LSP Bibliography

Ahdritz G, Bouatta N, 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]. bioRxiv; 2022 [cited 2022 Dec 2]. Available from: 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

Lin JR, Chen YA, Campton D, Cooper J, Coy S, Yapp C, Tefft J, McCarty E, Ligon K, Rodig SJ, Reese S, George T, Santagata S, Sorger PK. Multi-modal digital pathology for colorectal cancer diagnosis by high-plex immunofluorescence imaging and traditional histology of the same tissue section [Internet]. Cancer Biology; 2022 [cited 2023 Feb 22]. Available from: http://biorxiv.org/lookup/doi/10.1101/2022.09.28.509927

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

Nariya MK, Mills CE, Sorger PK, Sokolov A. Paired evaluation defines performance landscapes for machine learning models [Internet]. bioRxiv; 2022 [cited 2022 Oct 25]. Available from: http://biorxiv.org/lookup/doi/10.1101/2022.09.07.507020

Netterfield TS, Ostheimer GJ, Tentner AR, Sorger PK, Janes KA, Lauffenburger DA, Yaffe MB. Biphasic JNK–Erk Signaling Separates Induction and Maintenance of Cell Senescence after DNA Damage [Internet]. bioRxiv; 2022 [cited 2022 Jun 21]. Available from: DOI: 10.1101/2022.06.15.496288

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

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

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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

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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