The Human BioMolecular Atlas Program (HuBMAP)
The Human BioMolecular Atlas Program (HuBMAP)
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 |
|---|---|---|---|---|
| Dictionary learning for integrative, multimodal and scalable single-cell analysis. | Hao, Yuhan; Stuart, Tim; Kowalski, Madeline H; Choudhary, Saket; Hoffman, Paul; Hartman, Austin; Srivastava, Avi; Molla, Gesmira; Madad, Shaista; Fernandez-Granda, Carlos; Satija, Rahul | Nature biotechnology | 37231261 | 2024 Feb |
| ELISL: early-late integrated synthetic lethality prediction in cancer. | Tepeli, Yasin I; Seale, Colm; Gonçalves, Joana P | Bioinformatics (Oxford, England) | 38113447 | 2024 Jan 02 |
| Discussion: Commercial Insurance Rates and Coding for Lymphedema Procedures: The Current State of Confusion and Need for Consensus. | Friedman, Rosie; Lee, Bernard T; Chatterjee, Abhishek; Singhal, Dhruv | Plastic and reconstructive surgery | 38127452 | 2024 Jan 01 |
| Tumor proliferation and invasion are intrinsically coupled and unraveled through tunable spheroid and physics-based models. | Crawford, Ashleigh J; Gomez-Cruz, Clara; Russo, Gabriella C; Huang, Wilson; Bhorkar, Isha; Roy, Triya; Muñoz-Barrutia, Arrate; Wirtz, Denis; Garcia-Gonzalez, Daniel | Acta biomaterialia | 38160858 | 2024 Feb |
| Expanding the coverage of spatial proteomics: a machine learning approach. | Sun, Huangqingbo; Li, Jiayi; Murphy, Robert F | Bioinformatics (Oxford, England) | 38310340 | 2024 Feb 01 |
| Convergence of coronary artery disease genes onto endothelial cell programs. | Schnitzler, Gavin R; Kang, Helen; Fang, Shi; Angom, Ramcharan S; Lee-Kim, Vivian S; Ma, X Rosa; Zhou, Ronghao; Zeng, Tony; Guo, Katherine; Taylor, Martin S; Vellarikkal, Shamsudheen K; Barry, Aurelie E; Sias-Garcia, Oscar; Bloemendal, Alex; Munson, Glen; Guckelberger, Philine; Nguyen, Tung H; Bergman, Drew T; Hinshaw, Stephen; Cheng, Nathan; Cleary, Brian; Aragam, Krishna; Lander, Eric S; Finucane, Hilary K; Mukhopadhyay, Debabrata; Gupta, Rajat M; Engreitz, Jesse M | Nature | 38326615 | 2024 Feb |
| Multimodal mass spectrometry imaging identifies cell-type-specific metabolic and lipidomic variation in the mammalian liver. | Tian, Hua; Rajbhandari, Presha; Tarolli, Jay; Decker, Aubrianna M; Neelakantan, Taruna V; Angerer, Tina; Zandkarimi, Fereshteh; Remotti, Helen; Frache, Gilles; Winograd, Nicholas; Stockwell, Brent R | Developmental cell | 38359832 | 2024 Apr 08 |
| Spatially Exploring RNA Biology in Archival Formalin-Fixed Paraffin-Embedded Tissues. | Bai, Zhiliang; Zhang, Dingyao; Gao, Yan; Tao, Bo; Bao, Shuozhen; Enninful, Archibald; Zhang, Daiwei; Su, Graham; Tian, Xiaolong; Zhang, Ningning; Xiao, Yang; Liu, Yang; Gerstein, Mark; Li, Mingyao; Xing, Yi; Lu, Jun; Xu, Mina L; Fan, Rong | bioRxiv : the preprint server for biology | 38370833 | 2024 Feb 08 |
| Host-Microbe Multiomic Profiling Reveals Age-Dependent COVID-19 Immunopathology. | Van Phan, Hoang; Tsitsiklis, Alexandra; Maguire, Cole P; Haddad, Elias K; Becker, Patrice M; Kim-Schulze, Seunghee; Lee, Brian; Chen, Jing; Hoch, Annmarie; Pickering, Harry; Van Zalm, Patrick; Altman, Matthew C; Augustine, Alison D; Calfee, Carolyn S; Bosinger, Steve; Cairns, Charles; Eckalbar, Walter; Guan, Leying; Jayavelu, Naresh Doni; Kleinstein, Steven H; Krammer, Florian; Maecker, Holden T; Ozonoff, Al; Peters, Bjoern; Rouphael, Nadine; IMPACC Network; Montgomery, Ruth R; Reed, Elaine; Schaenman, Joanna; Steen, Hanno; Levy, Ofer; Diray-Arce, Joann; Langelier, Charles R | medRxiv : the preprint server for health sciences | 38405760 | 2024 Feb 13 |
| Spatial top-down proteomics for the functional characterization of human kidney. | Zemaitis, Kevin J; Fulcher, James M; Kumar, Rashmi; Degnan, David J; Lewis, Logan A; Liao, Yen-Chen; Veličković, Marija; Williams, Sarah M; Moore, Ronald J; Bramer, Lisa M; Veličković, Dušan; Zhu, Ying; Zhou, Mowei; Paša-Tolić, Ljiljana | bioRxiv : the preprint server for biology | 38405958 | 2024 Jul 05 |
| Advances in mass spectrometry-enabled multiomics at single-cell resolution. | Kumar, Rashmi; Zemaitis, Kevin J; Fulcher, James M; Paša-Tolić, Ljiljana | Current opinion in biotechnology | 38432187 | 2024 Jun |
| Modelling post-implantation human development to yolk sac blood emergence. | Hislop, Joshua; Song, Qi; Keshavarz F, Kamyar; Alavi, Amir; Schoenberger, Rayna; LeGraw, Ryan; Velazquez, Jeremy J; Mokhtari, Tahere; Taheri, Mohammad Naser; Rytel, Matthew; Chuva de Sousa Lopes, Susana M; Watkins, Simon; Stolz, Donna; Kiani, Samira; Sozen, Berna; Bar-Joseph, Ziv; Ebrahimkhani, Mo R | Nature | 38092041 | 2024 Feb |
| Slide-tags enables single-nucleus barcoding for multimodal spatial genomics. | Russell, Andrew J C; Weir, Jackson A; Nadaf, Naeem M; Shabet, Matthew; Kumar, Vipin; Kambhampati, Sandeep; Raichur, Ruth; Marrero, Giovanni J; Liu, Sophia; Balderrama, Karol S; Vanderburg, Charles R; Shanmugam, Vignesh; Tian, Luyi; Iorgulescu, J Bryan; Yoon, Charles H; Wu, Catherine J; Macosko, Evan Z; Chen, Fei | Nature | 38093010 | 2024 Jan |
| Features of acute COVID-19 associated with post-acute sequelae of SARS-CoV-2 phenotypes: results from the IMPACC study. | Ozonoff, Al; Jayavelu, Naresh Doni; Liu, Shanshan; Melamed, Esther; Milliren, Carly E; Qi, Jingjing; Geng, Linda N; McComsey, Grace A; Cairns, Charles B; Baden, Lindsey R; Schaenman, Joanna; Shaw, Albert C; Samaha, Hady; Seyfert-Margolis, Vicki; Krammer, Florian; Rosen, Lindsey B; Steen, Hanno; Syphurs, Caitlin; Dandekar, Ravi; Shannon, Casey P; Sekaly, Rafick P; Ehrlich, Lauren I R; Corry, David B; Kheradmand, Farrah; Atkinson, Mark A; Brakenridge, Scott C; Higuita, Nelson I Agudelo; Metcalf, Jordan P; Hough, Catherine L; Messer, William B; Pulendran, Bali; Nadeau, Kari C; Davis, Mark M; Sesma, Ana Fernandez; Simon, Viviana; van Bakel, Harm; Kim-Schulze, Seunghee; Hafler, David A; Levy, Ofer; Kraft, Monica; Bime, Chris; Haddad, Elias K; Calfee, Carolyn S; Erle, David J; Langelier, Charles R; Eckalbar, Walter; Bosinger, Steven E; IMPACC Network; Peters, Bjoern; Kleinstein, Steven H; Reed, Elaine F; Augustine, Alison D; Diray-Arce, Joann; Maecker, Holden T; Altman, Matthew C; Montgomery, Ruth R; Becker, Patrice M; Rouphael, Nadine | Nature communications | 38172101 | 2024 Jan 03 |
| Unsupervised and supervised discovery of tissue cellular neighborhoods from cell phenotypes. | Hu, Yuxuan; Rong, Jiazhen; Xu, Yafei; Xie, Runzhi; Peng, Jacqueline; Gao, Lin; Tan, Kai | Nature methods | 38191930 | 2024 Feb |
| Prediction of single-cell RNA expression profiles in live cells by Raman microscopy with Raman2RNA. | Kobayashi-Kirschvink, Koseki J; Comiter, Charles S; Gaddam, Shreya; Joren, Taylor; Grody, Emanuelle I; Ounadjela, Johain R; Zhang, Ke; Ge, Baoliang; Kang, Jeon Woong; Xavier, Ramnik J; So, Peter T C; Biancalani, Tommaso; Shu, Jian; Regev, Aviv | Nature biotechnology | 38200118 | 2024 Jan 10 |
| Toward a common standard for data and specimen provenance in life sciences. | Wittner, Rudolf; Holub, Petr; Mascia, Cecilia; Frexia, Francesca; Müller, Heimo; Plass, Markus; Allocca, Clare; Betsou, Fay; Burdett, Tony; Cancio, Ibon; Chapman, Adriane; Chapman, Martin; Courtot, Mélanie; Curcin, Vasa; Eder, Johann; Elliot, Mark; Exter, Katrina; Goble, Carole; Golebiewski, Martin; Kisler, Bron; Kremer, Andreas; Leo, Simone; Lin-Gibson, Sheng; Marsano, Anna; Mattavelli, Marco; Moore, Josh; Nakae, Hiroki; Perseil, Isabelle; Salman, Ayat; Sluka, James; Soiland-Reyes, Stian; Strambio-De-Castillia, Caterina; Sussman, Michael; Swedlow, Jason R; Zatloukal, Kurt; Geiger, Jörg | Learning health systems | 38249839 | 2024 Jan |
| Integrated longitudinal multiomics study identifies immune programs associated with acute COVID-19 severity and mortality. | Gygi, Jeremy P; Maguire, Cole; Patel, Ravi K; Shinde, Pramod; Konstorum, Anna; Shannon, Casey P; Xu, Leqi; Hoch, Annmarie; Jayavelu, Naresh Doni; Haddad, Elias K; IMPACC Network; Reed, Elaine F; Kraft, Monica; McComsey, Grace A; Metcalf, Jordan P; Ozonoff, Al; Esserman, Denise; Cairns, Charles B; Rouphael, Nadine; Bosinger, Steven E; Kim-Schulze, Seunghee; Krammer, Florian; Rosen, Lindsey B; van Bakel, Harm; Wilson, Michael; Eckalbar, Walter L; Maecker, Holden T; Langelier, Charles R; Steen, Hanno; Altman, Matthew C; Montgomery, Ruth R; Levy, Ofer; Melamed, Esther; Pulendran, Bali; Diray-Arce, Joann; Smolen, Kinga K; Fragiadakis, Gabriela K; Becker, Patrice M; Sekaly, Rafick P; Ehrlich, Lauren Ir; Fourati, Slim; Peters, Bjoern; Kleinstein, Steven H; Guan, Leying | The Journal of clinical investigation | 38690733 | 2024 May 01 |
| 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 |
| Predicting drug outcome of population via clinical knowledge graph. | Brbić, Maria; Yasunaga, Michihiro; Agarwal, Prabhat; Leskovec, Jure | medRxiv : the preprint server for health sciences | 38496488 | 2024 Mar 08 |
| Imaging Mass Spectrometry of Isotopically Resolved Intact Proteins on a Trapped Ion-Mobility Quadrupole Time-of-Flight Mass Spectrometer. | Klein, Dustin R; Rivera, Emilio S; Caprioli, Richard M; Spraggins, Jeffrey M | Analytical chemistry | 38517028 | 2024 Apr 02 |
| Mapping the Anatomy of the Human Lymphatic System. | Bustos, Valeria P; Wang, Robin; Pardo, Jaime; Boppana, Avinash; Weber, Griffin; Itkin, Max; Singhal, Dhruv | Journal of reconstructive microsurgery | 38547908 | 2024 Mar 28 |
| Mapping the Cellular Biogeography of Human Bone Marrow Niches Using Single-Cell Transcriptomics and Proteomic Imaging. | Bandyopadhyay, Shovik; Duffy, Michael; Ahn, Kyung Jin; Pang, Minxing; Smith, David; Duncan, Gwendolyn; Sussman, Jonathan; Zhang, Iris; Huang, Jeffrey; Lin, Yulieh; Xiong, Barbara; Imtiaz, Tamjid; Chen, Chia-Hui; Thadi, Anusha; Chen, Changya; Xu, Jason; Reichart, Melissa; Pillai, Vinodh; Snaith, Oraine; Oldridge, Derek; Bhattacharyya, Siddharth; Maillard, Ivan; Carroll, Martin; Nelson, Charles; Qin, Ling; Tan, Kai | bioRxiv : the preprint server for biology | 38559168 | 2024 Mar 16 |
| ComPRePS: An Automated Cloud-based Image Analysis tool to democratize AI in Digital Pathology. | Mimar, Sayat; Paul, Anindya S; Lucarelli, Nicholas; Border, Samuel; Santo, Briana A; Naglah, Ahmed; Barisoni, Laura; Hodgin, Jeffrey; Rosenberg, Avi Z; Clapp, William; Sarder, Pinaki; Kidney Precision Medicine Project | bioRxiv : the preprint server for biology | 38585837 | 2024 Apr 05 |
| Blind Polarization Demultiplexing of Shaped QAM Signals Assisted by Temporal Correlations. | Bajaj, Vinod; Van de Plas, Raf; Wahls, Sander | Journal of lightwave technology : a joint IEEE/OSA publication | 38586243 | 2024 Jan 15 |
| 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 |
| Robust Surfactant-Assisted One-Pot Sample Preparation for Label-Free Single-Cell and Nanoscale Proteomics. | Xu, Zhangyang; Zou, Rongge; Horn, Nina C; Kitata, Reta Birhanu; Shi, Tujin | Methods in molecular biology (Clifton, N.J.) | 38907149 | 2024 |
| Local, Sustained, and Targeted Co-Delivery of MEK Inhibitor and Doxorubicin Inhibits Tumor Progression in E-Cadherin-Positive Breast Cancer. | Kuhn, Paul M; Russo, Gabriella C; Crawford, Ashleigh J; Venkatraman, Aditya; Yang, Nanlan; Starich, Bartholomew A; Schneiderman, Zachary; Wu, Pei-Hsun; Vo, Thi; Wirtz, Denis; Kokkoli, Efrosini | Pharmaceutics | 39204325 | 2024 Jul 25 |
| Enhancing Hierarchical Transformers for Whole Brain Segmentation with Intracranial Measurements Integration. | Yu, Xin; Tang, Yucheng; Yang, Qi; Lee, Ho Hin; Bao, Shunxing; Huo, Yuankai; Landman, Bennett A | Proceedings of SPIE--the International Society for Optical Engineering | 39220623 | 2024 Feb |
| E-Cadherin Induces Serine Synthesis to Support Progression and Metastasis of Breast Cancer. | Lee, Geonhui; Wong, Claudia; Cho, Anna; West, Junior J; Crawford, Ashleigh J; Russo, Gabriella C; Si, Bishwa R; Kim, Jungwoo; Hoffner, Lauren; Jang, Cholsoon; Jung, Moonjung; Leone, Robert D; Konstantopoulos, Konstantinos; Ewald, Andrew J; Wirtz, Denis; Jeong, Sangmoo | Cancer research | 38959339 | 2024 Sep 04 |
| Top-down proteomics. | Roberts, David S; Loo, Joseph A; Tsybin, Yury O; Liu, Xiaowen; Wu, Si; Chamot-Rooke, Julia; Agar, Jeffrey N; Paša-Tolić, Ljiljana; Smith, Lloyd M; Ge, Ying | Nature reviews. Methods primers | 39006170 | 2024 |
| FUSION: A web-based application for in-depth exploration of multi-omics data with brightfield histology. | Border, Samuel; Ferreira, Ricardo Melo; Lucarelli, Nicholas; Manthey, David; Kumar, Suhas; Paul, Anindya; Mimar, Sayat; Naglah, Ahmed; Cheng, Ying-Hua; Barisoni, Laura; Ray, Jessica; Strekalova, Yulia; Rosenberg, Avi Z; Tomaszewski, John E; Hodgin, Jeffrey B; HuBMAP consortium; El-Achkar, Tarek M; Jain, Sanjay; Eadon, Michael T; Sarder, Pinaki | bioRxiv : the preprint server for biology | 39026885 | 2024 Aug 22 |
| Deep Learning for 3D Vascular Segmentation in Phase Contrast Tomography. | Yagis, Ekin; Aslani, Shahab; Jain, Yashvardhan; Zhou, Yang; Rahmani, Shahrokh; Brunet, Joseph; Bellier, Alexandre; Werlein, Christopher; Ackermann, Maximilian; Jonigk, Danny; Tafforeau, Paul; Lee, Peter D; Walsh, Claire | Research square | 39070623 | 2024 Jul 16 |
| Super-Resolution Stimulated Raman Scattering Microscopy with Graphical User Interface-Supported A-PoD. | Jang, Hongje; Li, Yajuan; Wu, Shuang; Shi, Lingyan | Current protocols | 38270527 | 2024 Jan |
| Single-cell multiomics guided mechanistic understanding of Fontan-associated liver disease. | Hu, Po; Rychik, Jack; Zhao, Juanjuan; Bai, Huajun; Bauer, Aidan; Yu, Wenbao; Rand, Elizabeth B; Dodds, Kathryn M; Goldberg, David J; Tan, Kai; Wilkins, Benjamin J; Pei, Liming | Science translational medicine | 38657025 | 2024 Apr 24 |
| PanIN or IPMN? Redefining Lesion Size in 3 Dimensions. | Kiemen, Ashley L; Dequiedt, Lucie; Shen, Yu; Zhu, Yutong; Matos-Romero, Valentina; Forjaz, André; Campbell, Kurtis; Dhana, Will; Cornish, Toby; Braxton, Alicia M; Wu, Pei-Hsun; Fishman, Elliot K; Wood, Laura D; Wirtz, Denis; Hruban, Ralph H | The American journal of surgical pathology | 38764379 | 2024 Jul 01 |
| Markov models for clinical decision-making in radiation oncology: A systematic review. | McCullum, Lucas B; Karagoz, Aysenur; Dede, Cem; Garcia, Raul; Nosrat, Fatemeh; Hemmati, Mehdi; Hosseinian, Seyedmohammadhossein; Schaefer, Andrew J; Fuller, Clifton D; Rice/MD Anderson Center for Operations Research in Cancer (CORC); MD Anderson Head and Neck Cancer Symptom Working Group | Journal of medical imaging and radiation oncology | 38766899 | 2024 May 20 |
| ComPRePS: An Automated Cloud-based Image Analysis tool to democratize AI in Digital Pathology. | Mimar, Sayat; Paul, Anindya S; Lucarelli, Nicholas; Border, Samuel; Naglah, Ahmed; Barisoni, Laura; Hodgin, Jeffrey; Rosenberg, Avi Z; Clapp, William; Sarder, Pinaki | Proceedings of SPIE--the International Society for Optical Engineering | 38813089 | 2024 Feb |
| Publication, funding, and experimental data in support of Human Reference Atlas construction and usage. | Kong, Yongxin; Börner, Katy | Scientific data | 38834597 | 2024 Jun 04 |
| Thermal-plex: fluidic-free, rapid sequential multiplexed imaging with DNA-encoded thermal channels. | Hong, Fan; Kishi, Jocelyn Y; Delgado, Ryan N; Jeong, Jiyoun; Saka, Sinem K; Su, Hanquan; Cepko, Constance L; Yin, Peng | Nature methods | 38151595 | 2024 Feb |
| Spatial transcriptomics in health and disease. | Jain, Sanjay; Eadon, Michael T | Nature reviews. Nephrology | 38719971 | 2024 Oct |
| The future of rapid and automated single-cell data analysis using reference mapping. | Lotfollahi, Mohammad; Yuhan Hao; Theis, Fabian J; Satija, Rahul | Cell | 38729109 | 2024 May 09 |
| Modeling blood-brain barrier formation and cerebral cavernous malformations in human PSC-derived organoids. | Dao, Lan; You, Zhen; Lu, Lu; Xu, Tianyang; Sarkar, Avijite Kumer; Zhu, Hui; Liu, Miao; Calandrelli, Riccardo; Yoshida, George; Lin, Pei; Miao, Yifei; Mierke, Sarah; Kalva, Srijan; Zhu, Haining; Gu, Mingxia; Vadivelu, Sudhakar; Zhong, Sheng; Huang, L Frank; Guo, Ziyuan | Cell stem cell | 38754427 | 2024 Jun 06 |
| Longitudinal plasma proteomic analysis of 1117 hospitalized patients with COVID-19 identifies features associated with severity and outcomes. | Viode, Arthur; Smolen, Kinga K; van Zalm, Patrick; Stevenson, David; Jha, Meenakshi; Parker, Kenneth; IMPACC Network‡; Levy, Ofer; Steen, Judith A; Steen, Hanno | Science advances | 38787940 | 2024 May 24 |
| Piezo1 regulates meningeal lymphatic vessel drainage and alleviates excessive CSF accumulation. | Choi, Dongwon; Park, Eunkyung; Choi, Joshua; Lu, Renhao; Yu, Jin Suh; Kim, Chiyoon; Zhao, Luping; Yu, James; Nakashima, Brandon; Lee, Sunju; Singhal, Dhruv; Scallan, Joshua P; Zhou, Bin; Koh, Chester J; Lee, Esak; Hong, Young-Kwon | Nature neuroscience | 38528202 | 2024 May |
| Single-cell multiplex chromatin and RNA interactions in ageing human brain. | Wen, Xingzhao; Luo, Zhifei; Zhao, Wenxin; Calandrelli, Riccardo; Nguyen, Tri C; Wan, Xueyi; Charles Richard, John Lalith; Zhong, Sheng | Nature | 38538789 | 2024 Apr |
| 3DCellComposer - A Versatile Pipeline Utilizing 2D Cell Segmentation Methods for 3D Cell Segmentation. | Chen, Haoran; Murphy, Robert F | bioRxiv : the preprint server for biology | 38559093 | 2024 Mar 12 |
| Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads. | Keskus, Ayse; Bryant, Asher; Ahmad, Tanveer; Yoo, Byunggil; Aganezov, Sergey; Goretsky, Anton; Donmez, Ataberk; Lansdon, Lisa A; Rodriguez, Isabel; Park, Jimin; Liu, Yuelin; Cui, Xiwen; Gardner, Joshua; McNulty, Brandy; Sacco, Samuel; Shetty, Jyoti; Zhao, Yongmei; Tran, Bao; Narzisi, Giuseppe; Helland, Adrienne; Cook, Daniel E; Chang, Pi-Chuan; Kolesnikov, Alexey; Carroll, Andrew; Molloy, Erin K; Pushel, Irina; Guest, Erin; Pastinen, Tomi; Shafin, Kishwar; Miga, Karen H; Malikic, Salem; Day, Chi-Ping; Robine, Nicolas; Sahinalp, Cenk; Dean, Michael; Farooqi, Midhat S; Paten, Benedict; Kolmogorov, Mikhail | medRxiv : the preprint server for health sciences | 38585974 | 2024 Mar 26 |
| Multiplexed in situ protein imaging using DNA-barcoded antibodies with extended hybridization chain reactions. | Wang, Yu; Liu, Xiaoyu; Zeng, Yitian; Saka, Sinem K; Xie, Wenxin; Goldaracena, Isabel; Kohman, Richie E; Yin, Peng; Church, George M | Nucleic acids research | 38966983 | 2024 Aug 27 |
| qMAP enabled microanatomical mapping of human skin aging. | Han, Kyu Sang; Sander, Inbal B; Kumer, Jacqueline; Resnick, Eric; Booth, Clare; Cheng, Guoqing; Im, Yebin; Starich, Bartholomew; Kiemen, Ashley L; Phillip, Jude M; Reddy, Sashank; Joshu, Corrine E; Sunshine, Joel C; Walston, Jeremy D; Wirtz, Denis; Wu, Pei-Hsun | bioRxiv : the preprint server for biology | 39005293 | 2024 Jul 06 |
| Characterizing Low-cost Registration for Photographic Images to Computed Tomography. | Kim, Michael E; Lee, Ho Hin; Ramadass, Karthik; Gao, Chenyu; Van Schaik, Katherine; Tkaczyk, Eric; Spraggins, Jeffrey; Moyer, Daniel C; Landman, Bennett A | Proceedings of SPIE--the International Society for Optical Engineering | 39220622 | 2024 Feb |
| Role of Artificial Intelligence in Kidney Pathology: Promises and Pitfalls. | Goodman, Kyle; Sarullo, Kathryn; Swamidass, S Joshua; Gaut, Joseph P; Jain, Sanjay | Kidney360 | 39254464 | 2024 Jul 01 |
| LungMAP Portal Ecosystem: Systems-level Exploration of the Lung. | Gaddis, Nathan; Fortriede, Joshua; Guo, Minzhe; Bardes, Eric E; Kouril, Michal; Tabar, Scott; Burns, Kevin; Ardini-Poleske, Maryanne E; Loos, Stephanie; Schnell, Daniel; Jin, Kang; Iyer, Balaji; Du, Yina; Huo, Bing-Xing; Bhattacharjee, Anukana; Korte, Jeff; Munshi, Ruchi; Smith, Victoria; Herbst, Andrew; Kitzmiller, Joseph A; Clair, Geremy C; Carson, James P; Adkins, Joshua; Morrisey, Edward E; Pryhuber, Gloria S; Misra, Ravi; Whitsett, Jeffrey A; Sun, Xin; Heathorn, Trevor; Paten, Benedict; Prasath, V B Surya; Xu, Yan; Tickle, Tim; Aronow, Bruce J; Salomonis, Nathan | American journal of respiratory cell and molecular biology | 36413377 | 2024 Feb |
| Three-dimensional reconstruction of fetal rhesus macaque kidneys at single-cell resolution reveals complex inter-relation of structures. | Dequiedt, Lucie; Forjaz, André; Lo, Jamie O; McCarty, Owen; Wu, Pei-Hsun; Rosenberg, Avi; Wirtz, Denis; Kiemen, Ashley | bioRxiv : the preprint server for biology | 38106004 | 2024 Apr 03 |
| Generative interpolation and restoration of images using deep learning for improved 3D tissue mapping. | Joshi, Saurabh; Forjaz, André; Han, Kyu Sang; Shen, Yu; Queiroga, Vasco; Xenes, Daniel; Matelsk, Jordan; Wester, Brock; Barrutia, Arrate Munoz; Kiemen, Ashley L; Wu, Pei-Hsun; Wirtz, Denis | bioRxiv : the preprint server for biology | 38496512 | 2024 Mar 28 |
| A longitudinal single-cell and spatial multiomic atlas of pediatric high-grade glioma. | Sussman, Jonathan H; Oldridge, Derek A; Yu, Wenbao; Chen, Chia-Hui; Zellmer, Abigail M; Rong, Jiazhen; Parvaresh-Rizi, Arianne; Thadi, Anusha; Xu, Jason; Bandyopadhyay, Shovik; Sun, Yusha; Wu, David; Emerson Hunter, C; Brosius, Stephanie; Ahn, Kyung Jin; Baxter, Amy E; Koptyra, Mateusz P; Vanguri, Rami S; McGrory, Stephanie; Resnick, Adam C; Storm, Phillip B; Amankulor, Nduka M; Santi, Mariarita; Viaene, Angela N; Zhang, Nancy; Raedt, Thomas De; Cole, Kristina; Tan, Kai | bioRxiv : the preprint server for biology | 38496580 | 2024 Mar 08 |
| Proteome-scale tissue mapping using mass spectrometry based on label-free and multiplexed workflows. | Kwon, Yumi; Woo, Jongmin; Yu, Fengchao; Williams, Sarah M; Markillie, Lye Meng; Moore, Ronald J; Nakayasu, Ernesto S; Chen, Jing; Campbell-Thompson, Martha; Mathews, Clayton E; Nesvizhskii, Alexey I; Qian, Wei-Jun; Zhu, Ying | bioRxiv : the preprint server for biology | 38496682 | 2024 Jul 10 |
| Heterogeneity of ovarian matrisome hydrogels elucidates factors that may influence follicle growth in vitro. | McDowell, Hannah B; Henning, Nathaniel F; Laronda, Monica M | Reproduction (Cambridge, England) | 38888996 | 2024 Sep 01 |
| SEraster: a rasterization preprocessing framework for scalable spatial omics data analysis. | Aihara, Gohta; Clifton, Kalen; Chen, Mayling; Li, Zhuoyan; Atta, Lyla; Miller, Brendan F; Satija, Rahul; Hickey, John W; Fan, Jean | Bioinformatics (Oxford, England) | 38902953 | 2024 Jul 01 |
| Application of Delta T1 maps for quantitative and objective assessment of extent of resection and survival prediction in glioblastoma. | Laing, Brandon R; Prah, Melissa A; Best, Benjamin J; Krucoff, Max O; Mueller, Wade M; Schmainda, Kathleen M | Neurosurgery practice | 38919518 | 2024 Mar |
| 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 |
| Pangenome graph construction from genome alignments with Minigraph-Cactus. | Hickey, Glenn; Monlong, Jean; Ebler, Jana; Novak, Adam M; Eizenga, Jordan M; Gao, Yan; Human Pangenome Reference Consortium; Marschall, Tobias; Li, Heng; Paten, Benedict | Nature biotechnology | 37165083 | 2024 Apr |
| Integration of spatial and single-cell data across modalities with weakly linked features. | Chen, Shuxiao; Zhu, Bokai; Huang, Sijia; Hickey, John W; Lin, Kevin Z; Snyder, Michael; Greenleaf, William J; Nolan, Garry P; Zhang, Nancy R; Ma, Zongming | Nature biotechnology | 37679544 | 2024 Jul |
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| Membrane marker selection for segmenting single cell spatial proteomics data. | Dayao, Monica T; Brusko, Maigan; Wasserfall, Clive; Bar-Joseph, Ziv | Nature communications | 35422106 | 2022 04 14 |
| A single-cell regulatory map of postnatal lung alveologenesis in humans and mice. | Duong, Thu Elizabeth; Wu, Yan; Sos, Brandon Chin; Dong, Weixiu; Limaye, Siddharth; Rivier, Lauraine H; Myers, Greg; Hagood, James S; Zhang, Kun | Cell genomics | 35434692 | 2022 Mar 09 |
| Human IL-10-producing B cells have diverse states that are induced from multiple B cell subsets. | Glass, Marla C; Glass, David R; Oliveria, John-Paul; Mbiribindi, Berenice; Esquivel, Carlos O; Krams, Sheri M; Bendall, Sean C; Martinez, Olivia M | Cell reports | 35443184 | 2022 04 19 |
| Proteoform-Selective Imaging of Tissues Using Mass Spectrometry. | Yang, Manxi; Hu, Hang; Su, Pei; Thomas, Paul M; Camarillo, Jeannie M; Greer, Joseph B; Early, Bryan P; Fellers, Ryan T; Kelleher, Neil L; Laskin, Julia | Angewandte Chemie (International ed. in English) | 35446460 | 2022 07 18 |
| Integrating transcription-factor abundance with chromatin accessibility in human erythroid lineage commitment. | Baskar, Reema; Chen, Amy F; Favaro, Patricia; Reynolds, Warren; Mueller, Fabian; Borges, Luciene; Jiang, Sizun; Park, Hyun Shin; Kool, Eric T; Greenleaf, William J; Bendall, Sean C | Cell reports methods | 35463156 | 2022 Mar 28 |
| Crowdsourced RNA design discovers diverse, reversible, efficient, self-contained molecular switches. | Andreasson, Johan O L; Gotrik, Michael R; Wu, Michelle J; Wayment-Steele, Hannah K; Kladwang, Wipapat; Portela, Fernando; Wellington-Oguri, Roger; Eterna Participants; Das, Rhiju; Greenleaf, William J | Proceedings of the National Academy of Sciences of the United States of America | 35471911 | 2022 05 03 |
| Computational tools for analyzing single-cell data in pluripotent cell differentiation studies. | Ding, Jun; Alavi, Amir; Ebrahimkhani, Mo R; Bar-Joseph, Ziv | Cell reports methods | 35474899 | 2021 Oct 25 |
| A complete pedigree-based graph workflow for rare candidate variant analysis. | Markello, Charles; Huang, Charles; Rodriguez, Alex; Carroll, Andrew; Chang, Pi-Chuan; Eizenga, Jordan; Markello, Thomas; Haussler, David; Paten, Benedict | Genome research | 35483961 | 2022 May |
| NEAT-seq: simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells. | Chen, Amy F; Parks, Benjamin; Kathiria, Arwa S; Ober-Reynolds, Benjamin; Goronzy, Jorg J; Greenleaf, William J | Nature methods | 35501385 | 2022 05 |
| Unilateral Radiation Therapy for Tonsillar Cancer: Treatment Outcomes in the Era of Human Papillomavirus, Positron-Emission Tomography, and Intensity Modulated Radiation Therapy. | Taku, Nicolette; Chronowski, Gregory; Brandon Gunn, G; Morrison, William H; Gross, Neil D; Moreno, Amy C; Ferrarotto, Renata; Frank, Steven J; Fuller, C David; Goepfert, Ryan P; Phan, Jack; Lai, Stephen Y; Reddy, Jay P; Rosenthal, David I; Garden, Adam S | International journal of radiation oncology, biology, physics | 35504500 | 2022 Aug 01 |
| PHGDH expression increases with progression of Alzheimer's disease pathology and symptoms. | Chen, Xu; Calandrelli, Riccardo; Girardini, John; Yan, Zhangming; Tan, Zhiqun; Xu, Xiangmin; Hiniker, Annie; Zhong, Sheng | Cell metabolism | 35508105 | 2022 05 03 |
| Multi-contrast computed tomography healthy kidney atlas. | Lee, Ho Hin; Tang, Yucheng; Xu, Kaiwen; Bao, Shunxing; Fogo, Agnes B; Harris, Raymond; de Caestecker, Mark P; Heinrich, Mattias; Spraggins, Jeffrey M; Huo, Yuankai; Landman, Bennett A | Computers in biology and medicine | 35533459 | 2022 07 |
| Deep learning identification of stiffness markers in breast cancer. | Sneider, Alexandra; Kiemen, Ashley; Kim, Joo Ho; Wu, Pei-Hsun; Habibi, Mehran; White, Marissa; Phillip, Jude M; Gu, Luo; Wirtz, Denis | Biomaterials | 35537336 | 2022 06 |
| Epigenetic Regulation of Heart-ECHS. | Gan, Lu; Pei, Liming | JACC. Basic to translational science | 35540104 | 2022 Apr |
| Viv: multiscale visualization of high-resolution multiplexed bioimaging data on the web. | Manz, Trevor; Gold, Ilan; Patterson, Nathan Heath; McCallum, Chuck; Keller, Mark S; Herr 2nd, Bruce W; Börner, Katy; Spraggins, Jeffrey M; Gehlenborg, Nils | Nature methods | 35545714 | 2022 May |
| Nuclear oligo hashing improves differential analysis of single-cell RNA-seq. | Kim, Hyeon-Jin; Booth, Greg; Saunders, Lauren; Srivatsan, Sanjay; McFaline-Figueroa, José L; Trapnell, Cole | Nature communications | 35562344 | 2022 May 13 |
| New Views of Old Proteins: Clarifying the Enigmatic Proteome. | Burnum-Johnson, Kristin E; Conrads, Thomas P; Drake, Richard R; Herr, Amy E; Iyengar, Ravi; Kelly, Ryan T; Lundberg, Emma; MacCoss, Michael J; Naba, Alexandra; Nolan, Garry P; Pevzner, Pavel A; Rodland, Karin D; Sechi, Salvatore; Slavov, Nikolai; Spraggins, Jeffrey M; Van Eyk, Jennifer E; Vidal, Marc; Vogel, Christine; Walt, David R; Kelleher, Neil L | Molecular & cellular proteomics : MCP | 35654359 | 2022 Jul |
| A reference tissue atlas for the human kidney. | Hansen, Jens; Sealfon, Rachel; Menon, Rajasree; Eadon, Michael T; Lake, Blue B; Steck, Becky; Anjani, Kavya; Parikh, Samir; Sigdel, Tara K; Zhang, Guanshi; Velickovic, Dusan; Barwinska, Daria; Alexandrov, Theodore; Dobi, Dejan; Rashmi, Priyanka; Otto, Edgar A; Rivera, Miguel; Rose, Michael P; Anderton, Christopher R; Shapiro, John P; Pamreddy, Annapurna; Winfree, Seth; Xiong, Yuguang; He, Yongqun; de Boer, Ian H; Hodgin, Jeffrey B; Barisoni, Laura; Naik, Abhijit S; Sharma, Kumar; Sarwal, Minnie M; Zhang, Kun; Himmelfarb, Jonathan; Rovin, Brad; El-Achkar, Tarek M; Laszik, Zoltan; He, John Cijiang; Dagher, Pierre C; Valerius, M Todd; Jain, Sanjay; Satlin, Lisa M; Troyanskaya, Olga G; Kretzler, Matthias; Iyengar, Ravi; Azeloglu, Evren U; Kidney Precision Medicine Project | Science advances | 35675394 | 2022 Jun 10 |
| Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer. | Becker, Winston R; Nevins, Stephanie A; Chen, Derek C; Chiu, Roxanne; Horning, Aaron M; Guha, Tuhin K; Laquindanum, Rozelle; Mills, Meredith; Chaib, Hassan; Ladabaum, Uri; Longacre, Teri; Shen, Jeanne; Esplin, Edward D; Kundaje, Anshul; Ford, James M; Curtis, Christina; Snyder, Michael P; Greenleaf, William J | Nature genetics | 35726067 | 2022 Jul |
| Unsupervised cell functional annotation for single-cell RNA-seq. | Li, Dongshunyi; Ding, Jun; Bar-Joseph, Ziv | Genome research | 35764397 | 2022 Jun 28 |
| High-Throughput Nano-DESI Mass Spectrometry Imaging of Biological Tissues Using an Integrated Microfluidic Probe. | Li, Xiangtang; Hu, Hang; Yin, Ruichuan; Li, Yingju; Sun, Xiaofei; Dey, Sudhansu K; Laskin, Julia | Analytical chemistry | 35770488 | 2022 07 12 |
| scSTEM: clustering pseudotime ordered single-cell data. | Song, Qi; Wang, Jingtao; Bar-Joseph, Ziv | Genome biology | 35799304 | 2022 07 07 |
| Ferroptosis turns 10: Emerging mechanisms, physiological functions, and therapeutic applications. | Stockwell, Brent R | Cell | 35803244 | 2022 07 07 |
| Hanging drop sample preparation improves sensitivity of spatial proteomics. | Kwon, Yumi; Piehowski, Paul D; Zhao, Rui; Sontag, Ryan L; Moore, Ronald J; Burnum-Johnson, Kristin E; Smith, Richard D; Qian, Wei-Jun; Kelly, Ryan T; Zhu, Ying | Lab on a chip | 35838077 | 2022 Jul 26 |
| Rapid Multivariate Analysis Approach to Explore Differential Spatial Protein Profiles in Tissue. | Sharman, Kavya; Patterson, Nathan Heath; Weiss, Andy; Neumann, Elizabeth K; Guiberson, Emma R; Ryan, Daniel J; Gutierrez, Danielle B; Spraggins, Jeffrey M; Van de Plas, Raf; Skaar, Eric P; Caprioli, Richard M | Journal of proteome research | 35849531 | 2023 May 05 |
| Overcoming Selection Bias In Synthetic Lethality Prediction. | Seale, Colm; Tepeli, Yasin; Gonçalves, Joana P | Bioinformatics (Oxford, England) | 35876858 | 2022 Jul 25 |
| Highly multiplexed, label-free proteoform imaging of tissues by individual ion mass spectrometry. | Su, Pei; McGee, John P; Durbin, Kenneth R; Hollas, Michael A R; Yang, Manxi; Neumann, Elizabeth K; Allen, Jamie L; Drown, Bryon S; Butun, Fatma Ayaloglu; Greer, Joseph B; Early, Bryan P; Fellers, Ryan T; Spraggins, Jeffrey M; Laskin, Julia; Camarillo, Jeannie M; Kafader, Jared O; Kelleher, Neil L | Science advances | 35947651 | 2022 Aug 12 |
| Revving an Engine of Human Metabolism: Activity Enhancement of Triosephosphate Isomerase via Hemi-Phosphorylation. | Schachner, Luis F; Soye, Benjamin Des; Ro, Soo; Kenney, Grace E; Ives, Ashley N; Su, Taojunfeng; Goo, Young Ah; Jewett, Michael C; Rosenzweig, Amy C; Kelleher, Neil L | ACS chemical biology | 35951581 | 2022 Aug 11 |
| Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: Results from the IMPACC study. | Ozonoff, Al; Schaenman, Joanna; Jayavelu, Naresh Doni; Milliren, Carly E; Calfee, Carolyn S; Cairns, Charles B; Kraft, Monica; Baden, Lindsey R; Shaw, Albert C; Krammer, Florian; van Bakel, Harm; Esserman, Denise A; Liu, Shanshan; Sesma, Ana Fernandez; Simon, Viviana; Hafler, David A; Montgomery, Ruth R; Kleinstein, Steven H; Levy, Ofer; Bime, Christian; Haddad, Elias K; Erle, David J; Pulendran, Bali; Nadeau, Kari C; Davis, Mark M; Hough, Catherine L; Messer, William B; Higuita, Nelson I Agudelo; Metcalf, Jordan P; Atkinson, Mark A; Brakenridge, Scott C; Corry, David; Kheradmand, Farrah; Ehrlich, Lauren I R; Melamed, Esther; McComsey, Grace A; Sekaly, Rafick; Diray-Arce, Joann; Peters, Bjoern; Augustine, Alison D; Reed, Elaine F; Altman, Matthew C; Becker, Patrice M; Rouphael, Nadine; IMPACC study group members | EBioMedicine | 35952496 | 2022 Sep |
| Spatial profiling of chromatin accessibility in mouse and human tissues. | Deng, Yanxiang; Bartosovic, Marek; Ma, Sai; Zhang, Di; Kukanja, Petra; Xiao, Yang; Su, Graham; Liu, Yang; Qin, Xiaoyu; Rosoklija, Gorazd B; Dwork, Andrew J; Mann, J John; Xu, Mina L; Halene, Stephanie; Craft, Joseph E; Leong, Kam W; Boldrini, Maura; Castelo-Branco, Gonçalo; Fan, Rong | Nature | 35978191 | 2022 09 |
| UNIFAN: A Tool for Unsupervised Single-Cell Clustering and Annotation. | Li, Dongshunyi; Ding, Jun; Bar-Joseph, Ziv | Journal of computational biology : a journal of computational molecular cell biology | 36036832 | 2022 Nov |
| Pharmacological inhibition and reversal of pancreatic acinar ductal metaplasia. | da Silva, Lais; Jiang, Jinmai; Perkins, Corey; Atanasova, Kalina Rosenova; Bray, Julie K; Bulut, Gamze; Azevedo-Pouly, Ana; Campbell-Thompson, Martha; Yang, Xiaozhi; Hakimjavadi, Hesamedin; Chamala, Srikar; Ratnayake, Ranjala; Gharaibeh, Raad Z; Li, Chenglong; Luesch, Hendrik; Schmittgen, Thomas D | Cell death discovery | 36055991 | 2022 Sep 02 |
| Enhanced Spatial Mapping of Histone Proteoforms in Human Kidney Through MALDI-MSI by High-Field UHMR-Orbitrap Detection. | Zemaitis, Kevin J; Veličković, Dušan; Kew, William; Fort, Kyle L; Reinhardt-Szyba, Maria; Pamreddy, Annapurna; Ding, Yanli; Kaushik, Dharam; Sharma, Kumar; Makarov, Alexander A; Zhou, Mowei; Paša-Tolić, Ljiljana | Analytical chemistry | 36067026 | 2022 09 20 |
| Incidence Trends of New-Onset Diabetes in Children and Adolescents Before and During the COVID-19 Pandemic: Findings From Florida. | Guo, Yi; Bian, Jiang; Chen, Aokun; Wang, Fei; Posgai, Amanda L; Schatz, Desmond A; Shenkman, Elizabeth A; Atkinson, Mark A | Diabetes | 36094294 | 2022 Dec 01 |
| CINS: Cell Interaction Network inference from Single cell expression data. | Yuan, Ye; Cosme Jr, Carlos; Adams, Taylor Sterling; Schupp, Jonas; Sakamoto, Koji; Xylourgidis, Nikos; Ruffalo, Matthew; Li, Jiachen; Kaminski, Naftali; Bar-Joseph, Ziv | PLoS computational biology | 36095011 | 2022 09 |
| Polyphony: An Interactive Transfer Learning Framework for Single-Cell Data Analysis. | Cheng, Furui; Keller, Mark S; Qu, Huamin; Gehlenborg, Nils; Wang, Qianwen | IEEE transactions on visualization and computer graphics | 36155452 | 2022 Sep 26 |
| GBZ file format for pangenome graphs. | Sirén, Jouni; Paten, Benedict | Bioinformatics (Oxford, England) | 36179091 | 2022 Nov 15 |
| Anatomic nomenclature and 3-dimensional regional model of the human ovary: call for a new paradigm. | O'Neill, Kathleen E; Maher, Jacqueline Y; Laronda, Monica M; Duncan, Francesca E; LeDuc, Richard D; Lujan, Marla E; Oktay, Kutluk H; Pouch, Alison M; Segars, James H; Tsui, Elizabeth L; Zelinski, Mary B; Halvorson, Lisa M; Gomez-Lobo, Veronica | American journal of obstetrics and gynecology | 36191605 | 2023 Mar |
| The expanding vistas of spatial transcriptomics. | Tian, Luyi; Chen, Fei; Macosko, Evan Z | Nature biotechnology | 36192637 | 2022 Oct 03 |
| Machine learning-assisted elucidation of CD81-CD44 interactions in promoting cancer stemness and extracellular vesicle integrity. | Ramos, Erika K; Tsai, Chia-Feng; Jia, Yuzhi; Cao, Yue; Manu, Megan; Taftaf, Rokana; Hoffmann, Andrew D; El-Shennawy, Lamiaa; Gritsenko, Marina A; Adorno-Cruz, Valery; Schuster, Emma J; Scholten, David; Patel, Dhwani; Liu, Xia; Patel, Priyam; Wray, Brian; Zhang, Youbin; Zhang, Shanshan; Moore, Ronald J; Mathews, Jeremy V; Schipma, Matthew J; Liu, Tao; Tokars, Valerie L; Cristofanilli, Massimo; Shi, Tujin; Shen, Yang; Dashzeveg, Nurmaa K; Liu, Huiping | eLife | 36193887 | 2022 Oct 04 |
| A Parallelization Strategy for the Time Efficient Analysis of Thousands of LC/MS Runs in High-Performance Computing Environment. | van Zalm, Patrick; Viodé, Arthur; Smolen, Kinga; Fatou, Benoit; Hayati, Arash Nemati; Schlaffner, Christoph N; Levy, Ofer; Steen, Judith; Steen, Hanno | Journal of proteome research | 36201825 | 2022 Nov 04 |
| Understanding islet dysfunction in type 2 diabetes through multidimensional pancreatic phenotyping: The Human Pancreas Analysis Program. | Shapira, Suzanne N; Naji, Ali; Atkinson, Mark A; Powers, Alvin C; Kaestner, Klaus H | Cell metabolism | 36206763 | 2022 Sep 30 |
| Light-Seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing. | Kishi, Jocelyn Y; Liu, Ninning; West, Emma R; Sheng, Kuanwei; Jordanides, Jack J; Serrata, Matthew; Cepko, Constance L; Saka, Sinem K; Yin, Peng | Nature methods | 36216958 | 2022 Nov |
| Spatial epitope barcoding reveals clonal tumor patch behaviors. | Rovira-Clavé, Xavier; Drainas, Alexandros P; Jiang, Sizun; Bai, Yunhao; Baron, Maya; Zhu, Bokai; Dallas, Alec E; Lee, Myung Chang; Chu, Theresa P; Holzem, Alessandra; Ayyagari, Ramya; Bhattacharya, Debadrita; McCaffrey, Erin F; Greenwald, Noah F; Markovic | Cancer cell | 36240778 | 2022 Nov 14 |
| Annotation of spatially resolved single-cell data with STELLAR. | Brbić, Maria; Cao, Kaidi; Hickey, John W; Tan, Yuqi; Snyder, Michael P; Nolan, Garry P; Leskovec, Jure | Nature methods | 36280720 | 2022 Nov |
| Supervised Deep Generation of High-Resolution Arterial Phase Computed Tomography Kidney Substructure Atlas. | Lee, Ho Hin; Tang, Yucheng; Bao, Shunxing; Yang, Qi; Xu, Xin; Fogo, Agnes B; Harris, Raymond; de Caestecker, Mark P; Spraggins, Jeffrey M; Heinrich, Mattias; Huo, Yuankai; Landman, Bennett A | Proceedings of SPIE--the International Society for Optical Engineering | 36303577 | 2022 Feb-Mar |
| Creating a common language for the subanatomy of the ovary. | Tsui, Elizabeth L; O'Neill, Kathleen E; LeDuc, Richard D; Shikanov, Ariella; Gomez-Lobo, Veronica; Laronda, Monica M | Biology of reproduction | 36308436 | 2023 Jan 14 |
| Single-cell spatial proteomic imaging for human neuropathology. | Vijayaragavan, Kausalia; Cannon, Bryan J; Tebaykin, Dmitry; Bossé, Marc; Baranski, Alex; Oliveria, J P; Bukhari, Syed A; Mrdjen, Dunja; Corces, M Ryan; McCaffrey, Erin F; Greenwald, Noah F; Sigal, Yari; Marquez, Diana; Khair, Zumana; Bruce, Trevor; Goldston, Mako; Bharadwaj, Anusha; Montine, Kathleen S; Angelo, R Michael; Montine, Thomas J; Bendall, Sean C | Acta neuropathologica communications | 36333818 | 2022 Nov 04 |
| Gestationally dependent immune organization at the maternal-fetal interface. | Moore, Amber R; Vivanco Gonzalez, Nora; Plummer, Katherine A; Mitchel, Olivia R; Kaur, Harleen; Rivera, Moises; Collica, Brian; Goldston, Mako; Filiz, Ferda; Angelo, Michael; Palmer, Theo D; Bendall, Sean C | Cell reports | 36384130 | 2022 Nov 15 |
| MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database. | Shao, Xinhao; Gomez, Clarissa D; Kapoor, Nandini; Considine, James M; Grams, Christopher; Gao, Yu Tom; Naba, Alexandra | Nucleic acids research | 36399478 | 2022 Nov 18 |
| Multiset multicover methods for discriminative marker selection. | Hasanaj, Euxhen; Alavi, Amir; Gupta, Anupam; Póczos, Barnabás; Bar-Joseph, Ziv | Cell reports methods | 36452867 | 2022 Nov 21 |
| An optimized approach and inflation media for obtaining complimentary mass spectrometry-based omics data from human lung tissue. | Lukowski, Jessica K; Olson, Heather; Velickovic, Marija; Wang, Juan; Kyle, Jennifer E; Kim, Young-Mo; Williams, Sarah M; Zhu, Ying; Huyck, Heidi L; McGraw, Matthew D; Poole, Cory; Rogers, Lisa; Misra, Ravi; Alexandrov, Theodore; Ansong, Charles; Pryhuber, Gloria S; Clair, Geremy; Adkins, Joshua N; Carson, James P; Anderton, Christopher R | Frontiers in molecular biosciences | 36465564 | 2022 |
| Long noncoding RNA LEENE promotes angiogenesis and ischemic recovery in diabetes models. | Tang, Xiaofang; Luo, Yingjun; Yuan, Dongqiang; Calandrelli, Riccardo; Malhi, Naseeb Kaur; Sriram, Kiran; Miao, Yifei; Lou, Chih-Hong; Tsark, Walter; Tapia, Alonso; Chen, Aleysha T; Zhang, Guangyu; Roeth, Daniel; Kalkum, Markus; Wang, Zhao V; Chien, Shu; N | The Journal of clinical investigation | 36512424 | 2023 Feb 01 |
| 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 |
| Evaluation of cell segmentation methods without reference segmentations. | Chen, Haoran; Murphy, Robert F | Molecular biology of the cell | 36515991 | 2023 May 15 |
| Nanobody-tethered transposition enables multifactorial chromatin profiling at single-cell resolution. | Stuart, Tim; Hao, Stephanie; Zhang, Bingjie; Mekerishvili, Levan; Landau, Dan A; Maniatis, Silas; Satija, Rahul; Raimondi, Ivan | Nature biotechnology | 36536150 | 2023 Jun |
| Senescent cell population with ZEB1 transcription factor as its main regulator promotes osteoarthritis in cartilage and meniscus. | Swahn, Hannah; Li, Kun; Duffy, Tomas; Olmer, Merissa; D'Lima, Darryl D; Mondala, Tony S; Natarajan, Padmaja; Head, Steven R; Lotz, Martin K | Annals of the rheumatic diseases | 36564153 | 2023 Mar |
| Machine-learning based investigation of prognostic indicators for oncological outcome of pancreatic ductal adenocarcinoma. | Chang, Jeremy; Liu, Yanan; Saey, Stephanie A; Chang, Kevin C; Shrader, Hannah R; Steckly, Kelsey L; Rajput, Maheen; Sonka, Milan; Chan, Carlos H F | Frontiers in oncology | 36568148 | 2022 |
| Spatially Resolved Top-Down Proteomics of Tissue Sections Based on a Microfluidic Nanodroplet Sample Preparation Platform. | Liao, Yen-Chen; Fulcher, James M; Degnan, David J; Williams, Sarah M; Bramer, Lisa M; Veličković, Dušan; Zemaitis, Kevin J; Veličković, Marija; Sontag, Ryan L; Moore, Ronald J; Paša-Tolić, Ljiljana; Zhu, Ying; Zhou, Mowei | Molecular & cellular proteomics : MCP | 36603806 | 2023 Feb |
| 193 nm Ultraviolet Photodissociation for the Characterization of Singly Charged Proteoforms Generated by MALDI. | Zemaitis, Kevin J; Zhou, Mowei; Kew, William; Paša-Tolić, Ljiljana | Journal of the American Society for Mass Spectrometry | 36622763 | 2023 Feb 01 |
| Haplotype-aware pantranscriptome analyses using spliced pangenome graphs. | Sibbesen, Jonas A; Eizenga, Jordan M; Novak, Adam M; Sirén, Jouni; Chang, Xian; Garrison, Erik; Paten, Benedict | Nature methods | 36646895 | 2023 Feb |
| A streamlined tandem tip-based workflow for sensitive nanoscale phosphoproteomics. | Tsai, Chia-Feng; Wang, Yi-Ting; Hsu, Chuan-Chih; Kitata, Reta Birhanu; Chu, Rosalie K; Velickovic, Marija; Zhao, Rui; Williams, Sarah M; Chrisler, William B; Jorgensen, Marda L; Moore, Ronald J; Zhu, Ying; Rodland, Karin D; Smith, Richard D; Wasserfall, Clive H; Shi, Tujin; Liu, Tao | Communications biology | 36653408 | 2023 Jan 18 |
| Human pancreatic capillaries and nerve fibers persist in type 1 diabetes despite beta cell loss. | Richardson, Tiffany M; Saunders, Diane C; Haliyur, Rachana; Shrestha, Shristi; Cartailler, Jean-Philippe; Reinert, Rachel B; Petronglo, Jenna; Bottino, Rita; Aramandla, Radhika; Bradley, Amber M; Jenkins, Regina; Phillips, Sharon; Kang, Hakmook; Human Pancreas Analysis Program; Caicedo, Alejandro; Powers, Alvin C; Brissova, Marcela | American journal of physiology. Endocrinology and metabolism | 36696598 | 2023 Mar 01 |
| A Multicompartmental Diffusion Model for Improved Assessment of Whole-Body Diffusion-weighted Imaging Data and Evaluation of Prostate Cancer Bone Metastases. | Conlin, Christopher C; Feng, Christine H; Digma, Leonardino A; Rodríguez-Soto, Ana E; Kuperman, Joshua M; Rakow-Penner, Rebecca; Karow, David S; White, Nathan S; Seibert, Tyler M; Hahn, Michael E; Dale, Anders M | Radiology. Imaging cancer | 36705559 | 2023 Jan |
| Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. | Kolmogorov, Mikhail; Billingsley, Kimberley J; Mastoras, Mira; Meredith, Melissa; Monlong, Jean; Lorig-Roach, Ryan; Asri, Mobin; Jerez, Pilar Alvarez; Malik, Laksh; Dewan, Ramita; Reed, Xylena; Genner, Rylee M; Daida, Kensuke; Behera, Sairam; Shafin, Kishwar; Pesout, Trevor; Prabakaran, Jeshuwin; Carnevali, Paolo; North American Brain Expression Consortium (NABEC); Yang, Jianzhi; Rhie, Arang; Scholz, Sonja W; Traynor, Bryan J; Miga, Karen H; Jain, Miten; Timp, Winston; Phillippy, Adam M; Chaisson, Mark; Sedlazeck, Fritz J; Blauwendraat, Cornelis; Paten, Benedict | bioRxiv : the preprint server for biology | 36711673 | 2023 Apr 05 |
| Integration of spatial and single-cell data across modalities with weak linkage. | Chen, Shuxiao; Zhu, Bokai; Huang, Sijia; Hickey, John W; Lin, Kevin Z; Snyder, Michael; Greenleaf, William J; Nolan, Garry P; Zhang, Nancy R; Ma, Zongming | bioRxiv : the preprint server for biology | 36711792 | 2023 Jan 16 |
| Segmenting functional tissue units across human organs using community-driven development of generalizable machine learning algorithms. | Jain, Yashvardhan; Godwin, Leah L; Joshi, Sripad; Mandarapu, Shriya; Le, Trang; Lindskog, Cecilia; Lundberg, Emma; Börner, Katy | bioRxiv : the preprint server for biology | 36711953 | 2023 Jan 06 |
| Multimodal characterization of antigen-specific CD8 + T cells across SARS-CoV-2 vaccination and infection. | Zhang, Bingjie; Upadhyay, Rabi; Hao, Yuhan; Samanovic, Marie I; Herati, Ramin S; Blair, John; Axelrad, Jordan; Mulligan, Mark J; Littman, Dan R; Satija, Rahul | bioRxiv : the preprint server for biology | 36747786 | 2023 Jan 24 |
| Optimal gap-affine alignment in O(s) space. | Marco-Sola, Santiago; Eizenga, Jordan M; Guarracino, Andrea; Paten, Benedict; Garrison, Erik; Moreto, Miquel | Bioinformatics (Oxford, England) | 36749013 | 2023 Feb 03 |
| Using single cell atlas data to reconstruct regulatory networks. | Song, Qi; Ruffalo, Matthew; Bar-Joseph, Ziv | Nucleic acids research | 36762475 | 2023 Apr 24 |
| Towards Universal Cell Embeddings: Integrating Single-cell RNA-seq Datasets across Species with SATURN. | Rosen, Yanay; Brbić, Maria; Roohani, Yusuf; Swanson, Kyle; Li, Ziang; Leskovec, Jure | bioRxiv : the preprint server for biology | 36778387 | 2023 Sep 24 |
| Super-resolution SRS microscopy with A-PoD. | Jang, Hongje; Li, Yajuan; Fung, Anthony A; Bagheri, Pegah; Hoang, Khang; Skowronska-Krawczyk, Dorota; Chen, Xiaoping; Wu, Jane Y; Bintu, Bogdan; Shi, Lingyan | Nature methods | 36797410 | 2023 Mar |
| Conundrums of choice of 'normal' kidney tissue for single cell studies. | Jain, Sanjay | Current opinion in nephrology and hypertension | 36811638 | 2023 May 01 |
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| Spatially Aware Transformer Networks for Contextual Prediction of Diabetic Nephropathy Progression from Whole Slide Images. | Shickel, Benjamin; Lucarelli, Nicholas; Rao, Adish S; Yun, Donghwan; Moon, Kyung Chul; Han, Seung Seok; Sarder, Pinaki | medRxiv : the preprint server for health sciences | 36865174 | 2023 Feb 23 |
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| Magnitude and kinetics of the human immune cell response associated with severe dengue progression by single-cell proteomics. | Robinson, Makeda L; Glass, David R; Duran, Veronica; Agudelo Rojas, Olga Lucia; Sanz, Ana Maria; Consuegra, Monika; Sahoo, Malaya Kumar; Hartmann, Felix J; Bosse, Marc; Gelvez, Rosa Margarita; Bueno, Nathalia; Pinsky, Benjamin A; Montoya, Jose G; Maecker, Holden; Estupiñan Cardenas, Maria Isabel; Villar Centeno, Luis Angel; Garrido, Elsa Marina Rojas; Rosso, Fernando; Bendall, Sean C; Einav, Shirit | Science advances | 36961888 | 2023 Mar 24 |
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| Multiomic Analysis and CRISPR Perturbation Screens Identify Endothelial Cell Programs and Novel Therapeutic Targets for Coronary Artery Disease. | Gupta, Rajat M; Schnitzler, Gavin R; Fang, Shi; Lee-Kim, Vivian S; Barry, Aurelie | Arteriosclerosis, thrombosis, and vascular biology | 36994731 | 2023 May |
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| Erratum. Integrated Physiology of the Exocrine and Endocrine Compartments in Pancreatic Diseases: Workshop Proceedings. Diabetes 2023;72:433-448. | Mastracci, Teresa L; Apte, Minoti; Amundadottir, Laufey T; Alvarsson, Alexandra; Artandi, Steven; Bellin, Melena D; Bernal-Mizrachi, Ernesto; Caicedo, Alejandro; Campbell-Thompson, Martha; Cruz-Monserrate, Zobeida; Ouaamari, Abdelfattah El; Gaulton, Kyle J; Geisz, Andrea; Goodarzi, Mark O; Hara, Manami; Hull-Meichle, Rebecca L; Kleger, Alexander; Klein, Alison P; Kopp, Janel L; Kulkarni, Rohit N; Muzumdar, Mandar D; Naren, Anjaparavanda P; Oakes, Scott A; Olesen, Søren S; Phelps, Edward A; Powers, Alvin C; Stabler, Cherie L; Tirkes, Temel; Whitcomb, David C; Yadav, Dhiraj; Yong, Jing; Zaghloul, Norann A; Pandol, Stephen J; Sander, Maike | Diabetes | 37116182 | 2023 Aug 01 |
| Matrisome AnalyzeR: A suite of tools to annotate and quantify ECM molecules in big datasets across organisms. | Petrov, Petar B; Considine, James M; Izzi, Valerio; Naba, Alexandra | bioRxiv : the preprint server for biology | 37131773 | 2023 Apr 20 |
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| High-Throughput Mass Spectrometry Imaging of Biological Systems: Current Approaches and Future Directions. | Jiang, Li-Xue; Yang, Manxi; Wali, Syeda Nazifa; Laskin, Julia | Trends in analytical chemistry : TRAC | 37206615 | 2023 Jun |
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| Bioorthogonal Chemical Imaging of Cell Metabolism Regulated by Aromatic Amino Acids. | Bagheri, Pegah; Hoang, Khang; Kuo, Chan-Yu; Trivedi, Hetvi; Jang, Hongje; Shi, Lingyan | Journal of visualized experiments : JoVE | 37246865 | 2023 May 12 |
| Polygenic prediction of preeclampsia and gestational hypertension. | Honigberg, Michael C; Truong, Buu; Khan, Raiyan R; Xiao, Brenda; Bhatta, Laxmi; Vy, Ha My T; Guerrero, Rafael F; Schuermans, Art; Selvaraj, Margaret Sunitha; Patel, Aniruddh P; Koyama, Satoshi; Cho, So Mi Jemma; Vellarikkal, Shamsudheen Karuthedath; Trinder, Mark; Urbut, Sarah M; Gray, Kathryn J; Brumpton, Ben M; Patil, Snehal; Zöllner, Sebastian; Antopia, Mariah C; Saxena, Richa; Nadkarni, Girish N; Do, Ron; Yan, Qi; Pe'er, Itsik; Verma, Shefali Setia; Gupta, Rajat M; Haas, David M; Martin, Hilary C; van Heel, David A; Laisk, Triin; Natarajan, Pradeep | Nature medicine | 37248299 | 2023 Jun |
| Dynamic glycoprotein hyposialylation promotes chemotherapy evasion and metastatic seeding of quiescent circulating tumor cell clusters in breast cancer. | Dashzeveg, Nurmaa K; Jia, Yuzhi; Zhang, Youbin; Gerratana, Lorenzo; Patel, Priyam; Shajahan, Asif; Dandar, Tsogbadrakh; Ramos, Erika K; Almubarak, Hannah F; Adorno-Cruz, Valery; Taftaf, Rokana; Schuster, Emma J; Scholten, David; Sokolowski, Michael T; Reduzzi, Carolina; El-Shennawy, Lamiaa; Hoffmann, Andrew D; Manai, Maroua; Zhang, Qiang; D'Amico, Paolo; Azadi, Parastoo; Colley, Karen J; Platanias, Leonidas C; Shah, Ami N; Gradishar, William J; Cristofanilli, Massimo; Muller, William A; Cobb, Brian A; Liu, Huiping | Cancer discovery | 37272843 | 2023 Jun 05 |
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| Correlating Deep Learning-Based Automated Reference Kidney Histomorphometry with Patient Demographics and Creatinine. | Ginley, Brandon; Lucarelli, Nicholas; Zee, Jarcy; Jain, Sanjay; Han, Seung Sook; Rodrigues, Luis; Ozrazgat-Baslanti, Tezcan; Wong, Michelle L; Nadkarni, Girish; Jen, Kuang-Yu; Sarder, Pinaki | bioRxiv : the preprint server for biology | 37292965 | 2023 May 18 |
| Tissue Mass Spectrometry: How Solid Is Our Future? | Unsihuay, Daisy; Phipps, William S; Paulovich, Amanda G; Chapman, Jessica R; Ducret, Axel; Eberlin, Livia S; Spraggins, Jeffrey M; Goodwin, Richard J A | Clinical chemistry | 37293883 | 2023 Jul 05 |
| Ex Vivo OCT-Based Multimodal Imaging of Human Donor Eyes for Research into Age-Related Macular Degeneration. | Messinger, Jeffrey D; Brinkmann, Max; Kimble, James A; Berlin, Andreas; Freund, K Bailey; Grossman, Gregory H; Ach, Thomas; Curcio, Christine A | Journal of visualized experiments : JoVE | 37306417 | 2023 May 26 |
| Semantic-Aware Contrastive Learning for Multi-Object Medical Image Segmentation. | Lee, Ho Hin; Tang, Yucheng; Yang, Qi; Yu, Xin; Cai, Leon Y; Remedios, Lucas W; Bao, Shunxing; Landman, Bennett A; Huo, Yuankai | IEEE journal of biomedical and health informatics | 37310834 | 2023 Sep |
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| Proteome Mapping of the Human Pancreatic Islet Microenvironment Reveals Endocrine-Exocrine Signaling Sphere of Influence. | Gosline, Sara J C; Veličković, Marija; Pino, James C; Day, Le Z; Attah, Isaac K; Swensen, Adam C; Danna, Vincent; Posso, Camilo; Rodland, Karin D; Chen, Jing; Matthews, Clayton E; Campbell-Thompson, Martha; Laskin, Julia; Burnum-Johnson, Kristin; Zhu, Ying; Piehowski, Paul D | Molecular & cellular proteomics : MCP | 37328065 | 2023 Aug |
| Surgical management of lymphedema: Does a microsurgeon's bias exist? | Friedman, Rosie; Ismail Aly, Mohamed Eldardiri; Singhal, Dhruv | Microsurgery | 37339916 | 2023 Sep |
| Proteome Landscapes of Human Hepatocellular Carcinoma and Intrahepatic Cholangiocarcinoma. | Yi, Xiao; Zhu, Jiang; Liu, Wei; Peng, Li; Lu, Cong; Sun, Ping; Huang, Lingling; Nie, Xiu; Huang, Shi'ang; Guo, Tiannan; Zhu, Yi | Molecular & cellular proteomics : MCP | 37353004 | 2023 Aug |
| Potential and risks of artificial intelligence models: Common in medicine practice and special in pediatric urology. | Wen, Yi; Di, Huajie | Journal of pediatric urology | 37355343 | 2023 Oct |
| Deriving spatial features from in situ proteomics imaging to enhance cancer survival analysis. | Dayao, Monica T; Trevino, Alexandro; Kim, Honesty; Ruffalo, Matthew; D'Angio, H Blaize; Preska, Ryan; Duvvuri, Umamaheswar; Mayer, Aaron T; Bar-Joseph, Ziv | Bioinformatics (Oxford, England) | 37387167 | 2023 Jun 30 |
| IgM N-glycosylation correlates with COVID-19 severity and rate of complement deposition. | Haslund-Gourley, Benjamin; Woloszcuk, Kyra; Hou, Jintong; Connors, Jennifer; Cusimano, Gina; Bell, Mathew; Taramangalam, Bhavani; Fourati, Slim; Mege, Nathan; Bernui, Mariana; Altman, Matthew; Krammer, Florian; van Bakel, Harm; Maecker, Holden; Wigdahl, Brian; Cairns, Charles; Haddad, Elias; Comunale, Mary | Research square | 37398192 | 2023 Jun 02 |
| SCS: cell segmentation for high-resolution spatial transcriptomics. | Chen, Hao; Li, Dongshunyi; Bar-Joseph, Ziv | bioRxiv : the preprint server for biology | 37398213 | 2023 Jun 16 |
| Ubiquitin-specific peptidase 22 controls integrin-dependent cancer cell stemness and metastasis. | Liu, Kun; Gao, Qiong; Jia, Yuzhi; Wei, Juncheng; Chaudhuri, Shuvam; Wang, Shengnan; Tang, Amy; Mani, Nikita; Iyer, Radhika; Cheng, Yang; Gao, Beixue; Lu, Weiyuan; Sun, Zhaolin; Liu, Huiping; Fang, Deyu | Research square | 37398311 | 2023 Jun 16 |
| Spatial proteomics reveals human microglial states shaped by anatomy and neuropathology. | Mrdjen, Dunja; Amouzgar, Meelad; Cannon, Bryan; Liu, Candace; Spence, Angie; McCaffrey, Erin; Bharadwaj, Anusha; Tebaykin, Dmitry; Bukhari, Syed; Hartmann, Felix J; Kagel, Adam; Vijayaragavan, Kausalia; Oliveria, John Paul; Yakabi, Koya; Serrano, Geidy E; Corrada, Maria M; Kawas, Claudia H; Camacho, Christine; Bosse, Marc; Tibshirani, Robert; Beach, Thomas G; Angelo, Michael; Montine, Thomas; Bendall, Sean C | Research square | 37398389 | 2023 Jun 02 |
| Modelling Human Post-Implantation Development via Extra-Embryonic Niche Engineering. | Hislop, Joshua; Alavi, Amir; Song, Qi; Schoenberger, Rayna; Kamyar, Keshavarz F; LeGraw, Ryan; Velazquez, Jeremy; Mokhtari, Tahere; Taheri, Mohammad Nasser; Rytel, Matthew; de Sousa Lopes, Susana M Chuva; Watkins, Simon; Stolz, Donna; Kiani, Samira; Sozen, Berna; Bar-Joseph, Ziv; Ebrahimkhani, Mo R | bioRxiv : the preprint server for biology | 37398391 | 2023 Jul 24 |
| Joint profiling of multiplex chromatin interactions, gene expression, and RNA-chromatin associations in single cells of the human brain. | Luo, Zhifei; Wen, Xingzhao; Zhao, Wenxin; Nguyen, Tri C; Wan, Xueyi; Richard, John Lalith Charles; Zhong, Sheng | bioRxiv : the preprint server for biology | 37425846 | 2023 Jun 28 |
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| SCS: cell segmentation for high-resolution spatial transcriptomics. | Chen, Hao; Li, Dongshunyi; Bar-Joseph, Ziv | Nature methods | 37429992 | 2023 Aug |
| Nanospray Desorption Electrospray Ionization (Nano-DESI) Mass Spectrometry Imaging with High Ion Mobility Resolution. | Jiang, Li-Xue; Hernly, Emerson; Hu, Hang; Hilger, Ryan T; Neuweger, Heiko; Yang, Manxi; Laskin, Julia | Journal of the American Society for Mass Spectrometry | 37463098 | 2023 Aug 02 |
| Unsupervised Registration Refinement for Generating Unbiased Eye Atlas. | Lee, Ho Hin; Tang, Yucheng; Bao, Shunxing; Yang, Qi; Xu, Xin; Schey, Kevin L; Spraggins, Jeffrey M; Huo, Yuankai; Landman, Bennett A | Proceedings of SPIE--the International Society for Optical Engineering | 37465097 | 2023 Feb |
| A spatially anchored transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease. | Canela, Victor Hugo; Bowen, William S; Ferreira, Ricardo Melo; Syed, Farooq; Lingeman, James E; Sabo, Angela R; Barwinska, Daria; Winfree, Seth; Lake, Blue B; Cheng, Ying-Hua; Gaut, Joseph P; Ferkowicz, Michael; LaFavers, Kaice A; Zhang, Kun; Coe, Fredric L; Worcester, Elaine; Kidney Precision Medicine Project; Jain, Sanjay; Eadon, Michael T; Williams Jr, James C; El-Achkar, Tarek M | Nature communications | 37468493 | 2023 Jul 19 |
| Anatomical structures, cell types, and biomarkers of the healthy human blood vasculature. | Boppana, Avinash; Lee, Sujin; Malhotra, Rajeev; Halushka, Marc; Gustilo, Katherine S; Quardokus, Ellen M; Herr 2nd, Bruce W; Börner, Katy; Weber, Griffin M | Scientific data | 37468503 | 2023 Jul 19 |
| Segmentation of human functional tissue units in support of a Human Reference Atlas. | Jain, Yashvardhan; Godwin, Leah L; Ju, Yingnan; Sood, Naveksha; Quardokus, Ellen M; Bueckle, Andreas; Longacre, Teri; Horning, Aaron; Lin, Yiing; Esplin, Edward D; Hickey, John W; Snyder, Michael P; Patterson, Nathan Heath; Spraggins, Jeffrey M; Börner, Katy | Communications biology | 37468557 | 2023 Jul 19 |
| An atlas of healthy and injured cell states and niches in the human kidney. | Lake, Blue B; Menon, Rajasree; Winfree, Seth; Hu, Qiwen; Melo Ferreira, Ricardo; Kalhor, Kian; Barwinska, Daria; Otto, Edgar A; Ferkowicz, Michael; Diep, Dinh; Plongthongkum, Nongluk; Knoten, Amanda; Urata, Sarah; Mariani, Laura H; Naik, Abhijit S; Eddy, Sean; Zhang, Bo; Wu, Yan; Salamon, Diane; Williams, James C; Wang, Xin; Balderrama, Karol S; Hoover, Paul J; Murray, Evan; Marshall, Jamie L; Noel, Teia; Vijayan, Anitha; Hartman, Austin; Chen, Fei; Waikar, Sushrut S; Rosas, Sylvia E; Wilson, Francis P; Palevsky, Paul M; Kiryluk, Krzysztof; Sedor, John R; Toto, Robert D; Parikh, Chirag R; Kim, Eric H; Satija, Rahul; Greka, Anna; Macosko, Evan Z; Kharchenko, Peter V; Gaut, Joseph P; Hodgin, Jeffrey B; KPMP Consortium; Eadon, Michael T; Dagher, Pierre C; El-Achkar, Tarek M; Zhang, Kun; Kretzler, Matthias; Jain, Sanjay | Nature | 37468583 | 2023 Jul |
| Organization of the human intestine at single-cell resolution. | Hickey, John W; Becker, Winston R; Nevins, Stephanie A; Horning, Aaron; Perez, Almudena Espin; Zhu, Chenchen; Zhu, Bokai; Wei, Bei; Chiu, Roxanne; Chen, Derek C; Cotter, Daniel L; Esplin, Edward D; Weimer, Annika K; Caraccio, Chiara; Venkataraaman, Vishal; Schürch, Christian M; Black, Sarah; Brbić, Maria; Cao, Kaidi; Chen, Shuxiao; Zhang, Weiruo; Monte, Emma; Zhang, Nancy R; Ma, Zongming; Leskovec, Jure; Zhang, Zhengyan; Lin, Shin; Longacre, Teri; Plevritis, Sylvia K; Lin, Yiing; Nolan, Garry P; Greenleaf, William J; Snyder, Michael | Nature | 37468586 | 2023 Jul |
| Organ Mapping Antibody Panels: a community resource for standardized multiplexed tissue imaging. | Quardokus, Ellen M; Saunders, Diane C; McDonough, Elizabeth; Hickey, John W; Werlein, Christopher; Surrette, Christine; Rajbhandari, Presha; Casals, Anna Martinez; Tian, Hua; Lowery, Lisa; Neumann, Elizabeth K; Björklund, Frida; Neelakantan, Taruna V; Croteau, Josh; Wiblin, Anne E; Fisher, Jeremy; Livengood, April J; Dowell, Karen G; Silverstein, Jonathan C; Spraggins, Jeffrey M; Pryhuber, Gloria S; Deutsch, Gail; Ginty, Fiona; Nolan, Garry P; Melov, Simon; Jonigk, Danny; Caldwell, Michael A; Vlachos, Ioannis S; Muller, Werner; Gehlenborg, Nils; Stockwell, Brent R; Lundberg, Emma; Snyder, Michael P; Germain, Ronald N; Camarillo, Jeannie M; Kelleher, Neil L; Börner, Katy; Radtke, Andrea J | Nature methods | 37468619 | 2023 Aug |
| KRAS(G12D) drives lepidic adenocarcinoma through stem-cell reprogramming. | Juul, Nicholas H; Yoon, Jung-Ki; Martinez, Marina C; Rishi, Neha; Kazadaeva, Yana I; Morri, Maurizio; Neff, Norma F; Trope, Winston L; Shrager, Joseph B; Sinha, Rahul; Desai, Tushar J | Nature | 37468622 | 2023 Jul |
| Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP). | Jain, Sanjay; Pei, Liming; Spraggins, Jeffrey M; Angelo, Michael; Carson, James P; Gehlenborg, Nils; Ginty, Fiona; Gonçalves, Joana P; Hagood, James S; Hickey, John W; Kelleher, Neil L; Laurent, Louise C; Lin, Shin; Lin, Yiing; Liu, Huiping; Naba, Alexandra; Nakayasu, Ernesto S; Qian, Wei-Jun; Radtke, Andrea; Robson, Paul; Stockwell, Brent R; Van de Plas, Raf; Vlachos, Ioannis S; Zhou, Mowei; HuBMAP Consortium; Börner, Katy; Snyder, Michael P | Nature cell biology | 37468756 | 2023 Aug |
| 3D reconstruction of skin and spatial mapping of immune cell density, vascular distance and effects of sun exposure and aging. | Ghose, Soumya; Ju, Yingnan; McDonough, Elizabeth; Ho, Jonhan; Karunamurthy, Arivarasan; Chadwick, Chrystal; Cho, Sanghee; Rose, Rachel; Corwin, Alex; Surrette, Christine; Martinez, Jessica; Williams, Eric; Sood, Anup; Al-Kofahi, Yousef; Falo Jr, Louis D; Börner, Katy; Ginty, Fiona | Communications biology | 37468758 | 2023 Jul 19 |
| Non-Linear Lymphatic Anatomy in Breast Cancer Patients Prior to Axillary Lymph Node Dissection: A Risk Factor For Lymphedema Development. | Kinney, JacqueLyn R; Friedman, Rosie; Kim, Erin; Tillotson, Elizabeth; Shillue, Kathy; Lee, Bernard T; Singhal, Dhruv | Journal of mammary gland biology and neoplasia | 37480365 | 2023 Jul 22 |
| Editorial: Global excellence in inflammatory diseases: North America 2021. | Kusner, Linda L; Misra, Ravi S; Lucas, Rudolf | Frontiers in immunology | 37483602 | 2023 |
| Integrated single-cell chromatin and transcriptomic analyses of human scalp identify gene-regulatory programs and critical cell types for hair and skin diseases. | Ober-Reynolds, Benjamin; Wang, Chen; Ko, Justin M; Rios, Eon J; Aasi, Sumaira Z; Davis, Mark M; Oro, Anthony E; Greenleaf, William J | Nature genetics | 37500727 | 2023 Aug |
| Segmenting functional tissue units across human organs using community-driven development of generalizable machine learning algorithms. | Jain, Yashvardhan; Godwin, Leah L; Joshi, Sripad; Mandarapu, Shriya; Le, Trang; Lindskog, Cecilia; Lundberg, Emma; Börner, Katy | Nature communications | 37537179 | 2023 Aug 03 |
| Matrisome AnalyzeR - a suite of tools to annotate and quantify ECM molecules in big datasets across organisms. | Petrov, Petar B; Considine, James M; Izzi, Valerio; Naba, Alexandra | Journal of cell science | 37555624 | 2023 Sep 01 |
| Systematic Sampling of the Female Reproductive System for Molecular Characterization. | Fisher, Stephen A; Grijalva, Marielena; Guo, Rong; Johnston, Sarah A; Laurent, Louise C; Nguyen, Hieu; Renz, John; Rosario, Jean G; Rudich, Steven; Gregory, Brian D; Kim, Junhyong; O'Neill, Kathleen | Current protocols | 37584588 | 2023 Aug |
| Segmentation quality assessment by automated detection of erroneous surface regions in medical images. | Zaman, Fahim Ahmed; Zhang, Lichun; Zhang, Honghai; Sonka, Milan; Wu, Xiaodong | Computers in biology and medicine | 37591161 | 2023 Sep |
| Edematous Dermal Thickening on Magnetic Resonance Imaging as a Biomarker for Lymphatic Surgical Outcomes. | Kinney, JacqueLyn R; Babapour, Sara; Kim, Erin; Friedman, Rosie; Singhal, Dhruv; Lee, Bernard T; Tsai, Leo L | Medicina (Kaunas, Lithuania) | 37629659 | 2023 Jul 26 |
| Mapping Human Tissues with Highly Multiplexed RNA in situ Hybridization. | Kalhor, Kian; Chen, Chien-Ju; Lee, Ho Suk; Cai, Matthew; Nafisi, Mahsa; Que, Richard; Palmer, Carter; Yuan, Yixu; Zhang, Yida; Song, Jinghui; Knoten, Amanda; Lake, Blue B; Gaut, Joseph P; Keene, Dirk; Lein, Ed; Kharchenko, Peter V; Chun, Jerold; Jain, Sanjay; Fan, Jian-Bing; Zhang, Kun | bioRxiv : the preprint server for biology | 37645998 | 2023 Aug 19 |
| Unravelling human hematopoietic progenitor cell diversity through association with intrinsic regulatory factors. | Favaro, Patricia; Glass, David R; Borges, Luciene; Baskar, Reema; Reynolds, Warren; Ho, Daniel; Bruce, Trevor; Tebaykin, Dmitry; Scanlon, Vanessa M; Shestopalov, Ilya; Bendall, Sean C | bioRxiv : the preprint server for biology | 37693547 | 2023 Aug 30 |
| Transcriptomic profiling of tissue environments critical for post-embryonic patterning and morphogenesis of zebrafish skin. | Aman, Andrew J; Saunders, Lauren M; Carr, August A; Srivatasan, Sanjay; Eberhard, Colten; Carrington, Blake; Watkins-Chow, Dawn; Pavan, William J; Trapnell, Cole; Parichy, David M | eLife | 37695017 | 2023 Sep 11 |
| Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. | Kolmogorov, Mikhail; Billingsley, Kimberley J; Mastoras, Mira; Meredith, Melissa; Monlong, Jean; Lorig-Roach, Ryan; Asri, Mobin; Alvarez Jerez, Pilar; Malik, Laksh; Dewan, Ramita; Reed, Xylena; Genner, Rylee M; Daida, Kensuke; Behera, Sairam; Shafin, Kishwar; Pesout, Trevor; Prabakaran, Jeshuwin; Carnevali, Paolo; Yang, Jianzhi; Rhie, Arang; Scholz, Sonja W; Traynor, Bryan J; Miga, Karen H; Jain, Miten; Timp, Winston; Phillippy, Adam M; Chaisson, Mark; Sedlazeck, Fritz J; Blauwendraat, Cornelis; Paten, Benedict | Nature methods | 37710018 | 2023 Oct |
| Early cancer detection by SERS spectroscopy and machine learning. | Shi, Lingyan; Li, Yajuan; Li, Zhi | Light, science & applications | 37714845 | 2023 Sep 15 |
| Multimodal single-cell datasets characterize antigen-specific CD8+ T cells across SARS-CoV-2 vaccination and infection. | Zhang, Bingjie; Upadhyay, Rabi; Hao, Yuhan; Samanovic, Marie I; Herati, Ramin S; Blair, John D; Axelrad, Jordan; Mulligan, Mark J; Littman, Dan R; Satija, Rahul | Nature immunology | 37735591 | 2023 Oct |
| Local read haplotagging enables accurate long-read small variant calling. | Kolesnikov, Alexey; Cook, Daniel; Nattestad, Maria; McNulty, Brandy; Gorzynski, John; Goenka, Sneha; Ashley, Euan A; Jain, Miten; Miga, Karen H; Paten, Benedict; Chang, Pi-Chuan; Carroll, Andrew; Shafin, Kishwar | bioRxiv : the preprint server for biology | 37745389 | 2023 Sep 12 |
| Navigating the kidney organoid: insights into assessment and enhancement of nephron function. | Tabibzadeh, Nahid; Satlin, Lisa M; Jain, Sanjay; Morizane, Ryuji | American journal of physiology. Renal physiology | 37767571 | 2023 Dec 01 |
| Rapid Setup of Tissue Microarray and Tiled Area Imaging on the Multiplexed Ion Beam Imaging Microscope using the Tile/SED/Array Interface. | Piyadasa, Hadeesha; Oberlton, Benjamin; Kong, Alex; Camacho Fullaway, Christine; Reddy Varra, Sricharan; Sowers, Cameron; Tsai, Albert G | Journal of visualized experiments : JoVE | 37782085 | 2023 Sep 15 |
| A monolithic microfluidic probe for ambient mass spectrometry imaging of biological tissues. | Jiang, Li-Xue; Polack, Matthias; Li, Xiangtang; Yang, Manxi; Belder, Detlev; Laskin, Julia | Lab on a chip | 37782224 | 2023 Oct 24 |
| Mechano-induced homotypic patterned domain formation by monocytes. | Wirtz, Denis; Du, Wenxuan; Zhu, Jingyi; Wu, Yufei; Kiemen, Ashley; Wan, Zeqi; Hanna, Eban; Sun, Sean | Research square | 37790337 | 2023 Sep 22 |
| The Role of Endothelial Cells in Atherosclerosis: Insights from Genetic Association Studies. | Pepin, Mark E; Gupta, Rajat | The American journal of pathology | 37827214 | 2023 Oct 10 |
| High-resolution integrated microfluidic probe for mass spectrometry imaging of biological tissues. | Li, Xiangtang; Hu, Hang; Laskin, Julia | Analytica chimica acta | 37827646 | 2023 Oct 23 |
| Automated imaging and identification of proteoforms directly from ovarian cancer tissue. | McGee, John P; Su, Pei; Durbin, Kenneth R; Hollas, Michael A R; Bateman, Nicholas W; Maxwell, G Larry; Conrads, Thomas P; Fellers, Ryan T; Melani, Rafael D; Camarillo, Jeannie M; Kafader, Jared O; Kelleher, Neil L | Nature communications | 37838706 | 2023 Oct 14 |
| Functional Tissue Units in the Human Reference Atlas. | Bidanta, Supriya; Börner, Katy; Herr 2nd, Bruce W; Nagy, Marcell; Gustilo, Katherine S; Bajema, Rachel; Maier, Libby; Molontay, Roland; Weber, Griffin | bioRxiv : the preprint server for biology | 37905079 | 2023 Oct 26 |
| Identification and targeting of treatment resistant progenitor populations in T-cell Acute Lymphoblastic Leukemia. | Tan, Kai; Xu, Jason; Chen, Changya; Vincent, Tiffaney; Pölönen, Petri; Hu, Jianzhong; Yoshimura, Satoshi; Yu, Wenbao; Sussman, Jonathan; Chen, Chia-Hui; Li, Elizabeth; Diorio, Caroline; Shraim, Rawan; Newman, Haley; Uppuluri, Lahari; Li, Alexander; Chen, Gregory; Bandyopadhyay, Shovik; Wu, David; Ding, Yang-Yang; Xu, Jessica; Lim, Tristan; Hsu, Miles; Thadi, Anusha; Ahn, Kyung Jin; Wu, Chi-Yun; Peng, Jacqueline; Sun, Yusha; Wang, Alice; Mehta, Rushabh; Frank, David; Meyer, Lauren; Loh, Mignon; Raetz, Elizabeth; Chen, Zhiguo; Wood, Brent; Devidas, Meenakshi; Dunsmore, Kimberly; Winter, Stuart; Chang, Ti-Cheng; Wu, Gang; Pounds, Stanley; Zhang, Nancy; Carroll, William; Hunger, Stephen; Bernt, Kathrin; Yang, Jun; Mullighan, Charles; Teachey, David | Research square | 37961674 | 2023 Oct 30 |
| Dimension-agnostic and granularity-based spatially variable gene identification using BSP. | Wang, Juexin; Li, Jinpu; Kramer, Skyler T; Su, Li; Chang, Yuzhou; Xu, Chunhui; Eadon, Michael T; Kiryluk, Krzysztof; Ma, Qin; Xu, Dong | Nature communications | 37963892 | 2023 Nov 14 |
| Correlating Deep Learning-Based Automated Reference Kidney Histomorphometry with Patient Demographics and Creatinine. | Lucarelli, Nicholas; Ginley, Brandon; Zee, Jarcy; Mimar, Sayat; Paul, Anindya S; Jain, Sanjay; Han, Seung Seok; Rodrigues, Luis; Ozrazgat-Baslanti, Tezcan; Wong, Michelle L; Nadkarni, Girish; Clapp, William L; Jen, Kuang-Yu; Sarder, Pinaki | Kidney360 | 37966063 | 2023 Dec 01 |
| Multimodal imaging of metabolic activities for distinguishing subtypes of breast cancer. | Li, Zhi; Nguyen, Chloe; Jang, Hongje; Hoang, David; Min, SoeSu; Ackerstaff, Ellen; Koutcher, Jason A; Shi, Lingyan | Biomedical optics express | 38021123 | 2023 Nov 01 |
| Human mobility networks reveal increased segregation in large cities. | Nilforoshan, Hamed; Looi, Wenli; Pierson, Emma; Villanueva, Blanca; Fishman, Nic; Chen, Yiling; Sholar, John; Redbird, Beth; Grusky, David; Leskovec, Jure | Nature | 38030732 | 2023 Dec |
| Author Correction: Automated imaging and identification of proteoforms directly from ovarian cancer tissue. | McGee, John P; Su, Pei; Durbin, Kenneth R; Hollas, Michael A R; Bateman, Nicholas W; Maxwell, G Larry; Conrads, Thomas P; Fellers, Ryan T; Melani, Rafael D; Camarillo, Jeannie M; Kafader, Jared O; Kelleher, Neil L | Nature communications | 38040721 | 2023 Dec 01 |
| Advances in Imaging Mass Spectrometry for Biomedical and Clinical Research. | Djambazova, Katerina V; van Ardenne, Jacqueline M; Spraggins, Jeffrey M | Trends in analytical chemistry : TRAC | 38045023 | 2023 Dec |
| A Foundation Model for Cell Segmentation. | Israel, Uriah; Marks, Markus; Dilip, Rohit; Li, Qilin; Schwartz, Morgan; Pradhan, Elora; Pao, Edward; Li, Shenyi; Pearson-Goulart, Alexander; Perona, Pietro; Gkioxari, Georgia; Barnowski, Ross; Yue, Yisong; Van Valen, David | bioRxiv : the preprint server for biology | 38045277 | 2023 Nov 20 |
| DRAVA: Aligning Human Concepts with Machine Learning Latent Dimensions for the Visual Exploration of Small Multiples. | Wang, Qianwen; L'Yi, Sehi; Gehlenborg, Nils | Proceedings of the SIGCHI conference on human factors in computing systems. CHI Conference | 38074525 | 2023 Apr |
| T cell-mediated curation and restructuring of tumor tissue coordinates an effective immune response. | Hickey, John W; Haist, Maximillian; Horowitz, Nina; Caraccio, Chiara; Tan, Yuqi; Rech, Andrew J; Baertsch, Marc-Andrea; Rovira-Clavé, Xavier; Zhu, Bokai; Vazquez, Gustavo; Barlow, Graham; Agmon, Eran; Goltsev, Yury; Sunwoo, John B; Covert, Markus; Nolan, | Cell reports | 38085642 | 2023 Dec 26 |
| Modelling post-implantation human development to yolk sac blood emergence. | Hislop, Joshua; Song, Qi; Keshavarz F, Kamyar; Alavi, Amir; Schoenberger, Rayna; LeGraw, Ryan; Velazquez, Jeremy J; Mokhtari, Tahere; Taheri, Mohammad Naser; Rytel, Matthew; Chuva de Sousa Lopes, Susana M; Watkins, Simon; Stolz, Donna; Kiani, Samira; Soze | Nature | 38092041 | 2024 Feb |
| Integrating Multiplexed Imaging and Multiscale Modeling Identifies Tumor Phenotype Transformation as a Critical Component of Therapeutic T Cell Efficacy. | Hickey, John W; Agmon, Eran; Horowitz, Nina; Lamore, Matthew; Sunwoo, John; Covert, Markus; Nolan, Garry P | bioRxiv : the preprint server for biology | 38106218 | 2023 Dec 08 |
| Personalized Pangenome References. | Sirén, Jouni; Eskandar, Parsa; Ungaro, Matteo Tommaso; Hickey, Glenn; Eizenga, Jordan M; Novak, Adam M; Chang, Xian; Chang, Pi-Chuan; Kolmogorov, Mikhail; Carroll, Andrew; Monlong, Jean; Paten, Benedict | bioRxiv : the preprint server for biology | 38168361 | 2023 Dec 15 |
| Lysolipids are prominent in subretinal drusenoid deposits, a high-risk phenotype in age-related macular degeneration. | Anderson, David M G; Kotnala, Ankita; Migas, Lukasz G; Patterson, Nathan Heath; Tideman, Léonore; Cao, Dongfeng; Adhikari, Bibek; Messinger, Jeffrey D; Ach, Thomas; Tortorella, Sara; Van de Plas, Raf; Curcio, Christine A; Schey, Kevin L | Frontiers in ophthalmology | 38186747 | 2023 |
| scResolve: Recovering single cell expression profiles from multi-cellular spatial transcriptomics. | Chen, Hao; Lee, Young Je; Ovando, Jose A; Rosas, Lorena; Rojas, Mauricio; Mora, Ana L; Bar-Joseph, Ziv; Lugo-Martinez, Jose | bioRxiv : the preprint server for biology | 38187629 | 2023 Dec 19 |
| Unsupervised and supervised discovery of tissue cellular neighborhoods from cell phenotypes. | Hu, Yuxuan; Rong, Jiazhen; Xu, Yafei; Xie, Runzhi; Peng, Jacqueline; Gao, Lin; Tan, Kai | Nature methods | 38191930 | 2024 Jan 08 |
| Host-Microbe Multi-omic Profiling Identifies a Unique Program of COVID-19 Inflammatory Dysregulation in Solid Organ Transplant Recipients. | Langelier, Charles; Pickering, Harry; Schaenman, Joanna; Phan, Hoang; Maguire, Cole; Tsitsiklis, Alexandra; Rouphael, Nadine; Higuita, Nelson; Atkinson, Mark; Breckenridge, Scott; Fung, Monica; Messer, William; IMPACC Network; Salehi-Rad, Ramin; Altman, M | Research square | 38196658 | 2023 Dec 20 |
| Spatial top-down proteomics for the functional characterization of human kidney. | Zemaitis, Kevin J; Fulcher, James M; Kumar, Rashmi; Degnan, David J; Lewis, Logan A; Liao, Yen-Chen; Veličković, Marija; Williams, Sarah M; Moore, Ronald J; Bramer, Lisa M; Veličković, Dušan; Zhu, Ying; Zhou, Mowei; Paša-Tolić, Ljiljana | bioRxiv : the preprint server for biology | 38405958 | 2024 Feb 13 |
| Proteome-scale tissue mapping using mass spectrometry based on label-free and multiplexed workflows. | Kwon, Yumi; Woo, Jongmin; Yu, Fengchao; Williams, Sarah M; Markillie, Lye Meng; Moore, Ronald J; Nakayasu, Ernesto S; Chen, Jing; Campbell-Thompson, Martha; Mathews, Clayton E; Nesvizhskii, Alexey I; Qia, Wei-Jun; Zhu, Ying | bioRxiv : the preprint server for biology | 38496682 | 2024 Mar 04 |
