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4. Author Correction: Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP)

Author

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, Börner, Katy, and Snyder, Michael P.

Published
2024
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5. Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP)

Author

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, Börner, Katy, and Snyder, Michael P.

Published
2023
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10. A strain-programmed patch for the healing of diabetic wounds

Author

Theocharidis, Georgios, Yuk, Hyunwoo, Roh, Heejung, Wang, Liu, Mezghani, Ikram, Wu, Jingjing, Kafanas, Antonios, Contreras, Mauricio, Sumpio, Brandon, Li, Zhuqing, Wang, Enya, Chen, Lihong, Guo, Chuan Fei, Jayaswal, Navin, Katopodi, Xanthi-Leda, Kalavros, Nikolaos, Nabzdyk, Christoph S., Vlachos, Ioannis S., Veves, Aristidis, and Zhao, Xuanhe

Published
2022
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13. The potential use of artificial intelligence for venous thromboembolism prophylaxis and management: clinician and healthcare informatician perspectives

Author

Lam, Barbara D., primary, Dodge, Laura E., additional, Zerbey, Sabrina, additional, Robertson, William, additional, Rosovsky, Rachel P., additional, Lake, Leslie, additional, Datta, Siddhant, additional, Elavakanar, Pavania, additional, Adamski, Alys, additional, Reyes, Nimia, additional, Abe, Karon, additional, Vlachos, Ioannis S., additional, Zwicker, Jeffrey I., additional, and Patell, Rushad, additional

Published
2024
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14. Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility

Author

Patsopoulos, Nikolaos A, Baranzini, Sergio E, Santaniello, Adam, Shoostari, Parisa, Cotsapas, Chris, Wong, Garrett, Beecham, Ashley H, James, Tojo, Replogle, Joseph, Vlachos, Ioannis S, McCabe, Cristin, Pers, Tune H, Brandes, Aaron, White, Charles, Keenan, Brendan, Cimpean, Maria, Winn, Phoebe, Panteliadis, Ioannis-Pavlos, Robbins, Allison, Andlauer, Till FM, Zarzycki, Onigiusz, Dubois, Bénédicte, Goris, An, Søndergaard, Helle Bach, Sellebjerg, Finn, Sorensen, Per Soelberg, Ullum, Henrik, Thørner, Lise Wegner, Saarela, Janna, Cournu-Rebeix, Isabelle, Damotte, Vincent, Fontaine, Bertrand, Guillot-Noel, Lena, Lathrop, Mark, Vukusic, Sandra, Berthele, Achim, Pongratz, Viola, Buck, Dorothea, Gasperi, Christiane, Graetz, Christiane, Grummel, Verena, Hemmer, Bernhard, Hoshi, Muni, Knier, Benjamin, Korn, Thomas, Lill, Christina M, Luessi, Felix, Mühlau, Mark, Zipp, Frauke, Dardiotis, Efthimios, Agliardi, Cristina, Amoroso, Antonio, Barizzone, Nadia, Benedetti, Maria D, Bernardinelli, Luisa, Cavalla, Paola, Clarelli, Ferdinando, Comi, Giancarlo, Cusi, Daniele, Esposito, Federica, Ferrè, Laura, Galimberti, Daniela, Guaschino, Clara, Leone, Maurizio A, Martinelli, Vittorio, Moiola, Lucia, Salvetti, Marco, Sorosina, Melissa, Vecchio, Domizia, Zauli, Andrea, Santoro, Silvia, Mancini, Nicasio, Zuccalà, Miriam, Mescheriakova, Julia, van Duijn, Cornelia, Bos, Steffan D, Celius, Elisabeth G, Spurkland, Anne, Comabella, Manuel, Montalban, Xavier, Alfredsson, Lars, Bomfim, Izaura L, Gomez-Cabrero, David, Hillert, Jan, Jagodic, Maja, Lindén, Magdalena, Piehl, Fredrik, Jelčić, Ilijas, Martin, Roland, Sospedra, Mirela, Baker, Amie, Ban, Maria, Hawkins, Clive, Hysi, Pirro, Kalra, Seema, Karpe, Fredrik, Khadake, Jyoti, Lachance, Genevieve, Molyneux, Paul, and Neville, Matthew

Subjects
Neurosciences, Brain Disorders, Multiple Sclerosis, Human Genome, Autoimmune Disease, Clinical Research, Genetics, Neurodegenerative, Aetiology, 2.1 Biological and endogenous factors, Inflammatory and immune system, Neurological, Case-Control Studies, Cell Cycle Proteins, Chromosome Mapping, Chromosomes, Human, X, GTPase-Activating Proteins, Gene Frequency, Genetic Loci, Genome-Wide Association Study, Genomics, Humans, Inheritance Patterns, Major Histocompatibility Complex, Microglia, Polymorphism, Single Nucleotide, Quantitative Trait Loci, RNA-Seq, Transcriptome, International Multiple Sclerosis Genetics Consortium, General Science & Technology
Abstract

We analyzed genetic data of 47,429 multiple sclerosis (MS) and 68,374 control subjects and established a reference map of the genetic architecture of MS that includes 200 autosomal susceptibility variants outside the major histocompatibility complex (MHC), one chromosome X variant, and 32 variants within the extended MHC. We used an ensemble of methods to prioritize 551 putative susceptibility genes that implicate multiple innate and adaptive pathways distributed across the cellular components of the immune system. Using expression profiles from purified human microglia, we observed enrichment for MS genes in these brain-resident immune cells, suggesting that these may have a role in targeting an autoimmune process to the central nervous system, although MS is most likely initially triggered by perturbation of peripheral immune responses.

Published
2019

18. Single cell transcriptomic landscape of diabetic foot ulcers

Author

Theocharidis, Georgios, Thomas, Beena E., Sarkar, Debasree, Mumme, Hope L., Pilcher, William J. R., Dwivedi, Bhakti, Sandoval-Schaefer, Teresa, Sîrbulescu, Ruxandra F., Kafanas, Antonios, Mezghani, Ikram, Wang, Peng, Lobao, Antonio, Vlachos, Ioannis S., Dash, Biraja, Hsia, Henry C., Horsley, Valerie, Bhasin, Swati S., Veves, Aristidis, and Bhasin, Manoj

Published
2022
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21. COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets

Author

Delorey, Toni M., Ziegler, Carly G. K., Heimberg, Graham, Normand, Rachelly, Yang, Yiming, Segerstolpe, Åsa, Abbondanza, Domenic, Fleming, Stephen J., Subramanian, Ayshwarya, Montoro, Daniel T., Jagadeesh, Karthik A., Dey, Kushal K., Sen, Pritha, Slyper, Michal, Pita-Juárez, Yered H., Phillips, Devan, Biermann, Jana, Bloom-Ackermann, Zohar, Barkas, Nikolaos, Ganna, Andrea, Gomez, James, Melms, Johannes C., Katsyv, Igor, Normandin, Erica, Naderi, Pourya, Popov, Yury V., Raju, Siddharth S., Niezen, Sebastian, Tsai, Linus T.-Y., Siddle, Katherine J., Sud, Malika, Tran, Victoria M., Vellarikkal, Shamsudheen K., Wang, Yiping, Amir-Zilberstein, Liat, Atri, Deepak S., Beechem, Joseph, Brook, Olga R., Chen, Jonathan, Divakar, Prajan, Dorceus, Phylicia, Engreitz, Jesse M., Essene, Adam, Fitzgerald, Donna M., Fropf, Robin, Gazal, Steven, Gould, Joshua, Grzyb, John, Harvey, Tyler, Hecht, Jonathan, Hether, Tyler, Jané-Valbuena, Judit, Leney-Greene, Michael, Ma, Hui, McCabe, Cristin, McLoughlin, Daniel E., Miller, Eric M., Muus, Christoph, Niemi, Mari, Padera, Robert, Pan, Liuliu, Pant, Deepti, Pe’er, Carmel, Pfiffner-Borges, Jenna, Pinto, Christopher J., Plaisted, Jacob, Reeves, Jason, Ross, Marty, Rudy, Melissa, Rueckert, Erroll H., Siciliano, Michelle, Sturm, Alexander, Todres, Ellen, Waghray, Avinash, Warren, Sarah, Zhang, Shuting, Zollinger, Daniel R., Cosimi, Lisa, Gupta, Rajat M., Hacohen, Nir, Hibshoosh, Hanina, Hide, Winston, Price, Alkes L., Rajagopal, Jayaraj, Tata, Purushothama Rao, Riedel, Stefan, Szabo, Gyongyi, Tickle, Timothy L., Ellinor, Patrick T., Hung, Deborah, Sabeti, Pardis C., Novak, Richard, Rogers, Robert, Ingber, Donald E., Jiang, Z. Gordon, Juric, Dejan, Babadi, Mehrtash, Farhi, Samouil L., Izar, Benjamin, Stone, James R., Vlachos, Ioannis S., Solomon, Isaac H., Ashenberg, Orr, Porter, Caroline B. M., Li, Bo, Shalek, Alex K., Villani, Alexandra-Chloé, Rozenblatt-Rosen, Orit, and Regev, Aviv

Published
2021
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22. RNAcentral: a comprehensive database of non-coding RNA sequences

Author

Petrov, Anton I, Kay, Simon JE, Kalvari, Ioanna, Howe, Kevin L, Gray, Kristian A, Bruford, Elspeth A, Kersey, Paul J, Cochrane, Guy, Finn, Robert D, Bateman, Alex, Kozomara, Ana, Griffiths-Jones, Sam, Frankish, Adam, Zwieb, Christian W, Lau, Britney Y, Williams, Kelly P, Chan, Patricia P, Lowe, Todd M, Cannone, Jamie J, Gutell, Robin, Machnicka, Magdalena A, Bujnicki, Janusz M, Yoshihama, Maki, Kenmochi, Naoya, Chai, Benli, Cole, James R, Szymanski, Maciej, Karlowski, Wojciech M, Wood, Valerie, Huala, Eva, Berardini, Tanya Z, Zhao, Yi, Chen, Runsheng, Zhu, Weimin, Paraskevopoulou, Maria D, Vlachos, Ioannis S, Hatzigeorgiou, Artemis G, Ma, Lina, Zhang, Zhang, Puetz, Joern, Stadler, Peter F, McDonald, Daniel, Basu, Siddhartha, Fey, Petra, Engel, Stacia R, Cherry, J Michael, Volders, Pieter-Jan, Mestdagh, Pieter, Wower, Jacek, Clark, Michael B, Quek, Xiu Cheng, and Dinger, Marcel E

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Generic health relevance, Animals, Databases, Nucleic Acid, Genomics, Humans, Nucleotides, RNA, Untranslated, Sequence Analysis, RNA, Species Specificity, The RNAcentral Consortium, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides a single entry point for accessing ncRNA sequences of all ncRNA types from all organisms. Since its launch in 2014, RNAcentral has integrated twelve new resources, taking the total number of collaborating database to 22, and began importing new types of data, such as modified nucleotides from MODOMICS and PDB. We created new species-specific identifiers that refer to unique RNA sequences within a context of single species. The website has been subject to continuous improvements focusing on text and sequence similarity searches as well as genome browsing functionality. All RNAcentral data is provided for free and is available for browsing, bulk downloads, and programmatic access at http://rnacentral.org/.

Published
2017

23. A Comparative Analysis of Imaging-Based Spatial Transcriptomics Platforms

Author

Cook, David P., primary, Jensen, Kirk B., additional, Wise, Kellie, additional, Roach, Michael J., additional, Dezem, Felipe Segato, additional, Ryan, Natalie K., additional, Zamojski, Michel, additional, Vlachos, Ioannis S., additional, Knott, Simon R. V., additional, Butler, Lisa M., additional, Wrana, Jeffrey L., additional, Banovich, Nicholas E., additional, Plummer, Jasmine T., additional, and Martelotto, Luciano G., additional

Published
2023
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25. Data from Randomized Phase II Trial of Dendritic Cell/Myeloma Fusion Vaccine with Lenalidomide Maintenance after Upfront Autologous Hematopoietic Cell Transplantation for Multiple Myeloma: BMT CTN 1401

Author

Chung, David J., primary, Shah, Nina, primary, Wu, Juan, primary, Logan, Brent, primary, Bisharat, Lina, primary, Callander, Natalie, primary, Cheloni, Giulia, primary, Anderson, Kenneth, primary, Chodon, Thinle, primary, Dhakal, Binod, primary, Devine, Steve, primary, Somaiya Dutt, Poorvi, primary, Efebera, Yvonne, primary, Geller, Nancy, primary, Ghiasuddin, Haider, primary, Hematti, Peiman, primary, Holmberg, Leona, primary, Howard, Alan, primary, Johnson, Bryon, primary, Karagkouni, Dimitra, primary, Lazarus, Hillard M., primary, Malek, Ehsan, primary, McCarthy, Philip, primary, McKenna, David, primary, Mendizabal, Adam, primary, Nooka, Ajay, primary, Munshi, Nikhil, primary, O'Donnell, Lynn, primary, Rapoport, Aaron P., primary, Reese, Jane, primary, Rosenblatt, Jacalyn, primary, Soiffer, Robert, primary, Stroopinsky, Dina, primary, Uhl, Lynne, primary, Vlachos, Ioannis S., primary, Waller, Edmund K., primary, Young, James W., primary, Pasquini, Marcelo C., primary, and Avigan, David, primary

Published
2023
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26. Attitudes towards venous thromboembolism prophylaxis including the use of artificial intelligence

Author

Lam, Barbara D., primary, Zerbey, Sabrina, additional, Pinson, Amanda, additional, Robertson, William, additional, Rosovsky, Rachel P., additional, Lake, Leslie, additional, Dodge, Laura E., additional, Adamski, Alys, additional, Reyes, Nimia, additional, Abe, Karon, additional, Vlachos, Ioannis S., additional, Zwicker, Jeffrey I., additional, Schonberg, Mara, additional, and Patell, Rushad, additional

Published
2023
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29. MicroRNA-22 Is a Key Regulator of Lipid and Metabolic Homeostasis

Author

Panella, Riccardo, primary, Petri, Andreas, additional, Desai, Bhavna N., additional, Fagoonee, Sharmila, additional, Cotton, Cody A., additional, Nguyen, Piercen K., additional, Lundin, Eric M., additional, Wagshal, Alexandre, additional, Wang, Da-Zhi, additional, Näär, Anders M., additional, Vlachos, Ioannis S., additional, Maratos-Flier, Eleftheria, additional, Altruda, Fiorella, additional, Kauppinen, Sakari, additional, and Paolo Pandolfi, Pier, additional

Published
2023
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30. Study Representativeness Table 1 from Randomized Phase II Trial of Dendritic Cell/Myeloma Fusion Vaccine with Lenalidomide Maintenance after Upfront Autologous Hematopoietic Cell Transplantation for Multiple Myeloma: BMT CTN 1401

Author

Chung, David J., primary, Shah, Nina, primary, Wu, Juan, primary, Logan, Brent, primary, Bisharat, Lina, primary, Callander, Natalie, primary, Cheloni, Giulia, primary, Anderson, Kenneth, primary, Chodon, Thinle, primary, Dhakal, Binod, primary, Devine, Steve, primary, Somaiya Dutt, Poorvi, primary, Efebera, Yvonne, primary, Geller, Nancy, primary, Ghiasuddin, Haider, primary, Hematti, Peiman, primary, Holmberg, Leona, primary, Howard, Alan, primary, Johnson, Bryon, primary, Karagkouni, Dimitra, primary, Lazarus, Hillard M., primary, Malek, Ehsan, primary, McCarthy, Philip, primary, McKenna, David, primary, Mendizabal, Adam, primary, Nooka, Ajay, primary, Munshi, Nikhil, primary, O'Donnell, Lynn, primary, Rapoport, Aaron P., primary, Reese, Jane, primary, Rosenblatt, Jacalyn, primary, Soiffer, Robert, primary, Stroopinsky, Dina, primary, Uhl, Lynne, primary, Vlachos, Ioannis S., primary, Waller, Edmund K., primary, Young, James W., primary, Pasquini, Marcelo C., primary, and Avigan, David, primary

Published
2023
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31. Figure S1 from Randomized Phase II Trial of Dendritic Cell/Myeloma Fusion Vaccine with Lenalidomide Maintenance after Upfront Autologous Hematopoietic Cell Transplantation for Multiple Myeloma: BMT CTN 1401

Author

Chung, David J., primary, Shah, Nina, primary, Wu, Juan, primary, Logan, Brent, primary, Bisharat, Lina, primary, Callander, Natalie, primary, Cheloni, Giulia, primary, Anderson, Kenneth, primary, Chodon, Thinle, primary, Dhakal, Binod, primary, Devine, Steve, primary, Somaiya Dutt, Poorvi, primary, Efebera, Yvonne, primary, Geller, Nancy, primary, Ghiasuddin, Haider, primary, Hematti, Peiman, primary, Holmberg, Leona, primary, Howard, Alan, primary, Johnson, Bryon, primary, Karagkouni, Dimitra, primary, Lazarus, Hillard M., primary, Malek, Ehsan, primary, McCarthy, Philip, primary, McKenna, David, primary, Mendizabal, Adam, primary, Nooka, Ajay, primary, Munshi, Nikhil, primary, O'Donnell, Lynn, primary, Rapoport, Aaron P., primary, Reese, Jane, primary, Rosenblatt, Jacalyn, primary, Soiffer, Robert, primary, Stroopinsky, Dina, primary, Uhl, Lynne, primary, Vlachos, Ioannis S., primary, Waller, Edmund K., primary, Young, James W., primary, Pasquini, Marcelo C., primary, and Avigan, David, primary

Published
2023
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32. Venous thromboembolism prophylaxis for hospitalized adult patients: A survey of U.S. healthcare providers on attitudes and practices

Author

Lam, Barbara D., primary, Dodge, Laura E., additional, Datta, Siddhant, additional, Rosovsky, Rachel P., additional, Robertson, William, additional, Lake, Leslie, additional, Reyes, Nimia, additional, Adamski, Alys, additional, Abe, Karon, additional, Panoff, Samuel, additional, Pinson, Amanda, additional, Elavalakanar, Pavania, additional, Vlachos, Ioannis S., additional, Zwicker, Jeffrey I., additional, and Patell, Rushad, additional

Published
2023
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33. Organ Mapping Antibody Panels: a community resource for standardized multiplexed tissue imaging

Author

Quardokus, Ellen M., primary, Saunders, Diane C., additional, McDonough, Elizabeth, additional, Hickey, John W., additional, Werlein, Christopher, additional, Surrette, Christine, additional, Rajbhandari, Presha, additional, Casals, Anna Martinez, additional, Tian, Hua, additional, Lowery, Lisa, additional, Neumann, Elizabeth K., additional, Björklund, Frida, additional, Neelakantan, Taruna V., additional, Croteau, Josh, additional, Wiblin, Anne E., additional, Fisher, Jeremy, additional, Livengood, April J., additional, Dowell, Karen G., additional, Silverstein, Jonathan C., additional, Spraggins, Jeffrey M., additional, Pryhuber, Gloria S., additional, Deutsch, Gail, additional, Ginty, Fiona, additional, Nolan, Garry P., additional, Melov, Simon, additional, Jonigk, Danny, additional, Caldwell, Michael A., additional, Vlachos, Ioannis S., additional, Muller, Werner, additional, Gehlenborg, Nils, additional, Stockwell, Brent R., additional, Lundberg, Emma, additional, Snyder, Michael P., additional, Germain, Ronald N., additional, Camarillo, Jeannie M., additional, Kelleher, Neil L., additional, Börner, Katy, additional, and Radtke, Andrea J., additional

Published
2023
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34. Randomized Trial of a Personalized Dendritic Cell Vaccine after Autologous Stem Cell Transplant for Multiple Myeloma

Author

Chung, David J., primary, Shah, Nina, additional, Wu, Juan, additional, Logan, Brent, additional, Bisharat, Lina, additional, Callander, Natalie, additional, Cheloni, Giulia, additional, Anderson, Kenneth, additional, Chodon, Thinle, additional, Dhakal, Binod, additional, Devine, Steven, additional, Somaiya Dutt, Poorvi, additional, Efebera, Yvonne, additional, Geller, Nancy, additional, Ghiasuddin, Haider, additional, Hematti, Peiman, additional, Holmberg, Leona, additional, Howard, Alan, additional, Johnson, Bryon, additional, Karagkouni, Dimitra, additional, Lazarus, Hillard M., additional, Malek, Ehsan, additional, McCarthy, Philip, additional, McKenna, David, additional, Mendizabal, Adam, additional, Nooka, Ajay, additional, Munshi, Nikhil, additional, O'Donnell, Lynn, additional, Rapoport, Aaron P., additional, Reese, Jane, additional, Rosenblatt, Jacalyn, additional, Soiffer, Robert, additional, Stroopinsky, Dina, additional, Uhl, Lynne, additional, Vlachos, Ioannis S., additional, Waller, Edmund K., additional, Young, James W., additional, Pasquini, Marcelo C., additional, and Avigan, David, additional

Published
2023
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35. Defective synaptic connectivity and axonal neuropathology in a human iPSC-based model of familial Parkinson’s disease

Author

Kouroupi, Georgia, Taoufik, Era, Vlachos, Ioannis S., Tsioras, Konstantinos, Antoniou, Nasia, Papastefanaki, Florentia, Chroni-Tzartou, Dafni, Wrasidlo, Wolfgang, Bohl, Delphine, Stellas, Dimitris, Politis, Panagiotis K., Vekrellis, Kostas, Papadimitriou, Dimitra, Stefanis, Leonidas, Bregestovski, Piotr, Hatzigeorgiou, Artemis G., Masliah, Eliezer, and Matsas, Rebecca

Published
2017

37. Supplementary Table TS1 from Comprehensive Characterization of the Multiple Myeloma Immune Microenvironment Using Integrated scRNA-seq, CyTOF, and CITE-seq Analysis

Author

Yao, Lijun, primary, Jayasinghe, Reyka G., primary, Lee, Brian H., primary, Bhasin, Swati S., primary, Pilcher, William, primary, Doxie, Deon Bryant, primary, Gonzalez-Kozlova, Edgar, primary, Dasari, Surendra, primary, Fiala, Mark A., primary, Pita-Juarez, Yered, primary, Strausbauch, Michael, primary, Kelly, Geoffrey, primary, Thomas, Beena E., primary, Kumar, Shaji K., primary, Cho, Hearn Jay, primary, Anderson, Emilie, primary, Wendl, Michael C., primary, Dawson, Travis, primary, D'souza, Darwin, primary, Oh, Stephen T., primary, Cheloni, Giulia, primary, Li, Ying, primary, DiPersio, John F., primary, Rahman, Adeeb H., primary, Dhodapkar, Kavita M., primary, Kim-Schulze, Seunghee, primary, Vij, Ravi, primary, Vlachos, Ioannis S., primary, Mehr, Shaadi, primary, Hamilton, Mark, primary, Auclair, Daniel, primary, Kourelis, Taxiarchis, primary, Avigan, David, primary, Dhodapkar, Madhav V., primary, Gnjatic, Sacha, primary, Bhasin, Manoj K., primary, and Ding, Li, primary

Published
2023
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38. Supplementary Figure FS2 from Comprehensive Characterization of the Multiple Myeloma Immune Microenvironment Using Integrated scRNA-seq, CyTOF, and CITE-seq Analysis

Author

Yao, Lijun, primary, Jayasinghe, Reyka G., primary, Lee, Brian H., primary, Bhasin, Swati S., primary, Pilcher, William, primary, Doxie, Deon Bryant, primary, Gonzalez-Kozlova, Edgar, primary, Dasari, Surendra, primary, Fiala, Mark A., primary, Pita-Juarez, Yered, primary, Strausbauch, Michael, primary, Kelly, Geoffrey, primary, Thomas, Beena E., primary, Kumar, Shaji K., primary, Cho, Hearn Jay, primary, Anderson, Emilie, primary, Wendl, Michael C., primary, Dawson, Travis, primary, D'souza, Darwin, primary, Oh, Stephen T., primary, Cheloni, Giulia, primary, Li, Ying, primary, DiPersio, John F., primary, Rahman, Adeeb H., primary, Dhodapkar, Kavita M., primary, Kim-Schulze, Seunghee, primary, Vij, Ravi, primary, Vlachos, Ioannis S., primary, Mehr, Shaadi, primary, Hamilton, Mark, primary, Auclair, Daniel, primary, Kourelis, Taxiarchis, primary, Avigan, David, primary, Dhodapkar, Madhav V., primary, Gnjatic, Sacha, primary, Bhasin, Manoj K., primary, and Ding, Li, primary

Published
2023
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39. Data from Comprehensive Characterization of the Multiple Myeloma Immune Microenvironment Using Integrated scRNA-seq, CyTOF, and CITE-seq Analysis

Author

Yao, Lijun, primary, Jayasinghe, Reyka G., primary, Lee, Brian H., primary, Bhasin, Swati S., primary, Pilcher, William, primary, Doxie, Deon Bryant, primary, Gonzalez-Kozlova, Edgar, primary, Dasari, Surendra, primary, Fiala, Mark A., primary, Pita-Juarez, Yered, primary, Strausbauch, Michael, primary, Kelly, Geoffrey, primary, Thomas, Beena E., primary, Kumar, Shaji K., primary, Cho, Hearn Jay, primary, Anderson, Emilie, primary, Wendl, Michael C., primary, Dawson, Travis, primary, D'souza, Darwin, primary, Oh, Stephen T., primary, Cheloni, Giulia, primary, Li, Ying, primary, DiPersio, John F., primary, Rahman, Adeeb H., primary, Dhodapkar, Kavita M., primary, Kim-Schulze, Seunghee, primary, Vij, Ravi, primary, Vlachos, Ioannis S., primary, Mehr, Shaadi, primary, Hamilton, Mark, primary, Auclair, Daniel, primary, Kourelis, Taxiarchis, primary, Avigan, David, primary, Dhodapkar, Madhav V., primary, Gnjatic, Sacha, primary, Bhasin, Manoj K., primary, and Ding, Li, primary

Published
2023
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44. Artificial intelligence in the prediction of venous thromboembolism: A systematic review and pooled analysis.

Author

Chiasakul, Thita, Lam, Barbara D., McNichol, Megan, Robertson, William, Rosovsky, Rachel P., Lake, Leslie, Vlachos, Ioannis S., Adamski, Alys, Reyes, Nimia, Abe, Karon, Zwicker, Jeffrey I., and Patell, Rushad

Subjects
MACHINE learning, THROMBOEMBOLISM, ARTIFICIAL intelligence, GENETIC programming, SUPPORT vector machines
Abstract

Background: Accurate diagnostic and prognostic predictions of venous thromboembolism (VTE) are crucial for VTE management. Artificial intelligence (AI) enables autonomous identification of the most predictive patterns from large complex data. Although evidence regarding its performance in VTE prediction is emerging, a comprehensive analysis of performance is lacking. Aims: To systematically review the performance of AI in the diagnosis and prediction of VTE and compare it to clinical risk assessment models (RAMs) or logistic regression models. Methods: A systematic literature search was performed using PubMed, MEDLINE, EMBASE, and Web of Science from inception to April 20, 2021. Search terms included "artificial intelligence" and "venous thromboembolism." Eligible criteria were original studies evaluating AI in the prediction of VTE in adults and reporting one of the following outcomes: sensitivity, specificity, positive predictive value, negative predictive value, or area under receiver operating curve (AUC). Risks of bias were assessed using the PROBAST tool. Unpaired t‐test was performed to compare the mean AUC from AI versus conventional methods (RAMs or logistic regression models). Results: A total of 20 studies were included. Number of participants ranged from 31 to 111 888. The AI‐based models included artificial neural network (six studies), support vector machines (four studies), Bayesian methods (one study), super learner ensemble (one study), genetic programming (one study), unspecified machine learning models (two studies), and multiple machine learning models (five studies). Twelve studies (60%) had both training and testing cohorts. Among 14 studies (70%) where AUCs were reported, the mean AUC for AI versus conventional methods were 0.79 (95% CI: 0.74–0.85) versus 0.61 (95% CI: 0.54–0.68), respectively (p <.001). However, the good to excellent discriminative performance of AI methods is unlikely to be replicated when used in clinical practice, because most studies had high risk of bias due to missing data handling and outcome determination. Conclusion: The use of AI appears to improve the accuracy of diagnostic and prognostic prediction of VTE over conventional risk models; however, there was a high risk of bias observed across studies. Future studies should focus on transparent reporting, external validation, and clinical application of these models. [ABSTRACT FROM AUTHOR]

Published
2023
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45. PanomiR: a systems biology framework for analysis of multi-pathway targeting by miRNAs.

Author

Yeganeh, Pourya Naderi, Teo, Yue Y, Karagkouni, Dimitra, Pita-Juárez, Yered, Morgan, Sarah L, Slack, Frank J, Vlachos, Ioannis S, and Hide, Winston A

Subjects
SYSTEMS biology, MICRORNA, GENE expression, COMPUTATIONAL biology, SYNTHETIC biology, RNA regulation, FUNCTIONAL groups
Abstract

Charting microRNA (miRNA) regulation across pathways is key to characterizing their function. Yet, no method currently exists that can quantify how miRNAs regulate multiple interconnected pathways or prioritize them for their ability to regulate coordinate transcriptional programs. Existing methods primarily infer one-to-one relationships between miRNAs and pathways using differentially expressed genes. We introduce PanomiR, an in silico framework for studying the interplay of miRNAs and disease functions. PanomiR integrates gene expression, mRNA–miRNA interactions and known biological pathways to reveal coordinated multi-pathway targeting by miRNAs. PanomiR utilizes pathway-activity profiling approaches, a pathway co-expression network and network clustering algorithms to prioritize miRNAs that target broad-scale transcriptional disease phenotypes. It directly resolves differential regulation of pathways, irrespective of their differential gene expression, and captures co-activity to establish functional pathway groupings and the miRNAs that may regulate them. PanomiR uses a systems biology approach to provide broad but precise insights into miRNA-regulated functional programs. It is available at https://bioconductor.org/packages/PanomiR. [ABSTRACT FROM AUTHOR]

Published
2023
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47. SHP-2 and PD-1-SHP-2 signaling regulate myeloid cell differentiation and antitumor responses

Author

Christofides, Anthos, primary, Katopodi, Xanthi-Lida, additional, Cao, Carol, additional, Karagkouni, Dimitra, additional, Aliazis, Konstantinos, additional, Yenyuwadee, Sasitorn, additional, Aksoylar, Halil-Ibrahim, additional, Pal, Rinku, additional, Mahmoud, Mohamed A. A., additional, Strauss, Laura, additional, Tijaro-Ovalle, Natalia M., additional, Boon, Louis, additional, Asara, John, additional, Vlachos, Ioannis S., additional, Patsoukis, Nikolaos, additional, and Boussiotis, Vassiliki A., additional

Published
2022
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48. Tissue-Specific Human Extracellular Matrix Scaffolds Promote Pancreatic Tumour Progression and Chemotherapy Resistance

Author

Al-Akkad, Walid, primary, Acedo, Pilar, additional, Vilia, Maria-Giovanna, additional, Frenguelli, Luca, additional, Ney, Alexander, additional, Rodriguez-Hernandez, Irene, additional, Labib, Peter L., additional, Tamburrino, Domenico, additional, Spoletini, Gabriele, additional, Hall, Andrew R., additional, Canestrari, Simone, additional, Osnato, Anna, additional, Garcia-Bernardo, Jose, additional, Sejour, Leinal, additional, Vassileva, Vessela, additional, Vlachos, Ioannis S., additional, Fusai, Giuseppe, additional, Luong, Tu Vinh, additional, Whittaker, Steven R., additional, Pereira, Stephen P., additional, Vallier, Ludovic, additional, Pinzani, Massimo, additional, Rombouts, Krista, additional, and Mazza, Giuseppe, additional

Published
2022
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49. A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients

Author

Pita-Juarez, Yered, primary, Karagkouni, Dimitra, additional, Kalavros, Nikolaos, additional, Melms, Johannes C., additional, Niezen, Sebastian, additional, Delorey, Toni M., additional, Essene, Adam L, additional, Brook, Olga R., additional, Pant, Deepti, additional, Skelton-Badlani, Disha, additional, Naderi, Pourya, additional, Huang, Pinzhu, additional, Pan, Liuliu, additional, Hether, Tyler, additional, Andrews, Tallulah S., additional, Ziegler, Carly G.K., additional, Reeves, Jason, additional, Myloserdnyy, Andriy, additional, Chen, Rachel, additional, Nam, Andy, additional, Phelan, Stefan, additional, Liang, Yan, additional, Amin, Amit Dipak, additional, Biermann, Jana, additional, Hibshoosh, Hanina, additional, Veregge, Molly, additional, Kramer, Zachary, additional, Jacobs, Christopher, additional, Yalcin, Yusuf, additional, Phillips, Devan, additional, Slyper, Michal, additional, Subramanian, Ayshwarya, additional, Ashenberg, Orr, additional, Bloom-Ackermann, Zohar, additional, Tran, Victoria M., additional, Gomez, James, additional, Sturm, Alexander, additional, Zhang, Shuting, additional, Fleming, Stephen J., additional, Warren, Sarah, additional, Beechem, Joseph, additional, Hung, Deborah, additional, Babadi, Mehrtash, additional, Padera, Robert F., additional, MacParland, Sonya A., additional, Bader, Gary D., additional, Imad, Nasser, additional, Solomon, Isaac H., additional, Miller, Eric, additional, Riedel, Stefan, additional, Porter, Caroline B.M., additional, Villani, Alexandra-Chloé, additional, Tsai, Linus T.-Y., additional, Hide, Winston, additional, Szabo, Gyongyi, additional, Hecht, Jonathan, additional, Rozenblatt-Rosen, Orit, additional, Shalek, Alex K., additional, Izar, Benjamin, additional, Regev, Aviv, additional, Popov, Yury, additional, Jiang, Z. Gordon, additional, and Vlachos, Ioannis S., additional

Published
2022
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50. Comprehensive Characterization of the Multiple Myeloma Immune Microenvironment Using Integrated scRNA-seq, CyTOF, and CITE-seq Analysis

Author

Yao, Lijun, primary, Jayasinghe, Reyka G., additional, Lee, Brian H., additional, Bhasin, Swati S., additional, Pilcher, William, additional, Doxie, Deon Bryant, additional, Gonzalez-Kozlova, Edgar, additional, Dasari, Surendra, additional, Fiala, Mark A., additional, Pita-Juarez, Yered, additional, Strausbauch, Michael, additional, Kelly, Geoffrey, additional, Thomas, Beena E., additional, Kumar, Shaji K., additional, Cho, Hearn Jay, additional, Anderson, Emilie, additional, Wendl, Michael C., additional, Dawson, Travis, additional, D'souza, Darwin, additional, Oh, Stephen T., additional, Cheloni, Giulia, additional, Li, Ying, additional, DiPersio, John F., additional, Rahman, Adeeb H., additional, Dhodapkar, Kavita M., additional, Kim-Schulze, Seunghee, additional, Vij, Ravi, additional, Vlachos, Ioannis S., additional, Mehr, Shaadi, additional, Hamilton, Mark, additional, Auclair, Daniel, additional, Kourelis, Taxiarchis, additional, Avigan, David, additional, Dhodapkar, Madhav V., additional, Gnjatic, Sacha, additional, Bhasin, Manoj K., additional, and Ding, Li, additional

Published
2022
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