HuBMAP (185)
Publication TitleAuthorsJournalPublication DatePage NoPubMedID
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, ZivPLoS computational biology2022 0936095011
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, RongNature2022 0935978191
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 LACS chemical biology2022 Aug 1135951581
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 LScience advances2022 Aug 1235947651
Overcoming Selection Bias In Synthetic Lethality Prediction.Seale, Colm; Tepeli, Yasin; Gonçalves, Joana PBioinformatics (Oxford, England)2022 Jul 2535876858
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, YingLab on a chip2022 Jul 2635838077
Ferroptosis turns 10: Emerging mechanisms, physiological functions, and therapeutic applications.Stockwell, Brent RCell2022 07 0735803244
scSTEM: clustering pseudotime ordered single-cell data.Song, Qi; Wang, Jingtao; Bar-Joseph, ZivGenome biology2022 07 0735799304
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, JuliaAnalytical chemistry2022 07 1235770488
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 JNature genetics2022 Jul35726067
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 LMolecular & cellular proteomics : MCP2022 Jul35654359
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, ColeNature communications2022 May 1335562344
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, NilsNature methods2022 May35545714
Epigenetic Regulation of Heart-ECHS.Gan, Lu; Pei, LimingJACC. Basic to translational science2022 Apr35540104
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 AComputers in biology and medicine2022 0735533459
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, ShengCell metabolism2022 05 0335508105
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 SInternational journal of radiation oncology, biology, physics2022 Aug 0135504500
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 JNature methods2022 0535501385
Computational tools for analyzing single-cell data in pluripotent cell differentiation studies.Ding, Jun; Alavi, Amir; Ebrahimkhani, Mo R; Bar-Joseph, ZivCell reports methods2021 Oct 2535474899
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 JProceedings of the National Academy of Sciences of the United States of America2022 05 0335471911
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 CCell reports methods2022 Mar 2835463156
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, JuliaAngewandte Chemie (International ed. in English)2022 07 1835446460
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 MCell reports2022 04 1935443184
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, KunCell genomics2022 Mar 0935434692
Membrane marker selection for segmenting single cell spatial proteomics data.Dayao, Monica T; Brusko, Maigan; Wasserfall, Clive; Bar-Joseph, ZivNature communications2022 04 1435422106
Interactive single-cell data analysis using Cellar.Hasanaj, Euxhen; Wang, Jingtao; Sarathi, Arjun; Ding, Jun; Bar-Joseph, ZivNature communications2022 04 1435422041
Mapping the Proteoform Landscape of Five Human Tissues.Drown, Bryon S; Jooß, Kevin; Melani, Rafael D; Lloyd-Jones, Cameron; Camarillo, Jeannie M; Kelleher, Neil LJournal of proteome research2022 05 0635413190
Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling.Bailey, Andrew D; Talkish, Jason; Ding, Hongxu; Igel, Haller; Duran, Alejandra; Mantripragada, Shreya; Paten, Benedict; Ares, ManueleLife2022 Apr 0635384842
Analyzing Spatial Transcriptomics Data Using Giotto.Del Rossi, Natalie; Chen, Jiaji G; Yuan, Guo-Cheng; Dries, RubenCurrent protocols2022 Apr35384407
Spatial-CITE-seq: spatially resolved high-plex protein and whole transcriptome co-mapping.Fan, Rong; Liu, Yang; DiStasio, Marcello; Su, Graham; Asashima, Hiromitsu; Enninful, Archibald; Qin, Xiaoyu; Deng, Yanxiang; Bordignon, Pino; Cassano, Marco; Tomayko, Mary; Xu, Mina; Halene, Stephanie; Craft, Joseph; Hafler, DavidResearch square2022 Mar 3035378748
Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation.Formenti, Giulio; Rhie, Arang; Walenz, Brian P; Thibaud-Nissen, Françoise; Shafin, Kishwar; Koren, Sergey; Myers, Eugene W; Jarvis, Erich D; Phillippy, Adam MNature methods2022 0635361932
Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies.Mc Cartney, Ann M; Shafin, Kishwar; Alonge, Michael; Bzikadze, Andrey V; Formenti, Giulio; Fungtammasan, Arkarachai; Howe, Kerstin; Jain, Chirag; Koren, Sergey; Logsdon, Glennis A; Miga, Karen H; Mikheenko, Alla; Paten, Benedict; Shumate, Alaina; Soto, Daniela C; Sović, Ivan; Wood, Jonathan M D; Zook, Justin M; Phillippy, Adam M; Rhie, ArangNature methods2022 0635361931
A complete reference genome improves analysis of human genetic variation.Aganezov, Sergey; Yan, Stephanie M; Soto, Daniela C; Kirsche, Melanie; Zarate, Samantha; Avdeyev, Pavel; Taylor, Dylan J; Shafin, Kishwar; Shumate, Alaina; Xiao, Chunlin; Wagner, Justin; McDaniel, Jennifer; Olson, Nathan D; Sauria, Michael E G; Vollger, Mitchell R; Rhie, Arang; Meredith, Melissa; Martin, Skylar; Lee, Joyce; Koren, Sergey; Rosenfeld, Jeffrey A; Paten, Benedict; Layer, Ryan; Chin, Chen-Shan; Sedlazeck, Fritz J; Hansen, Nancy F; Miller, Danny E; Phillippy, Adam M; Miga, Karen H; McCoy, Rajiv C; Dennis, Megan Y; Zook, Justin M; Schatz, Michael CScience (New York, N.Y.)2022 0435357935
Complete genomic and epigenetic maps of human centromeres.Altemose, Nicolas; Logsdon, Glennis A; Bzikadze, Andrey V; Sidhwani, Pragya; Langley, Sasha A; Caldas, Gina V; Hoyt, Savannah J; Uralsky, Lev; Ryabov, Fedor D; Shew, Colin J; Sauria, Michael E G; Borchers, Matthew; Gershman, Ariel; Mikheenko, Alla; Shepelev, Valery A; Dvorkina, Tatiana; Kunyavskaya, Olga; Vollger, Mitchell R; Rhie, Arang; McCartney, Ann M; Asri, Mobin; Lorig-Roach, Ryan; Shafin, Kishwar; Lucas, Julian K; Aganezov, Sergey; Olson, Daniel; de Lima, Leonardo Gomes; Potapova, Tamara; Hartley, Gabrielle A; Haukness, Marina; Kerpedjiev, Peter; Gusev, Fedor; Tigyi, Kristof; Brooks, Shelise; Young, Alice; Nurk, Sergey; Koren, Sergey; Salama, Sofie R; Paten, Benedict; Rogaev, Evgeny I; Streets, Aaron; Karpen, Gary H; Dernburg, Abby F; Sullivan, Beth A; Straight, Aaron F; Wheeler, Travis J; Gerton, Jennifer L; Eichler, Evan E; Phillippy, Adam M; Timp, Winston; Dennis, Megan Y; O'Neill, Rachel J; Zook, Justin M; Schatz, Michael C; Pevzner, Pavel A; Diekhans, Mark; Langley, Charles H; Alexandrov, Ivan A; Miga, Karen HScience (New York, N.Y.)2022 0435357911
Reproducible, high-dimensional imaging in archival human tissue by multiplexed ion beam imaging by time-of-flight (MIBI-TOF).Liu, Candace C; Bosse, Marc; Kong, Alex; Kagel, Adam; Kinders, Robert; Hewitt, Stephen M; Varma, Sushama; van de Rijn, Matt; Nowak, Stanisław H; Bendall, Sean C; Angelo, MichaelLaboratory investigation; a journal of technical methods and pathology2022 0735351966
Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing.Goenka, Sneha D; Gorzynski, John E; Shafin, Kishwar; Fisk, Dianna G; Pesout, Trevor; Jensen, Tanner D; Monlong, Jean; Chang, Pi-Chuan; Baid, Gunjan; Bernstein, Jonathan A; Christle, Jeffrey W; Dalton, Karen P; Garalde, Daniel R; Grove, Megan E; Guillory, Joseph; Kolesnikov, Alexey; Nattestad, Maria; Ruzhnikov, Maura R Z; Samadi, Mehrzad; Sethia, Ankit; Spiteri, Elizabeth; Wright, Christopher J; Xiong, Katherine; Zhu, Tong; Jain, Miten; Sedlazeck, Fritz J; Carroll, Andrew; Paten, Benedict; Ashley, Euan ANature biotechnology2022 Jul35347328
Referenced Kendrick Mass Defect Annotation and Class-Based Filtering of Imaging MS Lipidomics Experiments.Richardson, Luke T; Neumann, Elizabeth K; Caprioli, Richard M; Spraggins, Jeffrey M; Solouki, TouradjAnalytical chemistry2022 04 1235344335
Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro.Zhang, Bingjie; Srivastava, Avi; Mimitou, Eleni; Stuart, Tim; Raimondi, Ivan; Hao, Yuhan; Smibert, Peter; Satija, RahulNature biotechnology2022 Aug35332340
Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms.LeDuc, Richard D; Deutsch, Eric W; Binz, Pierre-Alain; Fellers, Ryan T; Cesnik, Anthony J; Klein, Joshua A; Van Den Bossche, Tim; Gabriels, Ralf; Yalavarthi, Arshika; Perez-Riverol, Yasset; Carver, Jeremy; Bittremieux, Wout; Kawano, Shin; Pullman, Benjamin; Bandeira, Nuno; Kelleher, Neil L; Thomas, Paul M; Vizcaíno, Juan AntonioJournal of proteome research2022 Apr 0135290070
Clinical Implementation and Initial Experience With a 1.5 Tesla MR-Linac for MR-Guided Radiation Therapy for Gynecologic Cancer: An R-IDEAL Stage 1 and 2a First in Humans Feasibility Study of New Technology Implementation.Lakomy, David S; Yang, Jinzhong; Vedam, Sastry; Wang, Jihong; Lee, Belinda; Sobremonte, Angela; Castillo, Pamela; Hughes, Neil; Mohammedsaid, Mustefa; Jhingran, Anuja; Klopp, Ann H; Choi, Seungtaek; Fuller, C David; Lin, Lilie LPractical radiation oncology2022 Jul-Aug35278717
MITI minimum information guidelines for highly multiplexed tissue images.Schapiro, Denis; Yapp, Clarence; Sokolov, Artem; Reynolds, Sheila M; Chen, Yu-An; Sudar, Damir; Xie, Yubin; Muhlich, Jeremy; Arias-Camison, Raquel; Arena, Sarah; Taylor, Adam J; Nikolov, Milen; Tyler, Madison; Lin, Jia-Ren; Burlingame, Erik A; Human Tumor Atlas Network; Chang, Young H; Farhi, Samouil L; Thorsson, Vésteinn; Venkatamohan, Nithya; Drewes, Julia L; Pe'er, Dana; Gutman, David A; Herrmann, Markus D; Gehlenborg, Nils; Bankhead, Peter; Roland, Joseph T; Herndon, John M; Snyder, Michael P; Angelo, Michael; Nolan, Garry; Swedlow, Jason R; Schultz, Nikolaus; Merrick, Daniel T; Mazzili, Sarah A; Cerami, Ethan; Rodig, Scott J; Santagata, Sandro; Sorger, Peter KNature methods2022 0335277708
TraSig: inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data.Li, Dongshunyi; Velazquez, Jeremy J; Ding, Jun; Hislop, Joshua; Ebrahimkhani, Mo R; Bar-Joseph, ZivGenome biology2022 Mar 0735255944
Limited extent and consequences of pancreatic SARS-CoV-2 infection.van der Heide, Verena; Jangra, Sonia; Cohen, Phillip; Rathnasinghe, Raveen; Aslam, Sadaf; Aydillo, Teresa; Geanon, Daniel; Handler, Diana; Kelley, Geoffrey; Lee, Brian; Rahman, Adeeb; Dawson, Travis; Qi, Jingjing; D'Souza, Darwin; Kim-Schulze, Seunghee; Panzer, Julia K; Caicedo, Alejandro; Kusmartseva, Irina; Posgai, Amanda L; Atkinson, Mark A; Albrecht, Randy A; García-Sastre, Adolfo; Rosenberg, Brad R; Schotsaert, Michael; Homann, DirkCell reports2022 Feb 2135247306
Machine Learning Classifies Ferroptosis and Apoptosis Cell Death Modalities with TfR1 Immunostaining.Jin, Jenny; Schorpp, Kenji; Samaga, Daniel; Unger, Kristian; Hadian, Kamyar; Stockwell, Brent RACS chemical biology2022 Mar 1835230809
Uncovering Molecular Heterogeneity in the Kidney With Spatially Targeted Mass Spectrometry.Kruse, Angela R S; Spraggins, Jeffrey MFrontiers in physiology202235222094
Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics?Plubell, Deanna L; Käll, Lukas; Webb-Robertson, Bobbie-Jo; Bramer, Lisa M; Ives, Ashley; Kelleher, Neil L; Smith, Lloyd M; Montine, Thomas J; Wu, Christine C; MacCoss, Michael JJournal of proteome research2022 Apr 0135220718
Revealing new biology from multiplexed, metal-isotope-tagged, single-cell readouts.Baskar, Reema; Kimmey, Sam C; Bendall, Sean CTrends in cell biology2022 Feb 1635181197
Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level.Deng, Yanxiang; Bartosovic, Marek; Kukanja, Petra; Zhang, Di; Liu, Yang; Su, Graham; Enninful, Archibald; Bai, Zhiliang; Castelo-Branco, Gonçalo; Fan, RongScience (New York, N.Y.)2022 02 1135143307
Temporal modelling using single-cell transcriptomics.Ding, Jun; Sharon, Nadav; Bar-Joseph, ZivNature reviews. Genetics2022 0635102309
The Blood Proteoform Atlas: A reference map of proteoforms in human hematopoietic cells.Melani, Rafael D; Gerbasi, Vincent R; Anderson, Lissa C; Sikora, Jacek W; Toby, Timothy K; Hutton, Josiah E; Butcher, David S; Negrão, Fernanda; Seckler, Henrique S; Srzentić, Kristina; Fornelli, Luca; Camarillo, Jeannie M; LeDuc, Richard D; Cesnik, Anthony J; Lundberg, Emma; Greer, Joseph B; Fellers, Ryan T; Robey, Matthew T; DeHart, Caroline J; Forte, Eleonora; Hendrickson, Christopher L; Abbatiello, Susan E; Thomas, Paul M; Kokaji, Andy I; Levitsky, Josh; Kelleher, Neil LScience (New York, N.Y.)2022 01 2835084980
Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma.Risom, Tyler; Glass, David R; Averbukh, Inna; Liu, Candace C; Baranski, Alex; Kagel, Adam; McCaffrey, Erin F; Greenwald, Noah F; Rivero-Gutiérrez, Belén; Strand, Siri H; Varma, Sushama; Kong, Alex; Keren, Leeat; Srivastava, Sucheta; Zhu, Chunfang; Khair, Zumana; Veis, Deborah J; Deschryver, Katherine; Vennam, Sujay; Maley, Carlo; Hwang, E Shelley; Marks, Jeffrey R; Bendall, Sean C; Colditz, Graham A; West, Robert B; Angelo, MichaelCell2022 01 2035063072
Comparison and evaluation of statistical error models for scRNA-seq.Choudhary, Saket; Satija, RahulGenome biology2022 01 1835042561
Author Correction: Single-cell chromatin state analysis with Signac.Nature methods2022 Feb34997233
Pangenomics enables genotyping of known structural variants in 5202 diverse genomes.Sirén, Jouni; Monlong, Jean; Chang, Xian; Novak, Adam M; Eizenga, Jordan M; Markello, Charles; Sibbesen, Jonas A; Hickey, Glenn; Chang, Pi-Chuan; Carroll, Andrew; Gupta, Namrata; Gabriel, Stacey; Blackwell, Thomas W; Ratan, Aakrosh; Taylor, Kent D; Rich, Stephen S; Rotter, Jerome I; Haussler, David; Garrison, Erik; Paten, BenedictScience (New York, N.Y.)2021 12 1734914532
Tissue fixation effects on human retinal lipid analysis by MALDI imaging and LC-MS/MS technologies.Kotnala, Ankita; Anderson, David M G; Patterson, Nathan Heath; Cantrell, Lee S; Messinger, Jeffrey D; Curcio, Christine A; Schey, Kevin LJournal of mass spectrometry : JMS2021 Dec34881479
Multicellular modules as clinical diagnostic and therapeutic targets.Baertsch, Marc-A; Nolan, Garry P; Hickey, John WTrends in cancer2022 Mar34872889
geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq.Missarova, Alsu; Jain, Jaison; Butler, Andrew; Ghazanfar, Shila; Stuart, Tim; Brusko, Maigan; Wasserfall, Clive; Nick, Harry; Brusko, Todd; Atkinson, Mark; Satija, Rahul; Marioni, John CGenome biology2021 12 0634872616
Cross-Laboratory Standardization of Preclinical Lipidomics Using Differential Mobility Spectrometry and Multiple Reaction Monitoring.Ghorasaini, Mohan; Mohammed, Yassene; Adamski, Jerzy; Bettcher, Lisa; Bowden, John A; Cabruja, Matias; Contrepois, Kévin; Ellenberger, Mathew; Gajera, Bharat; Haid, Mark; Hornburg, Daniel; Hunter, Christie; Jones, Christina M; Klein, Theo; Mayboroda, Oleg; Mirzaian, Mina; Moaddel, Ruin; Ferrucci, Luigi; Lovett, Jacqueline; Nazir, Kenneth; Pearson, Mackenzie; Ubhi, Baljit K; Raftery, Daniel; Riols, Fabien; Sayers, Rebekah; Sijbrands, Eric J G; Snyder, Michael P; Su, Baolong; Velagapudi, Vidya; Williams, Kevin J; de Rijke, Yolanda B; Giera, MartinAnalytical chemistry2021 12 1434859676
Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging.Hickey, John W; Neumann, Elizabeth K; Radtke, Andrea J; Camarillo, Jeannie M; Beuschel, Rebecca T; Albanese, Alexandre; McDonough, Elizabeth; Hatler, Julia; Wiblin, Anne E; Fisher, Jeremy; Croteau, Josh; Small, Eliza C; Sood, Anup; Caprioli, Richard M; Angelo, R Michael; Nolan, Garry P; Chung, Kwanghun; Hewitt, Stephen M; Germain, Ronald N; Spraggins, Jeffrey M; Lundberg, Emma; Snyder, Michael P; Kelleher, Neil L; Saka, Sinem KNature methods2022 0334811556
Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning.Greenwald, Noah F; Miller, Geneva; Moen, Erick; Kong, Alex; Kagel, Adam; Dougherty, Thomas; Fullaway, Christine Camacho; McIntosh, Brianna J; Leow, Ke Xuan; Schwartz, Morgan Sarah; Pavelchek, Cole; Cui, Sunny; Camplisson, Isabella; Bar-Tal, Omer; Singh, Jaiveer; Fong, Mara; Chaudhry, Gautam; Abraham, Zion; Moseley, Jackson; Warshawsky, Shiri; Soon, Erin; Greenbaum, Shirley; Risom, Tyler; Hollmann, Travis; Bendall, Sean C; Keren, Leeat; Graf, William; Angelo, Michael; Van Valen, DavidNature biotechnology2021 Nov 1834795433
Immune cell topography predicts response to PD-1 blockade in cutaneous T cell lymphoma.Phillips, Darci; Matusiak, Magdalena; Gutierrez, Belén Rivero; Bhate, Salil S; Barlow, Graham L; Jiang, Sizun; Demeter, Janos; Smythe, Kimberly S; Pierce, Robert H; Fling, Steven P; Ramchurren, Nirasha; Cheever, Martin A; Goltsev, Yury; West, Robert B; Khodadoust, Michael S; Kim, Youn H; Schürch, Christian M; Nolan, Garry PNature communications2021 Nov 1834795254
Magnetic resonance linear accelerator technology and adaptive radiation therapy: An overview for clinicians.Hall, William A; Paulson, Eric; Li, X Allen; Erickson, Beth; Schultz, Christopher; Tree, Alison; Awan, Musaddiq; Low, Daniel A; McDonald, Brigid A; Salzillo, Travis; Glide-Hurst, Carri K; Kishan, Amar U; Fuller, Clifton DCA: a cancer journal for clinicians2022 0134792808
Anatomical structures, cell types and biomarkers of the Human Reference Atlas.Börner, Katy; Teichmann, Sarah A; Quardokus, Ellen M; Gee, James C; Browne, Kristen; Osumi-Sutherland, David; Herr 2nd, Bruce W; Bueckle, Andreas; Paul, Hrishikesh; Haniffa, Muzlifah; Jardine, Laura; Bernard, Amy; Ding, Song-Lin; Miller, Jeremy A; Lin, Shin; Halushka, Marc K; Boppana, Avinash; Longacre, Teri A; Hickey, John; Lin, Yiing; Valerius, M Todd; He, Yongqun; Pryhuber, Gloria; Sun, Xin; Jorgensen, Marda; Radtke, Andrea J; Wasserfall, Clive; Ginty, Fiona; Ho, Jonhan; Sunshine, Joel; Beuschel, Rebecca T; Brusko, Maigan; Lee, Sujin; Malhotra, Rajeev; Jain, Sanjay; Weber, GriffinNature cell biology2021 1134750582
Cell type ontologies of the Human Cell Atlas.Osumi-Sutherland, David; Xu, Chuan; Keays, Maria; Levine, Adam P; Kharchenko, Peter V; Regev, Aviv; Lein, Ed; Teichmann, Sarah ANature cell biology2021 1134750578
Stratification of chemotherapy-treated stage III colorectal cancer patients using multiplexed imaging and single-cell analysis of T-cell populations.Stachtea, Xanthi; Loughrey, Maurice B; Salvucci, Manuela; Lindner, Andreas U; Cho, Sanghee; McDonough, Elizabeth; Sood, Anup; Graf, John; Santamaria-Pang, Alberto; Corwin, Alex; Laurent-Puig, Pierre; Dasgupta, Sonali; Shia, Jinru; Owens, Jonathan R; Abate, Samantha; Van Schaeybroeck, Sandra; Lawler, Mark; Prehn, Jochen H M; Ginty, Fiona; Longley, Daniel BModern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc2021 Nov 0334732839
Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads.Shafin, Kishwar; Pesout, Trevor; Chang, Pi-Chuan; Nattestad, Maria; Kolesnikov, Alexey; Goel, Sidharth; Baid, Gunjan; Kolmogorov, Mikhail; Eizenga, Jordan M; Miga, Karen H; Carnevali, Paolo; Jain, Miten; Carroll, Andrew; Paten, BenedictNature methods2021 Nov34725481
Single-cell chromatin state analysis with Signac.Stuart, Tim; Srivastava, Avi; Madad, Shaista; Lareau, Caleb A; Satija, RahulNature methods2021 Nov34725479
Deep Learning Approach for Dynamic Sparse Sampling for High-Throughput Mass Spectrometry Imaging.Helminiak, David; Hu, Hang; Laskin, Julia; Ye, Dong HyeIS&T International Symposium on Electronic Imaging202134722959
Editorial: Footprints of Immune Cells in the Type 1 Diabetic Pancreas.Brusko, Todd M; Mallone, Roberto; Rodriguez-Calvo, TeresaFrontiers in endocrinology202134721308
Mass spectrometry-based targeted proteomics for analysis of protein mutations.Lin, Tai-Tu; Zhang, Tong; Kitata, Reta B; Liu, Tao; Smith, Richard D; Qian, Wei-Jun; Shi, TujinMass spectrometry reviews2021 Oct 3134719806
Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram.Biancalani, Tommaso; Scalia, Gabriele; Buffoni, Lorenzo; Avasthi, Raghav; Lu, Ziqing; Sanger, Aman; Tokcan, Neriman; Vanderburg, Charles R; Segerstolpe, Åsa; Zhang, Meng; Avraham-Davidi, Inbal; Vickovic, Sanja; Nitzan, Mor; Ma, Sai; Subramanian, Ayshwarya; Lipinski, Michal; Buenrostro, Jason; Brown, Nik Bear; Fanelli, Duccio; Zhuang, Xiaowei; Macosko, Evan Z; Regev, AvivNature methods2021 Nov34711971
3D virtual reality vs. 2D desktop registration user interface comparison.Bueckle, Andreas; Buehling, Kilian; Shih, Patrick C; Börner, KatyPloS one202134705835
RAP-NET: COARSE-TO-FINE MULTI-ORGAN SEGMENTATION WITH SINGLE RANDOM ANATOMICAL PRIOR.Lee, Ho Hin; Tang, Yucheng; Bao, Shunxing; Abramson, Richard G; Huo, Yuankai; Landman, Bennett AProceedings. IEEE International Symposium on Biomedical Imaging2021 Apr34667487
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High spatial resolution imaging of biological tissues using nanospray desorption electrospray ionization mass spectrometry.Yin, Ruichuan; Burnum-Johnson, Kristin E; Sun, Xiaofei; Dey, Sudhansu K; Laskin, JuliaNature protocols.2019 12;31723300
High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell.Chen, Song; Lake, Blue B; Zhang, KunNature biotechnology.2019 12;31611697
Staphylococcus aureus exhibits heterogeneous siderophore production within the vertebrate host.Perry, William J; Spraggins, Jeffrey M; Sheldon, Jessica R; Grunenwald, Caroline M; Heinrichs, David E; Cassat, James E; Skaar, Eric P; Caprioli, Richard MProceedings of the National Academy of Sciences of the United States of America.2019 10 29;31611408
Unsupervised machine learning for exploratory data analysis in imaging mass spectrometry.Verbeeck, Nico; Caprioli, Richard M; Van de Plas, RafMass spectrometry reviews.2020 May;31602691
The human body at cellular resolution: the NIH Human Biomolecular Atlas Program.HuBMAP ConsortiumNature.2019 10;31597973
High-Performance Molecular Imaging with MALDI Trapped Ion-Mobility Time-of-Flight (timsTOF) Mass Spectrometry.Spraggins, Jeffrey M; Djambazova, Katerina V; Rivera, Emilio S; Migas, Lukasz G; Neumann, Elizabeth K; Fuetterer, Arne; Suetering, Juergen; Goedecke, Niels; Ly, Alice; Van de Plas, Raf; Caprioli, Richard MAnalytical chemistry.2019 11 19;31593446
High-Parameter Immune Profiling with CyTOF.Sahaf, Bita; Rahman, Adeeb; Maecker, Holden T; Bendall, Sean CMethods in molecular biology (Clifton, N.J.).2020;31502160
Supervised classification enables rapid annotation of cell atlases.Pliner, Hannah A; Shendure, Jay; Trapnell, ColeNature methods.2019 Oct;31501545
A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition.McFaline-Figueroa, José L; Hill, Andrew J; Qiu, Xiaojie; Jackson, Dana; Shendure, Jay; Trapnell, ColeNature genetics.2019 Sep;31477929
Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues.Saka, Sinem K; Wang, Yu; Kishi, Jocelyn Y; Zhu, Allen; Zeng, Yitian; Xie, Wenxin; Kirli, Koray; Yapp, Clarence; Cicconet, Marcelo; Beliveau, Brian J; Lapan, Sylvain W; Yin, Siyuan; Lin, Millicent; Boyden, Edward S; Kaeser, Pascal S; Pihan, German; Church, George M; Yin, PengNature biotechnology.2019 Sep;31427819
A recommended and verified procedure for in situ tryptic digestion of formalin-fixed paraffin-embedded tissues for analysis by matrix-assisted laser desorption/ionization imaging mass spectrometry.Judd, Audra M; Gutierrez, Danielle B; Moore, Jessica L; Patterson, Nathan Heath; Yang, Junhai; Romer, Carrie E; Norris, Jeremy L; Caprioli, Richard MJournal of mass spectrometry : JMS.2019 Aug;31254303
Two Specific Sulfatide Species Are Dysregulated during Renal Development in a Mouse Model of Alport Syndrome.Gessel, Megan M; Spraggins, Jeffrey M; Voziyan, Paul A; Abrahamson, Dale R; Caprioli, Richard M; Hudson, Billy GLipids.2019 06;31197846
Comprehensive Integration of Single-Cell Data.Stuart, Tim; Butler, Andrew; Hoffman, Paul; Hafemeister, Christoph; Papalexi, Efthymia; Mauck 3rd, William M; Hao, Yuhan; Stoeckius, Marlon; Smibert, Peter; Satija, RahulCell.2019 Jun 13;31178118
MicroLESA: Integrating Autofluorescence Microscopy, In Situ Micro-Digestions, and Liquid Extraction Surface Analysis for High Spatial Resolution Targeted Proteomic Studies.Ryan, Daniel J; Patterson, Nathan Heath; Putnam, Nicole E; Wilde, Aimee D; Weiss, Andy; Perry, William J; Cassat, James E; Skaar, Eric P; Caprioli, Richard M; Spraggins, Jeffrey MAnalytical chemistry.2019 06 18;31149808
SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues.Kishi, Jocelyn Y; Lapan, Sylvain W; Beliveau, Brian J; West, Emma R; Zhu, Allen; Sasaki, Hiroshi M; Saka, Sinem K; Wang, Yu; Cepko, Constance L; Yin, PengNature methods.2019 Jun;31110282
Visualizing learner engagement, performance, and trajectories to evaluate and optimize online course design.Ginda, Michael; Richey, Michael C; Cousino, Mark; Börner, KatyPloS one.2019;31059546
Continuous State HMMs for Modeling Time Series Single Cell RNA-Seq Data.Lin, Chieh; Bar-Joseph, ZivBioinformatics (Oxford, England).2019 Apr 30;31038684
The 2019 mathematical oncology roadmap.Rockne, Russell C; Hawkins-Daarud, Andrea; Swanson, Kristin R; Sluka, James P; Glazier, James A; Macklin, Paul; Hormuth, David A; Jarrett, Angela M; Lima, Ernesto A B F; Tinsley Oden, J; Biros, George; Yankeelov, Thomas E; Curtius, Kit; Al Bakir, Ibrahim; Wodarz, Dominik; Komarova, Natalia; Aparicio, Luis; Bordyuh, Mykola; Rabadan, Raul; Finley, Stacey D; Enderling, Heiko; Caudell, Jimmy; Moros, Eduardo G; Anderson, Alexander R A; Gatenby, Robert A; Kaznatcheev, Artem; Jeavons, Peter; Krishnan, Nikhil; Pelesko, Julia; Wadhwa, Raoul R; Yoon, Nara; Nichol, Daniel; Marusyk, Andriy; Hinczewski, Michael; Scott, Jacob GPhysical biology.2019 Jun 19;30991381
Imaging mass spectrometry enables molecular profiling of mouse and human pancreatic tissue.Prentice, Boone M; Hart, Nathaniel J; Phillips, Neil; Haliyur, Rachana; Judd, Audra; Armandala, Radhika; Spraggins, Jeffrey M; Lowe, Cindy L; Boyd, Kelli L; Stein, Roland W; Wright, Christopher V; Norris, Jeremy L; Powers, Alvin C; Brissova, Marcela; Caprioli, Richard MDiabetologia.2019 06;30955045
Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution.Rodriques, Samuel G; Stickels, Robert R; Goeva, Aleksandrina; Martin, Carly A; Murray, Evan; Vanderburg, Charles R; Welch, Joshua; Chen, Linlin M; Chen, Fei; Macosko, Evan ZScience (New York, N.Y.).2019 03 29;30923225
Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH.Eng, Chee-Huat Linus; Lawson, Michael; Zhu, Qian; Dries, Ruben; Koulena, Noushin; Takei, Yodai; Yun, Jina; Cronin, Christopher; Karp, Christoph; Yuan, Guo-Cheng; Cai, LongNature.2019 Apr;30911168
Multiple TOF/TOF Events in a Single Laser Shot for Multiplexed Lipid Identifications in MALDI Imaging Mass Spectrometry.Prentice, Boone M; McMillen, Josiah C; Caprioli, Richard MInternational journal of mass spectrometry.2019 Mar;30906202
Cell lineage inference from SNP and scRNA-Seq data.Ding, Jun; Lin, Chieh; Bar-Joseph, ZivNucleic acids research.2019 Jun 04;30820578
The single-cell transcriptional landscape of mammalian organogenesis.Cao, Junyue; Spielmann, Malte; Qiu, Xiaojie; Huang, Xingfan; Ibrahim, Daniel M; Hill, Andrew J; Zhang, Fan; Mundlos, Stefan; Christiansen, Lena; Steemers, Frank J; Trapnell, Cole; Shendure, JayNature.2019 02;30787437
Dhaka: Variational Autoencoder for Unmasking Tumor Heterogeneity from Single Cell Genomic Data.Rashid, Sabrina; Shah, Sohrab; Bar-Joseph, Ziv; Pandya, RaviBioinformatics (Oxford, England).2019 Feb 15;30768159
Data visualization literacy: Definitions, conceptual frameworks, exercises, and assessments.Börner, Katy; Bueckle, Andreas; Ginda, MichaelProceedings of the National Academy of Sciences of the United States of America.2019 Feb 05;30718386
Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics.Stoeckius, Marlon; Zheng, Shiwei; Houck-Loomis, Brian; Hao, Stephanie; Yeung, Bertrand Z; Mauck 3rd, William M; Smibert, Peter; Satija, RahulGenome biology.2018 12 19;30567574
Forecasting innovations in science, technology, and education.Börner, Katy; Rouse, William B; Trunfio, Paul; Stanley, H EugeneProceedings of the National Academy of Sciences of the United States of America.2018 12 11;30530683
Protein identification strategies in MALDI imaging mass spectrometry: a brief review.Ryan, Daniel J; Spraggins, Jeffrey M; Caprioli, Richard MCurrent opinion in chemical biology.2019 02;30476689
Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data.Zhu, Qian; Shah, Sheel; Dries, Ruben; Cai, Long; Yuan, Guo-ChengNature biotechnology.2018 Oct 29;30371680