Illuminating the Druggable Genome (IDG)
Illuminating the Druggable Genome (IDG)
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 |
|---|---|---|---|---|
| Electrically silent KvS subunits associate with native Kv2 channels in brain and impact diverse properties of channel function. | Ferns, Michael; van der List, Deborah; Vierra, Nicholas C; Lacey, Taylor; Murray, Karl; Kirmiz, Michael; Stewart, Robert G; Sack, Jon T; Trimmer, James S | bioRxiv : the preprint server for biology | 38328147 | 2024 Jan 25 |
| Overview of the Knowledge Management Center for Illuminating the Druggable Genome. | Oprea, Tudor I; Bologa, Cristian; Holmes, Jayme; Mathias, Stephen; Metzger, Vincent T; Waller, Anna; Yang, Jeremy J; Leach, Andrew R; Jensen, Lars Juhl; Kelleher, Keith J; Sheils, Timothy K; Mathé, Ewy; Avram, Sorin; Edwards, Jeremy S | Drug discovery today | 38218214 | 2024 Mar |
| Parathyroid hormone-PTH1R signaling in cardiovascular disease and homeostasis. | Towler, Dwight A | Trends in endocrinology and metabolism: TEM | 38429163 | 2024 Jul |
| Chlorogenic Acid: A Systematic Review on the Biological Functions, Mechanistic Actions, and Therapeutic Potentials. | Nguyen, Vi; Taine, Elaine G; Meng, Dehao; Cui, Taixing; Tan, Wenbin | Nutrients | 38612964 | 2024 Mar 23 |
| Exploring the role of pyroptosis in the pathogenicity of heart disease. | Bhatti, Rohail; Sato, Priscila Y | Frontiers in physiology | 38645692 | 2024 |
| PIP4K2C inhibition reverses autophagic flux impairment induced by SARS-CoV-2. | Karim, Marwah; Mishra, Manjari; Lo, Chieh-Wen; Saul, Sirle; Cagirici, Halise Busra; Tran, Do Hoang Nhu; Agrawal, Aditi; Ghita, Luca; Ojha, Amrita; East, Michael P; Gammeltoft, Karen Anbro; Sahoo, Malaya Kumar; Johnson, Gary L; Das, Soumita; Jochmans, Dirk; Cohen, Courtney A; Gottwein, Judith; Dye, John; Neff, Norma; Pinsky, Benjamin A; Laitinen, Tuomo; Pantsar, Tatu; Poso, Antti; Zanini, Fabio; Jonghe, Steven De; Asquith, Christopher R M; Einav, Shirit | bioRxiv : the preprint server for biology | 38659941 | 2024 Apr 17 |
| ReactomeGSA: new features to simplify public data reuse. | Grentner, Alexander; Ragueneau, Eliot; Gong, Chuqiao; Prinz, Adrian; Gansberger, Sabina; Oyarzun, Inigo; Hermjakob, Henning; Griss, Johannes | Bioinformatics (Oxford, England) | 38806182 | 2024 Jun 03 |
| Novel drug targets in 2023. | Avram, Sorin; Halip, Liliana; Curpan, Ramona; Oprea, Tudor I | Nature reviews. Drug discovery | 38565953 | 2024 May |
| Utilizing Low-Dimensional Molecular Embeddings for Rapid Chemical Similarity Search. | Kirchoff, Kathryn E; Wellnitz, James; Hochuli, Joshua E; Maxfield, Travis; Popov, Konstantin I; Gomez, Shawn; Tropsha, Alexander | Advances in information retrieval : ... European Conference on IR Research, ECIR ... proceedings. European Conference on IR Research | 38585224 | 2024 Mar |
| A comprehensive exploration of the druggable conformational space of protein kinases using AI-predicted structures. | Herrington, Noah B; Li, Yan Chak; Stein, David; Pandey, Gaurav; Schlessinger, Avner | PLoS computational biology | 39046952 | 2024 Jul |
| Drosophila tweety facilitates autophagy to regulate mitochondrial homeostasis and bioenergetics in Glia. | Leung, Ho Hang; Mansour, Christina; Rousseau, Morgan; Nakhla, Anwar; Kiselyov, Kirill; Venkatachalam, Kartik; Wong, Ching-On | Glia | 37870193 | 2024 Feb |
| CaV 2.1 α1 subunit motifs that control presynaptic CaV 2.1 subtype abundance are distinct from CaV 2.1 preference. | Li, Jianing; Veeraraghavan, Priyadharishini; Young Jr, Samuel M | The Journal of physiology | 38155373 | 2024 Feb |
| Alternative splicing of latrophilin-3 controls synapse formation. | Wang, Shuai; DeLeon, Chelsea; Sun, Wenfei; Quake, Stephen R; Roth, Bryan L; Südhof, Thomas C | Nature | 38233523 | 2024 Feb |
| Measuring conformational equilibria in allosteric proteins with time-resolved tmFRET. | Zagotta, William N; Evans, Eric G B; Eggan, Pierce; Tessmer, Maxx H; Shaffer, Kyle D; Petersson, E James; Stoll, Stefan; Gordon, Sharona E | Biophysical journal | 38303511 | 2024 Jul 16 |
| 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 |
| Environmental enrichment enhances ethanol preference over social reward in male swiss mice: Involvement of oxytocin-dopamine interactions. | Rae, Mariana; Gomes, Ivone; Spelta, Lidia Emmanuela Wiazowski; Bailey, Alexis; Marcourakis, Tania; Devi, Lakshmi; Camarini, Rosana | Neuropharmacology | 38705568 | 2024 Aug 01 |
| Testis-specific serine kinase 6 (TSSK6) is abnormally expressed in colorectal cancer and promotes oncogenic behaviors. | Delgado, Magdalena; Gallegos, Zachary; Stippec, Steve; McGlynn, Kathleen; Cobb, Melanie H; Whitehurst, Angelique W | The Journal of biological chemistry | 38762178 | 2024 Jun |
| Low-frequency ERK and Akt activity dynamics are predictive of stochastic cell division events. | Bennett, Jamie J R; Stern, Alan D; Zhang, Xiang; Birtwistle, Marc R; Pandey, Gaurav | NPJ systems biology and applications | 38834572 | 2024 Jun 04 |
| Development of adenoviral vectors that transduce Purkinje cells and other cerebellar cell-types in the cerebellum of a humanized mouse model. | Kul, Emre; Okoroafor, Uchechi; Dougherty, Amanda; Palkovic, Lauren; Li, Hao; Valiño-Ramos, Paula; Aberman, Leah; Young Jr, Samuel M | Molecular therapy. Methods & clinical development | 38605812 | 2024 Jun 13 |
| Best practices for managing and disseminating resources and outreach and evaluating the impact of the IDG Consortium. | Vidović, Dušica; Waller, Anna; Holmes, Jayme; Sklar, Larry A; Schürer, Stephan C | Drug discovery today | 38508231 | 2024 May |
| The BKCa (slo) channel regulates the cardiac function of Drosophila. | Gururaja Rao, Shubha; Lam, Alexander; Seeley, Sarah; Park, Jeniffer; Aruva, Shriya; Singh, Harpreet | Physiological reports | 38561252 | 2024 Apr |
| More than an Amide Bioisostere: Discovery of 1,2,4-Triazole-containing Pyrazolo[1,5-a]pyrimidine Host CSNK2 Inhibitors for Combatting β-Coronavirus Replication. | Ong, Han Wee; Yang, Xuan; Smith, Jeffery L; Dickmander, Rebekah J; Brown, Jason W; Havener, Tammy M; Taft-Benz, Sharon; Howell, Stefanie; Sanders, Marcia K; Capener, Jacob L; Couñago, Rafael M; Chang, Edcon; Krämer, Andreas; Moorman, Nathaniel J; Heise, Mark; Axtman, Alison D; Drewry, David H; Willson, Timothy M | Journal of medicinal chemistry | 38959455 | 2024 Jul 25 |
| 12-Lipoxygenase inhibition suppresses islet immune and inflammatory responses and delays autoimmune diabetes in human gene replacement mice. | Nargis, Titli; Muralidharan, Charanya; Enriquez, Jacob R; Wang, Jiayi E; Kaylan, Kerim; Chakraborty, Advaita; Pratuangtham, Sarida; Figatner, Kayla; Nelson, Jennifer B; May, Sarah C; Nadler, Jerry L; Boxer, Matthew B; Maloney, David J; Tersey, Sarah A; Mirmira, Raghavendra G | bioRxiv : the preprint server for biology | 39091839 | 2024 Jul 28 |
| Discovery and Characterization of a Chemical Probe for Cyclin-Dependent Kinase-Like 2. | Bashore, Frances M; Min, Sophia M; Chen, Xiangrong; Howell, Stefanie; Rinderle, Caroline H; Morel, Gabriel; Silvaroli, Josie A; Wells, Carrow I; Bunnell, Bruce A; Drewry, David H; Pabla, Navjot S; Ultanir, Sila K; Bullock, Alex N; Axtman, Alison D | ACS medicinal chemistry letters | 39140040 | 2024 Aug 08 |
| The ChEMBL Database in 2023: a drug discovery platform spanning multiple bioactivity data types and time periods. | Zdrazil, Barbara; Felix, Eloy; Hunter, Fiona; Manners, Emma J; Blackshaw, James; Corbett, Sybilla; de Veij, Marleen; Ioannidis, Harris; Lopez, David Mendez; Mosquera, Juan F; Magarinos, Maria Paula; Bosc, Nicolas; Arcila, Ricardo; Kizilören, Tevfik; Gaulton, Anna; Bento, A Patrícia; Adasme, Melissa F; Monecke, Peter; Landrum, Gregory A; Leach, Andrew R | Nucleic acids research | 37933841 | 2024 Jan 05 |
| The Reactome Pathway Knowledgebase 2024. | Milacic, Marija; Beavers, Deidre; Conley, Patrick; Gong, Chuqiao; Gillespie, Marc; Griss, Johannes; Haw, Robin; Jassal, Bijay; Matthews, Lisa; May, Bruce; Petryszak, Robert; Ragueneau, Eliot; Rothfels, Karen; Sevilla, Cristoffer; Shamovsky, Veronica; Stephan, Ralf; Tiwari, Krishna; Varusai, Thawfeek; Weiser, Joel; Wright, Adam; Wu, Guanming; Stein, Lincoln; Hermjakob, Henning; D'Eustachio, Peter | Nucleic acids research | 37941124 | 2024 Jan 05 |
| Illuminating function of the understudied druggable kinome. | Gomez, Shawn M; Axtman, Alison D; Willson, Timothy M; Major, Michael B; Townsend, Reid R; Sorger, Peter K; Johnson, Gary L | Drug discovery today | 38218213 | 2024 Mar |
| Measuring conformational equilibria in allosteric proteins with time-resolved tmFRET. | Zagotta, William N; Evans, Eric G B; Eggan, Pierce; Tessmer, Maxx H; Shaffer, Kyle D; Petersson, E James; Stoll, Stefan; Gordon, Sharona E | bioRxiv : the preprint server for biology | 37873384 | 2024 Jan 03 |
| Gpr149 is involved in energy homeostasis in the male mouse. | Wyler, Steven; Surbhi; Cao, Newton; Merchant, Warda; Bookout, Angie; Gautron, Laurent | PeerJ | 38282864 | 2024 |
| Discovery and optimization of narrow spectrum inhibitors of Tousled like kinase 2 (TLK2) using quantitative structure activity relationships. | Asquith, Christopher R M; East, Michael P; Laitinen, Tuomo; Alamillo-Ferrer, Carla; Hartikainen, Erkka; Wells, Carrow I; Axtman, Alison D; Drewry, David H; Tizzard, Graham J; Poso, Antti; Willson, Timothy M; Johnson, Gary L | European journal of medicinal chemistry | 38636130 | 2024 May 05 |
| Nuclear phosphoinositide signaling promotes YAP/TAZ-TEAD transcriptional activity in breast cancer. | Jung, Oisun; Baek, Min-Jeong; Wooldrik, Colin; Johnson, Keith R; Fisher, Kurt W; Lou, Jinchao; Ricks, Tanei J; Wen, Tianmu; Best, Michael D; Cryns, Vincent L; Anderson, Richard A; Choi, Suyong | The EMBO journal | 38565949 | 2024 May |
| Kinome-Wide Virtual Screening by Multi-Task Deep Learning. | Hu, Jiaming; Allen, Bryce K; Stathias, Vasileios; Ayad, Nagi G; Schürer, Stephan C | International journal of molecular sciences | 38473785 | 2024 Feb 22 |
| Illumination of understudied ciliary kinases. | Flax, Raymond G; Rosston, Peter; Rocha, Cecilia; Anderson, Brian; Capener, Jacob L; Durcan, Thomas M; Drewry, David H; Prinos, Panagiotis; Axtman, Alison D | Frontiers in molecular biosciences | 38523660 | 2024 |
| Genome-Wide CRISPR Screen Identifies Phospholipid Scramblase 3 as the Biological Target of Mitoprotective Drug SS-31. | Silvaroli, Josie A; Bisunke, Bijay; Kim, Ji Young; Stayton, Amanda; Jayne, Laura A; Martinez, Shirely A; Nguyen, Christopher; Patel, Prisha S; Vanichapol, Thitinee; Verma, Vivek; Akhter, Juheb; Bolisetty, Subhashini; Madhavan, Sethu M; Kuscu, Cem; Coss, Christopher C; Zepeda-Orozco, Diana; Parikh, Samir V; Satoskar, Anjali A; Davidson, Alan J; Eason, James D; Szeto, Hazel H; Pabla, Navjot S; Bajwa, Amandeep | Journal of the American Society of Nephrology : JASN | 38530359 | 2024 Jun 01 |
| 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 |
| Bioinformatic analysis of human ZPR1 gene pathogenic exome mutations. | Abok, Jeremiah I; Garver, William S; Edwards, Jeremy S | bioRxiv : the preprint server for biology | 38464185 | 2024 Mar 01 |
| Synthesis of 5-Benzylamino and 5-Alkylamino-Substituted Pyrimido[4,5-c]quinoline Derivatives as CSNK2A Inhibitors with Antiviral Activity. | Asressu, Kesatebrhan Haile; Smith, Jeffery L; Dickmander, Rebekah J; Moorman, Nathaniel J; Wellnitz, James; Popov, Konstantin I; Axtman, Alison D; Willson, Timothy M | Pharmaceuticals (Basel, Switzerland) | 38543092 | 2024 Feb 27 |
| Discovery and Characterization of a Chemical Probe for Cyclin-Dependent Kinase-Like 2. | Bashore, Frances M; Min, Sophia M; Chen, Xiangrong; Howell, Stefanie; Rinderle, Caroline H; Morel, Gabriel; Silvaroli, Josie A; Wells, Carrow I; Bunnell, Bruce A; Drewry, David H; Pabla, Navjot S; Ultanir, Sila K; Bullock, Alex N; Axtman, Alison D | bioRxiv : the preprint server for biology | 38798634 | 2024 May 14 |
| Modulation of TMEM16B channel activity by the calcium-activated chloride channel regulator 4 (CLCA4) in human cells. | Sala-Rabanal, Monica; Yurtsever, Zeynep; Berry, Kayla N; McClenaghan, Conor; Foy, Alyssa J; Hanson, Alex; Steinberg, Deborah F; Greven, Jessica A; Kluender, Colin E; Alexander-Brett, Jennifer M; Nichols, Colin G; Brett, Tom J | The Journal of biological chemistry | 38825009 | 2024 Jul |
| Chloride ions in health and disease. | Raut, Satish K; Singh, Kulwinder; Sanghvi, Shridhar; Loyo-Celis, Veronica; Varghese, Liyah; Singh, Ekam R; Gururaja Rao, Shubha; Singh, Harpreet | Bioscience reports | 38573803 | 2024 May 29 |
| Long-distance tmFRET using bipyridyl- and phenanthroline-based ligands. | Gordon, Sharona E; Evans, Eric G B; Otto, Shauna C; Tessmer, Maxx H; Shaffer, Kyle D; Gordon, Moshe T; Petersson, E James; Stoll, Stefan; Zagotta, William N | bioRxiv : the preprint server for biology | 37873407 | 2024 Jan 03 |
| Dissecting the biophysics and biology of intrinsically disordered proteins. | Banerjee, Priya R; Holehouse, Alex S; Kriwacki, Richard; Robustelli, Paul; Jiang, Hao; Sobolevsky, Alexander I; Hurley, Jennifer M; Mendell, Joshua T | Trends in biochemical sciences | 37949765 | 2024 Feb |
| Long-distance tmFRET using bipyridyl- and phenanthroline-based ligands. | Gordon, Sharona E; Evans, Eric G B; Otto, Shauna C; Tessmer, Maxx H; Shaffer, Kyle D; Gordon, Moshe T; Petersson, E James; Stoll, Stefan; Zagotta, William N | Biophysical journal | 38350449 | 2024 Jul 16 |
| Pan-cancer proteogenomics characterization of tumor immunity. | Petralia, Francesca; Ma, Weiping; Yaron, Tomer M; Caruso, Francesca Pia; Tignor, Nicole; Wang, Joshua M; Charytonowicz, Daniel; Johnson, Jared L; Huntsman, Emily M; Marino, Giacomo B; Calinawan, Anna; Evangelista, John Erol; Selvan, Myvizhi Esai; Chowdhury, Shrabanti; Rykunov, Dmitry; Krek, Azra; Song, Xiaoyu; Turhan, Berk; Christianson, Karen E; Lewis, David A; Deng, Eden Z; Clarke, Daniel J B; Whiteaker, Jeffrey R; Kennedy, Jacob J; Zhao, Lei; Segura, Rossana Lazcano; Batra, Harsh; Raso, Maria Gabriela; Parra, Edwin Roger; Soundararajan, Rama; Tang, Ximing; Li, Yize; Yi, Xinpei; Satpathy, Shankha; Wang, Ying; Wiznerowicz, Maciej; González-Robles, Tania J; Iavarone, Antonio; Gosline, Sara J C; Reva, Boris; Robles, Ana I; Nesvizhskii, Alexey I; Mani, D R; Gillette, Michael A; Klein, Robert J; Cieslik, Marcin; Zhang, Bing; Paulovich, Amanda G; Sebra, Robert; Gümüş, Zeynep H; Hostetter, Galen; Fenyö, David; Omenn, Gilbert S; Cantley, Lewis C; Ma'ayan, Avi; Lazar, Alexander J; Ceccarelli, Michele; Wang, Pei; Clinical Proteomic Tumor Analysis Consortium | Cell | 38359819 | 2024 Feb 29 |
| RIOK2 transcriptionally regulates TRiC and dyskerin complexes to prevent telomere shortening. | Ghosh, Shrestha; Nguyen, Mileena T; Choi, Ha Eun; Stahl, Maximilian; Kühn, Annemarie Luise; Van der Auwera, Sandra; Grabe, Hans J; Völzke, Henry; Homuth, Georg; Myers, Samuel A; Hogaboam, Cory M; Noth, Imre; Martinez, Fernando J; Petsko, Gregory A; Glimcher, Laurie H | Nature communications | 39164231 | 2024 Aug 20 |
| Unheralded Adrenergic Receptor Signaling in Cellular Oxidative Stress and Death. | Underwood, Lilly; Jiang, Chun-Sun; Oh, Joo-Yeun; Sato, Priscila Y | Current opinion in physiology | 39070968 | 2024 Aug |
| LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. | Duan, Qiaonan; Flynn, Corey; Niepel, Mario; Hafner, Marc; Muhlich, Jeremy L; Fernandez, Nicolas F; Rouillard, Andrew D; Tan, Christopher M; Chen, Edward Y; Golub, Todd R; Sorger, Peter K; Subramanian, Aravind; Ma'ayan, Avi | Nucleic acids research | 24906883 | 2014 Jul |
| Autophagy induction enhances TDP43 turnover and survival in neuronal ALS models. | Barmada, Sami J; Serio, Andrea; Arjun, Arpana; Bilican, Bilada; Daub, Aaron; Ando, D Michael; Tsvetkov, Andrey; Pleiss, Michael; Li, Xingli; Peisach, Daniel; Shaw, Christopher; Chandran, Siddharthan; Finkbeiner, Steven | Nature chemical biology | 24974230 | 2014 Aug |
| Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets. | Duan, Qiaonan; Wang, Zichen; Fernandez, Nicolas F; Rouillard, Andrew D; Tan, Christopher M; Benes, Cyril H; Ma'ayan, Avi | Bioinformatics (Oxford, England). | 25100688 | 2014 Nov 15; |
| Lean Big Data integration in systems biology and systems pharmacology. | Ma'ayan, Avi; Rouillard, Andrew D; Clark, Neil R; Wang, Zichen; Duan, Qiaonan; Kou, Yan | Trends in pharmacological sciences | 25109570 | 2014 Sep |
| The TLQP-21 peptide activates the G-protein-coupled receptor C3aR1 via a folding-upon-binding mechanism | Cero C, Vostrikov VV, Verardi R, Severini C, Gopinath T, Braun PD, Sassano MF, Gurney A, Roth BL, Vulchanova L, Possenti R, Veglia G, Bartolomucci A. | Structure | 25456411 | 2014 Dec 2 |
| REDD1 functions at the crossroads between the therapeutic and adverse effects of topical glucocorticoids. | Baida, Gleb; Bhalla, Pankaj; Kirsanov, Kirill; Lesovaya, Ekaterina; Yakubovskaya, Marianna; Yuen, Kit; Guo, Shuchi; Lavker, Robert M; Readhead, Ben; Dudley, Joel T; Budunova, Irina | EMBO molecular medicine. | 25504525 | 2015 Jan; |
| Computational and experimental advances in drug repositioning for accelerated therapeutic stratification | Shameer K, Readhead B, Dudley JT. | Current Topics in Medicinal Chemistry | 25579574 | 2015 |
| Genomic and network patterns of schizophrenia genetic variation in human evolutionary accelerated regions. | Xu, Ke; Schadt, Eric E; Pollard, Katherine S; Roussos, Panos; Dudley, Joel T | Molecular biology and evolution. | 25681384 | 2015 May; |
| Genome-wide significant loci: how important are they? Systems genetics to understand heritability of coronary artery disease and other common complex disorders. | Björkegren, Johan L M; Kovacic, Jason C; Dudley, Joel T; Schadt, Eric E | Journal of the American College of Cardiology. | 25720628 | 2015 Mar 3; |
| Cell-Based Screening: Extracting Meaning from Complex Data | Finkbeiner S., Frumkin M., Kassner PD | Neuron | 25856492 | 2015 Apr 8 |
| Inhibition of Lapatinib-Induced Kinome Reprogramming in ERBB2-Positive Breast Cancer by Targeting BET Family Bromodomains. | Stuhlmiller, Timothy J; Miller, Samantha M; Zawistowski, Jon S; Nakamura, Kazuhiro; Beltran, Adriana S; Duncan, James S; Angus, Steven P; Collins, Kyla A L; Granger, Deborah A; Reuther, Rachel A; Graves, Lee M; Gomez, Shawn M; Kuan, Pei-Fen; Parker, Joel | Cell reports. | 25865888 | 2015 Apr 21; |
| PRESTO-Tango as an open-source resource for interrogation of the druggable human GPCRome. | Kroeze, Wesley K; Sassano, Maria F; Huang, Xi-Ping; Lansu, Katherine; McCorvy, John D; Giguère, Patrick M; Sciaky, Noah; Roth, Bryan L | Nature structural & molecular biology. | 25895059 | 2015 May; |
| GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions. | Gundersen, Gregory W; Jones, Matthew R; Rouillard, Andrew D; Kou, Yan; Monteiro, Caroline D; Feldmann, Axel S; Hu, Kevin S; Ma'ayan, Avi | Bioinformatics (Oxford, England). | 25971742 | 2015 Sep 15; |
| Choosing the Right Tool for the Job: RNAi, TALEN, or CRISPR. | Boettcher, Michael; McManus, Michael T | Molecular cell. | 26000843 | 2015 May 21; |
| Dynamics of the discovery process of protein-protein interactions from low content studies. | Wang, Zichen; Clark, Neil R; Ma'ayan, Avi | BMC systems biology. | 26048415 | 2015; |
| Integrated Approaches for Genome-wide Interrogation of the Druggable Non-olfactory G Protein-coupled Receptor Superfamily. | Roth, Bryan L; Kroeze, Wesley K | The Journal of biological chemistry. | 26100629 | 2015 Aug 7; |
| Publisher?s Note:Abstraction for data integration:Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction. | Rouillard, Andrew D; Wang, Zichen; Ma'ayan, Avi | Computational biology and chemistry. | 26101093 | 2015 Oct; |
| Morphine Regulated Synaptic Networks Revealed by Integrated Proteomics and Network Analysis. | Stockton Jr, Steven D; Gomes, Ivone; Liu, Tong; Moraje, Chandrakala; Hipólito, Lucia; Jones, Matthew R; Ma'ayan, Avi; Morón, Jose A; Li, Hong; Devi, Lakshmi A | Molecular & cellular proteomics : MCP. | 26149443 | 2015 Oct; |
| Comprehensive comparison of large-scale tissue expression datasets | Santos A, Tsafou K, Stolte C, Pletscher-Frankild S, O'Donoghue SI, Jensen LJ. | Peer J | 26157623 | 2015 June 30 |
| HOODS: finding context-specific neighborhoods of proteins, chemicals and diseases. | Palleja, Albert; Jensen, Lars J | PeerJ. | 26157625 | 2015; |
| Computational and Practical Aspects of Drug Repositioning. | Oprea, Tudor I; Overington, John P | Assay and drug development technologies. | 26241209 | 2015 Jul-Aug; |
| An Integrated Transcriptome Atlas of Embryonic Hair Follicle Progenitors, Their Niche, and the Developing Skin. | Sennett, Rachel; Wang, Zichen; Rezza, Amélie; Grisanti, Laura; Roitershtein, Nataly; Sicchio, Cristina; Mok, Ka Wai; Heitman, Nicholas J; Clavel, Carlos; Ma'ayan, Avi; Rendl, Michael | Developmental cell. | 26256211 | 2015 Sep 14; |
| Reprint of ''Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction''. | Rouillard, Andrew D; Wang, Zichen; Ma'ayan, Avi | Computational biology and chemistry. | 26297300 | 2015 Dec; |
| Noribogaine is a G-protein biased ?-opioid receptor agonist. | Maillet, Emeline L; Milon, Nicolas; Heghinian, Mari D; Fishback, James; Schürer, Stephan C; Garamszegi, Nandor; Mash, Deborah C | Neuropharmacology. | 26302653 | 2015 Dec; |
| Identification of type 2 diabetes subgroups through topological analysis of patient similarity. | Li, Li; Cheng, Wei-Yi; Glicksberg, Benjamin S; Gottesman, Omri; Tamler, Ronald; Chen, Rong; Bottinger, Erwin P; Dudley, Joel T | Science translational medicine. | 26511511 | 2015 Oct 28; |
| Clinical Trials in a Dish: The Potential of Pluripotent Stem Cells to Develop Therapies for Neurodegenerative Diseases. | Haston, Kelly M; Finkbeiner, Steven | Annual review of pharmacology and toxicology. | 26514199 | 2016; |
| Allosteric ligands for the pharmacologically dark receptors GPR68 and GPR65. | Huang, Xi-Ping; Karpiak, Joel; Kroeze, Wesley K; Zhu, Hu; Chen, Xin; Moy, Sheryl S; Saddoris, Kara A; Nikolova, Viktoriya D; Farrell, Martilias S; Wang, Sheng; Mangano, Thomas J; Deshpande, Deepak A; Jiang, Alice; Penn, Raymond B; Jin, Jian; Koller, Bever | Nature. | 26550826 | 2015 Nov 26; |
| Molecular systems evaluation of oligomerogenic APP(E693Q) and fibrillogenic APP(KM670/671NL)/PSEN1(?exon9) mouse models identifies shared features with human Alzheimer's brain molecular pathology. | Readhead, B; Haure-Mirande, J-V; Zhang, B; Haroutunian, V; Gandy, S; Schadt, E E; Dudley, J T; Ehrlich, M E | Molecular psychiatry. | 26552589 | 2015 Nov 10; |
| Mapping the effects of drugs on the immune system. | Kidd, Brian A; Wroblewska, Aleksandra; Boland, Mary R; Agudo, Judith; Merad, Miriam; Tatonetti, Nicholas P; Brown, Brian D; Dudley, Joel T | Nature biotechnology. | 26619012 | 2016 Jan; |
| Fetal liver hematopoietic stem cell niches associate with portal vessels. | Khan, Jalal A; Mendelson, Avital; Kunisaki, Yuya; Birbrair, Alexander; Kou, Yan; Arnal-Estapé, Anna; Pinho, Sandra; Ciero, Paul; Nakahara, Fumio; Ma'ayan, Avi; Bergman, Aviv; Merad, Miriam; Frenette, Paul S | Science (New York, N.Y.). | 26634440 | 2016 Jan 8; |
| A three-groups model for high-throughput survival screens. | Shaby, Benjamin A; Skibinski, Gaia; Ando, Michael; LaDow, Eva S; Finkbeiner, Steven | Biometrics. | 26821783 | 2016 Jan 28; |
| Leveraging Large-scale Behavioral Profiling in Zebrafish to Explore Neuroactive Polypharmacology. | McCarroll, Matthew N; Gendelev, Leo; Keiser, Michael J; Kokel, David | ACS chemical biology. | 26845413 | 2016 Apr 15; |
| Principal Angle Enrichment Analysis (PAEA): Dimensionally Reduced Multivariate Gene Set Enrichment Analysis Tool. | Clark, Neil R; Szymkiewicz, Maciej; Wang, Zichen; Monteiro, Caroline D; Jones, Matthew R; Ma'ayan, Avi | Proceedings. IEEE International Conference on Bioinformatics and Biomedicine. | 26848405 | 2015 Nov; |
| Integrative radiogenomic analysis for multicentric radiophenotype in glioblastoma | Kong DS, Kim J, Lee IH, Kim ST, Seol HJ, Lee JI, Park WY, Ryu G, Wang Z, Ma'ayan A, Nam DH | Oncotarget | 26863628 | 2016 Feb 1 |
| Translational bioinformatics in the era of real-time biomedical, health care and wellness data streams | Shameer K, Badgeley MA, Miotto R, Glicksberg BS, Morgan JW, Dudley JT | Brief Bioinform | 26876889 | 2016 Feb 14 |
| Docking Screens for Novel Ligands Conferring New Biology. | Irwin, John J; Shoichet, Brian K | Journal of medicinal chemistry. | 26913380 | 2016 05 12; |
| Polygenic overlap between schizophrenia risk and antipsychotic response: a genomic medicine approach. | Ruderfer, Douglas M; Charney, Alexander W; Readhead, Ben; Kidd, Brian A; Kähler, Anna K; Kenny, Paul J; Keiser, Michael J; Moran, Jennifer L; Hultman, Christina M; Scott, Stuart A; Sullivan, Patrick F; Purcell, Shaun M; Dudley, Joel T; Sklar, Pamela | The lancet. Psychiatry. | 26915512 | 2016 Apr; |
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| A Chemical Probe for Dark Kinase STK17B Derives Its Potency and High Selectivity through a Unique P-Loop Conformation. | Picado, Alfredo; Chaikuad, Apirat; Wells, Carrow I; Shrestha, Safal; Zuercher, William J; Pickett, Julie E; Kwarcinski, Frank E; Sinha, Parvathi; de Silva, Chandi S; Zutshi, Reena; Liu, Shubin; Kannan, Natarajan; Knapp, Stefan; Drewry, David H; Willson, Timothy M | Journal of medicinal chemistry | 33215924 | 2020 12 10 |
| Activation of the ARCPOMC?MeA Projection Reduces Food Intake. | Kwon, Eunjin; Jo, Young-Hwan | Frontiers in neural circuits. | 33250721 | 2020; |
| Mapping the Degradable Kinome Provides a Resource for Expedited Degrader Development. | Donovan, Katherine A; Ferguson, Fleur M; Bushman, Jonathan W; Eleuteri, Nicholas A; Bhunia, Debabrata; Ryu, SeongShick; Tan, Li; Shi, Kun; Yue, Hong; Liu, Xiaoxi; Dobrovolsky, Dennis; Jiang, Baishan; Wang, Jinhua; Hao, Mingfeng; You, Inchul; Teng, Mingxing; Liang, Yanke; Hatcher, John; Li, Zhengnian; Manz, Theresa D; Groendyke, Brian; Hu, Wanyi; Nam, Yunju; Sengupta, Sandip; Cho, Hanna; Shin, Injae; Agius, Michael P; Ghobrial, Irene M; Ma, Michelle W; Che, Jianwei; Buhrlage, Sara J; Sim, Taebo; Gray, Nathanael S; Fischer, Eric S | Cell | 33275901 | 2020 12 10 |
| Optogenetic stimulation of the liver-projecting melanocortinergic pathway promotes hepatic glucose production. | Kwon, Eunjin; Joung, Hye-Young; Liu, Shun-Mei; Chua Jr, Streamson C; Schwartz, Gary J; Jo, Young-Hwan | Nature communications. | 33293550 | 2020 12 08; |
| Virtual and In Vitro Antiviral Screening Revive Therapeutic Drugs for COVID-19. | Bocci, Giovanni; Bradfute, Steven B; Ye, Chunyan; Garcia, Matthew J; Parvathareddy, Jyothi; Reichard, Walter; Surendranathan, Surekha; Bansal, Shruti; Bologa, Cristian G; Perkins, Douglas J; Jonsson, Colleen B; Sklar, Larry A; Oprea, Tudor I | ACS pharmacology & translational science | 33330842 | 2020 Dec 11 |
| The Kinase Chemogenomic Set (KCGS): An Open Science Resource for Kinase Vulnerability Identification. | Wells, Carrow I; Al-Ali, Hassan; Andrews, David M; Asquith, Christopher R M; Axtman, Alison D; Dikic, Ivan; Ebner, Daniel; Ettmayer, Peter; Fischer, Christian; Frederiksen, Mathias; Futrell, Robert E; Gray, Nathanael S; Hatch, Stephanie B; Knapp, Stefan; Lücking, Ulrich; Michaelides, Michael; Mills, Caitlin E; Müller, Susanne; Owen, Dafydd; Picado, Alfredo; Saikatendu, Kumar S; Schröder, Martin; Stolz, Alexandra; Tellechea, Mariana; Turunen, Brandon J; Vilar, Santiago; Wang, Jinhua; Zuercher, William J; Willson, Timothy M; Drewry, David H | International journal of molecular sciences | 33429995 | 2021 Jan 08 |
| SmartGraph: a network pharmacology investigation platform. | Zahoránszky-Kőhalmi, Gergely; Sheils, Timothy; Oprea, Tudor I | Journal of cheminformatics | 33430980 | 2020 Jan 21 |
| Development of a potent and selective chemical probe for the pleiotropic kinase CK2. | Wells, Carrow I; Drewry, David H; Pickett, Julie E; Tjaden, Amelie; Krämer, Andreas; Müller, Susanne; Gyenis, Laszlo; Menyhart, Daniel; Litchfield, David W; Knapp, Stefan; Axtman, Alison D | Cell chemical biology | 33484635 | 2021 04 15 |
| InContext: curation of medical context for drug indications. | Moodley, Kody; Rieswijk, Linda; Oprea, Tudor I; Dumontier, Michel | Journal of biomedical semantics | 33579375 | 2021 02 12 |
| Machine learning identifies candidates for drug repurposing in Alzheimer's disease. | Rodriguez, Steve; Hug, Clemens; Todorov, Petar; Moret, Nienke; Boswell, Sarah A; Evans, Kyle; Zhou, George; Johnson, Nathan T; Hyman, Bradley T; Sorger, Peter K; Albers, Mark W; Sokolov, Artem | Nature communications | 33589615 | 2021 02 15 |
| Prioritizing Pain-Associated Targets with Machine Learning. | Jeon, Minji; Jagodnik, Kathleen M; Kropiwnicki, Eryk; Stein, Daniel J; Ma'ayan, Avi | Biochemistry | 33606503 | 2021 05 11 |
| The Atypical Kinase RIOK3 Limits RVFV Propagation and Is Regulated by Alternative Splicing. | Havranek, Katherine E; White, Luke Adam; Bisom, Thomas C; Lanchy, Jean-Marc; Lodmell, J Stephen | Viruses | 33652597 | 2021 02 26 |
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| Blockade of IL-22 signaling reverses erythroid dysfunction in stress-induced anemias. | Raundhal, Mahesh; Ghosh, Shrestha; Myers, Samuel A; Cuoco, Michael S; Singer, Meromit; Carr, Steven A; Waikar, Sushrut S; Bonventre, Joseph V; Ritz, Jerome; Stone, Richard M; Steensma, David P; Regev, Aviv; Glimcher, Laurie H | Nature immunology | 33753942 | 2021 04 |
| Predicting Lyme Disease From Patients' Peripheral Blood Mononuclear Cells Profiled With RNA-Sequencing. | Clarke, Daniel J B; Rebman, Alison W; Bailey, Allison; Wojciechowicz, Megan L; Jenkins, Sherry L; Evangelista, John E; Danieletto, Matteo; Fan, Jinshui; Eshoo, Mark W; Mosel, Michael R; Robinson, William; Ramadoss, Nitya; Bobe, Jason; Soloski, Mark J; Aucott, John N; Ma'ayan, Avi | Frontiers in immunology | 33763080 | 2021 |
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| 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 |
| An Esrrb and Nanog Cell Fate Regulatory Module Controlled by Feed Forward Loop Interactions. | Sevilla, Ana; Papatsenko, Dimitri; Mazloom, Amin R; Xu, Huilei; Vasileva, Ana; Unwin, Richard D; LeRoy, Gary; Chen, Edward Y; Garrett-Bakelman, Francine E; Lee, Dung-Fang; Trinite, Benjamin; Webb, Ryan L; Wang, Zichen; Su, Jie; Gingold, Julian; Melnick, Ari; Garcia, Benjamin A; Whetton, Anthony D; MacArthur, Ben D; Ma'ayan, Avi; Lemischka, Ihor R | Frontiers in cell and developmental biology | 33816475 | 2021 |
| Highly Accurate Chip-Based Resequencing of SARS-CoV-2 Clinical Samples. | Hoff, Kendall; Ding, Xun; Carter, Lucas; Duque, John; Lin, Ju-Yu; Dung, Samantha; Singh, Priyanka; Sun, Jiayi; Crnogorac, Filip; Swaminathan, Radha; Alden, Emily N; Zhu, Xuechen; Shimada, Ryota; Posavi, Marijan; Hull, Noah; Dinwiddie, Darrell; Halasz, Adam M; McGall, Glenn; Zhou, Wei; Edwards, Jeremy S | Langmuir : the ACS journal of surfaces and colloids | 33848173 | 2021 Apr 27 |
| mTORC2 controls the activity of PKC and Akt by phosphorylating a conserved TOR interaction motif. | Baffi, Timothy R; Lordén, Gema; Wozniak, Jacob M; Feichtner, Andreas; Yeung, Wayland; Kornev, Alexandr P; King, Charles C; Del Rio, Jason C; Limaye, Ameya J; Bogomolovas, Julius; Gould, Christine M; Chen, Ju; Kennedy, Eileen J; Kannan, Natarajan; Gonzalez, David J; Stefan, Eduard; Taylor, Susan S; Newton, Alexandra C | Science signaling | 33850054 | 2021 Apr 13 |
| TMEM16C is involved in thermoregulation and protects rodent pups from febrile seizures. | Wang, Tongfei A; Chen, Chao; Huang, Fen; Feng, Shengjie; Tien, Jason; Braz, João M; Basbaum, Allan I; Jan, Yuh Nung; Jan, Lily Yeh | Proceedings of the National Academy of Sciences of the United States of America | 33972431 | 2021 05 18 |
| FOXA1 and adaptive response determinants to HER2 targeted therapy in TBCRC 036. | Angus, Steven P; Stuhlmiller, Timothy J; Mehta, Gaurav; Bevill, Samantha M; Goulet, Daniel R; Olivares-Quintero, J Felix; East, Michael P; Tanioka, Maki; Zawistowski, Jon S; Singh, Darshan; Sciaky, Noah; Chen, Xin; He, Xiaping; Rashid, Naim U; Chollet-Hinton, Lynn; Fan, Cheng; Soloway, Matthew G; Spears, Patricia A; Jefferys, Stuart; Parker, Joel S; Gallagher, Kristalyn K; Forero-Torres, Andres; Krop, Ian E; Thompson, Alastair M; Murthy, Rashmi; Gatza, Michael L; Perou, Charles M; Earp, H Shelton; Carey, Lisa A; Johnson, Gary L | NPJ breast cancer | 33980863 | 2021 May 12 |
| KEA3: improved kinase enrichment analysis via data integration. | Kuleshov, Maxim V; Xie, Zhuorui; London, Alexandra B K; Yang, Janice; Evangelista, John Erol; Lachmann, Alexander; Shu, Ingrid; Torre, Denis; Ma'ayan, Avi | Nucleic acids research | 34019655 | 2021 07 02 |
| Towards a RIOK2 chemical probe: cellular potency improvement of a selective 2-(acylamino)pyridine series. | Wang, Christopher B; Lorente-Macías, Álvaro; Wells, Carrow; Pickett, Julie E; Picado, Alfredo; Zuercher, William J; Axtman, Alison D | RSC medicinal chemistry | 34046605 | 2021 Jan 01 |
| Regulation of Tissue Inflammation by 12-Lipoxygenases. | Kulkarni, Abhishek; Nadler, Jerry L; Mirmira, Raghavendra G; Casimiro, Isabel | Biomolecules | 34064822 | 2021 05 11 |
| Krüppel-like factor 6-mediated loss of BCAA catabolism contributes to kidney injury in mice and humans. | Piret, Sian E; Guo, Yiqing; Attallah, Ahmed A; Horne, Sylvia J; Zollman, Amy; Owusu, Daniel; Henein, Justina; Sidorenko, Viktoriya S; Revelo, Monica P; Hato, Takashi; Ma'ayan, Avi; He, John Cijiang; Mallipattu, Sandeep K | Proceedings of the National Academy of Sciences of the United States of America | 34074766 | 2021 06 08 |
| Crowdsourced mapping of unexplored target space of kinase inhibitors. | Cichońska, Anna; Ravikumar, Balaguru; Allaway, Robert J; Wan, Fangping; Park, Sungjoon; Isayev, Olexandr; Li, Shuya; Mason, Michael; Lamb, Andrew; Tanoli, Ziaurrehman; Jeon, Minji; Kim, Sunkyu; Popova, Mariya; Capuzzi, Stephen; Zeng, Jianyang; Dang, Kristen; Koytiger, Gregory; Kang, Jaewoo; Wells, Carrow I; Willson, Timothy M; IDG-DREAM Drug-Kinase Binding Prediction Challenge Consortium; Oprea, Tudor I; Schlessinger, Avner; Drewry, David H; Stolovitzky, Gustavo; Wennerberg, Krister; Guinney, Justin; Aittokallio, Tero | Nature communications | 34083538 | 2021 06 03 |
| TIGA: Target illumination GWAS analytics. | Yang, Jeremy J; Grissa, Dhouha; Lambert, Christophe G; Bologa, Cristian G; Mathias, Stephen L; Waller, Anna; Wild, David J; Jensen, Lars Juhl; Oprea, Tudor I | Bioinformatics (Oxford, England) | 34086846 | 2021 Jun 04 |
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| NEK5 activity regulates the mesenchymal and migratory phenotype in breast cancer cells. | Matossian, Margarite D; Elliott, Steven; Van Hoang, T; Burks, Hope E; Wright, Maryl K; Alzoubi, Madlin S; Yan, Thomas; Chang, Tiffany; Wathieu, Henri; Windsor, Gabrielle O; Hartono, Alifiani Bo; Lee, Sean; Zuercher, William J; Drewry, David H; Wells, Carrow; Kapadia, Nirav; Buechlein, Aaron; Fang, Fang; Nephew, Kenneth P; Collins-Burow, Bridgette M; Burow, Matthew E | Breast cancer research and treatment | 34196902 | 2021 Jul 01 |
| A critical overview of computational approaches employed for COVID-19 drug discovery. | Muratov , Eugene N; Amaro , Rommie; Andrade , Carolina H; Brown , Nathan; Ekins , Sean; Fourches , Denis; Isayev , Olexandr; Kozakov , Dima; Medina-Franco , José L; Merz , Kenneth M; Oprea , Tudor I; Poroikov , Vladimir; Schneider , Gisbert; Todd , Matthew H; Varnek , Alexandre; Winkler , David A; Zakharov , Alexey V; Cherkasov , Artem; Tropsha , Alexander | Chemical Society reviews | 34212944 | 2021 Aug 21 |
| Hinge Binder Scaffold Hopping Identifies Potent Calcium/Calmodulin-Dependent Protein Kinase Kinase 2 (CAMKK2) Inhibitor Chemotypes. | Eduful, Benjamin J; O'Byrne, Sean N; Temme, Louisa; Asquith, Christopher R M; Liang, Yi; Picado, Alfredo; Pilotte, Joseph R; Hossain, Mohammad Anwar; Wells, Carrow I; Zuercher, William J; Catta-Preta, Carolina M C; Zonzini Ramos, Priscila; Santiago, André de S; Couñago, Rafael M; Langendorf, Christopher G; Nay, Kévin; Oakhill, Jonathan S; Pulliam, Thomas L; Lin, Chenchu; Awad, Dominik; Willson, Timothy M; Frigo, Daniel E; Scott, John W; Drewry, David H | Journal of medicinal chemistry | 34264658 | 2021 08 12 |
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| Identification of Pyrimidine-Based Lead Compounds for Understudied Kinases Implicated in Driving Neurodegeneration. | Drewry, David H; Annor-Gyamfi, Joel K; Wells, Carrow I; Pickett, Julie E; Dederer, Verena; Preuss, Franziska; Mathea, Sebastian; Axtman, Alison D | Journal of medicinal chemistry | 34333981 | 2022 01 27 |
| Post-translational modification of RAS proteins. | Campbell, Sharon L; Philips, Mark R | Current opinion in structural biology | 34365229 | 2021 12 |
| Evaluation of Amide Bioisosteres Leading to 1,2,3-Triazole Containing Compounds as GPR88 Agonists: Design, Synthesis, and Structure-Activity Relationship Studies. | Rahman, Md Toufiqur; Decker, Ann M; Laudermilk, Lucas; Maitra, Rangan; Ma, Weiya; Ben Hamida, Sami; Darcq, Emmanuel; Kieffer, Brigitte L; Jin, Chunyang | Journal of medicinal chemistry | 34387471 | 2021 Aug 26 |
| Adiponectin receptor fragmentation in mouse models of type 1 and type 2 diabetes. | Frabutt, Dylan; Stull, Natalie; Pineros, Annie R; Tersey, Sarah A; Scheuner, Donalyn; Mastracci, Teresa L; Pugia, Michael J | Archives of autoimmune diseases | 34414399 | 2020 |
| Non-canonical role of Hippo tumor suppressor serine/threonine kinase 3 STK3 in prostate cancer. | Schirmer, Amelia U; Driver, Lucy M; Zhao, Megan T; Wells, Carrow I; Pickett, Julie E; O'Bryne, Sean N; Eduful, Benjamin J; Yang, Xuan; Howard, Lauren; You, Sungyong; Devi, Gayathri R; DiGiovanni, John; Freedland, Stephen J; Chi, Jen-Tsan; Drewry, David H; Macias, Everardo | Molecular therapy : the journal of the American Society of Gene Therapy | 34450249 | 2022 01 05 |
| NeuriteNet: A convolutional neural network for assessing morphological parameters of neurite growth. | Vecchi, Joseph T; Mullan, Sean; Lopez, Josue A; Hansen, Marlan R; Sonka, Milan; Lee, Amy | Journal of neuroscience methods | 34480956 | 2021 11 01 |
| KinOrtho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases. | Huang, Liang-Chin; Taujale, Rahil; Gravel, Nathan; Venkat, Aarya; Yeung, Wayland; Byrne, Dominic P; Eyers, Patrick A; Kannan, Natarajan | BMC bioinformatics | 34537014 | 2021 Sep 18 |
| Characterizing the role of the dark kinome in neurodegenerative disease - A mini review. | Axtman, Alison D | Biochimica et biophysica acta. General subjects | 34547390 | 2021 Dec |
| PRM-LIVE with Trapped Ion Mobility Spectrometry and Its Application in Selectivity Profiling of Kinase Inhibitors. | Zhu, He; Ficarro, Scott B; Alexander, William M; Fleming, Laura E; Adelmant, Guillaume; Zhang, Tinghu; Willetts, Matthew; Decker, Jens; Brehmer, Sven; Krause, Michael; East, Michael P; Gray, Nathanael S; Johnson, Gary L; Kruppa, Gary; Marto, Jarrod A | Analytical chemistry | 34606255 | 2021 10 19 |
| Loss of proximal tubular transcription factor Krüppel-like factor 15 exacerbates kidney injury through loss of fatty acid oxidation. | Piret, Sian E; Attallah, Ahmed A; Gu, Xiangchen; Guo, Yiqing; Gujarati, Nehaben A; Henein, Justina; Zollman, Amy; Hato, Takashi; Ma'ayan, Avi; Revelo, Monica P; Dickman, Kathleen G; Chen, Chung-Hsin; Shun, Chia-Tung; Rosenquist, Thomas A; He, John C; Mallipattu, Sandeep K | Kidney international | 34634362 | 2021 Dec |
| Structural basis of human ghrelin receptor signaling by ghrelin and the synthetic agonist ibutamoren. | Liu, Heng; Sun, Dapeng; Myasnikov, Alexander; Damian, Marjorie; Baneres, Jean-Louis; Sun, Ji; Zhang, Cheng | Nature communications | 34737341 | 2021 11 04 |
| The reactome pathway knowledgebase 2022. | Gillespie, Marc; Jassal, Bijay; Stephan, Ralf; Milacic, Marija; Rothfels, Karen; Senff-Ribeiro, Andrea; Griss, Johannes; Sevilla, Cristoffer; Matthews, Lisa; Gong, Chuqiao; Deng, Chuan; Varusai, Thawfeek; Ragueneau, Eliot; Haider, Yusra; May, Bruce; Shamovsky, Veronica; Weiser, Joel; Brunson, Timothy; Sanati, Nasim; Beckman, Liam; Shao, Xiang; Fabregat, Antonio; Sidiropoulos, Konstantinos; Murillo, Julieth; Viteri, Guilherme; Cook, Justin; Shorser, Solomon; Bader, Gary; Demir, Emek; Sander, Chris; Haw, Robin; Wu, Guanming; Stein, Lincoln; Hermjakob, Henning; D'Eustachio, Peter | Nucleic acids research | 34788843 | 2022 01 07 |
| Structure, function and pharmacology of human itch GPCRs. | Cao, Can; Kang, Hye Jin; Singh, Isha; Chen, He; Zhang, Chengwei; Ye, Wenlei; Hayes, Byron W; Liu, Jing; Gumpper, Ryan H; Bender, Brian J; Slocum, Samuel T; Krumm, Brian E; Lansu, Katherine; McCorvy, John D; Kroeze, Wesley K; English, Justin G; DiBerto, Jeffrey F; Olsen, Reid H J; Huang, Xi-Ping; Zhang, Shicheng; Liu, Yongfeng; Kim, Kuglae; Karpiak, Joel; Jan, Lily Y; Abraham, Soman N; Jin, Jian; Shoichet, Brian K; Fay, Jonathan F; Roth, Bryan L | Nature | 34789874 | 2021 12 |
| A high-fat diet catalyzes progression to hyperglycemia in mice with selective impairment of insulin action in Glut4-expressing tissues. | Reilly, Austin M; Yan, Shijun; Huang, Menghao; Abhyankar, Surabhi D; Conley, Jason M; Bone, Robert N; Stull, Natalie D; Horan, Daniel J; Roh, Hyun C; Robling, Alexander G; Ericsson, Aaron C; Dong, Xiaocheng C; Evans-Molina, Carmella; Ren, Hongxia | The Journal of biological chemistry | 34801552 | 2022 Jan |
| Supervised learning with word embeddings derived from PubMed captures latent knowledge about protein kinases and cancer. | Ravanmehr, Vida; Blau, Hannah; Cappelletti, Luca; Fontana, Tommaso; Carmody, Leigh; Coleman, Ben; George, Joshy; Reese, Justin; Joachimiak, Marcin; Bocci, Giovanni; Hansen, Peter; Bult, Carol; Rueter, Jens; Casiraghi, Elena; Valentini, Giorgio; Mungall, Christopher; Oprea, Tudor I; Robinson, Peter N | NAR genomics and bioinformatics | 34888523 | 2021 Dec |
| Identification of RIOK2 as a master regulator of human blood cell development. | Ghosh, Shrestha; Raundhal, Mahesh; Myers, Samuel A; Carr, Steven A; Chen, Xi; Petsko, Gregory A; Glimcher, Laurie H | Nature immunology | 34937919 | 2022 01 |
| Adaptive chromatin remodeling and transcriptional changes of the functional kinome in tumor cells in response to targeted kinase inhibition. | East, Michael P; Johnson, Gary L | The Journal of biological chemistry | 34958800 | 2022 Feb |
| Intestinal Gpr17 deficiency improves glucose metabolism by promoting GLP-1 secretion. | Yan, Shijun; Conley, Jason M; Reilly, Austin M; Stull, Natalie D; Abhyankar, Surabhi D; Ericsson, Aaron C; Kono, Tatsuyoshi; Molosh, Andrei I; Kubal, Chandrashekhar A; Evans-Molina, Carmella; Ren, Hongxia | Cell reports | 34986353 | 2022 01 04 |
| Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients. | Kaur, Navchetan; Oskotsky, Boris; Butte, Atul J; Hu, Zicheng | Genome biology | 35012625 | 2022 01 10 |
| Host kinase CSNK2 is a target for inhibition of pathogenic β-coronaviruses including SARS-CoV-2. | Yang, Xuan; Dickmander, Rebekah J; Bayati, Armin; Taft-Benz, Sharon A; Smith, Jeffery L; Wells, Carrow I; Madden, Emily A; Brown, Jason W; Lenarcic, Erik M; Yount Jr, Boyd L; Chang, Edcon; Axtman, Alison D; Baric, Ralph S; Heise, Mark T; McPherson, Peter S; Moorman, Nathaniel J; Willson, Timothy M | bioRxiv : the preprint server for biology | 35018375 | 2022 Jan 26 |
| A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research. | Zahoránszky-Kőhalmi, Gergely; Siramshetty, Vishal B; Kumar, Praveen; Gurumurthy, Manideep; Grillo, Busola; Mathew, Biju; Metaxatos, Dimitrios; Backus, Mark; Mierzwa, Tim; Simon, Reid; Grishagin, Ivan; Brovold, Laura; Mathé, Ewy A; Hall, Matthew D; Michael, Samuel G; Godfrey, Alexander G; Mestres, Jordi; Jensen, Lars J; Oprea, Tudor I | Journal of chemical information and modeling | 35057621 | 2022 02 14 |
| A Learning Based Framework for Disease Prediction from Images of Human-Derived Pluripotent Stem Cells of Schizophrenia Patients. | Fularczyk, Nickolas; Di Re, Jessica; Stertz, Laura; Walss-Bass, Consuelo; Laezza, Fernanda; Labate, Demetrio | Neuroinformatics | 35064871 | 2022 Jan 22 |
| 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 |
| Neuropeptide B/W receptor 1 peptidomimetic agonists: Structure-activity relationships and plasma stability. | Nguyen, Thuy; Decker, Ann M; Snyder, Rodney W; Tonetti, Emma C; Gamage, Thomas F; Zhang, Yanan | European journal of medicinal chemistry | 35101647 | 2022 Mar 05 |
| Tra2beta-Dependent Regulation of RIO Kinase 3 Splicing During Rift Valley Fever Virus Infection Underscores the Links Between Alternative Splicing and Innate Antiviral Immunity. | White, Luke Adam; Bisom, Thomas C; Grimes, Hunter L; Hayashi, Miyuki; Lanchy, Jean-Marc; Lodmell, J Stephen | Frontiers in cellular and infection microbiology | 35127560 | 2021 |
| Tousled-like kinase 2 targets ASF1 histone chaperones through client mimicry. | Simon, Bertrand; Lou, Hua Jane; Huet-Calderwood, Clotilde; Shi, Guangda; Boggon, Titus J; Turk, Benjamin E; Calderwood, David A | Nature communications | 35136069 | 2022 02 08 |
| 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 |
| Machine learning prediction and tau-based screening identifies potential Alzheimer's disease genes relevant to immunity. | Binder, Jessica; Ursu, Oleg; Bologa, Cristian; Jiang, Shanya; Maphis, Nicole; Dadras, Somayeh; Chisholm, Devon; Weick, Jason; Myers, Orrin; Kumar, Praveen; Yang, Jeremy J; Bhaskar, Kiran; Oprea, Tudor I | Communications biology | 35149761 | 2022 02 11 |
| EMBER: Multi-label prediction of kinase-substrate phosphorylation events through deep learning. | Kirchoff, Kathryn E; Gomez, Shawn M | Bioinformatics (Oxford, England) | 35157015 | 2022 Feb 14 |
| 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 |
| Structure-Based Design of a Chemical Probe Set for the 5-HT5A Serotonin Receptor. | Levit Kaplan, Anat; Strachan, Ryan T; Braz, Joao M; Craik, Veronica; Slocum, Samuel; Mangano, Thomas; Amabo, Vanessa; O'Donnell, Henry; Lak, Parnian; Basbaum, Allan I; Roth, Bryan L; Shoichet, Brian K | Journal of medicinal chemistry | 35195401 | 2022 03 10 |
| State of the Art and Uses for the Biopharmaceutics Drug Disposition Classification System (BDDCS): New Additions, Revisions, and Citation References. | Bocci, Giovanni; Oprea, Tudor I; Benet, Leslie Z | The AAPS journal | 35199251 | 2022 02 23 |
| Molecular recognition of formylpeptides and diverse agonists by the formylpeptide receptors FPR1 and FPR2. | Zhuang, Youwen; Wang, Lei; Guo, Jia; Sun, Dapeng; Wang, Yue; Liu, Weiyi; Xu, H Eric; Zhang, Cheng | Nature communications | 35217703 | 2022 Feb 25 |
| The voltage-gated Ca2+ channel subunit α2δ-4 regulates locomotor behavior and sensorimotor gating in mice. | Klomp, Annette; Omichi, Ryotaro; Iwasa, Yoichiro; Smith, Richard J; Usachev, Yuriy M; Russo, Andrew F; Narayanan, Nandakumar S; Lee, Amy | PloS one | 35353835 | 2022 |
| 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 |
| Agonist and antagonist TRUPATH assays for G protein-coupled receptors. | DiBerto, Jeffrey F; Smart, Katie; Olsen, Reid H J; Roth, Bryan L | STAR protocols | 35403009 | 2022 06 17 |
| Identification of 4-Anilinoquin(az)oline as a Cell-Active Protein Kinase Novel 3 (PKN3) Inhibitor Chemotype. | Asquith, Christopher R M; Temme, Louisa; East, Michael P; Laitinen, Tuomo; Pickett, Julie; Kwarcinski, Frank E; Sinha, Parvathi; Wells, Carrow I; Johnson, Gary L; Zutshi, Reena; Drewry, David H | ChemMedChem | 35403825 | 2022 06 20 |
| AlphaFold illuminates half of the dark human proteins. | Binder, Jessica L; Berendzen, Joel; Stevens, Amy O; He, Yi; Wang, Jian; Dokholyan, Nikolay V; Oprea, Tudor I | Current opinion in structural biology | 35439658 | 2022 06 |
| Cavβ1 regulates T cell expansion and apoptosis independently of voltage-gated Ca2+ channel function. | Erdogmus, Serap; Concepcion, Axel R; Yamashita, Megumi; Sidhu, Ikjot; Tao, Anthony Y; Li, Wenyi; Rocha, Pedro P; Huang, Bonnie; Garippa, Ralph; Lee, Boram; Lee, Amy; Hell, Johannes W; Lewis, Richard S; Prakriya, Murali; Feske, Stefan | Nature communications | 35440113 | 2022 04 19 |
| Ectopic biomolecular phase transitions: fusion proteins in cancer pathologies. | Davis, Richoo B; Moosa, Mahdi Muhammad; Banerjee, Priya R | Trends in cell biology | 35484036 | 2022 Aug |
| Protein proximity networks and functional evaluation of the casein kinase 1 gamma family reveal unique roles for CK1γ3 in WNT signaling. | Agajanian, Megan J; Potjewyd, Frances M; Bowman, Brittany M; Solomon, Smaranda; LaPak, Kyle M; Bhatt, Dhaval P; Smith, Jeffery L; Goldfarb, Dennis; Axtman, Alison D; Major, Michael B | The Journal of biological chemistry | 35487243 | 2022 06 |
| Open source fraction collector/MALDI spotter for proteomics. | Ficarro, Scott B; Max Alexander, William; Tavares, Isidoro; Marto, Jarrod A | HardwareX | 35518277 | 2022 Apr |
| 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 |
| Computational tools and resources for pseudokinase research. | O'Boyle, Brady; Shrestha, Safal; Kochut, Krzysztof; Eyers, Patrick A; Kannan, Natarajan | Methods in enzymology | 35525549 | 2022 |
| Analysis of human Tribbles 2 (TRIB2) pseudokinase. | Harris, John A; Fairweather, Emma; Byrne, Dominic P; Eyers, Patrick A | Methods in enzymology | 35525562 | 2022 |
| Investigating the Therapeutic Potential of Cdk8 Small Molecule Inhibitors to Prevent Pathological Cardiac Remodeling and Heart Failure. | Oppman, Alexis M; Gardner, Richard N; Martins, Ines; Minerath, Rachel A; Hall, Duane D; Grueter, Chad E | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 35553110 | 2022 May |
| Orphan G-Protein Coupled Receptor GPRC5B Is Critical for Lymphatic Development. | Xu, Wenjing; Nelson-Maney, Nathan P; Bálint, László; Kwon, Hyouk-Bum; Davis, Reema B; Dy, Danielle C M; Dunleavey, James M; St Croix, Brad; Caron, Kathleen M | International journal of molecular sciences | 35628521 | 2022 May 20 |
| Calcium Channels in Retinal Function and Disease. | Williams, Brittany; Maddox, J Wesley; Lee, Amy | Annual review of vision science | 35650675 | 2022 09 15 |
| Host Kinase CSNK2 is a Target for Inhibition of Pathogenic SARS-like β-Coronaviruses. | Yang, Xuan; Dickmander, Rebekah J; Bayati, Armin; Taft-Benz, Sharon A; Smith, Jeffery L; Wells, Carrow I; Madden, Emily A; Brown, Jason W; Lenarcic, Erik M; Yount Jr, Boyd L; Chang, Edcon; Axtman, Alison D; Baric, Ralph S; Heise, Mark T; McPherson, Peter S; Moorman, Nathaniel J; Willson, Timothy M | ACS chemical biology | 35723434 | 2022 Jul 15 |
| Autophagy and Herpesvirus: A collaboration Contributing to Alzheimer's Disease. | Nafchi, Amir R; Esmaeili, Mona; Myers, Orrin; Oprea, Tudor; Bearer, Elane L | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 35723876 | 2022 05 |
| On-Chip Preconcentration Microchip Capillary Electrophoresis Based CE-PRM-LIVE for High-Throughput Selectivity Profiling of Deubiquitinase Inhibitors. | Zhu, He; Mellors, J Scott; Chan, Wai Cheung; Thompson, J Will; Ficarro, Scott B; Tavares, Isidoro; Bratt, Ariana S; Decker, Jens; Krause, Michael; Kruppa, Gary; Buhrlage, Sara J; Marto, Jarrod A | Analytical chemistry | 35729701 | 2022 07 12 |
| Temozolomide-induced guanine mutations create exploitable vulnerabilities of guanine-rich DNA and RNA regions in drug-resistant gliomas. | Tiek, Deanna M; Erdogdu, Beril; Razaghi, Roham; Jin, Lu; Sadowski, Norah; Alamillo-Ferrer, Carla; Hogg, J Robert; Haddad, Bassem R; Drewry, David H; Wells, Carrow I; Pickett, Julie E; Song, Xiao; Goenka, Anshika; Hu, Bo; Goldlust, Samuel A; Zuercher, William J; Pertea, Mihaela; Timp, Winston; Cheng, Shi-Yuan; Riggins, Rebecca B | Science advances | 35731869 | 2022 06 24 |
| Numb-associated kinases are required for SARS-CoV-2 infection and are cellular targets for antiviral strategies. | Karim, Marwah; Saul, Sirle; Ghita, Luca; Sahoo, Malaya Kumar; Ye, Chengjin; Bhalla, Nishank; Lo, Chieh-Wen; Jin, Jing; Park, Jun-Gyu; Martinez-Gualda, Belén; East, Michael Patrick; Johnson, Gary L; Pinsky, Benjamin A; Martinez-Sobrido, Luis; Asquith, Christopher R M; Narayanan, Aarthi; De Jonghe, Steven; Einav, Shirit | Antiviral research | 35738348 | 2022 08 |
| Evaluation of a Selective Chemical Probe Validates That CK2 Mediates Neuroinflammation in a Human Induced Pluripotent Stem Cell-Derived Microglial Model. | Mishra, Swati; Kinoshita, Chizuru; Axtman, Alison D; Young, Jessica E | Frontiers in molecular neuroscience | 35774866 | 2022 |
| CACHE (Critical Assessment of Computational Hit-finding Experiments): A public-private partnership benchmarking initiative to enable the development of computational methods for hit-finding. | Ackloo, Suzanne; Al-Awar, Rima; Amaro, Rommie E; Arrowsmith, Cheryl H; Azevedo, Hatylas; Batey, Robert A; Bengio, Yoshua; Betz, Ulrich A K; Bologa, Cristian G; Chodera, John D; Cornell, Wendy D; Dunham, Ian; Ecker, Gerhard F; Edfeldt, Kristina; Edwards, Aled M; Gilson, Michael K; Gordijo, Claudia R; Hessler, Gerhard; Hillisch, Alexander; Hogner, Anders; Irwin, John J; Jansen, Johanna M; Kuhn, Daniel; Leach, Andrew R; Lee, Alpha A; Lessel, Uta; Morgan, Maxwell R; Moult, John; Muegge, Ingo; Oprea, Tudor I; Perry, Benjamin G; Riley, Patrick; Rousseaux, Sophie A L; Saikatendu, Kumar Singh; Santhakumar, Vijayaratnam; Schapira, Matthieu; Scholten, Cora; Todd, Matthew H; Vedadi, Masoud; Volkamer, Andrea; Willson, Timothy M | Nature reviews. Chemistry | 35783295 | 2022 Apr |
| The potassium channel auxiliary subunit Kvβ2 (Kcnab2) regulates Kv1 channels and dopamine neuron firing. | Yee, Joshua X; Rastani, Ariana; Soden, Marta E | Journal of neurophysiology | 35788155 | 2022 07 01 |
| Overexpressing the hydroxycarboxylic acid receptor 1 in mouse brown adipose tissue restores glucose tolerance and insulin sensitivity in diet-induced obese mice. | Min, Hyeon-Young; Hwang, Jiyeon; Choi, Yuna; Jo, Young-Hwan | American journal of physiology. Endocrinology and metabolism | 35830691 | 2022 Sep 01 |
| Inactive and active state structures template selective tools for the human 5-HT5A receptor. | Zhang, Shicheng; Chen, He; Zhang, Chengwei; Yang, Ying; Popov, Petr; Liu, Jing; Krumm, Brian E; Cao, Can; Kim, Kuglae; Xiong, Yan; Katritch, Vsevolod; Shoichet, Brian K; Jin, Jian; Fay, Jonathan F; Roth, Bryan L | Nature structural & molecular biology | 35835867 | 2022 07 |
| TRUPATH: An Open-Source Biosensor Platform for Interrogating the GPCR Transducerome. | DiBerto, Jeffrey F; Olsen, Reid H J; Roth, Bryan L | Methods in molecular biology (Clifton, N.J.) | 35836068 | 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 |
| A Superfolder Green Fluorescent Protein-Based Biosensor Allows Monitoring of Chloride in the Endoplasmic Reticulum. | Shariati, Kaavian; Zhang, Yaohuan; Giubbolini, Simone; Parra, Riccardo; Liang, Steven; Edwards, Austin; Hejtmancik, J Fielding; Ratto, Gian Michele; Arosio, Daniele; Ku, Gregory | ACS sensors | 35951356 | 2022 Aug 26 |
| Production of Eukaryotic Glycoproteins for Structural and Functional Studies Using Expi293F Cells. | Greven, Jessica A; Brett, Tom J | Current protocols | 35998009 | 2022 Aug |
| Magel2 knockdown in hypothalamic POMC neurons innervating the medial amygdala reduces susceptibility to diet-induced obesity. | Choi, Yuna; Min, Hyeon-Young; Hwang, Jiyeon; Jo, Young-Hwan | Life science alliance | 36007929 | 2022 11 |
| 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 |
| Identification and Utilization of a Chemical Probe to Interrogate the Roles of PIKfyve in the Lifecycle of β-Coronaviruses. | Drewry, David H; Potjewyd, Frances M; Bayati, Armin; Smith, Jeffery L; Dickmander, Rebekah J; Howell, Stefanie; Taft-Benz, Sharon; Min, Sophia M; Hossain, Mohammad Anwar; Heise, Mark; McPherson, Peter S; Moorman, Nathaniel J; Axtman, Alison D | Journal of medicinal chemistry | 36111834 | 2022 10 13 |
| RIOK3 and Its Alternatively Spliced Isoform Have Disparate Roles in the Innate Immune Response to Rift Valley Fever Virus (MP12) Infection. | Bisom, Thomas C; White, Luke A; Lanchy, Jean-Marc; Lodmell, J Stephen | Viruses | 36146870 | 2022 09 17 |
| Agent-based modeling predicts RAC1 is critical for ovarian cancer metastasis. | Rivera, Melanie; Toledo-Jacobo, Leslie; Romero, Elsa; Oprea, Tudor I; Moses, Melanie E; Hudson, Laurie G; Wandinger-Ness, Angela; Grimes, Martha M | Molecular biology of the cell | 36200848 | 2022 Dec 01 |
| A PKA inhibitor motif within SMOOTHENED controls Hedgehog signal transduction. | Happ, John T; Arveseth, Corvin D; Bruystens, Jessica; Bertinetti, Daniela; Nelson, Isaac B; Olivieri, Cristina; Zhang, Jingyi; Hedeen, Danielle S; Zhu, Ju-Fen; Capener, Jacob L; Bröckel, Jan W; Vu, Lily; King, C C; Ruiz-Perez, Victor L; Ge, Xuecai; Veglia, Gianluigi; Herberg, Friedrich W; Taylor, Susan S; Myers, Benjamin R | Nature structural & molecular biology | 36202993 | 2022 Oct |
| CLIC4 localizes to mitochondrial-associated membranes and mediates cardioprotection. | Ponnalagu, Devasena; Hamilton, Shanna; Sanghvi, Shridhar; Antelo, Diego; Schwieterman, Neill; Hansra, Inderjot; Xu, Xianyao; Gao, Erhe; Edwards, John C; Bansal, Shyam S; Wold, Loren E; Terentyev, Dmitry; Janssen, Paul M L; Hund, Thomas J; Khan, Mahmood; Kohut, Andrew R; Koch, Walter J; Singh, Harpreet | Science advances | 36269835 | 2022 Oct 21 |
| Ligand recognition and allosteric modulation of the human MRGPRX1 receptor. | Liu, Yongfeng; Cao, Can; Huang, Xi-Ping; Gumpper, Ryan H; Rachman, Moira M; Shih, Sheng-Luen; Krumm, Brian E; Zhang, Shicheng; Shoichet, Brian K; Fay, Jonathan F; Roth, Bryan L | Nature chemical biology | 36302898 | 2023 Apr |
| TTBK2 controls cilium stability by regulating distinct modules of centrosomal proteins. | Nguyen, Abraham; Goetz, Sarah C | Molecular biology of the cell | 36322399 | 2023 Jan 01 |
| Multiplexed and reproducible high content screening of live and fixed cells using Dye Drop. | Mills, Caitlin E; Subramanian, Kartik; Hafner, Marc; Niepel, Mario; Gerosa, Luca; Chung, Mirra; Victor, Chiara; Gaudio, Benjamin; Yapp, Clarence; Nirmal, Ajit J; Clark, Nicholas; Sorger, Peter K | Nature communications | 36376301 | 2022 Nov 14 |
| Beyond PI3Ks: targeting phosphoinositide kinases in disease. | Burke, John E; Triscott, Joanna; Emerling, Brooke M; Hammond, Gerald R V | Nature reviews. Drug discovery | 36376561 | 2022 Nov 14 |
| Molecular basis for selective activation of DREADD-based chemogenetics. | Zhang, Shicheng; Gumpper, Ryan H; Huang, Xi-Ping; Liu, Yongfeng; Krumm, Brian E; Cao, Can; Fay, Jonathan F; Roth, Bryan L | Nature | 36450989 | 2022 Dec |
| Protein kinase inhibitor selectivity "hinges" on evolution. | Shrestha, Safal; Bendzunas, George; Kannan, Natarajan | Structure (London, England : 1993) | 36459973 | 2022 Dec 01 |
| Cellular and molecular effects of PNCK, a non-canonical kinase target in renal cell carcinoma. | Essegian, Derek J; Chavez, Valery; Bustamante, Floritza; Schürer, Stephan C; Merchan, Jaime R | iScience | 36465101 | 2022 Dec 22 |
| DrugCentral 2023 extends human clinical data and integrates veterinary drugs. | Avram, Sorin; Wilson, Thomas B; Curpan, Ramona; Halip, Liliana; Borota, Ana; Bora, Alina; Bologa, Cristian G; Holmes, Jayme; Knockel, Jeffrey; Yang, Jeremy J; Oprea, Tudor I | Nucleic acids research | 36484092 | 2022 Dec 09 |
| Evolutionary and cellular analysis of the 'dark' pseudokinase PSKH2. | Byrne, Dominic P; Shrestha, Safal; Daly, Leonard A; Marensi, Vanessa; Ramakrishnan, Krithika; Eyers, Claire E; Kannan, Natarajan; Eyers, Patrick A | The Biochemical journal | 36520605 | 2023 Jan 31 |
| Seeing spermine blocking of K+ ion movement through inward rectifier Kir2.2 channels. | Lee, Sun-Joo; Nichols, Colin G | The Journal of general physiology | 36524992 | 2023 Feb 06 |
| Centering on synaptic vesicle release. | Young Jr, Samuel M | Cell calcium | 36527762 | 2023 Jan |
| Activation of amygdala prokineticin receptor 2 neurons drives the anorexigenic activity of the neuropeptide PK2. | Yin, Terry C; Mittal, Ayushi; Buscaglia, Paul; Li, Wenxian; Sebag, Julien A | The Journal of biological chemistry | 36539034 | 2023 Jan |
| Leveraging biochemical reactions to unravel functional impacts of cancer somatic variants affecting protein interaction interfaces. | Raimondi, Francesco; Burkhart, Joshua G; Betts, Matthew J; Russell, Robert B; Wu, Guanming | F1000Research | 36569594 | 2021 |
| SARS-CoV-2 replication in airway epithelia requires motile cilia and microvillar reprogramming. | Wu, Chien-Ting; Lidsky, Peter V; Xiao, Yinghong; Cheng, Ran; Lee, Ivan T; Nakayama, Tsuguhisa; Jiang, Sizun; He, Wei; Demeter, Janos; Knight, Miguel G; Turn, Rachel E; Rojas-Hernandez, Laura S; Ye, Chengjin; Chiem, Kevin; Shon, Judy; Martinez-Sobrido, Luis; Bertozzi, Carolyn R; Nolan, Garry P; Nayak, Jayakar V; Milla, Carlos; Andino, Raul; Jackson, Peter K | Cell | 36580912 | 2023 Jan 05 |
| Synthesis and pharmacological validation of a novel radioligand for the orphan GPR88 receptor. | Decker, Ann M; Rahman, Md Toufiqur; Kormos, Chad M; Hesk, David; Darcq, Emmanuel; Kieffer, Brigitte L; Jin, Chunyang | Bioorganic & medicinal chemistry letters | 36587872 | 2023 Jan 15 |
| Pharos 2023: an integrated resource for the understudied human proteome. | Kelleher, Keith J; Sheils, Timothy K; Mathias, Stephen L; Yang, Jeremy J; Metzger, Vincent T; Siramshetty, Vishal B; Nguyen, Dac-Trung; Jensen, Lars Juhl; Vidović, Dušica; Schürer, Stephan C; Holmes, Jayme; Sharma, Karlie R; Pillai, Ajay; Bologa, Cristian G; Edwards, Jeremy S; Mathé, Ewy A; Oprea, Tudor I | Nucleic acids research | 36624666 | 2023 Jan 06 |
| An atlas of substrate specificities for the human serine/threonine kinome. | Johnson, Jared L; Yaron, Tomer M; Huntsman, Emily M; Kerelsky, Alexander; Song, Junho; Regev, Amit; Lin, Ting-Yu; Liberatore, Katarina; Cizin, Daniel M; Cohen, Benjamin M; Vasan, Neil; Ma, Yilun; Krismer, Konstantin; Robles, Jaylissa Torres; van de Kooij, Bert; van Vlimmeren, Anne E; Andrée-Busch, Nicole; Käufer, Norbert F; Dorovkov, Maxim V; Ryazanov, Alexey G; Takagi, Yuichiro; Kastenhuber, Edward R; Goncalves, Marcus D; Hopkins, Benjamin D; Elemento, Olivier; Taatjes, Dylan J; Maucuer, Alexandre; Yamashita, Akio; Degterev, Alexei; Uduman, Mohamed; Lu, Jingyi; Landry, Sean D; Zhang, Bin; Cossentino, Ian; Linding, Rune; Blenis, John; Hornbeck, Peter V; Turk, Benjamin E; Yaffe, Michael B; Cantley, Lewis C | Nature | 36631611 | 2023 Jan |
| SGC-CAMKK2-1: A Chemical Probe for CAMKK2. | Wells, Carrow; Liang, Yi; Pulliam, Thomas L; Lin, Chenchu; Awad, Dominik; Eduful, Benjamin; O'Byrne, Sean; Hossain, Mohammad Anwar; Catta-Preta, Carolina Moura Costa; Ramos, Priscila Zonzini; Gileadi, Opher; Gileadi, Carina; Couñago, Rafael M; Stork, Brittany; Langendorf, Christopher G; Nay, Kevin; Oakhill, Jonathan S; Mukherjee, Debarati; Racioppi, Luigi; Means, Anthony R; York, Brian; McDonnell, Donald P; Scott, John W; Frigo, Daniel E; Drewry, David H | Cells | 36672221 | 2023 Jan 11 |
| Multiplexed kinase interactome profiling quantifies cellular network activity and plasticity. | Golkowski, Martin; Lius, Andrea; Sapre, Tanmay; Lau, Ho-Tak; Moreno, Taylor; Maly, Dustin J; Ong, Shao-En | Molecular cell | 36736316 | 2023 Mar 02 |
| Accelerating inhibitor discovery for deubiquitinating enzymes. | Chan, Wai Cheung; Liu, Xiaoxi; Magin, Robert S; Girardi, Nicholas M; Ficarro, Scott B; Hu, Wanyi; Tarazona Guzman, Maria I; Starnbach, Cara A; Felix, Alejandra; Adelmant, Guillaume; Varca, Anthony C; Hu, Bin; Bratt, Ariana S; DaSilva, Ethan; Schauer, Nathan J; Jaen Maisonet, Isabella; Dolen, Emma K; Ayala, Anthony X; Marto, Jarrod A; Buhrlage, Sara J | Nature communications | 36754960 | 2023 Feb 08 |
| TTBK2 mutations associated with spinocerebellar ataxia type 11 disrupt peroxisome dynamics and ciliary localization of SHH signaling proteins. | Muñoz-Estrada, Jesús; Nguyen, Abraham V; Goetz, Sarah C | bioRxiv : the preprint server for biology | 36778451 | 2023 Feb 01 |
| A Potent and Selective CDKL5/GSK3 Chemical Probe is Neuroprotective. | Ong, Han Wee; Liang, Yi; Richardson, William; Lowry, Emily R; Wells, Carrow I; Chen, Xiangrong; Silvestre, Margaux; Dempster, Kelvin; Silvaroli, Josie A; Smith, Jeffery L; Wichterle, Hynek; Pabla, Navjot S; Ultanir, Sila K; Bullock, Alex N; Drewry, David H; Axtman, Alison D | bioRxiv : the preprint server for biology | 36798313 | 2023 Feb 10 |
| Kinome inhibition states and multiomics data enable prediction of cell viability in diverse cancer types. | Berginski, Matthew E; Joisa, Chinmaya U; Golitz, Brian T; Gomez, Shawn M | PLoS computational biology | 36809237 | 2023 Feb |
| The ion channel CALHM6 controls bacterial infection-induced cellular cross-talk at the immunological synapse. | Danielli, Sara; Ma, Zhongming; Pantazi, Eirini; Kumar, Amrendra; Demarco, Benjamin; Fischer, Fabian A; Paudel, Usha; Weissenrieder, Jillian; Lee, Robert J; Joyce, Sebastian; Foskett, J Kevin; Bezbradica, Jelena S | The EMBO journal | 36861806 | 2023 Apr 03 |
| Reversal of Lactate and PD-1-mediated Macrophage Immunosuppression Controls Growth of PTEN/p53-deficient Prostate Cancer. | Chaudagar, Kiranj; Hieromnimon, Hanna M; Khurana, Rimpi; Labadie, Brian; Hirz, Taghreed; Mei, Shenglin; Hasan, Raisa; Shafran, Jordan; Kelley, Anne; Apostolov, Eva; Al-Eryani, Ghamdan; Harvey, Kate; Rameshbabu, Srikrishnan; Loyd, Mayme; Bynoe, Kaela; Drovetsky, Catherine; Solanki, Ani; Markiewicz, Erica; Zamora, Marta; Fan, Xiaobing; Schürer, Stephan; Swarbrick, Alex; Sykes, David B; Patnaik, Akash | Clinical cancer research : an official journal of the American Association for Cancer Research | 36862086 | 2023 May 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 |
| The structure, function, and pharmacology of MRGPRs. | Cao, Can; Roth, Bryan L | Trends in pharmacological sciences | 36870785 | 2023 Apr |
| 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 |
| Zinc finger protein 24-dependent transcription factor SOX9 up-regulation protects tubular epithelial cells during acute kidney injury. | Kim, Ji Young; Silvaroli, Josie A; Martinez, Gabriela Vasquez; Bisunke, Bijay; Luna Ramirez, Alanys V; Jayne, Laura A; Feng, Mei Ji He Ho; Girotra, Bhavya; Acosta Martinez, Shirely M; Vermillion, Corynne R; Karel, Isaac Z; Ferrell, Nicholas; Weisleder, Noah; Chung, Sangwoon; Christman, John W; Brooks, Craig R; Madhavan, Sethu M; Hoyt, Kari R; Cianciolo, Rachel E; Satoskar, Anjali A; Zepeda-Orozco, Diana; Sullivan, Jennifer C; Davidson, Alan J; Bajwa, Amandeep; Pabla, Navjot Singh | Kidney international | 36921719 | 2023 Jun |
| Subunit gating resulting from individual protonation events in Kir2 channels. | Maksaev, Grigory; Bründl-Jirout, Michael; Stary-Weinzinger, Anna; Zangerl-Plessl, Eva-Maria; Lee, Sun-Joo; Nichols, Colin G | Research square | 36993294 | 2023 Mar 16 |
| Dissection of a down syndrome-associated trisomy to separate the gene dosage-dependent and -independent effects of an extra chromosome. | Xing, Zhuo; Li, Yichen; Cortes-Gomez, Eduardo; Jiang, Xiaoling; Gao, Shuang; Pao, Annie; Shan, Jidong; Song, Yinghui; Perez, Amanda; Yu, Tao; Highsmith, Max R; Boadu, Frimpong; Conroy, Jeffrey M; Singh, Prashant K; Bakin, Andrei V; Cheng, Jianlin; Duan, Zhijun; Wang, Jianmin; Liu, Song; Tycko, Benjamin; Yu, Y Eugene | Human molecular genetics | 37014740 | 2023 Apr 04 |
| SARS-CoV-2 ORF3A interacts with the Clic-like chloride channel-1 (CLCC1) and triggers an unfolded protein response. | Gruner, Hannah N; Zhang, Yaohuan; Shariati, Kaavian; Yiv, Nicholas; Hu, Zicheng; Wang, Yuhao; Hejtmancik, J Fielding; McManus, Michael T; Tharp, Kevin; Ku, Gregory | PeerJ | 37033725 | 2023 |
| Development of Cell Permeable NanoBRET Probes for the Measurement of PLK1 Target Engagement in Live Cells. | Yang, Xuan; Smith, Jeffery L; Beck, Michael T; Wilkinson, Jennifer M; Michaud, Ani; Vasta, James D; Robers, Matthew B; Willson, Timothy M | Molecules (Basel, Switzerland) | 37049713 | 2023 Mar 25 |
| Using the Reactome Database. | Rothfels, Karen; Milacic, Marija; Matthews, Lisa; Haw, Robin; Sevilla, Cristoffer; Gillespie, Marc; Stephan, Ralf; Gong, Chuqiao; Ragueneau, Eliot; May, Bruce; Shamovsky, Veronica; Wright, Adam; Weiser, Joel; Beavers, Deidre; Conley, Patrick; Tiwari, Krishna; Jassal, Bijay; Griss, Johannes; Senff-Ribeiro, Andrea; Brunson, Timothy; Petryszak, Robert; Hermjakob, Henning; D'Eustachio, Peter; Wu, Guanming; Stein, Lincoln | Current protocols | 37053306 | 2023 Apr |
| Modulation of tau tubulin kinases (TTBK1 and TTBK2) impacts ciliogenesis. | Bashore, Frances M; Marquez, Ariana B; Chaikuad, Apirat; Howell, Stefanie; Dunn, Andrea S; Beltran, Alvaro A; Smith, Jeffery L; Drewry, David H; Beltran, Adriana S; Axtman, Alison D | Scientific reports | 37059819 | 2023 Apr 14 |
| Discovery of a Potent and Selective Naphthyridine-Based Chemical Probe for Casein Kinase 2. | Davis-Gilbert, Zachary W; Krämer, Andreas; Dunford, James E; Howell, Stefanie; Senbabaoglu, Filiz; Wells, Carrow I; Bashore, Frances M; Havener, Tammy M; Smith, Jeffery L; Hossain, Mohammad A; Oppermann, Udo; Drewry, David H; Axtman, Alison D | ACS medicinal chemistry letters | 37077385 | 2023 Apr 13 |
| 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 |
| Discovery of a Potent and Selective CDKL5/GSK3 Chemical Probe That Is Neuroprotective. | Ong, Han Wee; Liang, Yi; Richardson, William; Lowry, Emily R; Wells, Carrow I; Chen, Xiangrong; Silvestre, Margaux; Dempster, Kelvin; Silvaroli, Josie A; Smith, Jeffery L; Wichterle, Hynek; Pabla, Navjot S; Ultanir, Sila K; Bullock, Alex N; Drewry, David H; Axtman, Alison D | ACS chemical neuroscience | 37084253 | 2023 May 03 |
| Proteomic approaches to study ubiquitinomics. | Sahu, Indrajit; Zhu, He; Buhrlage, Sara J; Marto, Jarrod A | Biochimica et biophysica acta. Gene regulatory mechanisms | 37121501 | 2023 Jun |
| Editorial: The next generation of tools and technologies for studying human neurons in a dish. | Durcan, Thomas M; Axtman, Alison D | Frontiers in cellular neuroscience | 37124399 | 2023 |
| Illuminating the druggable genome through patent bioactivity data. | Magariños, Maria P; Gaulton, Anna; Félix, Eloy; Kiziloren, Tevfik; Arcila, Ricardo; Oprea, Tudor I; Leach, Andrew R | PeerJ | 37151295 | 2023 |
| Single-molecule imaging in the primary cilium. | Weiss, Lucien E; Love, Julia F; Yoon, Joshua; Comerci, Colin J; Milenkovic, Ljiljana; Kanie, Tomoharu; Jackson, Peter K; Stearns, Tim; Gustavsson, Anna-Karin | Methods in cell biology | 37164543 | 2023 |
| 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 |
| Oxidation Driven Reversal of PIP2-dependent Gating in GIRK2 Channels. | Lee, Sun-Joo; Maeda, Shoji; Gao, Jian; Nichols, Colin G | Function (Oxford, England) | 37168492 | 2023 |
| VIGET: A web portal for study of vaccine-induced host responses based on Reactome pathways and ImmPort data. | Brunson, Timothy; Sanati, Nasim; Huffman, Anthony; Masci, Anna Maria; Zheng, Jie; Cooke, Michael F; Conley, Patrick; He, Yongqun; Wu, Guanming | Frontiers in immunology | 37180100 | 2023 |
| AI-Assisted chemical probe discovery for the understudied Calcium-Calmodulin Dependent Kinase, PNCK. | Essegian, Derek J; Chavez, Valery; Khurshid, Rabia; Merchan, Jaime R; Schürer, Stephan C | PLoS computational biology | 37235579 | 2023 May |
| Development and evaluation of helper dependent adenoviral vectors for inner ear gene delivery. | Tarabichi, Osama; Correa, Tatiana; Kul, Emre; Phillips, Stacia; Darkazanly, Bahaa; Young Jr, Samuel M; Hansen, Marlan R | Hearing research | 37276687 | 2023 Aug |
| Optimization of 3-Cyano-7-cyclopropylamino-pyrazolo[1,5-a]pyrimidines Toward the Development of an In Vivo Chemical Probe for CSNK2A. | Yang, Xuan; Ong, Han Wee; Dickmander, Rebekah J; Smith, Jeffery L; Brown, Jason W; Tao, William; Chang, Edcon; Moorman, Nathaniel J; Axtman, Alison D; Willson, Timothy M | bioRxiv : the preprint server for biology | 37292607 | 2023 Jul 23 |
| Illuminating Dark Proteins using Reactome Pathways. | Brunson, Timothy; Sanati, Nasim; Matthews, Lisa; Haw, Robin; Beavers, Deidre; Shorser, Solomon; Sevilla, Cristoffer; Viteri, Guilherme; Conley, Patrick; Rothfels, Karen; Hermjakob, Henning; Stein, Lincoln; D'Eustachio, Peter; Wu, Guanming | bioRxiv : the preprint server for biology | 37333417 | 2023 Jun 05 |
| KG-Hub-building and exchanging biological knowledge graphs. | Caufield, J Harry; Putman, Tim; Schaper, Kevin; Unni, Deepak R; Hegde, Harshad; Callahan, Tiffany J; Cappelletti, Luca; Moxon, Sierra A T; Ravanmehr, Vida; Carbon, Seth; Chan, Lauren E; Cortes, Katherina; Shefchek, Kent A; Elsarboukh, Glass; Balhoff, Jim; Fontana, Tommaso; Matentzoglu, Nicolas; Bruskiewich, Richard M; Thessen, Anne E; Harris, Nomi L; Munoz-Torres, Monica C; Haendel, Melissa A; Robinson, Peter N; Joachimiak, Marcin P; Mungall, Christopher J; Reese, Justin T | Bioinformatics (Oxford, England) | 37389415 | 2023 Jul 01 |
| Combined CDK4/6 and ERK1/2 Inhibition Enhances Antitumor Activity in NF1-Associated Plexiform Neurofibroma. | Flint, Alyssa C; Mitchell, Dana K; Angus, Steven P; Smith, Abbi E; Bessler, Waylan; Jiang, Li; Mang, Henry; Li, Xiaohong; Lu, Qingbo; Rodriguez, Brooke; Sandusky, George E; Masters, Andi R; Zhang, Chi; Dang, Pengtao; Koenig, Jenna; Johnson, Gary L; Shen, Weihua; Liu, Jiangang; Aggarwal, Amit; Donoho, Gregory P; Willard, Melinda D; Bhagwat, Shripad V; Clapp, D Wade; Rhodes, Steven D | Clinical cancer research : an official journal of the American Association for Cancer Research | 37406085 | 2023 Sep 01 |
| Illuminate the Functions of Dark Proteins Using the Reactome-IDG Web Portal. | Beavers, Deidre; Brunson, Timothy; Sanati, Nasim; Matthews, Lisa; Haw, Robin; Shorser, Solomon; Sevilla, Cristoffer; Viteri, Guilherme; Conley, Patrick; Rothfels, Karen; Hermjakob, Henning; Stein, Lincoln; D'Eustachio, Peter; Wu, Guanming | Current protocols | 37467006 | 2023 Jul |
| Discovery and characterization of a specific inhibitor of serine-threonine kinase cyclin-dependent kinase-like 5 (CDKL5) demonstrates role in hippocampal CA1 physiology. | Castano, Anna; Silvestre, Margaux; Wells, Carrow I; Sanderson, Jennifer L; Ferrer, Carla A; Ong, Han Wee; Lang, Yi; Richardson, William; Silvaroli, Josie A; Bashore, Frances M; Smith, Jeffery L; Genereux, Isabelle M; Dempster, Kelvin; Drewry, David H; Pabla, Navlot S; Bullock, Alex N; Benke, Tim A; Ultanir, Sila K; Axtman, Alison D | eLife | 37490324 | 2023 Jul 25 |
| Subunit gating resulting from individual protonation events in Kir2 channels. | Maksaev, Grigory; Bründl-Jirout, Michael; Stary-Weinzinger, Anna; Zangerl-Plessl, Eva-Maria; Lee, Sun-Joo; Nichols, Colin G | Nature communications | 37507406 | 2023 Jul 28 |
| Alternative Splicing of RIOK3 Engages the Noncanonical NFκB Pathway during Rift Valley Fever Virus Infection. | Bisom, Thomas Charles; Smelser, Hope; Lanchy, Jean-Marc; Lodmell, J Stephen | Viruses | 37515252 | 2023 Jul 18 |
| A novel homeostatic mechanism tunes PI(4,5)P2-dependent signaling at the plasma membrane. | Wills, Rachel C; Doyle, Colleen P; Zewe, James P; Pacheco, Jonathan; Hansen, Scott D; Hammond, Gerald R V | Journal of cell science | 37534432 | 2023 Aug 15 |
| Temporal scaling of dopamine neuron firing and dopamine release by distinct ion channels shape behavior. | Juarez, Barbara; Kong, Mi-Seon; Jo, Yong S; Elum, Jordan E; Yee, Joshua X; Ng-Evans, Scott; Cline, Marcella; Hunker, Avery C; Quinlan, Meagan A; Baird, Madison A; Elerding, Abigail J; Johnson, Mia; Ban, Derek; Mendez, Adriana; Goodwin, Nastacia L; Soden, Marta E; Zweifel, Larry S | Science advances | 37566654 | 2023 Aug 11 |
| Gα Protein Signaling Bias at Serotonin 1A Receptor. | Alabdali, Rana; Franchini, Luca; Orlandi, Cesare | Molecular pharmacology | 37567783 | 2023 Nov |
| A peroxiredoxin-P38 MAPK scaffold increases MAPK activity by MAP3K-independent mechanisms. | Cao, Min; Day, Alison M; Galler, Martin; Latimer, Heather R; Byrne, Dominic P; Foy, Thomas W; Dwyer, Emilia; Bennett, Elise; Palmer, Jeremy; Morgan, Brian A; Eyers, Patrick A; Veal, Elizabeth A | Molecular cell | 37572670 | 2023 Sep 07 |
| Combined kinome inhibition states are predictive of cancer cell line sensitivity to kinase inhibitor combination therapies. | Joisa, Chinmaya U; Chen, Kevin A; Beville, Samantha; Stuhlmiller, Timothy; Berginski, Matthew E; Okumu, Denis; Golitz, Brian T; Johnson, Gary L; Gomez, Shawn M | bioRxiv : the preprint server for biology | 37577663 | 2023 Aug 03 |
| A Hybrid Structure-Based Machine Learning Approach for Predicting Kinase Inhibition by Small Molecules. | Liu, Changchang; Kutchukian, Peter; Nguyen, Nhan D; AlQuraishi, Mohammed; Sorger, Peter K | Journal of chemical information and modeling | 37595065 | 2023 Sep 11 |
| A proteogenomics data-driven knowledge base of human cancer. | Liao, Yuxing; Savage, Sara R; Dou, Yongchao; Shi, Zhiao; Yi, Xinpei; Jiang, Wen; Lei, Jonathan T; Zhang, Bing | Cell systems | 37619559 | 2023 Sep 20 |
| Investigation of the Host Kinome Response to Coronavirus Infection Reveals PI3K/mTOR Inhibitors as Betacoronavirus Antivirals. | Fritch, Ethan J; Mordant, Angie L; Gilbert, Thomas S K; Wells, Carrow I; Yang, Xuan; Barker, Natalie K; Madden, Emily A; Dinnon 3rd, Kenneth H; Hou, Yixuan J; Tse, Longping V; Castillo, Izabella N; Sims, Amy C; Moorman, Nathaniel J; Lakshmanane, Premkumar; Willson, Timothy M; Herring, Laura E; Graves, Lee M; Baric, Ralph S | Journal of proteome research | 37634194 | 2023 Oct 06 |
| Stereotactic Delivery of Helper-dependent Adenoviral Viral Vectors at Distinct Developmental Time Points to Perform Age-dependent Molecular Manipulations of the Mouse Calyx of Held. | Keine, Christian; Al-Yaari, Mohammed; Radulovic, Tamara; Young Jr, Samuel M | Bio-protocol | 37638292 | 2023 Aug 20 |
| How many kinases are druggable? A review of our current understanding. | Anderson, Brian; Rosston, Peter; Ong, Han Wee; Hossain, Mohammad Anwar; Davis-Gilbert, Zachary W; Drewry, David H | The Biochemical journal | 37642371 | 2023 Aug 30 |
| Molecular Complexity: You Know It When You See It. | Oprea, Tudor I; Bologa, Cristian | Journal of medicinal chemistry | 37675804 | 2023 Sep 28 |
| Sex and Racial Disparities in Peripheral Artery Disease. | Divakaran, Sanjay; Krawisz, Anna K; Secemsky, Eric A; Kant, Shashi | Arteriosclerosis, thrombosis, and vascular biology | 37706319 | 2023 Nov |
| Exploring DrugCentral: from molecular structures to clinical effects. | Halip, Liliana; Avram, Sorin; Curpan, Ramona; Borota, Ana; Bora, Alina; Bologa, Cristian; Oprea, Tudor I | Journal of computer-aided molecular design | 37707619 | 2023 Dec |
| Targeted Proteomic Quantitation of NRF2 Signaling and Predictive Biomarkers in HNSCC. | Wamsley, Nathan T; Wilkerson, Emily M; Guan, Li; LaPak, Kyle M; Schrank, Travis P; Holmes, Brittany J; Sprung, Robert W; Gilmore, Petra Erdmann; Gerndt, Sophie P; Jackson, Ryan S; Paniello, Randal C; Pipkorn, Patrik; Puram, Sidharth V; Rich, Jason T; Townsend, Reid R; Zevallos, José P; Zolkind, Paul; Le, Quynh-Thu; Goldfarb, Dennis; Major, Michael B | Molecular & cellular proteomics : MCP | 37716475 | 2023 Nov |
| To block or not to block: Targeting SK channels in diseased hearts. | Terentyev, Dmitry; Belevych, Andriy E; Choi, Bum-Rak; Hamilton, Shanna | Journal of molecular and cellular cardiology | 37742783 | 2023 Oct |
| KSFinder-a knowledge graph model for link prediction of novel phosphorylated substrates of kinases. | Anandakrishnan, Manju; Ross, Karen E; Chen, Chuming; Shanker, Vijay; Cowart, Julie; Wu, Cathy H | PeerJ | 37818330 | 2023 |
| Biophysical characterization of chloride intracellular channel 6 (CLIC6). | Loyo-Celis, Veronica; Patel, Devendra; Sanghvi, Shridhar; Kaur, Kamalpreet; Ponnalagu, Devasena; Zheng, Yang; Bindra, Sahej; Bhachu, Harmeet Rireika; Deschenes, Isabelle; Gururaja Rao, Shubha; Singh, Harpreet | The Journal of biological chemistry | 37838179 | 2023 Nov |
| Dynamic regulation of pancreatic β cell function and gene expression by the SND1 coregulator in vitro. | Kanojia, Sukrati; Davidson, Rebecca K; Conley, Jason M; Xu, Jerry; Osmulski, Meredith; Sims, Emily K; Ren, Hongxia; Spaeth, Jason M | Islets | 37838950 | 2023 Dec 31 |
| Confocal Imaging and 3D Reconstruction to Determine How Genetic Perturbations Impact Presynaptic Morphology at the Mouse Calyx of Held. | Keine, Christian; Radulovic, Tamara; Al-Yaari, Mohammed; Young Jr, Samuel M | Bio-protocol | 37849785 | 2023 Sep 05 |
| Predicting protein and pathway associations for understudied dark kinases using pattern-constrained knowledge graph embedding. | Salcedo, Mariah V; Gravel, Nathan; Keshavarzi, Abbas; Huang, Liang-Chin; Kochut, Krzysztof J; Kannan, Natarajan | PeerJ | 37868056 | 2023 |
| Measuring conformational equilibria in allosteric proteins with time-resolved tmFRET. | Zagotta, William N; Evans, Eric G B; Eggan, Pierce; Tessmer, Maxx H; Shaffer, Kyle D; Petersson, E James; Stoll, Stefan; Gordon, Sharona E | bioRxiv : the preprint server for biology | 37873384 | 2023 Oct 11 |
| Long-distance tmFRET using bipyridyl- and phenanthroline-based ligands. | Gordon, Sharona E; Evans, Eric G B; Otto, Shauna C; Tessmer, Maxx H; Shaffer, Kyle D; Gordon, Moshe T; Petersson, E James; Stoll, Stefan; Zagotta, William N | bioRxiv : the preprint server for biology | 37873407 | 2023 Oct 12 |
| Optimization of 3-Cyano-7-cyclopropylamino-pyrazolo[1,5-a]pyrimidines toward the Development of an In Vivo Chemical Probe for CSNK2A. | Yang, Xuan; Ong, Han Wee; Dickmander, Rebekah J; Smith, Jeffery L; Brown, Jason W; Tao, William; Chang, Edcon; Moorman, Nathaniel J; Axtman, Alison D; Willson, Timothy M | ACS omega | 37901516 | 2023 Oct 24 |
| Inflammatory stress-mediated chromatin changes underlie dysfunction in endothelial cells. | Liu, Haibo; Caliz, Amada D; Learnard, Heather; Koupenova, Milka; Keaney, John F; Kant, Shashi; Zhu, Lihua Julie; Vertii, Anastassiia | bioRxiv : the preprint server for biology | 37905100 | 2023 Oct 16 |
| Development of a covalent cereblon-based PROTAC employing a fluorosulfate warhead. | Nowak, Radosław P; Ragosta, Leah; Huerta, Fidel; Liu, Hu; Ficarro, Scott B; Cruite, Justin T; Metivier, Rebecca J; Donovan, Katherine A; Marto, Jarrod A; Fischer, Eric S; Zerfas, Breanna L; Jones, Lyn H | RSC chemical biology | 37920397 | 2023 Nov 01 |
| Dissecting the biophysics and biology of intrinsically disordered proteins. | Banerjee, Priya R; Holehouse, Alex S; Kriwacki, Richard; Robustelli, Paul; Jiang, Hao; Sobolevsky, Alexander I; Hurley, Jennifer M; Mendell, Joshua T | Trends in biochemical sciences | 37949765 | 2023 Nov 08 |
| Dex-Benchmark: datasets and code to evaluate algorithms for transcriptomics data analysis. | Xie, Zhuorui; Chen, Clara; Ma'ayan, Avi | PeerJ | 37953774 | 2023 |
| Covalent Stapling of the Cereblon Sensor Loop Histidine Using Sulfur-Heterocycle Exchange. | Cruite, Justin T; Nowak, Radosław P; Donovan, Katherine A; Ficarro, Scott B; Huang, Huang; Liu, Hu; Liu, Yingpeng; Marto, Jarrod A; Metivier, Rebecca J; Fischer, Eric S; Jones, Lyn H | ACS medicinal chemistry letters | 37974938 | 2023 Nov 09 |
| A small molecule exerts selective antiviral activity by targeting the human cytomegalovirus nuclear egress complex. | Chen, Han; Lye, Ming F; Gorgulla, Christoph; Ficarro, Scott B; Cuny, Gregory D; Scott, David A; Wu, Fan; Rothlauf, Paul W; Wang, Xiaoou; Fernandez, Rosio; Pesola, Jean M; Draga, Sorin; Marto, Jarrod A; Hogle, James M; Arthanari, Haribabu; Coen, Donald M | PLoS pathogens | 37976321 | 2023 Nov |
| ChatGPT usage in the Reactome curation process. | Tiwari, Krishna; Matthews, Lisa; May, Bruce; Shamovsky, Veronica; Orlic-Milacic, Marija; Rothfels, Karen; Ragueneau, Eliot; Gong, Chuqiao; Stephan, Ralf; Li, Nancy; Wu, Guanming; Stein, Lincoln; D'Eustachio, Peter; Hermjakob, Henning | bioRxiv : the preprint server for biology | 37986970 | 2023 Nov 08 |
| SGC-CLK-1: A chemical probe for the Cdc2-like kinases CLK1, CLK2, and CLK4. | Tiek, Deanna; Wells, Carrow I; Schröder, Martin; Song, Xiao; Alamillo-Ferrer, Carla; Goenka, Anshika; Iglesia, Rebeca; Lu, Minghui; Hu, Bo; Kwarcinski, Frank; Sintha, Parvathi; de Silva, Chandi; Hossain, Mohammad Anwar; Picado, Alfredo; Zuercher, William; Zutshi, Reena; Knapp, Stefan; Riggins, Rebecca B; Cheng, Shi-Yuan; Drewry, David H | Current research in chemical biology | 38009092 | 2023 |
| Identification of Cellular Interactions in the Tumor Immune Microenvironment Underlying CD8 T Cell Exhaustion. | Klocke, Christopher; Moran, Amy; Adey, Andrew; McWeeney, Shannon; Wu, Guanming | bioRxiv : the preprint server for biology | 38014233 | 2023 Nov 13 |
| Integrated single-dose kinome profiling data is predictive of cancer cell line sensitivity to kinase inhibitors. | Joisa, Chinmaya U; Chen, Kevin A; Berginski, Matthew E; Golitz, Brian T; Jenner, Madison R; Herrera Loeza, Gabriela; Yeh, Jen Jen; Gomez, Shawn M | PeerJ | 38025707 | 2023 |
| Genome-wide prediction of pathogenic gain- and loss-of-function variants from ensemble learning of a diverse feature set. | Stein, David; Kars, Meltem Ece; Wu, Yiming; Bayrak, Çiğdem Sevim; Stenson, Peter D; Cooper, David N; Schlessinger, Avner; Itan, Yuval | Genome medicine | 38037155 | 2023 Nov 30 |
| pH-sensing G protein-coupled orphan receptor GPR68 is expressed in human cartilage and correlates with degradation of extracellular matrix during OA progression. | Khan, Nazir M; Diaz-Hernandez, Martha E; Martin, William N; Patel, Bhakti; Chihab, Samir; Drissi, Hicham | PeerJ | 38077417 | 2023 |
| Dark kinase annotation, mining, and visualization using the Protein Kinase Ontology. | Soleymani, Saber; Gravel, Nathan; Huang, Liang-Chin; Yeung, Wayland; Bozorgi, Elika; Bendzunas, Nathaniel G; Kochut, Krzysztof J; Kannan, Natarajan | PeerJ | 38077442 | 2023 |
| Detection of neoplastic-immune hybrid cells with metastatic properties in uveal melanoma. | Anderson, Ashley N; Conley, Patrick; Klocke, Christopher D; Sengupta, Sidharth K; Pang, Amara; Farley, Hannah C; Gillingham, Abigail R; Dawson, Aubrey D; Fan, Yichen; Jones, Jocelyn A; Gibbs, Summer L; Skalet, Alison H; Wu, Guanming; Wong, Melissa H | Research square | 38106024 | 2023 Dec 06 |
| Identification of 4-(6-((2-methoxyphenyl)amino)pyrazin-2-yl)benzoic acids as CSNK2A inhibitors with antiviral activity and improved selectivity over PIM3. | Galal, Kareem A; Krämer, Andreas; Strickland, Benjamin G; Smith, Jeffery L; Dickmander, Rebekah J; Moorman, Nathaniel J; Willson, Timothy M | bioRxiv : the preprint server for biology | 38106118 | 2023 Dec 05 |
| CaV 2.1 α1 subunit motifs that control presynaptic CaV 2.1 subtype abundance are distinct from CaV 2.1 preference. | Li, Jianing; Veeraraghavan, Priyadharishini; Young Jr, Samuel M | The Journal of physiology | 38155373 | 2023 Dec 28 |
| GRAPE for fast and scalable graph processing and random-walk-based embedding. | Cappelletti, Luca; Fontana, Tommaso; Casiraghi, Elena; Ravanmehr, Vida; Callahan, Tiffany J; Cano, Carlos; Joachimiak, Marcin P; Mungall, Christopher J; Robinson, Peter N; Reese, Justin; Valentini, Giorgio | Nature computational science | 38177435 | 2023 Jun |
| Illuminating function of the understudied druggable kinome. | Gomez, Shawn M; Axtman, Alison D; Willson, Timothy M; Major, Michael B; Townsend, Reid R; Sorger, Peter K; Johnson, Gary L | Drug discovery today | 38218213 | 2024 Jan 11 |
| Gpr149 is involved in energy homeostasis in the male mouse. | Wyler, Steven; Surbhi; Cao, Newton; Merchant, Warda; Bookout, Angie; Gautron, Laurent | PeerJ | 38282864 | 2024 |
