H; Earlie, Ethan M; Chung, Charlie; Deshmukh, Sachin K; Wu, Sharon; Sledge, George; Tang, Stephen; Ho, Patricia; Amin, Amit Dipak; Caprio, Lindsay; Gurjao, Carino; Tagore, Somnath; Ngo, Bryan; Lee, Michael J; Zanetti, Giorgia; Wang, Yiping; Chen, Sean; Ge, William; Melo, Luiza Martins Nascentes; Allies, Gabriele; Rösler, Jonas; Gibney, Goeffrey T; Schmitz, Oliver J; Sykes, Megan; Creusot, Rémi J; Tüting, Thomas; Schadendorf, Dirk; Röcken, Martin; Eigentler, Thomas K; Molotkov, Andrei; Mintz, Akiva; Bakhoum, Samuel F; Beyaz, Semir; Cantley, Lewis C; Sorger, Peter K; Meckelmann, Sven W; Tasdogan, Alpaslan; Liu, David; Laughney, Ashley M; Izar, Benjamin | Nature cancer | 38286827 | 2024 Mar |
| Transcriptional risk scores in Alzheimer's disease: From pathology to cognition. | Pyun, Jung-Min; Park, Young Ho; Wang, Jiebiao; Bennett, David A; Bice, Paula J; Kim, Jun Pyo; Kim, SangYun; Saykin, Andrew J; Nho, Kwangsik | Alzheimer's & dementia : the journal of the Alzheimer's Association | 37563770 | 2024 Jan |
| Modeling transcriptional regulation of the cell cycle using a novel cybernetic-inspired approach. | Raja, Rubesh; Khanum, Sana; Aboulmouna, Lina; Maurya, Mano R; Gupta, Shakti; Subramaniam, Shankar; Ramkrishna, Doraiswami | Biophysical journal | 38102827 | 2024 Jan 16 |
| Sex-biased gene expression and gene-regulatory networks of sex-biased adverse event drug targets and drug metabolism genes. | Fisher, Jennifer L; Clark, Amanda D; Jones, Emma F; Lasseigne, Brittany N | BMC pharmacology & toxicology | 38167211 | 2024 Jan 02 |
| scMD facilitates cell type deconvolution using single-cell DNA methylation references. | Cai, Manqi; Zhou, Jingtian; McKennan, Chris; Wang, Jiebiao | Communications biology | 38168620 | 2024 Jan 02 |
| Deficiency of the lipid flippase ATP10A causes diet-induced dyslipidemia in female mice. | Norris, Adriana C; Yazlovitskaya, Eugenia M; Zhu, Lin; Rose, Bailey S; May, Jody C; Gibson-Corley, Katherine N; McLean, John A; Stafford, John M; Graham, Todd R | Scientific reports | 38172157 | 2024 Jan 03 |
| Rummagene: massive mining of gene sets from supporting materials of biomedical research publications. | Clarke, Daniel J B; Marino, Giacomo B; Deng, Eden Z; Xie, Zhuorui; Evangelista, John Erol; Ma'ayan, Avi | Communications biology | 38643247 | 2024 Apr 20 |
| Loop Catalog: a comprehensive HiChIP database of human and mouse samples. | Reyna, Joaquin; Fetter, Kyra; Ignacio, Romeo; Marandi, Cemil Can Ali; Rao, Nikhil; Jiang, Zichen; Figueroa, Daniela Salgado; Bhattacharyya, Sourya; Ay, Ferhat | bioRxiv : the preprint server for biology | 38746164 | 2024 Apr 29 |
| SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models. | Gjoni, Ketrin; Pollard, Katherine S | Bioinformatics (Oxford, England) | 38796686 | 2024 Jun 03 |
| METTL3-mediated chromatin contacts promote stress granule phase separation through metabolic reprogramming during senescence. | Wang, Chen; Tanizawa, Hideki; Hill, Connor; Havas, Aaron; Zhang, Qiang; Liao, Liping; Hao, Xue; Lei, Xue; Wang, Lu; Nie, Hao; Qi, Yuan; Tian, Bin; Gardini, Alessandro; Kossenkov, Andrew V; Goldman, Aaron; Berger, Shelley L; Noma, Ken-Ichi; Adams, Peter D; Zhang, Rugang | Nature communications | 38926365 | 2024 Jun 26 |
| High-Resolution Mass Spectrometry for Human Exposomics: Expanding Chemical Space Coverage. | Lai, Yunjia; Koelmel, Jeremy P; Walker, Douglas I; Price, Elliott J; Papazian, Stefano; Manz, Katherine E; Castilla-Fernández, Delia; Bowden, John A; Nikiforov, Vladimir; David, Arthur; Bessonneau, Vincent; Amer, Bashar; Seethapathy, Suresh; Hu, Xin; Lin, Elizabeth Z; Jbebli, Akrem; McNeil, Brooklynn R; Barupal, Dinesh; Cerasa, Marina; Xie, Hongyu; Kalia, Vrinda; Nandakumar, Renu; Singh, Randolph; Tian, Zhenyu; Gao, Peng; Zhao, Yujia; Froment, Jean; Rostkowski, Pawel; Dubey, Saurabh; Coufalíková, Kateřina; Seličová, Hana; Hecht, Helge; Liu, Sheng; Udhani, Hanisha H; Restituito, Sophie; Tchou-Wong, Kam-Meng; Lu, Kun; Martin, Jonathan W; Warth, Benedikt; Godri Pollitt, Krystal J; Klánová, Jana; Fiehn, Oliver; Metz, Thomas O; Pennell, Kurt D; Jones, Dean P; Miller, Gary W | Environmental science & technology | 38984754 | 2024 Jul 23 |
| Multiomics2Targets identifies targets from cancer cohorts profiled with transcriptomics, proteomics, and phosphoproteomics. | Deng, Eden Z; Marino, Giacomo B; Clarke, Daniel J B; Diamant, Ido; Resnick, Adam C; Ma, Weiping; Wang, Pei; Ma'ayan, Avi | Cell reports methods | 39127042 | 2024 Aug 19 |
| Mitochondrial complex I promotes kidney cancer metastasis. | Bezwada, Divya; Perelli, Luigi; Lesner, Nicholas P; Cai, Ling; Brooks, Bailey; Wu, Zheng; Vu, Hieu S; Sondhi, Varun; Cassidy, Daniel L; Kasitinon, Stacy; Kelekar, Sherwin; Cai, Feng; Aurora, Arin B; Patrick, McKenzie; Leach, Ashley; Ghandour, Rashed; Zhang, Yuanyuan; Do, Duyen; McDaniel, Phyllis; Sudderth, Jessica; Dumesnil, Dennis; House, Sara; Rosales, Tracy; Poole, Alan M; Lotan, Yair; Woldu, Solomon; Bagrodia, Aditya; Meng, Xiaosong; Cadeddu, Jeffrey A; Mishra, Prashant; Garcia-Bermudez, Javier; Pedrosa, Ivan; Kapur, Payal; Courtney, Kevin D; Malloy, Craig R; Genovese, Giannicola; Margulis, Vitaly; DeBerardinis, Ralph J | Nature | 39143213 | 2024 Sep |
| Multiorgan locked-state model of chronic diseases and systems pharmacology opportunities. | Ung, Choong Yong; Correia, Cristina; Li, Hu; Adams, Christopher M; Westendorf, Jennifer J; Zhu, Shizhen | Drug discovery today | 37967790 | 2024 Jan |
| A fast, scalable and versatile tool for analysis of single-cell omics data. | Zhang, Kai; Zemke, Nathan R; Armand, Ethan J; Ren, Bing | Nature methods | 38191932 | 2024 Feb |
| Metabolic abnormalities in the bone marrow cells of young offspring born to obese mothers. | Alina, Maloyan; Phillips, Elysse; Alharithi, Yem; Kadam, Leena; Coussens, Lisa; Kumar, Sushil | Research square | 38313293 | 2024 Jan 16 |
| RummaGEO: Automatic Mining of Human and Mouse Gene Sets from GEO. | Marino, Giacomo B; Clarke, Daniel J B; Deng, Eden Z; Ma'ayan, Avi | bioRxiv : the preprint server for biology | 38645198 | 2024 Apr 13 |
| Discovery of optimal cell type classification marker genes from single cell RNA sequencing data. | Liu, Angela; Peng, Beverly; Pankajam, Ajith V; Duong, Thu Elizabeth; Pryhuber, Gloria; Scheuermann, Richard H; Zhang, Yun | bioRxiv : the preprint server for biology | 38712147 | 2024 Jun 26 |
| Repeated exposure to eucalyptus wood smoke alters pulmonary gene and metabolic profiles in male Long-Evans rats. | Cochran, Samuel J; Dunigan-Russell, Katelyn; Hutton, Grace M; Nguyen, Helen; Schladweiler, Mette C; Jones, Dean P; Williams, Wanda C; Fisher, Anna A; Gilmour, M Ian; Dye, Janice A; Smith, M Ryan; Miller, Colette N; Gowdy, Kymberly M | Toxicological sciences : an official journal of the Society of Toxicology | 38544285 | 2024 May 28 |
| Single-cell transcriptomics reveals stage- and side-specificity of gene modules in colorectal cancer. | Rahiminejad, Sara; Mukund, Kavitha; Maurya, Mano Ram; Subramaniam, Shankar | Research square | 38826219 | 2024 May 24 |
| Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage. | Börner, Katy; Blood, Philip D; Silverstein, Jonathan C; Ruffalo, Matthew; Satija, Rahul; Teichmann, Sarah A; Pryhuber, Gloria; Misra, Ravi S; Purkerson, Jeffrey; Fan, Jean; Hickey, John W; Molla, Gesmira; Xu, Chuan; Zhang, Yun; Weber, Griffin; Jain, Yashvardhan; Qaurooni, Danial; Kong, Yongxin; HRA Team; Bueckle, Andreas; Herr, Bruce W | bioRxiv : the preprint server for biology | 38826261 | 2024 Aug 14 |
| Nucleotide metabolism in cancer cells fuels a UDP-driven macrophage cross-talk, promoting immunosuppression and immunotherapy resistance. | Scolaro, Tommaso; Manco, Marta; Pecqueux, Mathieu; Amorim, Ricardo; Trotta, Rosa; Van Acker, Heleen H; Van Haele, Matthias; Shirgaonkar, Niranjan; Naulaerts, Stefan; Daniluk, Jan; Prenen, Fran; Varamo, Chiara; Ponti, Donatella; Doglioni, Ginevra; Ferreira Campos, Ana Margarida; Fernandez Garcia, Juan; Radenkovic, Silvia; Rouhi, Pegah; Beatovic, Aleksandar; Wang, Liwei; Wang, Yu; Tzoumpa, Amalia; Antoranz, Asier; Sargsian, Ara; Di Matteo, Mario; Berardi, Emanuele; Goveia, Jermaine; Ghesquière, Bart; Roskams, Tania; Soenen, Stefaan; Voets, Thomas; Manshian, Bella; Fendt, Sarah-Maria; Carmeliet, Peter; Garg, Abhishek D; DasGupta, Ramanuj; Topal, Baki; Mazzone, Massimiliano | Nature cancer | 38844817 | 2024 Aug |
| BLEND: Probabilistic Cellular Deconvolution with Automated Reference Selection. | Huang, Penghui; Cai, Manqi; McKennan, Chris; Wang, Jiebiao | bioRxiv : the preprint server for biology | 39149243 | 2024 Aug 06 |
| Deciphering tumour microenvironment and elucidating the origin of cancer cells in ovarian clear cell carcinoma. | Kamaraj, Uma S; Gautam, Pradeep; Cheng, Terence; Chin, Tham Su; Tay, Sun Kuie; Ho, Tew Hong; Nadarajah, Ravichandran; Goh, Ronald Chin Hong; Wong, Shing Lih; Mantoo, Sangeeta; Busmanis, Inny; Li, Hu; Le, Minh Tn; Li, Qi-Jing; Lim, Elaine Hsuen; Loh, Yuin-Han | bioRxiv : the preprint server for biology | 39149248 | 2024 Aug 08 |
| An Ensemble Spectral Prediction (ESP) model for metabolite annotation. | Li, Xinmeng; Zhou Chen, Yan; Kalia, Apurva; Zhu, Hao; Liu, Li-Ping; Hassoun, Soha | Bioinformatics (Oxford, England) | 39180771 | 2024 Aug 02 |
| Taurine modulates host cell responses to Helicobacter pylori VacA toxin. | Westland, Mandy D; Schrimpe-Rutledge, Alexandra C; Codreanu, Simona G; Sherrod, Stacy D; McLean, John A; McClain, Mark S; Cover, Timothy L | Infection and immunity | 38975764 | 2024 Aug 13 |
| Association studies of up to 1.2 million individuals yield new insights into the genetic etiology of tobacco and alcohol use. | Liu, Mengzhen; Jiang, Yu; Wedow, Robbee; Li, Yue; Brazel, David M; Chen, Fang; Datta, Gargi; Davila-Velderrain, Jose; McGuire, Daniel; Tian, Chao; Zhan, Xiaowei; 23andMe Research Team; HUNT All-In Psychiatry; Choquet, Hélène; Docherty, Anna R; Faul, Jessi | Nature genetics | 30643251 | 2019 Feb |
| Appyters: Turning Jupyter Notebooks into data-driven web apps. | Clarke, Daniel J B; Jeon, Minji; Stein, Daniel J; Moiseyev, Nicole; Kropiwnicki, Eryk; Dai, Charles; Xie, Zhuorui; Wojciechowicz, Megan L; Litz, Skylar; Hom, Jason; Evangelista, John Erol; Goldman, Lucas; Zhang, Serena; Yoon, Christine; Ahamed, Tahmid; Bhuiyan, Samantha; Cheng, Minxuan; Karam, Julie; Jagodnik, Kathleen M; Shu, Ingrid; Lachmann, Alexander; Ayling, Sam; Jenkins, Sherry L; Ma'ayan, Avi | Patterns (New York, N.Y.) | 33748796 | 2021 Mar 12 |
| Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning. | Kropiwnicki, Eryk; Evangelista, John E; Stein, Daniel J; Clarke, Daniel J B; Lachmann, Alexander; Kuleshov, Maxim V; Jeon, Minji; Jagodnik, Kathleen M; Ma'ayan, Avi | Database : the journal of biological databases and curation | 33787872 | 2021 03 31 |
| The mwtab Python Library for RESTful Access and Enhanced Quality Control, Deposition, and Curation of the Metabolomics Workbench Data Repository. | Powell, Christian D; Moseley, Hunter N B | Metabolites | 33808985 | 2021 Mar 12 |
| 3D virtual reality vs. 2D desktop registration user interface comparison. | Bueckle, Andreas; Buehling, Kilian; Shih, Patrick C; Börner, Katy | PloS one | 34705835 | 2021 |
| Immune Response in Severe and Non-Severe Coronavirus Disease 2019 (COVID-19) Infection: A Mechanistic Landscape. | Mukund, Kavitha; Nayak, Priya; Ashokkumar, Chethan; Rao, Sohail; Almeda, Jose; Betancourt-Garcia, Monica M; Sindhi, Rakesh; Subramaniam, Shankar | Frontiers in immunology | 34721400 | 2021 |
| GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser. | Petras, Daniel; Phelan, Vanessa V; Acharya, Deepa; Allen, Andrew E; Aron, Allegra T; Bandeira, Nuno; Bowen, Benjamin P; Belle-Oudry, Deirdre; Boecker, Simon; Cummings Jr, Dale A; Deutsch, Jessica M; Fahy, Eoin; Garg, Neha; Gregor, Rachel; Handelsman, Jo; Navarro-Hoyos, Mirtha; Jarmusch, Alan K; Jarmusch, Scott A; Louie, Katherine; Maloney, Katherine N; Marty, Michael T; Meijler, Michael M; Mizrahi, Itzhak; Neve, Rachel L; Northen, Trent R; Molina-Santiago, Carlos; Panitchpakdi, Morgan; Pullman, Benjamin; Puri, Aaron W; Schmid, Robin; Subramaniam, Shankar; Thukral, Monica; Vasquez-Castro, Felipe; Dorrestein, Pieter C; Wang, Mingxun | Nature methods | 34862502 | 2022 02 |
| Getting Started with the IDG KMC Datasets and Tools. | Kropiwnicki, Eryk; Binder, Jessica L; Yang, Jeremy J; Holmes, Jayme; Lachmann, Alexander; Clarke, Daniel J B; Sheils, Timothy; Kelleher, Keith J; Metzger, Vincent T; Bologa, Cristian G; Oprea, Tudor I; Ma'ayan, Avi | Current protocols | 35085427 | 2022 Jan |
| blitzGSEA: Efficient computation of Gene Set Enrichment Analysis through Gamma distribution approximation. | Lachmann, Alexander; Xie, Zhuorui; Ma'ayan, Avi | Bioinformatics (Oxford, England) | 35143610 | 2022 Feb 10 |
| Assessing reproducibility of high-throughput experiments in the case of missing data. | Singh, Roopali; Zhang, Feipeng; Li, Qunhua | Statistics in medicine | 35178743 | 2022 May 10 |
| DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules. | Kropiwnicki, Eryk; Lachmann, Alexander; Clarke, Daniel J B; Xie, Zhuorui; Jagodnik, Kathleen M; Ma'ayan, Avi | BMC bioinformatics | 35183110 | 2022 Feb 19 |
| LMOD2-related dilated cardiomyopathy presenting in late infancy. | Lay, Erica; Azamian, Mahshid S; Denfield, Susan W; Dreyer, William; Spinner, Joseph A; Kearney, Debra; Zhang, Lilei; Worley, Kim C; Bi, Weimin; Lalani, Seema R | American journal of medical genetics. Part A | 35188328 | 2022 Feb 21 |
| Considerations and challenges for sex-aware drug repurposing. | Fisher, Jennifer L; Jones, Emma F; Flanary, Victoria L; Williams, Avery S; Ramsey, Elizabeth J; Lasseigne, Brittany N | Biology of sex differences | 35337371 | 2022 03 25 |
| Gene and drug landing page aggregator. | Clarke, Daniel J B; Kuleshov, Maxim V; Xie, Zhuorui; Evangelista, John E; Meyers, Marilyn R; Kropiwnicki, Eryk; Jenkins, Sherry L; Ma'ayan, Avi | Bioinformatics advances | 35368424 | 2022 |
| Connecting high-resolution 3D chromatin organization with epigenomics. | Feng, Fan; Yao, Yuan; Wang, Xue Qing David; Zhang, Xiaotian; Liu, Jie | Nature communications | 35440119 | 2022 Apr 19 |
| Modular and mechanistic changes across stages of colorectal cancer. | Rahiminejad, Sara; Maurya, Mano R; Mukund, Kavitha; Subramaniam, Shankar | BMC cancer | 35448980 | 2022 Apr 21 |
| SigCom LINCS: data and metadata search engine for a million gene expression signatures. | Evangelista, John Erol; Clarke, Daniel J B; Xie, Zhuorui; Lachmann, Alexander; Jeon, Minji; Chen, Kerwin; Jagodnik, Kathleen M; Jenkins, Sherry L; Kuleshov, Maxim V; Wojciechowicz, Megan L; Schürer, Stephan C; Medvedovic, Mario; Ma'ayan, Avi | Nucleic acids research | 35524556 | 2022 May 07 |
| Harmonizing Labeling and Analytical Strategies to Obtain Protein Turnover Rates in Intact Adult Animals. | Hammond, Dean E; Simpson, Deborah M; Franco, Catarina; Wright Muelas, Marina; Waters, John; Ludwig, R W; Prescott, Mark C; Hurst, Jane L; Beynon, Robert J; Lau, Edward | Molecular & cellular proteomics : MCP | 35636728 | 2022 07 |
| Integrating 3D genomic and epigenomic data to enhance target gene discovery and drug repurposing in transcriptome-wide association studies. | Khunsriraksakul, Chachrit; McGuire, Daniel; Sauteraud, Renan; Chen, Fang; Yang, Lina; Wang, Lida; Hughey, Jordan; Eckert, Scott; Dylan Weissenkampen, J; Shenoy, Ganesh; Marx, Olivia; Carrel, Laura; Jiang, Bibo; Liu, Dajiang J | Nature communications | 35672318 | 2022 06 07 |
| Arap1 loss causes retinal pigment epithelium phagocytic dysfunction and subsequent photoreceptor death. | Shao, Andy; Lopez, Antonio Jacobo; Chen, JiaJia; Tham, Addy; Javier, Seanne; Quiroz, Alejandra; Frick, Sonia; Levine, Edward M; Lloyd, K C Kent; Leonard, Brian C; Murphy, Christopher J; Glaser, Thomas M; Moshiri, Ala | Disease models & mechanisms | 35758026 | 2022 Jul 01 |
| Defining the Roles of Cardiokines in Human Aging and Age-Associated Diseases. | Srivastava, Himangi; Pozzoli, Marina; Lau, Edward | Frontiers in aging | 35821831 | 2022 |
| Construction and Application of Polygenic Risk Scores in Autoimmune Diseases. | Khunsriraksakul, Chachrit; Markus, Havell; Olsen, Nancy J; Carrel, Laura; Jiang, Bibo; Liu, Dajiang J | Frontiers in immunology | 35833142 | 2022 |
| Getting Started with LINCS Datasets and Tools. | Xie, Zhuorui; Kropiwnicki, Eryk; Wojciechowicz, Megan L; Jagodnik, Kathleen M; Shu, Ingrid; Bailey, Allison; Clarke, Daniel J B; Jeon, Minji; Evangelista, John Erol; V Kuleshov, Maxim; Lachmann, Alexander; Parigi, Abhijna A; Sanchez, Jose M; Jenkins, Sherry L; Ma'ayan, Avi | Current protocols | 35876555 | 2022 Jul |
| Pan-African genome demonstrates how population-specific genome graphs improve high-throughput sequencing data analysis. | Tetikol, H Serhat; Turgut, Deniz; Narci, Kubra; Budak, Gungor; Kalay, Ozem; Arslan, Elif; Demirkaya-Budak, Sinem; Dolgoborodov, Alexey; Kabakci-Zorlu, Duygu; Semenyuk, Vladimir; Jain, Amit; Davis-Dusenbery, Brandi N | Nature communications | 35927245 | 2022 Aug 04 |
| Rare genetic variants explain missing heritability in smoking. | Jang, Seon-Kyeong; Evans, Luke; Fialkowski, Allison; Arnett, Donna K; Ashley-Koch, Allison E; Barnes, Kathleen C; Becker, Diane M; Bis, Joshua C; Blangero, John; Bleecker, Eugene R; Boorgula, Meher Preethi; Bowden, Donald W; Brody, Jennifer A; Cade, Brian | Nature human behaviour | 35927319 | 2022 Nov |
| Proteogenomics reveals sex biased aging genes and coordinated splicing in cardiac aging. | Han, Yu; Wennersten, Sara A; Wright, Julianna M; Ludwig, R W; Lau, Edward; Lam, Maggie P Y | American journal of physiology. Heart and circulatory physiology | 35930447 | 2022 Aug 05 |
| Proteogenomic Markers of Chemotherapy Resistance and Response in Triple-Negative Breast Cancer. | Anurag, Meenakshi; Jaehnig, Eric J; Krug, Karsten; Lei, Jonathan T; Bergstrom, Erik J; Kim, Beom-Jun; Vashist, Tanmayi D; Huynh, Anh Minh Tran; Dou, Yongchao; Gou, Xuxu; Huang, Chen; Shi, Zhiao; Wen, Bo; Korchina, Viktoriya; Gibbs, Richard A; Muzny, Donna | Cancer discovery | 36001024 | 2022 Nov 02 |
| Social and scientific motivations to move beyond groups in allele frequencies: The TOPMed experience. | Nelson, Sarah C; Gogarten, Stephanie M; Fullerton, Stephanie M; Isasi, Carmen R; Mitchell, Braxton D; North, Kari E; Rich, Stephen S; Taylor, Matthew R G; Zöllner, Sebastian; Sofer, Tamar | American journal of human genetics | 36055210 | 2022 Sep 01 |
| Clinical exome sequencing uncovers a high frequency of Mendelian disorders in infants with stroke: A retrospective analysis. | Kumar, Runjun D; Meng, Linyan; Liu, Pengfei; Miyake, Christina Y; Worley, Kim C; Bi, Weimin; Lalani, Seema R | American journal of medical genetics. Part A | 36065636 | 2022 Sep 06 |
| Transforming L1000 profiles to RNA-seq-like profiles with deep learning. | Jeon, Minji; Xie, Zhuorui; Evangelista, John E; Wojciechowicz, Megan L; Clarke, Daniel J B; Ma'ayan, Avi | BMC bioinformatics | 36100892 | 2022 Sep 13 |
| Mucoadhesive carriers for oral drug delivery. | Kumar, Raj; Islam, Tamanna; Nurunnabi, Md | Journal of controlled release : official journal of the Controlled Release Society | 36116580 | 2022 Nov |
| Promoting validation and cross-phylogenetic integration in model organism research. | Cheng, Keith C; Burdine, Rebecca D; Dickinson, Mary E; Ekker, Stephen C; Lin, Alex Y; Lloyd, K C Kent; Lutz, Cathleen M; MacRae, Calum A; Morrison, John H; O'Connor, David H; Postlethwait, John H; Rogers, Crystal D; Sanchez, Susan; Simpson, Julie H; Talbot, William S; Wallace, Douglas C; Weimer, Jill M; Bellen, Hugo J | Disease models & mechanisms | 36125045 | 2022 09 01 |
| A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies. | Li, Zilin; Li, Xihao; Zhou, Hufeng; Gaynor, Sheila M; Selvaraj, Margaret Sunitha; Arapoglou, Theodore; Quick, Corbin; Liu, Yaowu; Chen, Han; Sun, Ryan; Dey, Rounak; Arnett, Donna K; Auer, Paul L; Bielak, Lawrence F; Bis, Joshua C; Blackwell, Thomas W; Blangero, John; Boerwinkle, Eric; Bowden, Donald W; Brody, Jennifer A; Cade, Brian E; Conomos, Matthew P; Correa, Adolfo; Cupples, L Adrienne; Curran, Joanne E; de Vries, Paul S; Duggirala, Ravindranath; Franceschini, Nora; Freedman, Barry I; Göring, Harald H H; Guo, Xiuqing; Kalyani, Rita R; Kooperberg, Charles; Kral, Brian G; Lange, Leslie A; Lin, Bridget M; Manichaikul, Ani; Manning, Alisa K; Martin, Lisa W; Mathias, Rasika A; Meigs, James B; Mitchell, Braxton D; Montasser, May E; Morrison, Alanna C; Naseri, Take; O'Connell, Jeffrey R; Palmer, Nicholette D; Peyser, Patricia A; Psaty, Bruce M; Raffield, Laura M; Redline, Susan; Reiner, Alexander P; Reupena, Muagututi'a Sefuiva; Rice, Kenneth M; Rich, Stephen S; Smith, Jennifer A; Taylor, Kent D; Taub, Margaret A; Vasan, Ramachandran S; Weeks, Daniel E; Wilson, James G; Yanek, Lisa R; Zhao, Wei; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; TOPMed Lipids Working Group; Rotter, Jerome I; Willer, Cristen J; Natarajan, Pradeep; Peloso, Gina M; Lin, Xihong | Nature methods | 36303018 | 2022 Dec |
| FAVOR: functional annotation of variants online resource and annotator for variation across the human genome. | Zhou, Hufeng; Arapoglou, Theodore; Li, Xihao; Li, Zilin; Zheng, Xiuwen; Moore, Jill; Asok, Abhijith; Kumar, Sushant; Blue, Elizabeth E; Buyske, Steven; Cox, Nancy; Felsenfeld, Adam; Gerstein, Mark; Kenny, Eimear; Li, Bingshan; Matise, Tara; Philippakis, Anthony; Rehm, Heidi L; Sofia, Heidi J; Snyder, Grace; NHGRI Genome Sequencing Program Variant Functional Annotation Working Group; Weng, Zhiping; Neale, Benjamin; Sunyaev, Shamil R; Lin, Xihong | Nucleic acids research | 36350676 | 2023 Jan 06 |
| Protein prediction models support widespread post-transcriptional regulation of protein abundance by interacting partners. | Srivastava, Himangi; Lippincott, Michael J; Currie, Jordan; Canfield, Robert; Lam, Maggie P Y; Lau, Edward | PLoS computational biology | 36356032 | 2022 Nov |
| Making Common Fund data more findable: catalyzing a data ecosystem. | Charbonneau, Amanda L; Brady, Arthur; Czajkowski, Karl; Aluvathingal, Jain; Canchi, Saranya; Carter, Robert; Chard, Kyle; Clarke, Daniel J B; Crabtree, Jonathan; Creasy, Heather H; D'Arcy, Mike; Felix, Victor; Giglio, Michelle; Gingrich, Alicia; Harris, Rayna M; Hodges, Theresa K; Ifeonu, Olukemi; Jeon, Minji; Kropiwnicki, Eryk; Lim, Marisa C W; Liming, R Lee; Lumian, Jessica; Mahurkar, Anup A; Mandal, Meisha; Munro, James B; Nadendla, Suvarna; Richter, Rudyard; Romano, Cia; Rocca-Serra, Philippe; Schor, Michael; Schuler, Robert E; Tangmunarunkit, Hongsuda; Waldrop, Alex; Williams, Cris; Word, Karen; Sansone, Susanna-Assunta; Ma'ayan, Avi; Wagner, Rick; Foster, Ian; Kesselman, Carl; Brown, C Titus; White, Owen | GigaScience | 36409836 | 2022 Nov 21 |
| Myofibroblast specific targeting approaches to improve fibrosis treatment. | Beaven, Elfa; Kumar, Raj; Bhatt, Himanshu N; Esquivel, Stephanie V; Nurunnabi, Md | Chemical communications (Cambridge, England) | 36445310 | 2022 Dec 08 |
| Analysis of genome-wide knockout mouse database identifies candidate ciliopathy genes. | Higgins, Kendall; Moore, Bret A; Berberovic, Zorana; Adissu, Hibret A; Eskandarian, Mohammad; Flenniken, Ann M; Shao, Andy; Imai, Denise M; Clary, Dave; Lanoue, Louise; Newbigging, Susan; Nutter, Lauryl M J; Adams, David J; Bosch, Fatima; Braun, Robert E; Brown, Steve D M; Dickinson, Mary E; Dobbie, Michael; Flicek, Paul; Gao, Xiang; Galande, Sanjeev; Grobler, Anne; Heaney, Jason D; Herault, Yann; de Angelis, Martin Hrabe; Chin, Hsian-Jean Genie; Mammano, Fabio; Qin, Chuan; Shiroishi, Toshihiko; Sedlacek, Radislav; Seong, J-K; Xu, Ying; IMPC Consortium; Lloyd, K C Kent; McKerlie, Colin; Moshiri, Ala | Scientific reports | 36456625 | 2022 Dec 01 |
| Genetic diversity fuels gene discovery for tobacco and alcohol use. | Saunders, Gretchen R B; Wang, Xingyan; Chen, Fang; Jang, Seon-Kyeong; Liu, Mengzhen; Wang, Chen; Gao, Shuang; Jiang, Yu; Khunsriraksakul, Chachrit; Otto, Jacqueline M; Addison, Clifton; Akiyama, Masato; Albert, Christine M; Aliev, Fazil; Alonso, Alvaro; A | Nature | 36477530 | 2022 Dec |
| Tissue registration and exploration user interfaces in support of a human reference atlas. | Börner, Katy; Bueckle, Andreas; Herr 2nd, Bruce W; Cross, Leonard E; Quardokus, Ellen M; Record, Elizabeth G; Ju, Yingnan; Silverstein, Jonathan C; Browne, Kristen M; Jain, Sanjay; Wasserfall, Clive H; Jorgensen, Marda L; Spraggins, Jeffrey M; Patterson, N Heath; Weber, Griffin M | Communications biology | 36513738 | 2022 Dec 13 |
| Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies. | Li, Xihao; Quick, Corbin; Zhou, Hufeng; Gaynor, Sheila M; Liu, Yaowu; Chen, Han; Selvaraj, Margaret Sunitha; Sun, Ryan; Dey, Rounak; Arnett, Donna K; Bielak, Lawrence F; Bis, Joshua C; Blangero, John; Boerwinkle, Eric; Bowden, Donald W; Brody, Jennifer A; Cade, Brian E; Correa, Adolfo; Cupples, L Adrienne; Curran, Joanne E; de Vries, Paul S; Duggirala, Ravindranath; Freedman, Barry I; Göring, Harald H H; Guo, Xiuqing; Haessler, Jeffrey; Kalyani, Rita R; Kooperberg, Charles; Kral, Brian G; Lange, Leslie A; Manichaikul, Ani; Martin, Lisa W; McGarvey, Stephen T; Mitchell, Braxton D; Montasser, May E; Morrison, Alanna C; Naseri, Take; O'Connell, Jeffrey R; Palmer, Nicholette D; Peyser, Patricia A; Psaty, Bruce M; Raffield, Laura M; Redline, Susan; Reiner, Alexander P; Reupena, Muagututi'a Sefuiva; Rice, Kenneth M; Rich, Stephen S; Sitlani, Colleen M; Smith, Jennifer A; Taylor, Kent D; Vasan, Ramachandran S; Willer, Cristen J; Wilson, James G; Yanek, Lisa R; Zhao, Wei; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Lipids Working Group; Rotter, Jerome I; Natarajan, Pradeep; Peloso, Gina M; Li, Zilin; Lin, Xihong | Nature genetics | 36564505 | 2023 Jan |
| Ten simple rules for using public biological data for your research. | Oza, Vishal H; Whitlock, Jordan H; Wilk, Elizabeth J; Uno-Antonison, Angelina; Wilk, Brandon; Gajapathy, Manavalan; Howton, Timothy C; Trull, Austyn; Ianov, Lara; Worthey, Elizabeth A; Lasseigne, Brittany N | PLoS computational biology | 36602970 | 2023 Jan |
| Unified and Standardized Mass Spectrometry Data Processing in Python Using spectrum_utils. | Bittremieux, Wout; Levitsky, Lev; Pilz, Matteo; Sachsenberg, Timo; Huber, Florian; Wang, Mingxun; Dorrestein, Pieter C | Journal of proteome research | 36688502 | 2023 Feb 03 |
| Multi-ancestry transcriptome-wide association analyses yield insights into tobacco use biology and drug repurposing. | Chen, Fang; Wang, Xingyan; Jang, Seon-Kyeong; Quach, Bryan C; Weissenkampen, J Dylan; Khunsriraksakul, Chachrit; Yang, Lina; Sauteraud, Renan; Albert, Christine M; Allred, Nicholette D D; Arnett, Donna K; Ashley-Koch, Allison E; Barnes, Kathleen C; Barr, R Graham; Becker, Diane M; Bielak, Lawrence F; Bis, Joshua C; Blangero, John; Boorgula, Meher Preethi; Chasman, Daniel I; Chavan, Sameer; Chen, Yii-Der I; Chuang, Lee-Ming; Correa, Adolfo; Curran, Joanne E; David, Sean P; Fuentes, Lisa de Las; Deka, Ranjan; Duggirala, Ravindranath; Faul, Jessica D; Garrett, Melanie E; Gharib, Sina A; Guo, Xiuqing; Hall, Michael E; Hawley, Nicola L; He, Jiang; Hobbs, Brian D; Hokanson, John E; Hsiung, Chao A; Hwang, Shih-Jen; Hyde, Thomas M; Irvin, Marguerite R; Jaffe, Andrew E; Johnson, Eric O; Kaplan, Robert; Kardia, Sharon L R; Kaufman, Joel D; Kelly, Tanika N; Kleinman, Joel E; Kooperberg, Charles; Lee, I-Te; Levy, Daniel; Lutz, Sharon M; Manichaikul, Ani W; Martin, Lisa W; Marx, Olivia; McGarvey, Stephen T; Minster, Ryan L; Moll, Matthew; Moussa, Karine A; Naseri, Take; North, Kari E; Oelsner, Elizabeth C; Peralta, Juan M; Peyser, Patricia A; Psaty, Bruce M; Rafaels, Nicholas; Raffield, Laura M; Reupena, Muagututi'a Sefuiva; Rich, Stephen S; Rotter, Jerome I; Schwartz, David A; Shadyab, Aladdin H; Sheu, Wayne H-H; Sims, Mario; Smith, Jennifer A; Sun, Xiao; Taylor, Kent D; Telen, Marilyn J; Watson, Harold; Weeks, Daniel E; Weir, David R; Yanek, Lisa R; Young, Kendra A; Young, Kristin L; Zhao, Wei; Hancock, Dana B; Jiang, Bibo; Vrieze, Scott; Liu, Dajiang J | Nature genetics | 36702996 | 2023 Feb |
| Genome-wide screening reveals the genetic basis of mammalian embryonic eye development. | Chee, Justine M; Lanoue, Louise; Clary, Dave; Higgins, Kendall; Bower, Lynette; Flenniken, Ann; Guo, Ruolin; Adams, David J; Bosch, Fatima; Braun, Robert E; Brown, Steve D M; Chin, H-J Genie; Dickinson, Mary E; Hsu, Chih-Wei; Dobbie, Michael; Gao, Xiang; Galande, Sanjeev; Grobler, Anne; Heaney, Jason D; Herault, Yann; de Angelis, Martin Hrabe; Mammano, Fabio; Nutter, Lauryl M J; Parkinson, Helen; Qin, Chuan; Shiroishi, Toshi; Sedlacek, Radislav; Seong, J-K; Xu, Ying; International Mouse Phenotyping Consortium; Brooks, Brian; McKerlie, Colin; Lloyd, K C Kent; Westerberg, Henrik; Moshiri, Ala | BMC biology | 36737727 | 2023 Feb 03 |
| Multi-ancestry and multi-trait genome-wide association meta-analyses inform clinical risk prediction for systemic lupus erythematosus. | Khunsriraksakul, Chachrit; Li, Qinmengge; Markus, Havell; Patrick, Matthew T; Sauteraud, Renan; McGuire, Daniel; Wang, Xingyan; Wang, Chen; Wang, Lida; Chen, Siyuan; Shenoy, Ganesh; Li, Bingshan; Zhong, Xue; Olsen, Nancy J; Carrel, Laura; Tsoi, Lam C; Jiang, Bibo; Liu, Dajiang J | Nature communications | 36750564 | 2023 Feb 07 |
| Potential and Progress of 2D Materials in Photomedicine for Cancer Treatment. | Bhatt, Himanshu N; Pena-Zacarias, Jaqueline; Beaven, Elfa; Zahid, Md Ikhtiar; Ahmad, Sheikh Shafin; Diwan, Rimpy; Nurunnabi, Md | ACS applied bio materials | 36753355 | 2023 Feb 20 |
| Deep learning enabled multi-organ segmentation of mouse embryos. | Rolfe, S M; Whikehart, S M; Maga, A M | Biology open | 36802342 | 2023 Feb 15 |
| lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs. | Marino, Giacomo B; Wojciechowicz, Megan L; Clarke, Daniel J B; Kuleshov, Maxim V; Xie, Zhuorui; Jeon, Minji; Lachmann, Alexander; Ma'ayan, Avi | Database : the journal of biological databases and curation | 36869839 | 2023 Mar 04 |
| kegg_pull: a software package for the RESTful access and pulling from the Kyoto Encyclopedia of Gene and Genomes. | Huckvale, Erik; Moseley, Hunter N B | BMC bioinformatics | 36870946 | 2023 Mar 04 |
| PrismEXP: gene annotation prediction from stratified gene-gene co-expression matrices. | Lachmann, Alexander; Rizzo, Kaeli A; Bartal, Alon; Jeon, Minji; Clarke, Daniel J B; Ma'ayan, Avi | PeerJ | 36874981 | 2023 |
| RNAget: an API to securely retrieve RNA quantifications. | Upchurch, Sean; Palumbo, Emilio; Adams, Jeremy; Bujold, David; Bourque, Guillaume; Nedzel, Jared; Graham, Keenan; Kagda, Meenakshi S; Assis, Pedro; Hitz, Benjamin; Righi, Emilio; Guigó, Roderic; Wold, Barbara J; GA4GH RNA-Seq Task Team | Bioinformatics (Oxford, England) | 36897015 | 2023 Apr 03 |
| A pilot study on metabolomic characterization of human glioblastomas and patient plasma. | Liu, Allison; Aboud, Orwa; Dahabiyeh, Lina A; Bloch, Orin; Fiehn, Oliver | Research square | 36945517 | 2023 Mar 10 |
| Oral delivery of RNAi for cancer therapy. | Afrin, Humayra; Geetha Bai, Renu; Kumar, Raj; Ahmad, Sheikh Shafin; Agarwal, Sandeep K; Nurunnabi, Md | Cancer metastasis reviews | 36971908 | 2023 Mar 27 |
| Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas. | Herr 2nd, Bruce W; Hardi, Josef; Quardokus, Ellen M; Bueckle, Andreas; Chen, Lu; Wang, Fusheng; Caron, Anita R; Osumi-Sutherland, David; Musen, Mark A; Börner, Katy | Scientific data | 36973309 | 2023 Mar 27 |
| Computational screen to identify potential targets for immunotherapeutic identification and removal of senescence cells. | Deng, Eden Z; Fleishman, Reid H; Xie, Zhuorui; Marino, Giacomo B; Clarke, Daniel J B; Ma'ayan, Avi | Aging cell | 37082798 | 2023 Jun |
| Evaluating cancer cell line and patient-derived xenograft recapitulation of tumor and non-diseased tissue gene expression profiles in silico. | Williams, Avery S; Wilk, Elizabeth J; Fisher, Jennifer L; Lasseigne, Brittany N | bioRxiv : the preprint server for biology | 37090499 | 2023 Jun 15 |
| GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery. | Marino, Giacomo B; Ngai, Michael; Clarke, Daniel J B; Fleishman, Reid H; Deng, Eden Z; Xie, Zhuorui; Ahmed, Nasheath; Ma'ayan, Avi | Nucleic acids research | 37166966 | 2023 Jul 05 |
| Enrichr-KG: bridging enrichment analysis across multiple libraries. | Evangelista, John Erol; Xie, Zhuorui; Marino, Giacomo B; Nguyen, Nhi; Clarke, Daniel J B; Ma'ayan, Avi | Nucleic acids research | 37166973 | 2023 Jul 05 |
| Prioritized polycystic kidney disease drug targets and repurposing candidates from pre-cystic and cystic mouse Pkd2 model gene expression reversion. | Wilk, Elizabeth J; Howton, Timothy C; Fisher, Jennifer L; Oza, Vishal H; Brownlee, Ryan T; McPherson, Kasi C; Cleary, Hannah L; Yoder, Bradley K; George, James F; Mrug, Michal; Lasseigne, Brittany N | Molecular medicine (Cambridge, Mass.) | 37217845 | 2023 May 22 |
| β-Glucan and Fatty Acid Based Mucoadhesive Carrier for Gastrointestinal Tract Specific Local and Sustained Drug Delivery. | Esquivel, Stephanie Vargas; Bhatt, Himanshu N; Diwan, Rimpy; Habib, Ahsan; Lee, Wen-Yee; Khatun, Zehedina; Nurunnabi, Md | Biomolecules | 37238639 | 2023 Apr 28 |
| Senescent alveolar macrophages promote early-stage lung tumorigenesis. | Prieto, Luis I; Sturmlechner, Ines; Graves, Sara I; Zhang, Cheng; Goplen, Nick P; Yi, Eunhee S; Sun, Jie; Li, Hu; Baker, Darren J | Cancer cell | 37267954 | 2023 Jul 10 |
| Comparing chromatin contact maps at scale: methods and insights. | Gunsalus, Laura; McArthur, Evonne; Gjoni, Ketrin; Kuang, Shuzhen; Pittman, Maureen; Capra, John; Pollard, Katherine | Research square | 37292728 | 2023 May 23 |
| Defining diurnal fluctuations in mouse choroid plexus and CSF at high molecular, spatial, and temporal resolution. | Fame, Ryann M; Kalugin, Peter N; Petrova, Boryana; Xu, Huixin; Soden, Paul A; Shipley, Frederick B; Dani, Neil; Grant, Bradford; Pragana, Aja; Head, Joshua P; Gupta, Suhasini; Shannon, Morgan L; Chifamba, Fortunate F; Hawks-Mayer, Hannah; Vernon, Amanda; Gao, Fan; Zhang, Yong; Holtzman, Michael J; Heiman, Myriam; Andermann, Mark L; Kanarek, Naama; Lipton, Jonathan O; Lehtinen, Maria K | Nature communications | 37349305 | 2023 Jun 22 |
| β-Glucan-Mediated Oral Codelivery of 5FU and Bcl2 siRNA Attenuates Stomach Cancer. | Afrin, Humayra; Esquivel, Stephanie Vargas; Kumar, Raj; Zahid, Md Ikhtiar; Oporeza, Beu; Rahman, Md Fashiar; Boland, Thomas; Nurunnabi, Md | ACS applied materials & interfaces | 37350332 | 2023 Jul 12 |
| Sex-biased gene expression and gene-regulatory networks of sex-biased adverse event drug targets and drug metabolism genes. | Fisher, Jennifer L; Clark, Amanda D; Jones, Emma F; Lasseigne, Brittany N | bioRxiv : the preprint server for biology | 37362157 | 2023 Nov 15 |
| SPIN-AI: A Deep Learning Model That Identifies Spatially Predictive Genes. | Meng-Lin, Kevin; Ung, Choong-Yong; Zhang, Cheng; Weiskittel, Taylor M; Wisniewski, Philip; Zhang, Zhuofei; Tan, Shyang-Hong; Yeo, Kok-Siong; Zhu, Shizhen; Correia, Cristina; Li, Hu | Biomolecules | 37371475 | 2023 May 27 |
| Alternative Identification of Glycosides Using MS/MS Matching with an In Silico-Modified Aglycone Mass Spectra Library. | Rodríguez, Elys P; Li, Yuanyue; Vaniya, Arpana; Shih, Patrick M; Fiehn, Oliver | Analytical chemistry | 37390485 | 2023 Jul 18 |
| ATP10A promotes endothelial cell insulin sensitivity and protects against diet-induced dyslipidemia in female mice. | Norris, Adriana C; Yazlovitskaya, Eugenia M; Zhu, Lin; Rose, Bailey S; Mansueto, Alex; Gibson-Corley, Katherine N; May, Jody C; McLean, John A; Stafford, John M; Graham, Todd R | bioRxiv : the preprint server for biology | 37398141 | 2023 Jun 27 |
| Contribution of Circulating Host and Microbial Tryptophan Metabolites Toward Ah Receptor Activation. | Morgan, Ethan W; Dong, Fangcong; Annalora, Andrew J; Murray, Iain A; Wolfe, Trenton; Erickson, Reece; Gowda, Krishne; Amin, Shantu G; Petersen, Kristina S; Kris-Etherton, Penny M; Marcus, Craig B; Walk, Seth T; Patterson, Andrew D; Perdew, Gary H | International journal of tryptophan research : IJTR | 37441265 | 2023 |
| Lactate-dependent transcriptional regulation controls mammalian eye morphogenesis. | Takata, Nozomu; Miska, Jason M; Morgan, Marc A; Patel, Priyam; Billingham, Leah K; Joshi, Neha; Schipma, Matthew J; Dumar, Zachary J; Joshi, Nikita R; Misharin, Alexander V; Embry, Ryan B; Fiore, Luciano; Gao, Peng; Diebold, Lauren P; McElroy, Gregory S; Shilatifard, Ali; Chandel, Navdeep S; Oliver, Guillermo | Nature communications | 37452018 | 2023 Jul 14 |
| Toxicology knowledge graph for structural birth defects. | Evangelista, John Erol; Clarke, Daniel J B; Xie, Zhuorui; Marino, Giacomo B; Utti, Vivian; Jenkins, Sherry L; Ahooyi, Taha Mohseni; Bologa, Cristian G; Yang, Jeremy J; Binder, Jessica L; Kumar, Praveen; Lambert, Christophe G; Grethe, Jeffrey S; Wenger, Eric; Taylor, Deanne; Oprea, Tudor I; de Bono, Bernard; Ma'ayan, Avi | Communications medicine | 37460679 | 2023 Jul 17 |
| The stability of the myelinating oligodendrocyte transcriptome is regulated by the nuclear lamina. | Pruvost, Mathilde; Patzig, Julia; Yattah, Camila; Selcen, Ipek; Hernandez, Marylens; Park, Hye-Jin; Moyon, Sarah; Liu, Shibo; Morioka, Malia S; Shopland, Lindsay; Al-Dalahmah, Osama; Bendl, Jaroslav; Fullard, John F; Roussos, Panos; Goldman, James; He, Ye; Dupree, Jeffrey L; Casaccia, Patrizia | Cell reports | 37515770 | 2023 Aug 29 |
| Evaluating cancer cell line and patient-derived xenograft recapitulation of tumor and non-diseased tissue gene expression profiles in silico. | Williams, Avery S; Wilk, Elizabeth J; Fisher, Jennifer L; Lasseigne, Brittany N | Cancer reports (Hoboken, N.J.) | 37533331 | 2023 Sep |
| Spatially resolved metabolomics and isotope tracing reveal dynamic metabolic responses of dentate granule neurons with acute stimulation. | Miller, Anne; York, Elisa; Stopka, Sylwia; Martínez-François, Juan; Hossain, Md Amin; Baquer, Gerard; Regan, Michael; Agar, Nathalie; Yellen, Gary | Research square | 37546759 | 2023 Jul 25 |
| Carbon Coated Iron-Cobalt Nanoparticles for Magnetic Particle Imaging. | Kumar, Raj; Huda, Md Nurul; Habib, Ahsan; Nafiujjaman, Md; Woo, Hyun-Joo; Kim, Taeho; Nurunnabi, Md | ACS applied bio materials | 37554053 | 2023 Aug 21 |
| A photothermal driven chemotherapy for the treatment of metastatic melanoma. | Bhatt, Himanshu N; Diwan, Rimpy; Borrego, Edgar A; Pérez, Carlos Alberto Martínez; Varela-Ramirez, Armando; Kumar, Raj; Aguilera, Renato J; Nurunnabi, Md | Journal of controlled release : official journal of the Controlled Release Society | 37562554 | 2023 Sep |
| Transcriptional risk scores in Alzheimer's disease: From pathology to cognition. | Pyun, Jung-Min; Park, Young Ho; Wang, Jiebiao; Bennett, David A; Bice, Paula J; Kim, Jun Pyo; Kim, SangYun; Saykin, Andrew J; Nho, Kwangsik | Alzheimer's & dementia : the journal of the Alzheimer's Association | 37563770 | 2023 Aug 10 |
| scMD: cell type deconvolution using single-cell DNA methylation references. | Cai, Manqi; Zhou, Jingtian; McKennan, Chris; Wang, Jiebiao | bioRxiv : the preprint server for biology | 37577715 | 2023 Aug 06 |
| Differences in the Stool Metabolome between Vegans and Omnivores: Analyzing the NIST Stool Reference Material. | Cumeras, Raquel; Shen, Tong; Valdiviez, Luis; Tippins, Zakery; Haffner, Bennett D; Fiehn, Oliver | Metabolites | 37623865 | 2023 Aug 07 |
| Systems immunology-based drug repurposing framework to target inflammation in atherosclerosis. | Amadori, Letizia; Calcagno, Claudia; Fernandez, Dawn M; Koplev, Simon; Fernandez, Nicolas; Kaur, Ravneet; Mury, Pauline; Khan, Nayaab S; Sajja, Swathy; Shamailova, Roza; Cyr, Yannick; Jeon, Minji; Hill, Christopher A; Chong, Peik Sean; Naidu, Sonum; Sakurai, Ken; Ghotbi, Adam Ali; Soler, Raphael; Eberhardt, Natalia; Rahman, Adeeb; Faries, Peter; Moore, Kathryn J; Fayad, Zahi A; Ma'ayan, Avi; Giannarelli, Chiara | Nature cardiovascular research | 37771373 | 2023 Jun |
| Spatially resolved metabolomics and isotope tracing reveal dynamic metabolic responses of dentate granule neurons with acute stimulation. | Miller, Anne; York, Elisa M; Stopka, Sylwia A; Martínez-François, Juan Ramón; Hossain, Md Amin; Baquer, Gerard; Regan, Michael S; Agar, Nathalie Y R; Yellen, Gary | Nature metabolism | 37798473 | 2023 Oct |
| MYC is a regulator of androgen receptor inhibition-induced metabolic requirements in prostate cancer. | Crowell, Preston D; Giafaglione, Jenna M; Jones, Anthony E; Nunley, Nicholas M; Hashimoto, Takao; Delcourt, Amelie M L; Petcherski, Anton; Agrawal, Raag; Bernard, Matthew J; Diaz, Johnny A; Heering, Kylie Y; Huang, Rong Rong; Low, Jin-Yih; Matulionis, Nedas; Navone, Nora M; Ye, Huihui; Zoubeidi, Amina; Christofk, Heather R; Rettig, Matthew B; Reiter, Robert E; Haffner, Michael C; Boutros, Paul C; Shirihai, Orian S; Divakaruni, Ajit S; Goldstein, Andrew S | Cell reports | 37815914 | 2023 Oct 31 |
| Endotype Characterization Reveals Mechanistic Differences Across Brain Regions in Sporadic Alzheimer's Disease. | Patel, Ashay O; Caldwell, Andrew B; Ramachandran, Srinivasan; Subramaniam, Shankar | Journal of Alzheimer's disease reports | 37849634 | 2023 |
| Dex-Benchmark: datasets and code to evaluate algorithms for transcriptomics data analysis. | Xie, Zhuorui; Chen, Clara; Ma'ayan, Avi | PeerJ | 37953774 | 2023 |
| SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models. | Gjoni, Ketrin; Pollard, Katherine S | bioRxiv : the preprint server for biology | 37961123 | 2023 Nov 05 |
| IL-1β-mediated adaptive reprogramming of endogenous human cardiac fibroblasts to cells with immune features during fibrotic remodeling. | Siamwala, Jamila H; Pagano, Francesco S; Dubielecka, Patrycja M; Ivey, Malina J; Guirao-Abad, Jose Pedro; Zhao, Alexander; Chen, Sonja; Granston, Haley; Jeong, Jae Yun; Rounds, Sharon; Kanisicak, Onur; Sadayappan, Sakthivel; Gilbert, Richard J | Communications biology | 38001239 | 2023 Nov 25 |
| Gut microbiota and metabolites in estrus cycle and their changes in a menopausal transition rat model with typical neuroendocrine aging. | Dai, Ruoxi; Huang, Jianqin; Cui, Liyuan; Sun, Ruiqi; Qiu, Xuemin; Wang, Yan; Sun, Yan | Frontiers in endocrinology | 38161977 | 2023 |
| Matrix Linear Models for connecting metabolite composition to individual characteristics. | Farage, Gregory; Zhao, Chenhao; Choi, Hyo Young; Garrett, Timothy J; Kechris, Katerina; Elam, Marshall B; Sen, Śaunak | bioRxiv : the preprint server for biology | 38187579 | 2023 Dec 20 |
| Less-is-more: selecting transcription factor binding regions informative for motif inference. | Xu, Jinrui; Gao, Jiahao; Ni, Pengyu; Gerstein, Mark | Nucleic acids research | 38214231 | 2024 Jan 12 |
| Exploring the interplay between running exercises, microbial diversity, and tryptophan metabolism along the microbiota-gut-brain axis. | Vazquez-Medina, Alejandra; Rodriguez-Trujillo, Nicole; Ayuso-Rodriguez, Kiara; Marini-Martinez, Fabiana; Angeli-Morales, Roberto; Caussade-Silvestrini, Gerardo; Godoy-Vitorino, Filipa; Chorna, Nataliya | Frontiers in microbiology | 38318337 | 2024 |
| Liver fibrosis pathologies and potentials of RNA based therapeutics modalities. | Diwan, Rimpy; Gaytan, Samantha Lynn; Bhatt, Himanshu Narendrakumar; Pena-Zacarias, Jacqueline; Nurunnabi, Md | Drug delivery and translational research | 38446352 | 2024 Mar 06 |
