LSP Bibliography

Aguilar F, Yu S, Grant RA, Swanson S, Ghose D, Su BG, Sarosiek KA, Keating AE. Peptides from human BNIP5 and PXT1 and non-native binders of pro-apoptotic BAK can directly activate or inhibit BAK-mediated membrane permeabilization. Structure. 2023 Jan 23;S0969-2126(23)00001–1. PMID: 36706751

Bachman JA, Gyori BM, Sorger PK. Automated assembly of molecular mechanisms at scale from text mining and curated databases. Mol Syst Biol. 2023 May 9;19(5):e11325. PMCID: PMC10167483

Bergholz JS, Wang Q, Wang Q, Ramseier M, Prakadan S, Wang W, Fang R, Kabraji S, Zhou Q, Gray GK, Abell-Hart K, Xie S, Guo X, Gu H, Von T, Jiang T, Tang S, Freeman GJ, Kim HJ, Shalek AK, Roberts TM, Zhao JJ. PI3Kβ controls immune evasion in PTEN-deficient breast tumours. Nature. 2023 May;617(7959):139–146. PMID: 37076617

Bouatta N, AlQuraishi M. Structural biology at the scale of proteomes. Nat Struct Mol Biol. 2023 Feb;30(2):129–130. PMCID: PMC10389299

Brastianos PK, Twohy E, Geyer S, Gerstner ER, Kaufmann TJ, Tabrizi S, Kabat B, Thierauf J, Ruff MW, Bota DA, Reardon DA, Cohen AL, De La Fuente MI, Lesser GJ, Campian J, Agarwalla PK, Kumthekar P, Mann B, Vora S, Knopp M, Iafrate AJ, Curry WT, Cahill DP, Shih HA, Brown PD, Santagata S, Barker FG, Galanis E. BRAF-MEK Inhibition in Newly Diagnosed Papillary Craniopharyngiomas. N Engl J Med. 2023 Jul 13;389(2):118–126. PMID: 37437144

Brastianos PK, Twohy EL, Gerstner ER, Kaufmann TJ, Iafrate AJ, Lennerz J, Jeyapalan S, Piccioni DE, Monga V, Fadul CE, Schiff D, Taylor JW, Chowdhary SA, Bettegowda C, Ansstas G, De La Fuente M, Anderson MD, Shonka N, Damek D, Carrillo J, Kunschner-Ronan LJ, Chaudhary R, Jaeckle KA, Senecal FM, Kaley T, Morrison T, Thomas AA, Welch MR, Iwamoto F, Cachia D, Cohen AL, Vora S, Knopp M, Dunn IF, Kumthekar P, Sarkaria J, Geyer S, Carrero XW, Martinez-Lage M, Cahill DP, Brown PD, Giannini C, Santagata S, Barker FG, Galanis E. Alliance A071401: Phase II Trial of Focal Adhesion Kinase Inhibition in Meningiomas With Somatic NF2 Mutations. J Clin Oncol. 2023 Jan 20;41(3):618–628. PMCID: PMC9870228

Cello G, Patel RV, McMahon JT, Santagata S, Bi WL. Impact of H3K27 trimethylation loss in meningiomas: a meta-analysis. Acta Neuropathol Commun. 2023 Jul 25;11(1):122. PMCID: PMC10369842

Chen JY, Hug C, Reyes J, Tian C, Gerosa L, Fröhlich F, Ponsioen B, Snippert HJG, Spencer SL, Jambhekar A, Sorger PK, Lahav G. Multi-range ERK responses shape the proliferative trajectory of single cells following oncogene induction. Cell Rep. 2023 Mar 28;42(3):112252. PMCID: PMC10153468

Chidley C, Darnell AM, Gaudio BL, Lien EC, Barbeau AM, Vander Heiden MG, Sorger PK. A CRISPRi/a screening platform to study cellular nutrient transport in diverse microenvironments [Internet]. Cancer Biology; 2023 [cited 2023 Jan 30]. Available from: http://biorxiv.org/lookup/doi/10.1101/2023.01.26.525375

Choudhury A, Chen WC, Lucas CHG, Bayley JC, Harmanci AS, Maas SLN, Santagata S, Klisch T, Perry A, Bi WL, Sahm F, Patel AJ, Magill ST, Raleigh DR. Hypermitotic meningiomas harbor DNA methylation subgroups with distinct biological and clinical features. Neuro Oncol. 2023 Mar 14;25(3):520–530. PMCID: PMC10013643

Dulberger CL, Guerrero-Bustamante CA, Owen SV, Wilson S, Wuo MG, Garlena RA, Serpa LA, Russell DA, Zhu J, Braunecker BJ, Squyres GR, Baym M, Kiessling LL, Garner EC, Rubin EJ, Hatfull GF. Mycobacterial nucleoid-associated protein Lsr2 is required for productive mycobacteriophage infection. Nat Microbiol. 2023 Feb 23; PMID: 36823286

Fröhlich F, Gerosa L, Muhlich J, Sorger PK. Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance. Mol Syst Biol. 2023 Feb 10;19(2):e10988. PMCID: PMC9912026

Gaglia G, Burger ML, Ritch CC, Rammos D, Dai Y, Crossland GE, Tavana SZ, Warchol S, Jaeger AM, Naranjo S, Coy S, Nirmal AJ, Krueger R, Lin JR, Pfister H, Sorger PK, Jacks T, Santagata S. Lymphocyte networks are dynamic cellular communities in the immunoregulatory landscape of lung adenocarcinoma. Cancer Cell. 2023 May 8;41(5):871-886.e10. PMCID: PMC10193529

Hermida-Prado F, Xie Y, Sherman S, Nagy Z, Russo D, Akhshi T, Chu Z, Feit A, Campisi M, Chen M, Nardone A, Guarducci C, Lim K, Font-Tello A, Lee I, García-Pedrero J, Canadas I, Agudo J, Huang Y, Sella T, Jin Q, Tayob N, Mittendorf EA, Tolaney SM, Qiu X, Long H, Symmans WF, Lin JR, Santagata S, Bedrosian I, Yardley DA, Mayer IA, Richardson ET, Oliveira G, Wu CJ, Schuster EF, Dowsett M, Welm AL, Barbie D, Metzger O, Jeselsohn R. Endocrine therapy synergizes with SMAC mimetics to potentiate antigen presentation and tumor regression in hormone receptor-positive breast cancer. Cancer Res. 2023 Jul 14;CAN-23-1711. PMID: 37450351

Hoyt CT, Hoyt AL, Gyori BM. Prediction and Curation of Missing Biomedical Identifier Mappings with Biomappings. Bioinformatics. 2023 Mar 14;btad130. PMID: 36916735

Hoyt CT, Zdrazil B, Guha R, Jeliazkova N, Martinez-Mayorga K, Nittinger E. Improving reproducibility and reusability in the Journal of Cheminformatics. J Cheminform. 2023 Jun 30;15(1):62. PMCID: PMC10314397

Jain A, Gyori BM, Hakim S, Bunga S, Taub DG, Ruiz-Cantero MC, Tong-Li C, Andrews N, Sorger PK, Woolf CJ. Nociceptor neuroimmune interactomes reveal cell type- and injury-specific inflammatory pain pathways. bioRxiv; 2023. PMCID: PMC9915698

Kalocsay M, Berberich MJ, Everley RA, Nariya MK, Chung M, Gaudio B, Victor C, Bradshaw GA, Eisert RJ, Hafner M, Sorger PK, Mills CE, Subramanian K. Proteomic profiling across breast cancer cell lines and models. Sci Data. 2023 Aug 4;10(1):514. PMCID: PMC10403526

Lecky E, Mukherji A, German R, Antonellis G, Lin JR, Yorsz M, McQueeney KE, Ryan J, Ng K, Sicinska E, Sorger PK, Letai A, Bhola PD. Sequential apoptotic and multiplexed proteomic evaluation of single cancer cells. Sci Adv. 2023 Jun 23;9(25):eadg4128. PMCID: PMC10289660

Limdi A, Baym M. Resolving Deleterious and Near-Neutral Effects Requires Different Pooled Fitness Assay Designs. J Mol Evol. 2023 Jun;91(3):325–333. PMID: 37160452

Lin JR, Wang S, Coy S, Chen YA, Yapp C, Tyler M, Nariya MK, Heiser CN, Lau KS, Santagata S, Sorger PK. Multiplexed 3D atlas of state transitions and immune interaction in colorectal cancer. Cell. 2023 Jan 19;186(2):363-381.e19. PMCID: PMC10019067

Lin JR, Chen YA, Campton D, Cooper J, Coy S, Yapp C, Tefft JB, McCarty E, Ligon KL, Rodig SJ, Reese S, George T, Santagata S, Sorger PK. High-plex immunofluorescence imaging and traditional histology of the same tissue section for discovering image-based biomarkers. Nat Cancer. 2023 Jul;4(7):1036–1052. PMCID: PMC10368530

Liu C, Kutchukian P, Nguyen ND, AlQuraishi M, Sorger PK. A Hybrid Structure-Based Machine Learning Approach for Predicting Kinase Inhibition by Small Molecules. J Chem Inf Model. 2023 Aug 18; PMCID: PMC10498990

Lobentanzer S, Aloy P, Baumbach J, Bohar B, Carey VJ, Charoentong P, Danhauser K, Doğan T, Dreo J, Dunham I, Farr E, Fernandez-Torras A, Gyori BM, Hartung M, Hoyt CT, Klein C, Korcsmaros T, Maier A, Mann M, Ochoa D, Pareja-Lorente E, Popp F, Preusse M, Probul N, Schwikowski B, Sen B, Strauss MT, Turei D, Ulusoy E, Waltemath D, Wodke JAH, Saez-Rodriguez J. Democratizing knowledge representation with BioCypher. Nat Biotechnol. 2023 Jun 19; PMID: 37337100

Maliga Z, Kim DY, Bui ATN, Lin JR, Dewan AK, Murphy GF, Nirmal AJ, Lian CG, Sorger PK, LeBoeuf NR. Immune Profiling of Dermatologic Adverse Events from Checkpoint Blockade using Tissue Cyclic Immunofluorescence [Internet]. Immunology; 2023 [cited 2023 Apr 7]. Available from: http://biorxiv.org/lookup/doi/10.1101/2023.04.03.535435

Mohammad-Taheri S, Tewari V, Kapre R, Rahiminasab E, Sachs K, Taply Hoyt C, Zucker J, Vitek O. Optimal adjustment sets for causal query estimation in partially observed biomolecular networks. Bioinformatics. 2023 Jun 30;39(39 Suppl 1):i494–i503. PMCID: PMC10311316

Nariya MK, Mills CE, Sorger PK, Sokolov A. Paired evaluation of machine-learning models characterizes effects of confounders and outliers. Patterns (N Y). 2023 Aug 11;4(8):100791. PMCID: PMC10435952

Netterfield TS, Ostheimer GJ, Tentner AR, Joughin BA, Dakoyannis AM, Sharma CD, Sorger PK, Janes KA, Lauffenburger DA, Yaffe MB. Biphasic JNK-Erk signaling separates the induction and maintenance of cell senescence after DNA damage induced by topoisomerase II inhibition. Cell Syst. 2023 Jul 19;14(7):582-604.e10. PMID: 37473730

Nyerges A, Vinke S, Flynn R, Owen SV, Rand EA, Budnik B, Keen E, Narasimhan K, Marchand JA, Baas-Thomas M, Liu M, Chen K, Chiappino-Pepe A, Hu F, Baym M, Church GM. A swapped genetic code prevents viral infections and gene transfer. Nature. 2023 Mar;615(7953):720–727. PMID: 36922599

Perurena N, Lock R, Davis RA, Raghavan S, Pilla NF, Ng R, Loi P, Guild CJ, Miller AL, Sicinska E, Cleary JM, Rubinson DA, Wolpin BM, Gray NS, Santagata S, Hahn WC, Morton JP, Sansom OJ, Aguirre AJ, Cichowski K. USP9X mediates an acute adaptive response to MAPK suppression in pancreatic cancer but creates multiple actionable therapeutic vulnerabilities. Cell Rep Med. 2023 Apr 18;4(4):101007. PMCID: PMC10140597

Pillich RT, Chen J, Churas C, Fong D, Gyori BM, Ideker T, Karis K, Liu SN, Ono K, Pico A, Pratt D. NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange. Bioinformatics. 2023 Mar 1;39(3):btad118. PMCID: PMC10023220

Prabhakaran S, Yapp C, Baker GJ, Beyer J, Chang YH, Creason AL, Krueger R, Muhlich J, Patterson NH, Sidak K, Sudar D, Taylor AJ, Ternes L, Troidl J, Xie Y, Sokolov A, Tyson DR, the Cell Imaging Hackathon 2022 Participants (Alphabetical authorship, apart from primary contributors). Addressing persistent challenges in digital image analysis of cancerous tissues [Internet]. bioRxiv; 2023 [cited 2023 Aug 18]. Available from: http://biorxiv.org/lookup/doi/10.1101/2023.07.21.548450

Raleigh D, Chen W, Choudhury A, Youngblood M, Polley MY, Lucas CH, Mirchia K, Maas S, Suwala A, Won M, Bayley J, Harmanci A, Harmanci A, Klisch T, Nguyen M, Vasudevan H, McCortney K, Yu T, Bhave V, Lam TC, Pu J, Leung G, Chang J, Perlow H, Palmer J, Haberler C, Berghoff A, Preusser M, Nicolaides T, Mawrin C, Agnihotri S, Resnick A, Rood B, Chew J, Young J, Boreta L, Braunstein S, Schulte J, Butowski N, Santagata S, Spetzler D, Bush NAO, Villanueva-Meyer J, Chandler J, Solomon D, Rogers C, Pugh S, Mehta M, Sneed P, Berger M, Horbinski C, McDermott M, Perry A, Bi W, Patel A, Sahm F, Magill S. Targeted gene expression profiling predicts meningioma outcomes and radiotherapy responses. Res Sq. 2023 Mar 20;rs.3.rs-2663611. PMCID: PMC10055655

Stopka SA, Ruiz D, Baquer G, Bodineau C, Hossain MA, Pellens VT, Regan MS, Pourquié O, Haigis MC, Bi WL, Coy SM, Santagata S, Agar NYR, Basu SS. Chemical QuantArray: A Quantitative Tool for Mass Spectrometry Imaging. Anal Chem. 2023 Jul 19; PMID: 37469028

Sun Y, Revach OY, Anderson S, Kessler EA, Wolfe CH, Jenney A, Mills CE, Robitschek EJ, Davis TGR, Kim S, Fu A, Ma X, Gwee J, Tiwari P, Du PP, Sindurakar P, Tian J, Mehta A, Schneider AM, Yizhak K, Sade-Feldman M, LaSalle T, Sharova T, Xie H, Liu S, Michaud WA, Saad-Beretta R, Yates KB, Iracheta-Vellve A, Spetz JKE, Qin X, Sarosiek KA, Zhang G, Kim JW, Su MY, Cicerchia AM, Rasmussen MQ, Klempner SJ, Juric D, Pai SI, Miller DM, Giobbie-Hurder A, Chen JH, Pelka K, Frederick DT, Stinson S, Ivanova E, Aref AR, Paweletz CP, Barbie DA, Sen DR, Fisher DE, Corcoran RB, Hacohen N, Sorger PK, Flaherty KT, Boland GM, Manguso RT, Jenkins RW. Targeting TBK1 to overcome resistance to cancer immunotherapy. Nature. 2023 Jan 12; PMID: 36634707

Wan G, Leung B, Nguyen N, DeSimone MS, Liu F, Choi MS, Ho D, Laucks V, Duey S, Sullivan RJ, Boland GM, LeBoeuf NR, Liu D, Gusev A, Kwatra SG, Sorger PK, Yu KH, Semenov YR. The impact of stage-related features in melanoma recurrence prediction: A machine learning approach. JAAD Int. 2023 Mar;10:28–30. PMCID: PMC9678753

Wang H, Wang Y, Li J, He Z, Boswell SA, Chung M, You F, Han S. Three tyrosine kinase inhibitors cause cardiotoxicity by inducing endoplasmic reticulum stress and inflammation in cardiomyocytes. BMC Med. 2023 Apr 17;21(1):147. PMCID: PMC10108821

Wang Y, Fan JL, Melms JC, Amin AD, Georgis Y, Barrera I, Ho P, Tagore S, Abril-Rodríguez G, He S, Jin Y, Biermann J, Hofree M, Caprio L, Berhe S, Khan SA, Henick BS, Ribas A, Macosko EZ, Chen F, Taylor AM, Schwartz GK, Carvajal RD, Azizi E, Izar B. Multimodal single-cell and whole-genome sequencing of small, frozen clinical specimens. Nat Genet. 2023 Jan;55(1):19–25. PMCID: PMC10155259

Warchol S, Krueger R, Nirmal AJ, Gaglia G, Jessup J, Ritch CC, Hoffer J, Muhlich J, Burger ML, Jacks T, Santagata S, Sorger PK, Pfister H. Visinity: Visual Spatial Neighborhood Analysis for Multiplexed Tissue Imaging Data. IEEE Trans Vis Comput Graph. 2023 Jan;29(1):106–116. PMCID: PMC10043053

Williams EA, Brastianos PK, Wakimoto H, Zolal A, Filbin MG, Cahill DP, Santagata S, Juratli TA. A comprehensive genomic study of 390 H3F3A-mutant pediatric and adult diffuse high-grade gliomas, CNS WHO grade 4. Acta Neuropathol. 2023 Sep;146(3):515–525. PMCID: PMC10412483

Zhang S, Tang K, Wan G, Nguyen N, Lu C, Ugwu-Dike P, Raval N, Seo J, Alexander NA, Jairath R, Phillipps J, Leung BW, Roster K, Chen W, Zubiri L, Boland G, Chen ST, Tsao H, Demehri S, LeBoeuf NR, Reynolds KL, Yu KH, Gusev A, Kwatra SG, Semenov YR. Cutaneous immune-related adverse events are associated with longer overall survival in advanced cancer patients on immune checkpoint inhibitors: A multi-institutional cohort study. J Am Acad Dermatol. 2023 May;88(5):1024–1032. PMCID: PMC10283025

Ahdritz G, Bouatta N, Floristean C, Kadyan S, Xia Q, Gerecke W, O’Donnell TJ, Berenberg D, Fisk I, Zanichelli N, Zhang B, Nowaczynski A, Wang B, Stepniewska-Dziubinska MM, Zhang S, Ojewole A, Guney ME, Biderman S, Watkins AM, Ra S, Lorenzo PR, Nivon L, Weitzner B, Ban YEA, Sorger PK, Mostaque E, Zhang Z, Bonneau R, AlQuraishi M. OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization [Internet]. Bioinformatics; 2022 [cited 2023 Aug 18]. Available from: http://biorxiv.org/lookup/doi/10.1101/2022.11.20.517210

Anderson AC, Yanai I, Yates LR, Wang L, Swarbrick A, Sorger P, Santagata S, Fridman WH, Gao Q, Jerby L, Izar B, Shang L, Zhou X. Spatial transcriptomics. Cancer Cell. 2022 Sep 12;40(9):895–900. PMID: 36099884

Balabin H, Hoyt CT, Birkenbihl C, Gyori BM, Bachman J, Kodamullil AT, Plöger PG, Hofmann-Apitius M, Domingo-Fernández D. STonKGs: a sophisticated transformer trained on biomedical text and knowledge graphs. Bioinformatics. 2022 Mar 4;38(6):1648–1656. PMCID: PMC8896635

Bi WL, Santagata S. Skull Base Tumors: Neuropathology and Clinical Implications. Neurosurgery. 2022 Mar 1;90(3):243–261. PMID: 34164689

Bi WL, Nayak L, Meredith DM, Driver J, Du Z, Hoffman S, Li Y, Lee EQ, Beroukhim R, Rinne M, McFaline-Figueroa R, Chukwueke U, McCluskey C, Gaffey S, Cherniack AD, Stefanik J, Doherty L, Taubert C, Cifrino M, LaFrankie D, Graillon T, Wen PY, Ligon KL, Al-Mefty O, Huang RY, Muzikansky A, Chiocca EA, Santagata S, Dunn IF, Reardon DA. Activity of PD-1 blockade with nivolumab among patients with recurrent atypical/anaplastic meningioma: phase II trial results. Neuro Oncol. 2022 Jan 5;24(1):101–113. PMCID: PMC8730772

Bonner S, Barrett IP, Ye C, Swiers R, Engkvist O, Bender A, Hoyt CT, Hamilton WL. A review of biomedical datasets relating to drug discovery: a knowledge graph perspective. Briefings in Bioinformatics [Internet]. 2022 Sep 23 [cited 2022 Sep 26];bbac404. Available from: https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbac404/6712301

Brastianos PK, Kim AE, Giobbie-Hurder A, Lee EQ, Wang N, Eichler AF, Chukwueke U, Forst DA, Arrillaga-Romany IC, Dietrich J, Corbin Z, Moliterno J, Baehring J, White M, Lou KW, Larson J, de Sauvage MA, Evancic K, Mora J, Nayyar N, Loeffler J, Oh K, Shih HA, Curry WT, Cahill DP, Barker FG, Gerstner ER, Santagata S. Phase 2 study of pembrolizumab in patients with recurrent and residual high-grade meningiomas. Nat Commun. 2022 Mar 14;13(1):1325. PMCID: PMC8921328

Charpignon ML, Vakulenko-Lagun B, Zheng B, Magdamo C, Su B, Evans K, Rodriguez S, Sokolov A, Boswell S, Sheu YH, Somai M, Middleton L, Hyman BT, Betensky RA, Finkelstein SN, Welsch RE, Tzoulaki I, Blacker D, Das S, Albers MW. Causal inference in medical records and complementary systems pharmacology for metformin drug repurposing towards dementia. Nat Commun. 2022 Dec 10;13(1):7652. PMCID: PMC9741618

Chowdhury R, Bouatta N, Biswas S, Floristean C, Kharkar A, Roy K, Rochereau C, Ahdritz G, Zhang J, Church GM, Sorger PK, AlQuraishi M. Single-sequence protein structure prediction using a language model and deep learning. Nat Biotechnol. 2022 Oct 3; PMID: 36192636

Coy S, Wang S, Stopka SA, Lin JR, Yapp C, Ritch CC, Salhi L, Baker GJ, Rashid R, Baquer G, Regan M, Khadka P, Cole KA, Hwang J, Wen PY, Bandopadhayay P, Santi M, De Raedt T, Ligon KL, Agar NYR, Sorger PK, Touat M, Santagata S. Single cell spatial analysis reveals the topology of immunomodulatory purinergic signaling in glioblastoma. Nat Commun. 2022 Aug 16;13(1):4814. PMCID: PMC9381513

Creason AL, Watson C, Gu Q, Persson D, Sargent LL, Chen YA, Lin JR, Sivagnanam S, Wünnemann F, Nirmal AJ, Chin K, Feiler HS, Coussens LM, Schapiro D, Grüning BA, Sorger PK, Sokolov A, Goecks J. A Web-based Software Resource for Interactive Analysis of Multiplex Tissue Imaging Datasets [Internet]. bioRxiv; 2022 [cited 2022 Aug 22]. Available from: DOI: 10.1101/2022.08.18.504436

CSBC/PS-ON Image Analysis Working Group, Vizcarra JC, Burlingame EA, Hug CB, Goltsev Y, White BS, Tyson DR, Sokolov A. A community-based approach to image analysis of cells, tissues and tumors. Comput Med Imaging Graph. 2022 Jan;95:102013. PMCID: PMC8761177

de Crécy-Lagard V, Amorin de Hegedus R, Arighi C, Babor J, Bateman A, Blaby I, Blaby-Haas C, Bridge AJ, Burley SK, Cleveland S, Colwell LJ, Conesa A, Dallago C, Danchin A, de Waard A, Deutschbauer A, Dias R, Ding Y, Fang G, Friedberg I, Gerlt J, Goldford J, Gorelik M, Gyori BM, Henry C, Hutinet G, Jaroch M, Karp PD, Kondratova L, Lu Z, Marchler-Bauer A, Martin MJ, McWhite C, Moghe GD, Monaghan P, Morgat A, Mungall CJ, Natale DA, Nelson WC, O’Donoghue S, Orengo C, O’Toole KH, Radivojac P, Reed C, Roberts RJ, Rodionov D, Rodionova IA, Rudolf JD, Saleh L, Sheynkman G, Thibaud-Nissen F, Thomas PD, Uetz P, Vallenet D, Carter EW, Weigele PR, Wood V, Wood-Charlson EM, Xu J. A roadmap for the functional annotation of protein families: a community perspective. Database (Oxford). 2022 Aug 12;2022:baac062. PMCID: PMC9374478

Doherty LM, Mills CE, Boswell SA, Liu X, Hoyt CT, Gyori B, Buhrlage SJ, Sorger PK. Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes. Elife. 2022 Jun 23;11:e72879. PMCID: PMC9225015

Fraser CS, Spetz JKE, Qin X, Presser A, Choiniere J, Li C, Yu S, Blevins F, Hata AN, Miller JW, Bradshaw GA, Kalocsay M, Sanchorawala V, Sarosiek S, Sarosiek KA. Exploiting endogenous and therapy-induced apoptotic vulnerabilities in immunoglobulin light chain amyloidosis with BH3 mimetics. Nat Commun. 2022 Oct 2;13(1):5789. PMCID: PMC9527241

Fröhlich F, Sorger PK. Fides: Reliable trust-region optimization for parameter estimation of ordinary differential equation models. PLoS Comput Biol. 2022 Jul 13;18(7):e1010322. PMCID: PMC9312381

Gaglia G, Kabraji S, Rammos D, Dai Y, Verma A, Wang S, Mills CE, Chung M, Bergholz JS, Coy S, Lin JR, Jeselsohn R, Metzger O, Winer EP, Dillon DA, Zhao JJ, Sorger PK, Santagata S. Temporal and spatial topography of cell proliferation in cancer. Nat Cell Biol. 2022 Mar;24(3):316–326. PMCID: PMC8959396

Gray GK, Li CMC, Rosenbluth JM, Selfors LM, Girnius N, Lin JR, Schackmann RCJ, Goh WL, Moore K, Shapiro HK, Mei S, D’Andrea K, Nathanson KL, Sorger PK, Santagata S, Regev A, Garber JE, Dillon DA, Brugge JS. A human breast atlas integrating single-cell proteomics and transcriptomics. Dev Cell. 2022 Jun 6;57(11):1400-1420.e7. PMCID: PMC9202341

Gross SM, Dane MA, Smith RL, Devlin KL, McLean IC, Derrick DS, Mills CE, Subramanian K, London AB, Torre D, Evangelista JE, Clarke DJB, Xie Z, Erdem C, Lyons N, Natoli T, Pessa S, Lu X, Mullahoo J, Li J, Adam M, Wassie B, Liu M, Kilburn DF, Liby TA, Bucher E, Sanchez-Aguila C, Daily K, Omberg L, Wang Y, Jacobson C, Yapp C, Chung M, Vidovic D, Lu Y, Schurer S, Lee A, Pillai A, Subramanian A, Papanastasiou M, Fraenkel E, Feiler HS, Mills GB, Jaffe JD, Ma’ayan A, Birtwistle MR, Sorger PK, Korkola JE, Gray JW, Heiser LM. A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses. Commun Biol. 2022 Oct 7;5(1):1066. PMCID: PMC9546880

Gyori BM, Hoyt CT. PyBioPAX: biological pathway exchange in Python. JOSS [Internet]. 2022 Mar 11 [cited 2022 Apr 7];7(71):4136. Available from: https://joss.theoj.org/papers/10.21105/joss.04136 PMCID: PMC9447860

Gyori BM, Hoyt CT, Steppi A. Gilda: biomedical entity text normalization with machine-learned disambiguation as a service. Arighi C, editor. Bioinformatics Advances [Internet]. 2022 Jan 10 [cited 2022 Aug 9];2(1):vbac034. Available from: https://academic.oup.com/bioinformaticsadvances/article/doi/10.1093/bioadv/vbac034/6584365

Hodis E, Triglia ET, Kwon JYH, Biancalani T, Zakka LR, Parkar S, Hütter JC, Buffoni L, Delorey TM, Phillips D, Dionne D, Nguyen LT, Schapiro D, Maliga Z, Jacobson CA, Hendel A, Rozenblatt-Rosen O, Mihm MC, Garraway LA, Regev A. Stepwise-edited, human melanoma models reveal mutations’ effect on tumor and microenvironment. Science. 2022 Apr 29;376(6592):eabi8175. PMID: 35482859

Hoyt CT, Balk M, Callahan TJ, Domingo-Fernández D, Haendel MA, Hegde HB, Himmelstein DS, Karis K, Kunze J, Lubiana T, Matentzoglu N, McMurry J, Moxon S, Mungall CJ, Rutz A, Unni DR, Willighagen E, Winston D, Gyori BM. Unifying the identification of biomedical entities with the Bioregistry. Sci Data. 2022 Nov 19;9(1):714. PMCID: PMC9675740

Jessup J, Krueger R, Warchol S, Hoffer J, Muhlich J, Ritch CC, Gaglia G, Coy S, Chen YA, Lin JR, Santagata S, Sorger PK, Pfister H. Scope2Screen: focus+context techniques for pathology tumor assessment in multivariate image data. IEEE Trans Vis Comput Graph. 2022 Jan;28(1):259–269. PMCID: PMC8805697

Jiménez A, Lu D, Kalocsay M, Berberich MJ, Balbi P, Jambhekar A, Lahav G. Time-series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations. Mol Syst Biol. 2022 Mar;18(3):e10588. PMCID: PMC8919251

Larkins-Ford J, Degefu YN, Van N, Sokolov A, Aldridge BB. Design principles to assemble drug combinations for effective tuberculosis therapy using interpretable pairwise drug response measurements. Cell Rep Med. 2022 Sep 20;3(9):100737. PMCID: PMC9512659

Launonen IM, Lyytikäinen N, Casado J, Anttila EA, Szabó A, Haltia UM, Jacobson CA, Lin JR, Maliga Z, Howitt BE, Strickland KC, Santagata S, Elias K, D’Andrea AD, Konstantinopoulos PA, Sorger PK, Färkkilä A. Single-cell tumor-immune microenvironment of BRCA1/2 mutated high-grade serous ovarian cancer. Nat Commun. 2022 Feb 11;13(1):835. PMCID: PMC8837628

Lomakin A, Svedlund J, Strell C, Gataric M, Shmatko A, Rukhovich G, Park JS, Ju YS, Dentro S, Kleshchevnikov V, Vaskivskyi V, Li T, Bayraktar OA, Pinder S, Richardson AL, Santagata S, Campbell PJ, Russnes H, Gerstung M, Nilsson M, Yates LR. Spatial genomics maps the structure, nature and evolution of cancer clones. Nature. 2022 Nov;611(7936):594–602. PMCID: PMC9668746

Matentzoglu N, Goutte-Gattat D, Tan SZK, Balhoff JP, Carbon S, Caron AR, Duncan WD, Flack JE, Haendel M, Harris NL, Hogan WR, Hoyt CT, Jackson RC, Kim H, Kir H, Larralde M, McMurry JA, Overton JA, Peters B, Pilgrim C, Stefancsik R, Robb SM, Toro S, Vasilevsky NA, Walls R, Mungall CJ, Osumi-Sutherland D. Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies. Database (Oxford). 2022 Oct 8;2022:baac087. PMCID: PMC9547537

Mills CE, Subramanian K, Hafner M, Niepel M, Gerosa L, Chung M, Victor C, Gaudio B, Yapp C, Nirmal AJ, Clark N, Sorger PK. Multiplexed and reproducible high content screening of live and fixed cells using Dye Drop. Nat Commun. 2022 Nov 14;13(1):6918. PMCID: PMC9663587

Mohammad-Taheri S, Zucker J, Hoyt CT, Sachs K, Tewari V, Ness R, Vitek O. Do-calculus enables estimation of causal effects in partially observed biomolecular pathways. Bioinformatics. 2022 Jun 24;38(Suppl 1):i350–i358. PMID: 35758817

Muhlich JL, Chen YA, Yapp C, Russell D, Santagata S, Sorger PK. Stitching and registering highly multiplexed whole slide images of tissues and tumors using ASHLAR. Bioinformatics. 2022 Aug 16;btac544. PMCID: PMC9525007

Ng TSC, Hu H, Kronister S, Lee C, Li R, Gerosa L, Stopka SA, Burgenske DM, Khurana I, Regan MS, Vallabhaneni S, Putta N, Scott E, Matvey D, Giobbie-Hurder A, Kohler RH, Sarkaria JN, Parangi S, Sorger PK, Agar NYR, Jacene HA, Sullivan RJ, Buchbinder E, Mikula H, Weissleder R, Miller MA. Overcoming differential tumor penetration of BRAF inhibitors using computationally guided combination therapy. Sci Adv. 2022 Apr 29;8(17):eabl6339. PMCID: PMC9054019

Nirmal AJ, Maliga Z, Vallius T, Quattrochi B, Chen AA, Jacobson CA, Pelletier RJ, Yapp C, Arias-Camison R, Chen YA, Lian CG, Murphy GF, Santagata S, Sorger PK. The Spatial Landscape of Progression and Immunoediting in Primary Melanoma at Single-Cell Resolution. Cancer Discov. 2022 Jun 2;12(6):1518–1541. PMCID: PMC9167783

Notarangelo G, Spinelli JB, Perez EM, Baker GJ, Kurmi K, Elia I, Stopka SA, Baquer G, Lin JR, Golby AJ, Joshi S, Baron HF, Drijvers JM, Georgiev P, Ringel AE, Zaganjor E, McBrayer SK, Sorger PK, Sharpe AH, Wucherpfennig KW, Santagata S, Agar NYR, Suvà ML, Haigis MC. Oncometabolite d-2HG alters T cell metabolism to impair CD8+ T cell function. Science. 2022 Sep 30;377(6614):1519–1529. PMCID: PMC9629749

Palmer AC, Izar B, Hwangbo H, Sorger PK. Predictable Clinical Benefits without Evidence of Synergy in Trials of Combination Therapies with Immune-Checkpoint Inhibitors. Clin Cancer Res. 2022 Jan 15;28(2):368–377. PMCID: PMC9068233

Papa A, Zakharov SI, Katchman AN, Kushner JS, Chen BX, Yang L, Liu G, Jimenez AS, Eisert RJ, Bradshaw GA, Dun W, Ali SR, Rodriques A, Zhou K, Topkara V, Yang M, Morrow JP, Tsai EJ, Karlin A, Wan E, Kalocsay M, Pitt GS, Colecraft HM, Ben-Johny M, Marx SO. Rad regulation of CaV1.2 channels controls cardiac fight-or-flight response. Nat Cardiovasc Res. 2022 Nov;1(11):1022–1038. PMCID: PMC9681059

Pernas S, Guerriero JL, Naumenko S, Goel S, Regan MM, Hu J, Harrison BT, Lynce F, Lin NU, Partridge A, Morikawa A, Hutchinson J, Mittendorf EA, Sokolov A, Overmoyer B. Early on-treatment transcriptional profiling as a tool for improving pathological response prediction in HER2-positive inflammatory breast cancer. Ther Adv Med Oncol. 2022 Jul 30;14:17588359221113268. PMCID: PMC9340890

Plana D, Fell G, Alexander BM, Palmer AC, Sorger PK. Cancer patient survival can be parametrized to improve trial precision and reveal time-dependent therapeutic effects. Nat Commun. 2022 Feb 15;13(1):873. PMCID: PMC8847344

Plana D, Palmer AC, Sorger PK. Independent drug action in combination therapy: implications for precision oncology. Cancer Discov. 2022 Mar 1;12(3):606–624. PMCID: PMC8904281

Pomeroy AE, Schmidt EV, Sorger PK, Palmer AC. Drug independence and the curability of cancer by combination chemotherapy. Trends Cancer. 2022 Nov;8(11):915–929. PMCID: PMC9588605

Rashid R, Chen YA, Hoffer J, Muhlich JL, Lin JR, Krueger R, Pfister H, Mitchell R, Santagata S, Sorger PK. Narrative online guides for the interpretation of digital-pathology images and tissue-atlas data. Nat Biomed Eng. 2022 May;6(5):515–526. PMCID: PMC9079188

Reichart D, Lindberg EL, Maatz H, Miranda AMA, Viveiros A, Shvetsov N, Gärtner A, Nadelmann ER, Lee M, Kanemaru K, Ruiz-Orera J, Strohmenger V, DeLaughter DM, Patone G, Zhang H, Woehler A, Lippert C, Kim Y, Adami E, Gorham JM, Barnett SN, Brown K, Buchan RJ, Chowdhury RA, Constantinou C, Cranley J, Felkin LE, Fox H, Ghauri A, Gummert J, Kanda M, Li R, Mach L, McDonough B, Samari S, Shahriaran F, Yapp C, Stanasiuk C, Theotokis PI, Theis FJ, van den Bogaerdt A, Wakimoto H, Ware JS, Worth CL, Barton PJR, Lee YA, Teichmann SA, Milting H, Noseda M, Oudit GY, Heinig M, Seidman JG, Hubner N, Seidman CE. Pathogenic variants damage cell composition and single cell transcription in cardiomyopathies. Science. 2022 Aug 5;377(6606):eabo1984. PMCID: PMC9528698

Schapiro D, Yapp C, Sokolov A, Reynolds SM, Chen YA, Sudar D, Xie Y, Muhlich J, Arias-Camison R, Arena S, Taylor AJ, Nikolov M, Tyler M, Lin JR, Burlingame EA, Human Tumor Atlas Network, Chang YH, Farhi SL, Thorsson V, Venkatamohan N, Drewes JL, Pe’er D, Gutman DA, Herrmann MD, Gehlenborg N, Bankhead P, Roland JT, Herndon JM, Snyder MP, Angelo M, Nolan G, Swedlow JR, Schultz N, Merrick DT, Mazzili SA, Cerami E, Rodig SJ, Santagata S, Sorger PK. MITI minimum information guidelines for highly multiplexed tissue images. Nat Methods. 2022 Mar;19(3):262–267. PMCID: PMC9009186

Schapiro D, Sokolov A, Yapp C, Chen YA, Muhlich JL, Hess J, Creason AL, Nirmal AJ, Baker GJ, Nariya MK, Lin JR, Maliga Z, Jacobson CA, Hodgman MW, Ruokonen J, Farhi SL, Abbondanza D, McKinley ET, Persson D, Betts C, Sivagnanam S, Regev A, Goecks J, Coffey RJ, Coussens LM, Santagata S, Sorger PK. MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging. Nat Methods. 2022 Mar;19(3):311–315. PMCID: PMC8916956

Schink SJ, Christodoulou D, Mukherjee A, Athaide E, Brunner V, Fuhrer T, Bradshaw GA, Sauer U, Basan M. Glycolysis/gluconeogenesis specialization in microbes is driven by biochemical constraints of flux sensing. Mol Syst Biol. 2022 Jan;18(1):e10704. PMID: 34994048

Scholten B, Simón LG, Krishnan S, Vermeulen R, Pronk A, Gyori BM, Bachman JA, Vlaanderen J, Stierum R. Automated Network Assembly of Mechanistic Literature for Informed Evidence Identification to Support Cancer Risk Assessment. Environ Health Perspect. 2022 Mar;130(3):37002. PMID: 35238605

Sekar G, Singh G, Qin X, Guibao CD, Schwam B, Inde Z, Grace CR, Zhang W, Slavish PJ, Lin W, Chen T, Lee RE, Rankovic Z, Sarosiek K, Moldoveanu T. Small molecule SJ572946 activates BAK to initiate apoptosis. iScience [Internet]. 2022 [cited 2022 Sep 26];25(10):105064. Available from: https://linkinghub.elsevier.com/retrieve/pii/S2589004222013360

Spetz JKE, Florido MHC, Fraser CS, Qin X, Choiniere J, Yu SJ, Singh R, Friesen M, Rubin LL, Salem JE, Moslehi JJ, Sarosiek KA. Heightened apoptotic priming of vascular cells across tissues and life span predisposes them to cancer therapy-induced toxicities. Sci Adv. 2022 Nov 11;8(45):eabn6579. PMCID: PMC9645721

Abtahi S, Gliksman NR, Heneghan JF, Nilsen SP, Muhlich JL, Copeland J, Rozbicki E, Allan C, Dudeja PK, Turner JR. A Simple Method for Creating a High-Content Microscope for Imaging Multiplexed Tissue Microarrays. Curr Protoc. 2021 Apr;1(4):e68. PMCID: PMC8103673

AlQuraishi M, Sorger PK. Differentiable biology: using deep learning for biophysics-based and data-driven modeling of molecular mechanisms. Nat Methods. 2021 Oct;18(10):1169–1180. PMCID: PMC8793939

Antonini MJ, Plana D, Srinivasan S, Atta L, Achanta A, Yang H, Cramer AK, Freake J, Sinha MS, Yu SH, LeBoeuf NR, Linville-Engler B, Sorger PK. A crisis-responsive framework for medical device development applied to the COVID-19 pandemic. Front Digit Health. 2021 Mar;3:617106. PMCID: PMC8064560

Bouatta N, Sorger P, AlQuraishi M. Protein structure prediction by AlphaFold2: are attention and symmetries all you need? Acta Crystallogr D Struct Biol. 2021 Aug 1;77(Pt 8):982–991. PMCID: PMC8329862

Břinda K, Baym M, Kucherov G. Simplitigs as an efficient and scalable representation of de Bruijn graphs. Genome Biol. 2021 Apr 6;22(1):96. PMCID: PMC8025321

Burger ML, Cruz AM, Crossland GE, Gaglia G, Ritch CC, Blatt SE, Bhutkar A, Canner D, Kienka T, Tavana SZ, Barandiaran AL, Garmilla A, Schenkel JM, Hillman M, de Los Rios Kobara I, Li A, Jaeger AM, Hwang WL, Westcott PMK, Manos MP, Holovatska MM, Hodi FS, Regev A, Santagata S, Jacks T. Antigen dominance hierarchies shape TCF1+ progenitor CD8 T cell phenotypes in tumors. Cell. 2021 Sep 16;184(19):4996-5014.e26. PMCID: PMC8522630

Cramer AK, Plana D, Yang H, Carmack MM, Tian E, Sinha MS, Krikorian D, Turner D, Mo J, Li J, Gupta R, Manning H, Bourgeois FT, Yu SH, Sorger PK, LeBoeuf NR. Analysis of SteraMist ionized hydrogen peroxide technology in the sterilization of N95 respirators and other PPE. Sci Rep. 2021 Jan 21;11(1):2051. PMCID: PMC7819989

Drijvers JM, Gillis JE, Muijlwijk T, Nguyen TH, Gaudiano EF, Harris IS, LaFleur MW, Ringel AE, Yao CH, Kurmi K, Juneja VR, Trombley JD, Haigis MC, Sharpe AH. Pharmacologic screening identifies metabolic vulnerabilities of CD8+ T cells. Cancer Immunol Res. 2021 Feb;9(2):184–199. PMCID: PMC7864883

Duraiswamy J, Turrini R, Minasyan A, Barras D, Crespo I, Grimm AJ, Casado J, Genolet R, Benedetti F, Wicky A, Ioannidou K, Castro W, Neal C, Moriot A, Renaud-Tissot S, Anstett V, Fahr N, Tanyi JL, Eiva MA, Jacobson CA, Montone KT, Westergaard MCW, Svane IM, Kandalaft LE, Delorenzi M, Sorger PK, Färkkilä A, Michielin O, Zoete V, Carmona SJ, Foukas PG, Powell DJ, Rusakiewicz S, Doucey MA, Dangaj Laniti D, Coukos G. Myeloid antigen-presenting cell niches sustain antitumor T cells and license PD-1 blockade via CD28 costimulation. Cancer Cell. 2021 Dec 13;39(12):1623-1642.e20. PMCID: PMC8861565

Färkkilä A, Rodríguez A, Oikkonen J, Gulhan DC, Nguyen H, Domínguez J, Ramos S, Mills CE, Pérez-Villatoro F, Lazaro JB, Zhou J, Clairmont CS, Moreau LA, Park PJ, Sorger PK, Hautaniemi S, Frias S, D’Andrea AD. Heterogeneity and Clonal Evolution of Acquired PARP Inhibitor Resistance in TP53- and BRCA1-Deficient Cells. Cancer Res. 2021 May 15;81(10):2774–2787. PMCID: PMC8323804

Fröhlich F, Weindl D, Schälte Y, Pathirana D, Paszkowski Ł, Lines GT, Stapor P, Hasenauer J. AMICI: high-performance sensitivity analysis for large ordinary differential equation models. Bioinformatics. 2021 Apr 2;btab227. PMCID: PMC8545331

Goldberg J, Pastorello RG, Vallius T, Davis J, Cui YX, Agudo J, Waks AG, Keenan T, McAllister SS, Tolaney SM, Mittendorf EA, Guerriero JL. The Immunology of Hormone Receptor Positive Breast Cancer. Front Immunol. 2021;12:674192. PMCID: PMC8202289

Gyori BM, Bachman JA. From knowledge to models: Automated modeling in systems and synthetic biology. Current Opinion in Systems Biology. 2021;28:100362.

Hemming ML, Coy S, Lin JR, Andersen JL, Przybyl J, Mazzola E, Abdelhamid Ahmed AH, van de Rijn M, Sorger PK, Armstrong SA, Demetri GD, Santagata S. HAND1 and BARX1 act as transcriptional and anatomic determinants of malignancy in gastrointestinal stromal tumor. Clin Cancer Res. 2021 Mar 15;27(6):1706–1719. PMCID: PMC7956056

Ietswaart R, Gyori BM, Bachman JA, Sorger PK, Churchman LS. GeneWalk identifies relevant gene functions for a biological context using network representation learning. Genome Biol. 2021 Feb 2;22(1):55. PMCID: PMC7852222

Inde Z, Croker BA, Yapp C, Joshi GN, Spetz J, Fraser C, Qin X, Xu L, Deskin B, Ghelfi E, Webb G, Carlin AF, Zhu YP, Leibel SL, Garretson AF, Clark AE, Duran JM, Pretorius V, Crotty-Alexander LE, Li C, Lee JC, Sodhi C, Hackam DJ, Sun X, Hata AN, Kobzik L, Miller J, Park JA, Brownfield D, Jia H, Sarosiek KA. Age-dependent regulation of SARS-CoV-2 cell entry genes and cell death programs correlates with COVID-19 severity. Sci Adv. 2021 Aug 18;7(34):eabf8609. PMCID: PMC8373124

Jerby-Arnon L, Neftel C, Shore ME, Weisman HR, Mathewson ND, McBride MJ, Haas B, Izar B, Volorio A, Boulay G, Cironi L, Richman AR, Broye LC, Gurski JM, Luo CC, Mylvaganam R, Nguyen L, Mei S, Melms JC, Georgescu C, Cohen O, Buendia-Buendia JE, Segerstolpe A, Sud M, Cuoco MS, Labes D, Gritsch S, Zollinger DR, Ortogero N, Beechem JM, Petur Nielsen G, Chebib I, Nguyen-Ngoc T, Montemurro M, Cote GM, Choy E, Letovanec I, Cherix S, Wagle N, Sorger PK, Haynes AB, Mullen JT, Stamenkovic I, Rivera MN, Kadoch C, Wucherpfennig KW, Rozenblatt-Rosen O, Suvà ML, Riggi N, Regev A. Opposing immune and genetic mechanisms shape oncogenic programs in synovial sarcoma. Nat Med. 2021 Feb;27(2):289–300. PMCID: PMC8817899

Jiang B, Gao Y, Che J, Lu W, Kaltheuner IH, Dries R, Kalocsay M, Berberich MJ, Jiang J, You I, Kwiatkowski N, Riching KM, Daniels DL, Sorger PK, Geyer M, Zhang T, Gray NS. Discovery and resistance mechanism of a selective CDK12 degrader. Nat Chem Biol. 2021 Jun;17(6):675–683. PMCID: PMC8590456

Kassamali B, Yu Z, Davis C, Carmack M, Bui ATN, Said JT, Plana D, Yang H, Sorger P, LeBoeuf NR, LaChance AH. Conversion of existing UVB phototherapy units to UVC germicidal chambers for N95 decontamination: lessons learned. Photobiomodul Photomed Laser Surg. 2021 Feb;39(2):83–85. PMCID: PMC8106246

Keenan TE, Li T, Vallius T, Guerriero JL, Tayob N, Kochupurakkal B, Davis J, Pastorello R, Tahara RK, Anderson L, Conway J, He MX, Shannon E, Godin RE, Sorger PK, D’Andrea A, Overmoyer B, Winer EP, Mittendorf EA, Van Allen EM, Shapiro GI, Tolaney SM. Clinical efficacy and molecular response correlates of the WEE1 inhibitor adavosertib combined with cisplatin in patients with metastatic triple-negative breast cancer. Clin Cancer Res. 2021 Feb 15;27(4):983–991. PMCID: PMC7887044

Koikawa K, Kibe S, Suizu F, Sekino N, Kim N, Manz TD, Pinch BJ, Akshinthala D, Verma A, Gaglia G, Nezu Y, Ke S, Qiu C, Ohuchida K, Oda Y, Lee TH, Wegiel B, Clohessy JG, London N, Santagata S, Wulf GM, Hidalgo M, Muthuswamy SK, Nakamura M, Gray NS, Zhou XZ, Lu KP. Targeting Pin1 renders pancreatic cancer eradicable by synergizing with immunochemotherapy. Cell. 2021 Sep 2;184(18):4753-4771.e27. PMCID: PMC8557351

Kothakonda A, Atta L, Plana D, Ward F, Davis C, Cramer A, Moran R, Freake J, Tian E, Mazor O, Gorelik P, Van C, Hansen C, Yang H, Li Y, Sinha MS, Li J, Yu SH, LeBoeuf NR, Sorger PK. De novo powered air-purifying respirator design and fabrication for pandemic response. Front Bioeng Biotechnol. 2021 Sep 6;9:690905. PMCID: PMC8450396

Larkins-Ford J, Greenstein T, Van N, Degefu YN, Olson MC, Sokolov A, Aldridge BB. Systematic measurement of combination-drug landscapes to predict in vivo treatment outcomes for tuberculosis. Cell Syst. 2021 Nov 17;12(11):1046-1063.e7. PMCID: PMC8617591

Lee J, Vernet A, Gruber NG, Kready KM, Burrill DR, Way JC, Silver PA. Rational engineering of an erythropoietin fusion protein to treat hypoxia. Protein Eng Des Sel. 2021 Feb 15;34:gzab025. PMID: 34725710

Leipzig J, Nüst D, Hoyt CT, Ram K, Greenberg J. The role of metadata in reproducible computational research. Patterns (N Y). 2021 Sep 10;2(9):100322. PMCID: PMC8441584

Li J, Duran MA, Dhanota N, Chatila WK, Bettigole SE, Kwon J, Sriram RK, Humphries MP, Salto-Tellez M, James JA, Hanna MG, Melms JC, Vallabhaneni S, Litchfield K, Usaite I, Biswas D, Bareja R, Li HW, Martin ML, Dorsaint P, Cavallo JA, Li P, Pauli C, Gottesdiener L, DiPardo BJ, Hollmann TJ, Merghoub T, Wen HY, Reis-Filho JS, Riaz N, Su SSM, Kalbasi A, Vasan N, Powell SN, Wolchok JD, Elemento O, Swanton C, Shoushtari AN, Parkes EE, Izar B, Bakhoum SF. Metastasis and immune evasion from extracellular cGAMP hydrolysis. Cancer Discov. 2021 May;11(5):1212–1227. PMCID: PMC8102348

Lukyanenko S, Jang WD, Wei D, Struyven R, Kim Y, Leahy B, Yang H, Rush A, Ben-Yosef D, Needleman D, Pfister H. Developmental stage classification of embryos using two-stream neural network with linear-chain conditional random field. Med Image Comput Comput Assist Interv. 2021 Sep;12908:363–372. PMCID: PMC8526069

Maliga Z, Nirmal AJ, Ericson NG, Boswell SA, U’Ren L, Podyminogin R, Chow J, Chen YA, Chen AA, Weinstock DM, Lian CG, Murphy GF, Kaldjian EP, Santagata S, Sorger PK. Micro-region transcriptomics of fixed human tissue using Pick-Seq [Internet]. bioRxiv; 2021 [cited 2021 Mar 19]. Available from: DOI: 10.1101/2021.03.18.431004

Mancuso CP, Lu ZX, Qian J, Boswell SA, Springer M. A Semi-Quantitative Isothermal Diagnostic Assay Utilizing Competitive Amplification. Anal Chem. 2021 Jun 28;acs.analchem.1c01576. PMID: 34180655

May EA, Kalocsay M, D’Auriac IG, Schuster PS, Gygi SP, Nachury MV, Mick DU. Time-resolved proteomics profiling of the ciliary Hedgehog response. J Cell Biol. 2021 May 3;220(5). PMCID: PMC8054476

McAvoy M, Bui ATN, Hansen C, Plana D, Said JT, Yu Z, Yang H, Freake J, Van C, Krikorian D, Cramer A, Smith L, Jiang L, Lee KJ, Li SJ, Beller B, Huggins K, Short MP, Yu SH, Mostaghimi A, Sorger PK, LeBoeuf NR. 3D Printed frames to enable reuse and improve the fit of N95 and KN95 respirators. BMC Biomed Eng. 2021 Jun 7;3(1):10. PMCID: PMC8182357

Mehta AK, Cheney EM, Hartl CA, Pantelidou C, Oliwa M, Castrillon JA, Lin JR, Hurst KE, de Oliveira Taveira M, Johnson NT, Oldham WM, Kalocsay M, Berberich MJ, Boswell SA, Kothari A, Johnson S, Dillon DA, Lipschitz M, Rodig S, Santagata S, Garber JE, Tung N, Yélamos J, Thaxton JE, Mittendorf EA, Sorger PK, Shapiro GI, Guerriero JL. Targeting immunosuppressive macrophages overcomes PARP inhibitor resistance in BRCA1-associated triple-negative breast cancer. Nat Cancer. 2021 Jan;2(1):66–82. PMCID: PMC7963404

Melms JC, Biermann J, Huang H, Wang Y, Nair A, Tagore S, Katsyv I, Rendeiro AF, Amin AD, Schapiro D, Frangieh CJ, Luoma AM, Filliol A, Fang Y, Ravichandran H, Clausi MG, Alba GA, Rogava M, Chen SW, Ho P, Montoro DT, Kornberg AE, Han AS, Bakhoum MF, Anandasabapathy N, Suárez-Fariñas M, Bakhoum SF, Bram Y, Borczuk A, Guo XV, Lefkowitch JH, Marboe C, Lagana SM, Del Portillo A, Tsai EJ, Zorn E, Markowitz GS, Schwabe RF, Schwartz RE, Elemento O, Saqi A, Hibshoosh H, Que J, Izar B. A molecular single-cell lung atlas of lethal COVID-19. Nature. 2021 Jul;595(7865):114–119. PMCID: PMC8814825

Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Monraz Gómez LC, Somers J, Hoch M, Kumar Gupta S, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Ponce de Leon M, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic-Milacic M, Senff Ribeiro A, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel JM, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, de Waard A, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Esteban-Medina M, Peña-Chilet M, Rian K, Helikar T, Puniya BL, Modos D, Treveil A, Olbei M, De Meulder B, Ballereau S, Dugourd A, Naldi A, Noël V, Calzone L, Sander C, Demir E, Korcsmaros T, Freeman TC, Augé F, Beckmann JS, Hasenauer J, Wolkenhauer O, Wilighagen EL, Pico AR, Evelo CT, Gillespie ME, Stein LD, Hermjakob H, D’Eustachio P, Saez-Rodriguez J, Dopazo J, Valencia A, Kitano H, Barillot E, Auffray C, Balling R, Schneider R, COVID-19 Disease Map Community. COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Mol Syst Biol. 2021 Oct;17(10):e10387. PMCID: PMC8524328

Owen SV, Wenner N, Dulberger CL, Rodwell EV, Bowers-Barnard A, Quinones-Olvera N, Rigden DJ, Rubin EJ, Garner EC, Baym M, Hinton JCD. Prophages encode phage-defense systems with cognate self-immunity. Cell Host Microbe. 2021 Nov 10;29(11):1620-1633.e8. PMCID: PMC8585504

Patiño-Galindo JÁ, Filip I, Chowdhury R, Maranas CD, Sorger PK, AlQuraishi M, Rabadan R. Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2. Genome Med. 2021 Aug 6;13(1):124. PMCID: PMC8343217

Pence IJ, Evans CL. Translational biophotonics with Raman imaging: clinical applications and beyond. Analyst. 2021 Oct 25;146(21):6379–6393. PMCID: PMC8543123

Pettit ME, Boswell SA, Qian J, Novak R, Springer M. Accessioning and automation compatible anterior nares swab design. J Virol Methods. 2021 May 10;114153. PMCID: PMC8108477

Plana D, Tian E, Cramer AK, Yang H, Carmack MM, Sinha MS, Bourgeois FT, Yu SH, Masse P, Boyer J, Kim M, Mo J, LeBoeuf NR, Li J, Sorger PK. Assessing the filtration efficiency and regulatory status of N95s and nontraditional filtering face-piece respirators available during the COVID-19 pandemic. BMC Infect Dis. 2021 Jul 29;21(1):712. PMCID: PMC8319695

Pomeranz Krummel DA, Nasti TH, Kaluzova M, Kallay L, Bhattacharya D, Melms JC, Izar B, Xu M, Burnham A, Ahmed T, Li G, Lawson D, Kowalski J, Cao Y, Switchenko JM, Ionascu D, Cook JM, Medvedovic M, Jenkins A, Khan MK, Sengupta S. Melanoma cell intrinsic GABAA receptor enhancement potentiates radiation and immune checkpoint inhibitor response by promoting direct and T cell-mediated antitumor activity. Int J Radiat Oncol Biol Phys. 2021 Mar 15;109(4):1040–1053. PMCID: PMC8329598

Rodriguez S, Sahin A, Schrank BR, Al-Lawati H, Costantino I, Benz E, Fard D, Albers AD, Cao L, Gomez AC, Evans K, Ratti E, Cudkowicz M, Frosch MP, Talkowski M, Sorger PK, Hyman BT, Albers MW. Genome-encoded cytoplasmic double-stranded RNAs, found in C9ORF72 ALS-FTD brain, propagate neuronal loss. Sci Transl Med. 2021 Jul 7;13(601):eaaz4699. PMID: 34233951

Rodriguez S, Hug C, Todorov P, Moret N, Boswell SA, Evans K, Zhou G, Johnson NT, Hyman BT, Sorger PK, Albers MW, Sokolov A. Machine learning identifies candidates for drug repurposing in Alzheimer’s disease. Nat Commun. 2021 Feb 15;12(1):1033. PMCID: PMC7884393

Schmiester L, Schälte Y, Bergmann FT, Camba T, Dudkin E, Egert J, Fröhlich F, Fuhrmann L, Hauber AL, Kemmer S, Lakrisenko P, Loos C, Merkt S, Müller W, Pathirana D, Raimúndez E, Refisch L, Rosenblatt M, Stapor PL, Städter P, Wang D, Wieland FG, Banga JR, Timmer J, Villaverde AF, Sahle S, Kreutz C, Hasenauer J, Weindl D. PEtab-Interoperable specification of parameter estimation problems in systems biology. PLoS Comput Biol. 2021 Jan 26;17(1):e1008646. PMCID: PMC7864467

Schmucker R, Farina G, Faeder J, Fröhlich F, Saglam AS, Sandholm T. Combination treatment optimization using a pan-cancer pathway model. PLoS Comput Biol. 2021 Dec 28;17(12):e1009689. PMCID: PMC8747684

Shimada K, Bachman JA, Muhlich JL, Mitchison TJ. shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data. Elife. 2021 Feb 8;10:e57116. PMCID: PMC7924953

Sritharan D, Wang S, Hormoz S. Computing the Riemannian curvature of image patch and single-cell RNA sequencing data manifolds using extrinsic differential geometry. Proc Natl Acad Sci U S A. 2021 Jul 20;118(29):e2100473118. PMCID: PMC8307776

Tsabar M, Lovitch SB, Jambhekar A, Lahav G. Connecting Timescales in Biology: Can Early Dynamical Measurements Predict Long-Term Outcomes? Trends Cancer. 2021 Apr;7(4):301–308. PMCID: PMC8796003

Vemulapalli V, Chylek LA, Erickson A, Pfeiffer A, Gabriel KH, LaRochelle J, Subramanian K, Cao R, Stegmaier K, Mohseni M, LaMarche MJ, Acker MG, Sorger PK, Gygi SP, Blacklow SC. Time-resolved phosphoproteomics reveals scaffolding and catalysis-responsive patterns of SHP2-dependent signaling. Elife. 2021 Mar 23;10:e64251. PMCID: PMC8024022

Wong JV, Franz M, Siper MC, Fong D, Durupinar F, Dallago C, Luna A, Giorgi J, Rodchenkov I, Babur Ö, Bachman JA, Gyori BM, Demir E, Bader GD, Sander C. Author-sourced capture of pathway knowledge in computable form using Biofactoid. Elife [Internet]. 2021 Dec 3 [cited 2022 Aug 9];10:e68292. Available from: https://elifesciences.org/articles/68292 PMCID: PMC8683078

Aid M, Busman-Sahay K, Vidal SJ, Maliga Z, Bondoc S, Starke C, Terry M, Jacobson CA, Wrijil L, Ducat S, Brook OR, Miller AD, Porto M, Pellegrini KL, Pino M, Hoang TN, Chandrashekar A, Patel S, Stephenson K, Bosinger SE, Andersen H, Lewis MG, Hecht JL, Sorger PK, Martinot AJ, Estes JD, Barouch DH. Vascular disease and thrombosis in SARS-CoV-2-infected rhesus macaques. Cell. 2020 Nov 25;183(5):1354-1366.e13. PMCID: PMC7546181

Berginski ME, Moret N, Liu C, Goldfarb D, Sorger PK, Gomez SM. The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases. Nucleic Acids Res. 2020 Oct 20;49(D1):D529–D535. PMCID: PMC7778917

Bhola PD, Ahmed E, Guerriero JL, Sicinska E, Su E, Lavrova E, Ni J, Chipashvili O, Hagan T, Pioso MS, McQueeney K, Ng K, Aguirre AJ, Cleary JM, Cocozziello D, Sotayo A, Ryan J, Zhao JJ, Letai A. High-throughput dynamic BH3 profiling may quickly and accurately predict effective therapies in solid tumors. Sci Signal. 2020 Jun 16;13(636). PMCID: PMC8023011

Břinda K, Callendrello A, Ma KC, MacFadden DR, Charalampous T, Lee RS, Cowley L, Wadsworth CB, Grad YH, Kucherov G, O’Grady J, Baym M, Hanage WP. Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing. Nat Microbiol. 2020;5(3):455–464. PMCID: PMC7044115

Chopra SS, Jenney A, Palmer A, Niepel M, Chung M, Mills C, Sivakumaren SC, Liu Q, Chen JY, Yapp C, Asara JM, Gray NS, Sorger PK. Torin2 exploits replication and checkpoint vulnerabilities to cause death of PI3K-activated triple-negative breast cancer cells. Cell Syst. 2020 Jan 22;10(1):66-81.e11. PMCID: PMC7000271

Coy S, Rashid R, Stemmer-Rachamimov A, Santagata S. An update on the CNS manifestations of neurofibromatosis type 2. Acta Neuropathol. 2020 Apr;139(4):643–665. PMCID: PMC7038792

Cunningham JM, Koytiger G, Sorger PK, AlQuraishi M. Biophysical prediction of protein-peptide interactions and signaling networks using machine learning. Nat Methods. 2020 Feb;17(2):175–183. PMCID: PMC7004877

Drijvers JM, Sharpe AH, Haigis MC. The effects of age and systemic metabolism on anti-tumor T cell responses. Elife. 2020 Nov 10;9:e62420. PMCID: PMC7655106

Drouin A, Wallbillich N, Theberge M, Liu S, Katz J, Bellovoda K, Se Yun Cheon S, Gootkind F, Bierman E, Zavras J, Berberich MJ, Kalocsay M, Guastaldi F, Salvadori N, Troulis M, Fusco DN. Impact of Zika virus on the human type I interferon osteoimmune response. Cytokine. 2020 Oct 29;137:155342. PMID: 33130337

Du G, Rao S, Gurbani D, Henning NJ, Jiang J, Che J, Yang A, Ficarro SB, Marto JA, Aguirre AJ, Sorger PK, Westover KD, Zhang T, Gray NS. Structure-Based Design of a Potent and Selective Covalent Inhibitor for SRC Kinase That Targets a P-Loop Cysteine. J Med Chem. 2020 Jan 30; PMID: 31935084

Färkkilä A, Gulhan DC, Casado J, Jacobson CA, Nguyen H, Kochupurakkal B, Maliga Z, Yapp C, Chen YA, Schapiro D, Zhou Y, Graham JR, Dezube BJ, Munster P, Santagata S, Garcia E, Rodig S, Lako A, Chowdhury D, Shapiro GI, Matulonis UA, Park PJ, Hautaniemi S, Sorger PK, Swisher EM, D’Andrea AD, Konstantinopoulos PA. Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer. Nat Commun. 2020 Mar 19;11(1):1459. PMCID: PMC7081234

Gaglia G, Rashid R, Yapp C, Joshi GN, Li CG, Lindquist SL, Sarosiek KA, Whitesell L, Sorger PK, Santagata S. HSF1 phase transition mediates stress adaptation and cell fate decisions. Nat Cell Biol. 2020 Feb;22(2):151–158. PMCID: PMC7135912

Gerosa L, Chidley C, Fröhlich F, Sanchez G, Lim SK, Muhlich J, Chen JY, Vallabhaneni S, Baker GJ, Schapiro D, Atanasova MI, Chylek LA, Shi T, Yi L, Nicora CD, Claas A, Ng TSC, Kohler RH, Lauffenburger DA, Weissleder R, Miller MA, Qian WJ, Wiley HS, Sorger PK. Receptor-driven ERK pulses reconfigure MAPK signaling and enable persistence of drug-adapted BRAF-mutant melanoma cells. Cell Syst. 2020 Nov 18;11(5):478-494.e9. PMCID: PMC8009031

Gevertz JL, Greene JM, Sanchez-Tapia CH, Sontag ED. A novel COVID-19 epidemiological model with explicit susceptible and asymptomatic isolation compartments reveals unexpected consequences of timing social distancing. J Theor Biol. 2020 Nov 23;110539. PMID: 33242489

Hafner A, Reyes J, Stewart-Ornstein J, Tsabar M, Jambhekar A, Lahav G. Quantifying the Central Dogma in the p53 Pathway in Live Single Cells. Cell Syst. 2020 Jun 24;10(6):495-505.e4. PMCID: PMC7413213

Hemming ML, Nathenson MJ, Lin JR, Mei S, Du Z, Malik K, Marino-Enriquez A, Jagannathan JP, Sorger PK, Bertagnolli M, Sicinska E, Demetri GD, Santagata S. Response and mechanisms of resistance to larotrectinib and selitrectinib in metastatic undifferentiated sarcoma harboring oncogenic fusion of NTRK1. JCO Precis Oncol. 2020 Feb 14;4:79–90. PMCID: PMC7055910

Hoffer J, Rashid R, Muhlich JL, Chen YA, Russell DPW, Ruokonen J, Krueger R, Pfister H, Santagata S, Sorger PK. Minerva: a light-weight, narrative image browser for multiplexed tissue images. J Open Source Softw. 2020 Oct 15;5(54):2579. PMCID: PMC7989801

Izar B, Tirosh I, Stover EH, Wakiro I, Cuoco MS, Alter I, Rodman C, Leeson R, Su MJ, Shah P, Iwanicki M, Walker SR, Kanodia A, Melms JC, Mei S, Lin JR, Porter CBM, Slyper M, Waldman J, Jerby-Arnon L, Ashenberg O, Brinker TJ, Mills C, Rogava M, Vigneau S, Sorger PK, Garraway LA, Konstantinopoulos PA, Liu JF, Matulonis U, Johnson BE, Rozenblatt-Rosen O, Rotem A, Regev A. A single-cell landscape of high-grade serous ovarian cancer. Nat Med. 2020 Aug;26(8):1271–1279. PMCID: PMC7723336

Kalocsay M, Berberich M, Everley R, Nariya M, Chung M, Gaudio B, Victor C, Bradshaw G, Hafner M, Sorger PK, Mills C, Subramanian K. Proteomic profiling of breast cancer cell lines and models [Internet]. bioRxiv; 2020. Available from: DOI: 10.1101/2020.12.15.422823

Kalocsay M, Maliga Z, Nirmal AJ, Eisert RJ, Bradshaw GA, Solomon IH, Chen YA, Pelletier RJ, Jacobson CA, Mintseris J, Padera RF, Martinot AJ, Barouch DH, Santagata S, Sorger PK. Multiplexed proteomics and imaging of resolving and lethal SARS-CoV-2 infection in the lung [Internet]. bioRxiv; 2020 [cited 2020 Dec 5]. Available from: DOI: 10.1101/2020.10.14.339952

Krueger R, Beyer J, Jang WD, Kim NW, Sokolov A, Sorger PK, Pfister H. Facetto: combining unsupervised and supervised learning for hierarchical phenotype analysis in multi-channel image data. IEEE Trans Vis Comput Graph. 2020 Jan;26(1):227–237. PMCID: PMC7045445

Leahy BD, Jang WD, Yang HY, Struyven R, Wei D, Sun Z, Lee KR, Royston C, Cam L, Kalma Y, Azem F, Ben-Yosef D, Pfister H, Needleman D. Automated measurements of key morphological features of human embryos for IVF. Med Image Comput Comput Assist Interv. 2020 Oct;12265:25–35. PMCID: PMC7732604

Lin Z, Wei D, Jang WD, Zhou S, Chen X, Wang X, Schalek R, Berger D, Matejek B, Kamentsky L, Peleg A, Haehn D, Jones T, Parag T, Lichtman J, Pfister H. Two stream active query suggestion for active learning in connectomics. Comput Vis ECCV. 2020 Aug;12363:103–120. PMCID: PMC7746018

Liu Y, Ferguson FM, Li L, Kuljanin M, Mills CE, Subramanian K, Harshbarger W, Gondi S, Wang J, Sorger PK, Mancias JD, Gray NS, Westover KD. Chemical Biology Toolkit for DCLK1 Reveals Connection to RNA Processing. Cell Chem Biol. 2020 Oct 15;27(10):1229-1240.e4. PMCID: PMC8053042

Lyashenko E, Niepel M, Dixit PD, Lim SK, Sorger PK, Vitkup D. Receptor-based mechanism of relative sensing and cell memory in mammalian signaling networks. Elife. 2020 Jan 21;9:e50342. PMCID: PMC7046471

Magid SA, Jang WD, Schapiro D, Wei D, Tompkin J, Sorger PK, Pfister H. Channel Embedding for Informative Protein Identification from Highly Multiplexed Images. Med Image Comput Comput Assist Interv. 2020 Oct;12265:3–13. PMCID: PMC7713713

Mallela A, Nariya MK, Deeds EJ. Crosstalk and ultrasensitivity in protein degradation pathways. PLoS Comput Biol. 2020 Dec;16(12):e1008492. PMCID: PMC7793289

Melms JC, Vallabhaneni S, Mills CE, Yapp C, Chen JY, Morelli E, Waszyk P, Kumar S, Deming D, Moret N, Rodriguez S, Subramanian K, Rogava M, Cartwright ANR, Luoma A, Mei S, Brinker TJ, Miller DM, Spektor A, Schadendorf D, Riggi N, Wucherpfennig KW, Sorger PK, Izar B. Inhibition of haspin kinase promotes cell-intrinsic and extrinsic antitumor activity. Cancer Res. 2020 Feb 15;80(4):798–810. PMCID: PMC7029677

Moret N, Liu C, Gyori BM, Bachman JA, Steppi A, Hug C, Taujale R, Huang LC, Berginski ME, Gomez SM, Kannan N, Sorger PK. A resource for exploring the understudied human kinome for research and therapeutic opportunities [Internet]. bioRxiv; 2020 [cited 2021 Mar 22]. Available from: http://biorxiv.org/lookup/doi/10.1101/2020.04.02.022277

Mostaghimi A, Antonini MJ, Plana D, Anderson PD, Beller B, Boyer EW, Fannin A, Freake J, Oakley R, Sinha MS, Smith L, Van C, Yang H, Sorger PK, LeBoeuf NR, Yu SH. Regulatory and safety considerations in deploying a locally fabricated, reusable face shield in a hospital responding to the COVID-19 pandemic. Med (N Y). 2020 Dec 18;1(1):139-151.e4. PMCID: PMC7304404

Nam KM, Gyori BM, Amethyst SV, Bates DJ, Gunawardena J. Robustness and parameter geography in post-translational modification systems. Mendes P, editor. PLoS Comput Biol [Internet]. 2020 May 4 [cited 2022 Jun 13];16(5):e1007573. Available from: https://dx.plos.org/10.1371/journal.pcbi.1007573

Palmer AC, Plana D, Sorger PK. Comparing the efficacy of cancer therapies between subgroups in basket trials. Cell Syst. 2020 Nov 18;11(5):449-460.e2. PMCID: PMC8022348

Palmer AC, Plana D, Gao H, Korn JM, Yang G, Green J, Zhang X, Velazquez R, McLaughlin ME, Ruddy DA, Kowal C, Muszynski J, Bullock C, Rivera S, Rakiec DP, Elliott G, Fordjour P, Meyer R, Loo A, Kurth E, Engelman JA, Bitter H, Sellers WR, Williams JA, Sorger PK. A proof of concept for biomarker-guided targeted therapy against ovarian cancer based on patient-derived tumor xenografts. Cancer Res. 2020 Oct 1;80(19):4278–4287. PMCID: PMC7541581

Pena AM, Chen X, Pence IJ, Bornschlögl T, Jeong S, Grégoire S, Luengo GS, Hallegot P, Obeidy P, Feizpour A, Chan KF, Evans CL. Imaging and quantifying drug delivery in skin - Part 2: Fluorescence andvibrational spectroscopic imaging methods. Adv Drug Deliv Rev. 2020 Jan 1;153:147–168. PMCID: PMC7483684

Pomeranz Krummel DA, Nasti TH, Izar B, Press RH, Xu M, Lowder L, Kallay L, Rupji M, Rosen H, Su J, Curran W, Olson J, Weinberg B, Schniederjan M, Neill S, Lawson D, Kowalski J, Khan MK, Sengupta S. Impact of sequencing radiation therapy and immune checkpoint inhibitors in the treatment of melanoma brain metastases. Int J Radiat Oncol Biol Phys. 2020 Sep 1;108(1):157–163. PMCID: PMC7839060

Qian J, Lu ZX, Mancuso CP, Jhuang HY, Del Carmen Barajas-Ornelas R, Boswell SA, Ramírez-Guadiana FH, Jones V, Sonti A, Sedlack K, Artzi L, Jung G, Arammash M, Pettit ME, Melfi M, Lyon L, Owen SV, Baym M, Khalil AS, Silver PA, Rudner DZ, Springer M. Barcoded microbial system for high-resolution object provenance. Science. 2020 05;368(6495):1135–1140. PMID: 32499444

Qu J, Steppi A, Zhong D, Hao J, Wang J, Lung PY, Zhao T, He Z, Zhang J. Triage of documents containing protein interactions affected by mutations using an NLP based machine learning approach. BMC Genomics. 2020 Nov 10;21(1):773. PMCID: PMC7654050

Revach OY, Liu S, Jenkins RW. Targeting TANK-binding kinase 1 (TBK1) in cancer. Expert Opin Ther Targets. 2020 Oct 5;1–14. PMID: 32962465

Ringel AE, Drijvers JM, Baker GJ, Catozzi A, García-Cañaveras JC, Gassaway BM, Miller BC, Juneja VR, Nguyen TH, Joshi S, Yao CH, Yoon H, Sage PT, LaFleur MW, Trombley JD, Jacobson CA, Maliga Z, Gygi SP, Sorger PK, Rabinowitz JD, Sharpe AH, Haigis MC. Obesity shapes metabolism in the tumor microenvironment to suppress anti-tumor immunity. Cell. 2020 Dec 23;183(7):1848-1866.e26. PMCID: PMC8064125

Rozenblatt-Rosen O, Regev A, Oberdoerffer P, Nawy T, Hupalowska A, Rood JE, Ashenberg O, Cerami E, Coffey RJ, Demir E, Ding L, Esplin ED, Ford JM, Goecks J, Ghosh S, Gray JW, Guinney J, Hanlon SE, Hughes SK, Hwang ES, Iacobuzio-Donahue CA, Jané-Valbuena J, Johnson BE, Lau KS, Lively T, Mazzilli SA, Pe’er D, Santagata S, Shalek AK, Schapiro D, Snyder MP, Sorger PK, Spira AE, Srivastava S, Tan K, West RB, Williams EH, Human Tumor Atlas Network. The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution. Cell. 2020 Apr 16;181(2):236–249. PMCID: PMC7376497

Russell-Goldman E, Murphy GF. The Pathobiology of Skin Aging: New Insights into an Old Dilemma. Am J Pathol. 2020 Jul;190(7):1356–1369. PMCID: PMC7481755

Santoriello C, Sporrij A, Yang S, Flynn RA, Henriques T, Dorjsuren B, Custo Greig E, McCall W, Stanhope ME, Fazio M, Superdock M, Lichtig A, Adatto I, Abraham BJ, Kalocsay M, Jurynec M, Zhou Y, Adelman K, Calo E, Zon LI. RNA helicase DDX21 mediates nucleotide stress responses in neural crest and melanoma cells. Nat Cell Biol. 2020 Apr;22(4):372–379. PMCID: PMC7185069

Shamsaei B, Chojnacki S, Pilarczyk M, Najafabadi M, Niu W, Chen C, Ross K, Matlock A, Muhlich J, Chutipongtanate S, Zheng J, Turner J, Vidović D, Jaffe J, MacCoss M, Wu C, Pillai A, Ma’ayan A, Schürer S, Kouril M, Medvedovic M, Meller J. piNET: a versatile web platform for downstream analysis and visualization of proteomics data. Nucleic Acids Res. 2020 Jul 2;48(W1):W85–W93.

Slyper M, Porter CBM, Ashenberg O, Waldman J, Drokhlyansky E, Wakiro I, Smillie C, Smith-Rosario G, Wu J, Dionne D, Vigneau S, Jané-Valbuena J, Tickle TL, Napolitano S, Su MJ, Patel AG, Karlstrom A, Gritsch S, Nomura M, Waghray A, Gohil SH, Tsankov AM, Jerby-Arnon L, Cohen O, Klughammer J, Rosen Y, Gould J, Nguyen L, Hofree M, Tramontozzi PJ, Li B, Wu CJ, Izar B, Haq R, Hodi FS, Yoon CH, Hata AN, Baker SJ, Suvà ML, Bueno R, Stover EH, Clay MR, Dyer MA, Collins NB, Matulonis UA, Wagle N, Johnson BE, Rotem A, Rozenblatt-Rosen O, Regev A. A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors. Nat Med. 2020 May;26(5):792–802. PMCID: PMC7220853

Steppi A, Gyori BM, Bachman JA. Adeft: Acromine-based Disambiguation of Entities from Text with applications to the biomedical literature. J Open Source Softw. 2020 Jan 16;5(45):1708. PMCID: PMC7182313

Teng M, Jiang J, He Z, Kwiatkowski NP, Donovan KA, Mills CE, Victor C, Hatcher JM, Fischer ES, Sorger PK, Zhang T, Gray NS. Development of CDK2 and CDK5 Dual Degrader TMX-2172. Angew Chem Int Ed Engl. 2020 Aug 10;59(33):13865–13870. PMCID: PMC7703486

Tran AP, Ali Al-Radhawi M, Kareva I, Wu J, Waxman DJ, Sontag ED. Delicate Balances in Cancer Chemotherapy: Modeling Immune Recruitment and Emergence of Systemic Drug Resistance. Front Immunol. 2020;11:1376. PMCID: PMC7338613

Tsabar M, Mock CS, Venkatachalam V, Reyes J, Karhohs KW, Oliver TG, Regev A, Jambhekar A, Lahav G. A Switch in p53 Dynamics Marks Cells That Escape from DSB-Induced Cell Cycle Arrest. Cell Rep. 2020 Aug 4;32(5):107995. PMCID: PMC7521664

Tyan K, Levin A, Avalos-Pacheco A, Plana D, Rand EA, Yang H, Maliszewski LE, Chylek LA, Atta L, Tye MA, Carmack MM, Oglesby NS, Burgin S, Yu SH, LeBoeuf NR, Kemp JM. Considerations for the selection and use of disinfectants against SARS-CoV-2 in a health care setting. Open Forum Infect Dis. 2020 Sep;7(9):ofaa396. PMCID: PMC7499694

Wei D, Lin Z, Franco-Barranco D, Wendt N, Liu X, Yin W, Huang X, Gupta A, Jang WD, Wang X, Arganda-Carreras I, Lichtman JW, Pfister H. MitoEM dataset: large-scale 3D mitochondria instance segmentation from EM images. Med Image Comput Comput Assist Interv. 2020 Oct;12265:66–76. PMCID: PMC7713709

Alley EC, Khimulya G, Biswas S, AlQuraishi M, Church GM. Unified rational protein engineering with sequence-based deep representation learning. Nat Methods. 2019 Dec;16(12):1315–1322. PMCID: PMC7067682

AlQuraishi M. Parallelized Natural Extension Reference Frame: Parallelized Conversion from Internal to Cartesian Coordinates. J Comput Chem. 2019 Mar 15;40(7):885–892. PMID: 30614534

AlQuraishi M. End-to-end differentiable learning of protein structure. Cell Syst. 2019 Apr 24;8(4):292-301.e3. PMCID: PMC6513320

AlQuraishi M. ProteinNet: a standardized data set for machine learning of protein structure. BMC Bioinformatics. 2019 Jun 11;20(1):311. PMCID: PMC6560865

AlQuraishi M. AlphaFold at CASP13. Bioinformatics. 2019 Nov 1;35(22):4862–4865. PMCID: PMC6907002

Bachman JA, Sorger PK, Gyori BM. Assembling a corpus of phosphoproteomic annotations using ProtMapper to normalize site information from databases and text mining [Internet]. bioRxiv; 2019 [cited 2022 Oct 31]. Available from: DOI: 10.1101/822668

Bandopadhayay P, Piccioni F, O’Rourke R, Ho P, Gonzalez EM, Buchan G, Qian K, Gionet G, Girard E, Coxon M, Rees MG, Brenan L, Dubois F, Shapira O, Greenwald NF, Pages M, Balboni Iniguez A, Paolella BR, Meng A, Sinai C, Roti G, Dharia NV, Creech A, Tanenbaum B, Khadka P, Tracy A, Tiv HL, Hong AL, Coy S, Rashid R, Lin JR, Cowley GS, Lam FC, Goodale A, Lee Y, Schoolcraft K, Vazquez F, Hahn WC, Tsherniak A, Bradner JE, Yaffe MB, Milde T, Pfister SM, Qi J, Schenone M, Carr SA, Ligon KL, Kieran MW, Santagata S, Olson JM, Gokhale PC, Jaffe JD, Root DE, Stegmaier K, Johannessen CM, Beroukhim R. Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma. Nat Commun. 2019 Jun 3;10(1):2400. PMCID: PMC6546744

Du Z, Lin JR, Rashid R, Maliga Z, Wang S, Aster JC, Izar B, Sorger PK, Santagata S. Qualifying antibodies for image-based immune profiling and multiplexed tissue imaging. Nat Protoc. 2019 Oct;14(10):2900–2930. PMCID: PMC6959005

Ferguson FM, Doctor ZM, Ficarro SB, Browne CM, Marto JA, Johnson JL, Yaron TM, Cantley LC, Kim ND, Sim T, Berberich MJ, Kalocsay M, Sorger PK, Gray NS. Discovery of Covalent CDK14 Inhibitors with Pan-TAIRE Family Specificity. Cell Chem Biol [Internet]. 2019 Jun 20;26(6):804-817.e12. Available from: https://pubmed.ncbi.nlm.nih.gov/30930164/ PMCID: PMC6588450

Hafner M, Mills CE, Subramanian K, Chen C, Chung M, Boswell SA, Everley RA, Liu C, Walmsley CS, Juric D, Sorger PK. Multiomics profiling establishes the polypharmacology of FDA-approved CDK4/6 inhibitors and the potential for differential clinical activity. Cell Chem Biol. 2019 Aug 15;26(8):1067-1080.e8. PMCID: PMC6936329

Hoyt CT, Domingo-Fernández D, Aldisi R, Xu L, Kolpeja K, Spalek S, Wollert E, Bachman J, Gyori BM, Greene P, Hofmann-Apitius M. Re-curation and rational enrichment of knowledge graphs in Biological Expression Language. Database. 2019 Jan 1;2019:baz068.

Juratli TA, Jones PS, Wang N, Subramanian M, Aylwin SJB, Odia Y, Rostami E, Gudjonsson O, Shaw BL, Cahill DP, Galanis E, Barker FG, Santagata S, Brastianos PK. Targeted treatment of papillary craniopharyngiomas harboring BRAF V600E mutations. Cancer. 2019 Sep 1;125(17):2910–2914. PMCID: PMC7032527

Kalocsay M. APEX Peroxidase-Catalyzed Proximity Labeling and Multiplexed Quantitative Proteomics. Methods Mol Biol. 2019 May 4;2008:41–55. PMID: 31124087

Katzir I, Cokol M, Aldridge BB, Alon U. Prediction of ultra-high-order antibiotic combinations based on pairwise interactions. PLoS Comput Biol. 2019 Jan 30;15(1):e1006774. PMCID: PMC6370231

Koch R, Christie AL, Crombie JL, Palmer AC, Plana D, Shigemori K, Morrow SN, Van Scoyk A, Wu W, Brem EA, Secrist JP, Drew L, Schuller AG, Cidado J, Letai A, Weinstock DM. Biomarker-driven strategy for MCL1 inhibition in T-cell lymphomas. Blood. 2019 Feb 7;133(6):566–575. PMCID: PMC6367646

Li Z, Pinch BJ, Olson CM, Donovan KA, Nowak RP, Mills CE, Scott DA, Doctor ZM, Eleuteri NA, Chung M, Sorger PK, Fischer ES, Gray NS. Development and Characterization of a Wee1 Kinase Degrader. Cell Chem Biol. 2019 Nov 13;27(1):57-65.e9. PMCID: PMC6980656

Liu B, Gyori BM, Thiagarajan PS. Statistical Model Checking-Based Analysis of Biological Networks. In: Liò P, Zuliani P, editors. Automated Reasoning for Systems Biology and Medicine [Internet]. Cham: Springer International Publishing; 2019. p. 63–92. Available from: https://doi.org/10.1007/978-3-030-17297-8_3

Moret N, Clark NA, Hafner M, Wang Y, Lounkine E, Medvedovic M, Wang J, Gray N, Jenkins J, Sorger PK. Cheminformatics Tools for Analyzing and Designing Optimized Small-Molecule Collections and Libraries. Cell Chem Biol. 2019 May 16;26(5):765-777.e3. PMCID: PMC6526536

Niepel M, Hafner M, Mills CE, Subramanian K, Williams EH, Chung M, Gaudio B, Barrette AM, Stern AD, Hu B, Korkola JE, LINCS Consortium, Gray JW, Birtwistle MR, Heiser LM, Sorger PK. A Multi-center Study on the Reproducibility of Drug-Response Assays in Mammalian Cell Lines. Cell Syst. 2019 Jul 5;9(1):35-48.e5. PMCID: PMC6700527

Olson CM, Liang Y, Leggett A, Park WD, Li L, Mills CE, Elsarrag SZ, Ficarro SB, Zhang T, Düster R, Geyer M, Sim T, Marto JA, Sorger PK, Westover KD, Lin CY, Kwiatkowski N, Gray NS. Development of a Selective CDK7 Covalent Inhibitor Reveals Predominant Cell-Cycle Phenotype. Cell Chem Biol. 2019 Jun 20;26(6):792-803.e10. PMCID: PMC6588464

Palmer AC, Chidley C, Sorger PK. A curative combination cancer therapy achieves high fractional cell killing through low cross-resistance and drug additivity. Elife. 2019 Nov 19;8:e50036. PMCID: PMC6897534

Pavkovic M, Pantano L, Gerlach CV, Brutus S, Boswell SA, Everley RA, Shah JV, Sui SH, Vaidya VS. Multi omics analysis of fibrotic kidneys in two mouse models. Scientific Data. 2019 Jun 14;6(1):92.

Ramm S, Todorov P, Chandrasekaran V, Dohlman A, Monteiro MB, Pavkovic M, Muhlich J, Shankaran H, Chen WW, Mettetal JT, Vaidya VS. A Systems Toxicology Approach for the Prediction of Kidney Toxicity and Its Mechanisms In Vitro. Toxicol Sci. 2019 01;169(1):54–69. PMCID: PMC6484891

Rao S, Gurbani D, Du G, Everley RA, Browne CM, Chaikuad A, Tan L, Schröder M, Gondi S, Ficarro SB, Sim T, Kim ND, Berberich MJ, Knapp S, Marto JA, Westover KD, Sorger PK, Gray NS. Leveraging compound promiscuity to identify targetable cysteines within the kinome. Cell Chem Biol. 2019 Jun 20;26(6):818-829.e9. PMCID: PMC6634314

Rao S, Du G, Hafner M, Subramanian K, Sorger PK, Gray NS. A multitargeted probe-based strategy to identify signaling vulnerabilities in cancers. J Biol Chem. 2019 May 24;294(21):8664–8673. PMCID: PMC6544847

Rashid R, Gaglia G, Chen YA, Lin JR, Du Z, Maliga Z, Schapiro D, Yapp C, Muhlich J, Sokolov A, Sorger P, Santagata S. Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer. Sci Data. 2019 Dec 17;6(1):323. PMCID: PMC6917801

Rogava M, Izar B. CXCR3: Here to stay to enhance cancer immunotherapy? EBioMedicine. 2019 Nov;49:11–12. PMCID: PMC6945198

Sokolov A, Ashenden S, Sahin N, Lewis R, Erdem N, Ozaltan E, Bender A, Roth FP, Cokol M. Characterizing ABC-transporter substrate-likeness using a clean-slate genetic background. Front Pharmacol. 2019 Apr 25;10:448. PMCID: PMC6494965

Song Y, Subramanian K, Berberich MJ, Rodriguez S, Latorre IJ, Luria CM, Everley R, Albers MW, Mitchison TJ, Sorger PK. A dynamic view of the proteomic landscape during differentiation of ReNcell VM cells, an immortalized human neural progenitor line. Sci Data. 2019 Feb 19;6:190016. PMCID: PMC6380223

Todorov PV, Gyori BM, Bachman JA, Sorger PK. INDRA-IPM: interactive pathway modeling using natural language with automated assembly. Bioinformatics. 2019 May 9; PMID: 31070726

Wang H, Sheehan RP, Palmer AC, Everley RA, Boswell SA, Ron-Harel N, Ringel AE, Holton KM, Jacobson CA, Erickson AR, Maliszewski L, Haigis MC, Sorger PK. Adaptation of human iPSC-derived cardiomyocytes to tyrosine kinase inhibitors reduces acute cardiotoxicity via metabolic reprogramming. Cell Syst. 2019 May 22;8(5):412-426.e7. PMCID: PMC6657491

Wang S, Lin JR, Sontag ED, Sorger PK. Inferring reaction network structure from single-cell, multiplex data, using toric systems theory. PLoS Comput Biol. 2019 Dec;15(12):e1007311. PMCID: PMC6919632

Bachman JA, Gyori BM, Sorger PK. FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining. BMC Bioinformatics. 2018 Jun 28;19(1):248. PMCID: PMC6022344

Cokol M, Li C, Chandrasekaran S. Chemogenomic model identifies synergistic drug combinations robust to the pathogen microenvironment. PLoS Comput Biol. 2018 Dec 31;14(12):e1006677. PMCID: PMC6329523

Cokol-Cakmak M, Bakan F, Cetiner S, Cokol M. Diagonal Method to Measure Synergy Among Any Number of Drugs. J Vis Exp. 2018 Jun 21;(136). PMID: 29985330

Coy S, Rashid R, Lin JR, Du Z, Donson AM, Hankinson TC, Foreman NK, Manley PE, Kieran MW, Reardon DA, Sorger PK, Santagata S. Multiplexed Immunofluorescence Reveals Potential PD-1/PD-L1 Pathway Vulnerabilities in Craniopharyngioma. Neuro Oncol [Internet]. 2018 Mar 2;20(8):1101–1112. Available from: https://pubmed.ncbi.nlm.nih.gov/29509940/ PMCID: PMC6280314

de Souza CF, Sabedot TS, Malta TM, Stetson L, Morozova O, Sokolov A, Laird PW, Wiznerowicz M, Iavarone A, Snyder J, deCarvalho A, Sanborn Z, McDonald KL, Friedman WA, Tirapelli D, Poisson L, Mikkelsen T, Carlotti CG, Kalkanis S, Zenklusen J, Salama SR, Barnholtz-Sloan JS, Noushmehr H. A Distinct DNA Methylation Shift in a Subset of Glioma CpG Island Methylator Phenotypes during Tumor Recurrence. Cell Rep. 2018 Apr 10;23(2):637–651. PMID: 29642018

Dunn IF, Du Z, Touat M, Sisti MB, Wen PY, Umeton R, Dubuc AM, Ducar M, Canoll PD, Severson E, Elvin JA, Ramkissoon SH, Lin JR, Cabrera L, Acevedo B, Sorger PK, Ligon KL, Santagata S, Reardon DA. Mismatch repair deficiency in high-grade meningioma: a rare but recurrent event associated with dramatic immune activation and clinical response to PD-1 blockade. JCO Precis Oncol. 2018 Nov 27;2018. PMCID: PMC6383717

Gonzalez Herrera KN, Zaganjor E, Ishikawa Y, Spinelli JB, Yoon H, Lin JR, Satterstrom FK, Ringel A, Mulei S, Souza A, Gorham JM, Benson CC, Seidman JG, Sorger PK, Clish CB, Haigis MC. Small-Molecule Screen Identifies De Novo Nucleotide Synthesis as a Vulnerability of Cells Lacking SIRT3. Cell Rep. 2018 Feb 20;22(8):1945–1955. PMID: 29466723

Iglesias N, Currie MA, Jih G, Paulo JA, Siuti N, Kalocsay M, Gygi SP, Moazed D. Automethylation-induced conformational switch in Clr4 (Suv39h) maintains epigenetic stability. Nature. 2018 Jul 23;560(7719):504–508. PMCID: PMC6287498

Jerby-Arnon L, Shah P, Cuoco MS, Rodman C, Su MJ, Melms JC, Leeson R, Kanodia A, Mei S, Lin JR, Wang S, Rabasha B, Liu D, Zhang G, Margolais C, Ashenberg O, Ott PA, Buchbinder EI, Haq R, Hodi FS, Boland GM, Sullivan RJ, Frederick DT, Miao B, Moll T, Flaherty KT, Herlyn M, Jenkins RW, Thummalapalli R, Kowalczyk MS, Cañadas I, Schilling B, Cartwright ANR, Luoma AM, Malu S, Hwu P, Bernatchez C, Forget MA, Barbie DA, Shalek AK, Tirosh I, Sorger PK, Wucherpfennig K, Van Allen EM, Schadendorf D, Johnson BE, Rotem A, Rozenblatt-Rosen O, Garraway LA, Yoon CH, Izar B, Regev A. A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade. Cell. 2018 Nov 1;175(4):984-997.e24. PMCID: PMC6410377

Keenan AB, Jenkins SL, Jagodnik KM, Koplev S, He E, Torre D, Wang Z, Dohlman AB, Silverstein MC, Lachmann A, Kuleshov MV, Ma’ayan A, Stathias V, Terryn R, Cooper D, Forlin M, Koleti A, Vidovic D, Chung C, Schürer SC, Vasiliauskas J, Pilarczyk M, Shamsaei B, Fazel M, Ren Y, Niu W, Clark NA, White S, Mahi N, Zhang L, Kouril M, Reichard JF, Sivaganesan S, Medvedovic M, Meller J, Koch RJ, Birtwistle MR, Iyengar R, Sobie EA, Azeloglu EU, Kaye J, Osterloh J, Haston K, Kalra J, Finkbiener S, Li J, Milani P, Adam M, Escalante-Chong R, Sachs K, Lenail A, Ramamoorthy D, Fraenkel E, Daigle G, Hussain U, Coye A, Rothstein J, Sareen D, Ornelas L, Banuelos M, Mandefro B, Ho R, Svendsen CN, Lim RG, Stocksdale J, Casale MS, Thompson TG, Wu J, Thompson LM, Dardov V, Venkatraman V, Matlock A, Van Eyk JE, Jaffe JD, Papanastasiou M, Subramanian A, Golub TR, Erickson SD, Fallahi-Sichani M, Hafner M, Gray NS, Lin JR, Mills CE, Muhlich JL, Niepel M, Shamu CE, Williams EH, Wrobel D, Sorger PK, Heiser LM, Gray JW, Korkola JE, Mills GB, LaBarge M, Feiler HS, Dane MA, Bucher E, Nederlof M, Sudar D, Gross S, Kilburn DF, Smith R, Devlin K, Margolis R, Derr L, Lee A, Pillai A. The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations. Cell Syst. 2018 Jan 24;6(1):13–24. PMCID: PMC5799026

Lin JR, Izar B, Wang S, Yapp C, Mei S, Shah PM, Santagata S, Sorger PK. Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes. Elife. 2018 Jul 11;7. PMCID: PMC6075866

Shimada K, Reznik E, Stokes ME, Krishnamoorthy L, Bos PH, Song Y, Quartararo CE, Pagano NC, Carpizo DR, deCarvalho AC, Lo DC, Stockwell BR. Copper-Binding Small Molecule Induces Oxidative Stress and Cell-Cycle Arrest in Glioblastoma-Patient-Derived Cells. Cell Chem Biol. 2018 Mar 7; PMID: 29576531

Spady ES, Wyche TP, Rollins NJ, Clardy J, Way JC, Silver PA. Mammalian Cells Engineered To Produce New Steroids. Chembiochem. 2018 Sep 4;19(17):1827–1833. PMCID: PMC6156985

Wang J, Erazo T, Ferguson FM, Buckley DL, Gomez N, Muñoz-Guardiola P, Diéguez-Martínez N, Deng X, Hao M, Massefski W, Fedorov O, Offei-Addo NK, Park PM, Dai L, DiBona A, Becht K, Kim ND, McKeown MR, Roberts JM, Zhang J, Sim T, Alessi DR, Bradner JE, Lizcano JM, Blacklow SC, Qi J, Xu X, Gray NS. Structural and Atropisomeric Factors Governing the Selectivity of Pyrimido-benzodiazipinones as Inhibitors of Kinases and Bromodomains. ACS Chem Biol. 2018 Sep 21;13(9):2438–2448. PMCID: PMC6333101

Weinstein ZB, Kuru N, Kiriakov S, Palmer AC, Khalil AS, Clemons PA, Zaman MH, Roth FP, Cokol M. Modeling the impact of drug interactions on therapeutic selectivity. Nat Commun. 2018 Aug 27;9(1):3452. PMCID: PMC6110842

Cardenas-Gonzalez M, Srivastava A, Pavkovic M, Bijol V, Rennke HG, Stillman IE, Zhang X, Parikh S, Rovin BH, Afkarian M, de Boer IH, Himmelfarb J, Waikar SS, Vaidya VS. Identification, Confirmation, and Replication of Novel Urinary MicroRNA Biomarkers in Lupus Nephritis and Diabetic Nephropathy. Clin Chem. 2017 Jun 30; PMID: 28667184

Carlin DE, Paull EO, Graim K, Wong CK, Bivol A, Ryabinin P, Ellrott K, Sokolov A, Stuart JM. Prophetic Granger Causality to infer gene regulatory networks. PLoS One. 2017;12(12):e0170340. PMCID: PMC5718405

Cokol M, Kuru N, Bicak E, Larkins-Ford J, Aldridge BB. Efficient measurement and factorization of high-order drug interactions in Mycobacterium tuberculosis. Sci Adv. 2017 Oct;3(10):e1701881. PMCID: PMC5636204

Fallahi-Sichani M, Becker V, Izar B, Baker GJ, Lin JR, Boswell SA, Shah P, Rotem A, Garraway LA, Sorger PK. Adaptive resistance of melanoma cells to RAF inhibition via reversible induction of a slowly dividing de-differentiated state. Mol Syst Biol [Internet]. 2017 Jan 9;13(1):905. Available from: http://www.ncbi.nlm.nih.gov/pubmed/28069687 PMCID: PMC5248573

Fusco DN, Pratt H, Kandilas S, Cheon SS, Lin W, Cronkite DA, Basavappa M, Jeffrey KL, Anselmo A, Sadreyev R, Yapp C, Shi X, O’Sullivan JF, Gerszten RE, Tomaru T, Yoshino S, Satoh T, Chung RT. HELZ2 Is an IFN Effector Mediating Suppression of Dengue Virus. Front Microbiol [Internet]. 2017;8:240. Available from: https://www.ncbi.nlm.nih.gov/pubmed/28265266

Gerlach CV, Vaidya VS. MicroRNAs in injury and repair. Arch Toxicol [Internet]. 2017 Aug;91(8):2781–2797. Available from: http://link.springer.com/10.1007/s00204-017-1974-1 PMCID: PMC5843992

Goel S, DeCristo MJ, Watt AC, BrinJones H, Sceneay J, Li BB, Khan N, Ubellacker JM, Xie S, Metzger-Filho O, Hoog J, Ellis MJ, Ma CX, Ramm S, Krop IE, Winer EP, Roberts TM, Kim HJ, McAllister SS, Zhao JJ. CDK4/6 inhibition triggers anti-tumour immunity. Nature. 2017 Aug 16; PMID: 28813415

Gönen M, Weir BA, Cowley GS, Vazquez F, Guan Y, Jaiswal A, Karasuyama M, Uzunangelov V, Wang T, Tsherniak A, Howell S, Marbach D, Hoff B, Norman TC, Airola A, Bivol A, Bunte K, Carlin D, Chopra S, Deran A, Ellrott K, Gopalacharyulu P, Graim K, Kaski S, Khan SA, Newton Y, Ng S, Pahikkala T, Paull E, Sokolov A, Tang H, Tang J, Wennerberg K, Xie Y, Zhan X, Zhu F, Broad-DREAM Community, Aittokallio T, Mamitsuka H, Stuart JM, Boehm JS, Root DE, Xiao G, Stolovitzky G, Hahn WC, Margolin AA. A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines. Cell Syst. 2017 Nov 22;5(5):485-497.e3. PMCID: PMC5814247

Gyori BM, Bachman JA, Subramanian K, Muhlich JL, Galescu L, Sorger PK. From word models to executable models of signaling networks using automated assembly. Mol Syst Biol [Internet]. 2017 Nov 24;13(11):954. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5731347/ PMCID: PMC5731347

Hafner M, Niepel M, Subramanian K, Sorger PK. Designing Drug-Response Experiments and Quantifying their Results. Curr Protoc Chem Biol. 2017 Jun 19;9(2):96–116. PMCID: PMC5729909

Lin JR. Multiplexed Single-Cell Imaging: Past, Present, and Future. ASSAY and Drug Development Technologies. 2017;15(1):8–10.

Logsdon MM, Ho PY, Papavinasasundaram K, Richardson K, Cokol M, Sassetti CM, Amir A, Aldridge BB. A Parallel Adder Coordinates Mycobacterial Cell-Cycle Progression and Cell-Size Homeostasis in the Context of Asymmetric Growth and Organization. Curr Biol. 2017 Nov 6;27(21):3367-3374.e7. PMCID: PMC5687851

Mason DJ, Stott I, Ashenden S, Weinstein ZB, Karakoc I, Meral S, Kuru N, Bender A, Cokol M. Prediction of Antibiotic Interactions Using Descriptors Derived from Molecular Structure. J Med Chem. 2017 May 11;60(9):3902–3912. PMID: 28383902

Niepel M, Hafner M, Chung M, Sorger PK. Measuring Cancer Drug Sensitivity and Resistance in Cultured Cells. Curr Protoc Chem Biol. 2017 Jun 19;9(2):55–74. PMCID: PMC5538315

Niepel M, Hafner M, Duan Q, Wang Z, Paull EO, Chung M, Lu X, Stuart JM, Golub TR, Subramanian A, Ma’ayan A, Sorger PK. Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling. Nat Commun. 2017 Oct 30;8(1):1186. PMCID: PMC5662764

Paek J, Kalocsay M, Staus DP, Wingler L, Pascolutti R, Paulo JA, Gygi SP, Kruse AC. Multidimensional Tracking of GPCR Signaling via Peroxidase-Catalyzed Proximity Labeling. Cell. 2017 Apr 6;169(2):338-349.e11. PMCID: PMC5514552

Subramanian K, Tyson JJ. Spatiotemporal Models of the Asymmetric Division Cycle of Caulobacter crescentus. In: Tassan JP, Kubiak JZ, editors. Asymmetric Cell Division in Development, Differentiation and Cancer [Internet]. Cham: Springer International Publishing; 2017. p. 23–48. Available from: http://link.springer.com/10.1007/978-3-319-53150-2_2

Tan L, Gurbani D, Weisberg EL, Hunter JC, Li L, Jones DS, Ficarro SB, Mowafy S, Tam CP, Rao S, Du G, Griffin JD, Sorger PK, Marto JA, Westover KD, Gray NS. Structure-guided development of covalent TAK1 inhibitors. Bioorg Med Chem [Internet]. 2017 Feb 1;25(3):838–846. Available from: http://www.ncbi.nlm.nih.gov/pubmed/28011204 PMCID: PMC5484537

Tanguturi SK, Trippa L, Ramkissoon SH, Pelton K, Knoff D, Sandak D, Lindeman NI, Ligon AH, Beroukhim R, Parmigiani G, Wen PY, Ligon KL, Alexander BM. Leveraging molecular datasets for biomarker-based clinical trial design in glioblastoma. Neuro-oncology. 2017 Feb 20;

Viswanathan VS, Ryan MJ, Dhruv HD, Gill S, Eichhoff OM, Seashore-Ludlow B, Kaffenberger SD, Eaton JK, Shimada K, Aguirre AJ, Viswanathan SR, Chattopadhyay S, Tamayo P, Yang WS, Rees MG, Chen S, Boskovic ZV, Javaid S, Huang C, Wu X, Tseng YY, Roider EM, Gao D, Cleary JM, Wolpin BM, Mesirov JP, Haber DA, Engelman JA, Boehm JS, Kotz JD, Hon CS, Chen Y, Hahn WC, Levesque MP, Doench JG, Berens ME, Shamji AF, Clemons PA, Stockwell BR, Schreiber SL. Dependency of a therapy-resistant state of cancer cells on a lipid peroxidase pathway. Nature. 2017 27;547(7664):453–457. PMCID: PMC5667900

Wang Y, Woehrstein JB, Donoghue N, Dai M, Avendaño MS, Schackmann RCJ, Zoeller JJ, Wang SSH, Tillberg PW, Park D, Lapan SW, Boyden ES, Brugge JS, Kaeser PS, Church GM, Agasti SS, Jungmann R, Yin P. Rapid Sequential in Situ Multiplexing with DNA Exchange Imaging in Neuronal Cells and Tissues. Nano Lett [Internet]. 2017 Oct 11;17(10):6131–6139. Available from: https://doi.org/10.1021/acs.nanolett.7b02716

Zhou J, Ramanathan R, Wong WF, Thiagarajan PS. Automated Property Synthesis of ODEs Based Bio-pathways Models. In: Feret J, Koeppl H, editors. Computational Methods in Systems Biology. Cham: Springer International Publishing; 2017. p. 265–282.

AlQuraishi M, Sorger PK. Reproducibility will only come with data liberation. Sci Transl Med [Internet]. 2016 May 18;8(339):339ed7. Available from: http://www.ncbi.nlm.nih.gov/pubmed/27194726 PMCID: PMC5084089

Cárdenas-González M, Jacobo Estrada T, Rodríguez-Muñoz R, Barrera-Chimal J, Bobadilla NA, Barbier OC, Del Razo LM. Sub-chronic exposure to fluoride impacts the response to a subsequent nephrotoxic treatment with gentamicin: Fluoride exposure impacts the response to treatment with gentamicin. Journal of Applied Toxicology. 2016;36(2):309–319.

Goel S, Wang Q, Watt AC, Tolaney SM, Dillon DA, Li W, Ramm S, Palmer AC, Yuzugullu H, Varadan V, Tuck D, Harris LN, Wong KK, Liu XS, Sicinski P, Winer EP, Krop IE, Zhao JJ. Overcoming Therapeutic Resistance in HER2-Positive Breast Cancers with CDK4/6 Inhibitors. Cancer Cell. 2016;29(3):255–269.

Hafner M, Niepel M, Chung M, Sorger PK. Growth rate inhibition metrics correct for confounders in measuring sensitivity to cancer drugs. Nat Methods [Internet]. 2016 Jun 1;13(6):521–527. Available from: http://www.ncbi.nlm.nih.gov/pubmed/27135972 PMCID: PMC4887336

Jadhav S, Ajay AK, Trivedi P, Seematti J, Pellegrini K, Craciun F, Vaidya VS. RNA-binding Protein Musashi Homologue 1 Regulates Kidney Fibrosis by Translational Inhibition of p21 and Numb mRNA. Journal of Biological Chemistry [Internet]. 2016 Jul 1 [cited 2017 Jun 8];291(27):14085–14094. Available from: http://www.jbc.org/lookup/doi/10.1074/jbc.M115.713289

Lee JK, Phillips JW, Smith BA, Park JW, Stoyanova T, McCaffrey EF, Baertsch R, Sokolov A, Meyerowitz JG, Mathis C, Cheng D, Stuart JM, Shokat KM, Gustafson WC, Huang J, Witte ON. N-Myc Drives Neuroendocrine Prostate Cancer Initiated from Human Prostate Epithelial Cells. Cancer Cell. 2016 Apr 11;29(4):536–547. PMCID: PMC4829466

Lin JR, Fallahi-Sichani M, Chen JY, Sorger PK. Cyclic Immunofluorescence (CycIF), A Highly Multiplexed Method for Single-cell Imaging. Curr Protoc Chem Biol [Internet]. 2016 Dec 7;8(4):251–264. Available from: http://www.ncbi.nlm.nih.gov/pubmed/27925668 PMCID: PMC5233430

Pavkovic M, Vaidya VS. MicroRNAs and drug-induced kidney injury. Pharmacology & Therapeutics. 2016 Jul 1;163:48–57.

Pavkovic M, Robinson-Cohen C, Chua AS, Nicoara O, Cárdenas-González M, Bijol V, Ramachandran K, Hampson L, Pirmohamed M, Antoine DJ, Frendl G, Himmelfarb J, Waikar SS, Vaidya VS. Detection of Drug-Induced Acute Kidney Injury in Humans Using Urinary KIM-1, miR-21, -200c, and -423. Toxicological Sciences [Internet]. 2016 [cited 2017 Jun 8];152(1):205–213. Available from: https://academic.oup.com/toxsci/article-lookup/doi/10.1093/toxsci/kfw077

Pellegrini KL, Gerlach CV, Craciun FL, Ramachandran K, Bijol V, Kissick HT, Vaidya VS. Application of small RNA sequencing to identify microRNAs in acute kidney injury and fibrosis. Toxicology and Applied Pharmacology. 2016;312:42–52.

Ramm S, Adler M, Vaidya VS. A High-Throughput Screening Assay to Identify Kidney Toxic Compounds. Curr Protoc Toxicol [Internet]. 2016 Aug 1;69:9.10.1-9.10.26. Available from: http://doi.wiley.com/10.1002/cptx.12 PMCID: PMC4981919

Richardson K, Bennion OT, Tan S, Hoang AN, Cokol M, Aldridge BB. Temporal and intrinsic factors of rifampicin tolerance in mycobacteria. PNAS. 2016 Jul 19;113(29):8302–8307. PMCID: PMC4961206

Sokolov A, Carlin DE, Paull EO, Baertsch R, Stuart JM. Pathway-Based Genomics Prediction using Generalized Elastic Net. PLoS Comput Biol. 2016 Mar;12(3):e1004790. PMCID: PMC4784899

Sokolov A, Paull EO, Stuart JM. One-Class Detection of Cell States in Tumor Subtypes. Pac Symp Biocomput [Internet]. 2016 Jan 19;21:405–416. Available from: http://www.ncbi.nlm.nih.gov/pubmed/26776204 PMCID: 4856035

Tan L, Gurbani D, Weisberg EL, Jones DS, Rao S, Singer WD, Bernard FM, Mowafy S, Jenney A, Du G, Nonami A, Griffin JD, Lauffenburger DA, Westover KD, Sorger PK, Gray NS. Studies of TAK1-centered polypharmacology with novel covalent TAK1 inhibitors. Bioorg Med Chem [Internet]. 2016 Dec 7;25(4):1320–1328. Available from: http://www.ncbi.nlm.nih.gov/pubmed/28038940 PMCID: PMC5484535

Tirosh I, Izar B, Prakadan SM, Wadsworth MH, Treacy D, Trombetta JJ, Rotem A, Rodman C, Lian C, Murphy G, Fallahi-Sichani M, Dutton-Regester K, Lin JR, Cohen O, Shah P, Lu D, Genshaft AS, Hughes TK, Ziegler CGK, Kazer SW, Gaillard A, Kolb KE, Villani AC, Johannessen CM, Andreev AY, Van Allen EM, Bertagnolli M, Sorger PK, Sullivan RJ, Flaherty KT, Frederick DT, Jané-Valbuena J, Yoon CH, Rozenblatt-Rosen O, Shalek AK, Regev A, Garraway LA. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science [Internet]. 2016 Apr 8;352(6282):189–196. Available from: http://www.ncbi.nlm.nih.gov/pubmed/27124452 PMCID: PMC4944528

AlQuraishi M, Tang S, Xia X. An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system. BMC Bioinformatics [Internet]. 2015 Nov 19;16(1):390. Available from: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0819-2 PMCID: PMC4653904

Baym M, Kryazhimskiy S, Lieberman TD, Chung H, Desai MM, Kishony R. Inexpensive multiplexed library preparation for megabase-sized genomes. PLoS One [Internet]. 2015 May 22;10(5):e0128036. Available from: http://dx.doi.org/10.1371/journal.pone.0128036 https://www.ncbi.nlm.nih.gov/pubmed/26000737 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4441430 http://dx.plos.org/10.1371/journal.pone.0128036

Elia AE, Boardman AP, Wang DC, Huttlin EL, Everley RA, Dephoure N, Zhou C, Koren I, Gygi SP, Elledge SJ. Quantitative Proteomic Atlas of Ubiquitination and Acetylation in the DNA Damage Response. Mol Cell. 2015 Sep;59(5):867–81.

Fallahi-Sichani M, Moerke NJ, Niepel M, Zhang T, Gray NS, Sorger PK. Systematic analysis of BRAF(V600E) melanomas reveals a role for JNK/c-Jun pathway in adaptive resistance to drug-induced apoptosis. Mol Syst Biol [Internet]. 2015 Mar 31;11(3):797. Available from: http://www.ncbi.nlm.nih.gov/pubmed/25814555 PMCID: PMC4380931

Krukenberg KA, Kim S, Tan ES, Maliga Z, Mitchison TJ. Extracellular Poly(ADP-Ribose) Is a Pro-inflammatory Signal for Macrophages. Chemistry & Biology. 2015;22(4):446–452.

Lin JR, Fallahi-Sichani M, Sorger PK. Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method. Nat Commun [Internet]. 2015 Sep 25;6:8390. Available from: http://www.ncbi.nlm.nih.gov/pubmed/26399630 PMCID: PMC4587398

Muntel J, Boswell SA, Tang S, Ahmed S, Wapinski I, Foley G, Steen H, Springer M. Abundance-based Classifier for the Prediction of Mass Spectrometric Peptide Detectability Upon Enrichment (PPA). Molecular & Cellular Proteomics [Internet]. 2015;14(2):430–440. Available from: http://www.mcponline.org/lookup/doi/10.1074/mcp.M114.044321

Palmer AC, Toprak E, Baym M, Kim S, Veres A, Bershtein S, Kishony R. Delayed commitment to evolutionary fate in antibiotic resistance fitness landscapes. Nature Communications [Internet]. 2015 Jun 10;6:7385. Available from: http://www.nature.com/doifinder/10.1038/ncomms8385

Pavkovic M, Riefke B, Frisk AL, Gröticke I, Ellinger-Ziegelbauer H. Glomerulonephritis-induced changes in kidney gene expression in rats. Genom Data [Internet]. 2015 Dec;6:81–82. Available from: http://linkinghub.elsevier.com/retrieve/pii/S2213596015300131 PMCID: PMC4664719

Pavkovic M, Riefke B, Frisk AL, Gröticke I, Ellinger-Ziegelbauer H. Glomerulonephritis-Induced Changes in Urinary and Kidney MicroRNA Profiles in Rats. Toxicological Sciences. 2015;145(2):348–359.

Xu X, Choi SH, Hu T, Tiyanont K, Habets R, Groot AJ, Vooijs M, Aster JC, Chopra R, Fryer C, Blacklow SC. Insights into Autoregulation of Notch3 from Structural and Functional Studies of Its Negative Regulatory Region. Structure. 2015;23(7):1227–1235.

AlQuraishi M, Koytiger G, Jenney A, MacBeath G, Sorger PK. A multiscale statistical mechanical framework integrates biophysical and genomic data to assemble cancer networks. Nat Genet [Internet]. 2014 Dec 1;46(12):1363–1371. Available from: http://www.ncbi.nlm.nih.gov/pubmed/25362484 PMCID: PMC4244270

Chung JJ, Shim SH, Everley RA, Gygi SP, Zhuang X, Clapham DE. Structurally distinct Ca(2+) signaling domains of sperm flagella orchestrate tyrosine phosphorylation and motility. Cell. 2014 May;157(4):808–22.

Palmer AC, Kishony R. Opposing effects of target overexpression reveal drug mechanisms. Nat Commun. 2014 Jul 1;5:4296. PMCID: PMC4408919

Pellegrini KL, Han T, Bijol V, Saikumar J, Craciun FL, Chen WW, Fuscoe JC, Vaidya VS. MicroRNA-155 Deficient Mice Experience Heightened Kidney Toxicity When Dosed with Cisplatin. Toxicological Sciences. 2014 Oct 1;141(2):484–492.

Everley RA, Kunz RC, McAllister FE, Gygi SP. Increasing throughput in targeted proteomics assays: 54-plex quantitation in a single mass spectrometry run. Anal Chem. 2013 Jun;85(11):5340–6.

Orth JD, Kohler RH, Foijer F, Sorger PK, Weissleder R, Mitchison TJ. Analysis of mitosis and antimitotic drug responses in tumors by in vivo microscopy and single-cell pharmacodynamics. Cancer Res [Internet]. 2011 Jul 1;71(13):4608–16. Available from: http://www.ncbi.nlm.nih.gov/pubmed/21712408 PMCID: 3129392