2022 Publications

Burden of Rare Genetic Variants in Spontaneous Coronary Artery Dissection with High-risk Features, Wang Y, Starovoytov A, Murad AM, Hunker KL, Brunham LR, Li JZ, Saw J, Ganesh SK, JAMA Cardiology, 10.1001/jamacardio.2022.2970

A Crowdsourcing Approach to Develop Machine Learning Models to Quantify Radiographic Joint Damage in Rheumatoid Arthritis, Sun D, Nguyen TM, Allaway RJ, Wang J, Chung V, Yu TV, Mason M, Dimitrovsky I, Ericson L, Li H, Guan Y, Israel A, Olar A, Pataki BA, Stolovitzky G, Guinney J, Gulko PS, Frazier MB, Chen JY, Costello JC, Bridges SL, JAMA Network Open, 10.1001/jamanetworkopen.2022.27423

Multilevel Modeling of Joint Damage in Rheumatoid Arthritis, Li H, Guan Y, Advanced Intelligent Systems, 10.1002/aisy.202200184

Optimal dynamic treatment regime estimation using information extraction from unstructured clinical text, Zhou N, Brook RD, Dinov ID, Wang L, Biometrical Journal, 10.1002/bimj.202100077

NetCellMatch: Multiscale Network-Based Matching of Cancer Cell Lines to Patients Using Graphical Wavelets, Desai N, Morris JS, Baladandayuthapani V, Chemistry and Biodiversity, 10.1002/cbdv.202200746

Integrating information from existing risk prediction models with no model details, Han P, Taylor JMG, Mukherjee B, Canadian Journal of Statistics, 10.1002/cjs.11701

A Dual-Filtration System for Single-Cell Sequencing of Circulating Tumor Cells and Clusters in HCC, Chen VL, Huang Q, Harouaka R, Du Y, Lok AS, Parikh ND, Garmire LX, Wicha MS, Hepatology Communications, 10.1002/hep4.1900

Population-based meta-analysis and gene-set enrichment identifies FXR/RXR pathway as common to fatty liver disease and serum lipids, Handelman SK, Puentes YM, Kuppa A, Chen Y, Du X, Feitosa MF, Palmer ND, Speliotes EK, Hepatology Communications, 10.1002/hep4.2066

Body mass index associates with amyotrophic lateral sclerosis survival and metabolomic profiles, Goutman SA, Boss J, Iyer G, Habra H, Savelieff MG, Karnovsky A, Mukherjee B, Feldman EL, Muscle and Nerve, 10.1002/mus.27744

Differential responses to taxanes and PARP inhibitors in ATM- versus BRCA2-mutated metastatic castrate-resistant prostate cancer, Su CT, Nizialek E, Berchuck JE, Vlachostergios PJ, Ashkar R, Sokolova A, Barata PC, Aggarwal RR, McKay RR, Agarwal N, McClure HM, Nafissi N, Bryce AH, Sartor O, Sayegh N, Cheng HH, Adra N, Sternberg CN, Taplin ME, Cieslik M, Alva AS, Antonarakis ES, Prostate, 10.1002/pros.24454

Genetic variation of the blood coagulation regulator tissue factor pathway inhibitor and venous thromboembolism among middle-aged and older adults: A population-based cohort study, Manderstedt E, Lind-Halldén C, Halldén C, Elf J, Svensson PJ, Engström G, Melander O, Baras A, Lotta LA, Zöller B, Abecasis G, Baras A, Cantor M, Coppola G, Economides A, Lotta LA, Overton JD, Reid JG, Shuldiner A, Beechert C, Forsythe C, Fuller ED, Gu Z,, Research and Practice in Thrombosis and Haemostasis, 10.1002/rth2.12842

Kimesurface representation and tensor linear modeling of longitudinal data, Zhang R, Zhang Y, Liu Y, Guo Y, Shen Y, Deng D, Qiu YJ, Dinov ID, Neural Computing and Applications, 10.1007/s00521-021-06789-8

Bayesian graphical models for modern biological applications, Ni Y, Baladandayuthapani V, Vannucci M, Stingo FC, Statistical Methods and Applications, 10.1007/s10260-021-00572-8

Rejoinder to the discussion of “Bayesian graphical models for modern biological applications”, Ni Y, Baladandayuthapani V, Vannucci M, Stingo FC, Statistical Methods and Applications, 10.1007/s10260-022-00634-5

Using Genomic Structural Equation Modeling to Partition the Genetic Covariance Between Birthweight and Cardiometabolic Risk Factors into Maternal and Offspring Components in the Norwegian HUNT Study, Moen GH, Nivard M, Bhatta L, Warrington NM, Willer C, Åsvold BO, Brumpton B, Evans DM, Behavior Genetics, 10.1007/s10519-022-10116-9

DataSifterText: Partially Synthetic Text Generation for Sensitive Clinical Notes, Zhou N, Wu Q, Wu Z, Marino S, Dinov ID, Journal of Medical Systems, 10.1007/s10916-022-01880-6

Interactive Visualization and Computation of 2D and 3D Probability Distributions, Bobrovnikov M, Chai JT, Dinov ID, SN Computer Science, 10.1007/s42979-022-01206-w

Identification of secreted proteins by comparison of protein abundance in conditioned media and cell lysates, Abbineni PS, Tang VT, da Veiga Leprevost F, Basrur V, Xiang J, Nesvizhskii AI, Ginsburg D, Analytical Biochemistry, 10.1016/j.ab.2022.114846

Head and Neck Radiotherapy Patterns of Practice Variability Identified as a Challenge to Real-World Big Data: results from the Learning from Analysis of Multicentre Big Data Aggregation (LAMBDA) Consortium, Caissie A, Mierzwa M, Fuller CD, Rajaraman M, Lin A, MacDonald A, Popple R, Xiao Y, VanDijk L, Balter P, Fong H, Xu H, Kovoor M, Lee J, Rao A, Martel M, Thompson R, Merz B, Yao J, Mayo C, Advances in Radiation Oncology, 10.1016/j.adro.2022.100925

Meta-imputation: An efficient method to combine genotype data after imputation with multiple reference panels, Yu K, Das S, LeFaive J, Kwong A, Pleiness J, Forer L, Schönherr S, Fuchsberger C, Smith AV, Abecasis GR, American Journal of Human Genetics, 10.1016/j.ajhg.2022.04.002

A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids, Ramdas S, Judd J, Graham SE, Kanoni S, Wang Y, Surakka I, Wenz B, Clarke SL, Chesi A, Wells A, Bhatti KF, Vedantam S, Winkler TW, Locke AE, Marouli E, Zajac GJM, Wu KHH, Ntalla I, Hui Q, Klarin D, Hilliard AT, Wang Z, Xue C, Thorleifsson G, Helgadottir A, American Journal of Human Genetics, 10.1016/j.ajhg.2022.06.012

Development of an automated screen for Kv7.2 potassium channels and discovery of a new agonist chemotype, Hernandez CC, Tarfa RA, Miguel I. Limcaoco J, Liu R, Mondal P, Hill C, Keith Duncan R, Tzounopoulos T, Stephenson CRJ, O'Meara MJ, Wipf P, Bioorganic and Medicinal Chemistry Letters, 10.1016/j.bmcl.2022.128841

High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios, Byrska-Bishop M, Evani US, Zhao X, Basile AO, Abel HJ, Regier AA, Corvelo A, Clarke WE, Musunuri R, Nagulapalli K, Fairley S, Runnels A, Winterkorn L, Lowy E, Eichler EE, Korbel JO, Lee C, Marschall T, Devine SE, Harvey WT, Zhou W, Mills RE, Rausch T, Kum, Cell, 10.1016/j.cell.2022.08.004

ATRX loss in glioma results in dysregulation of cell-cycle phase transition and ATM inhibitor radio-sensitization, Qin T, Mullan B, Ravindran R, Messinger D, Siada R, Cummings JR, Harris M, Muruganand A, Pyaram K, Miklja Z, Reiber M, Garcia T, Tran D, Danussi C, Brosnan-Cashman J, Pratt D, Zhao X, Rehemtulla A, Sartor MA, Venneti S, Meeker AK, Huse JT, Morgan MA, Lowe, Cell Reports, 10.1016/j.celrep.2021.110216

Biomarkers for the Prediction and Diagnosis of Fibrostenosing Crohn's Disease: A Systematic Review, Steiner CA, Berinstein JA, Louissaint J, Higgins PDR, Spence JR, Shannon C, Lu C, Stidham RW, Fletcher JG, Bruining DH, Feagan BG, Jairath V, Baker ME, Bettenworth D, Rieder F, Clinical Gastroenterology and Hepatology, 10.1016/j.cgh.2021.05.054

EML2-S constitutes a new class of proteins that recognizes and regulates the dynamics of tyrosinated microtubules, Hotta T, McAlear TS, Yue Y, Higaki T, Haynes SE, Nesvizhskii AI, Sept D, Verhey KJ, Bechstedt S, Ohi R, Current Biology, 10.1016/j.cub.2022.07.027

Molecular Characterization of Clear Cell Renal Cell Carcinoma Reveals Prognostic Significance of Epithelial-mesenchymal Transition Gene Expression Signature, Nallandhighal S, Vince R, Karim R, Groves S, Stangl-Kremser J, Russell C, Hu K, Pham T, Cani AK, Liu CJ, Zaslavsky A, Mehra R, Cieslik M, Morgan TM, Palapattu GS, Udager AM, Salami SS, European urology oncology, 10.1016/j.euo.2021.10.007

Outcomes of cold snare piecemeal EMR for nonampullary small-bowel adenomas larger than 1 cm: a retrospective study, Dang DT, Suresh S, Vance RB, Singla S, Javia S, Watson A, Chathadi KV, Katukuri V, Pompa R, Stidham RW, Zuchelli T, Piraka C, Gastrointestinal Endoscopy, 10.1016/j.gie.2021.12.018

Performance of polygenic risk scores for cancer prediction in a racially diverse academic biobank, Wang L, Desai H, Verma SS, Le A, Hausler R, Verma A, Judy R, Doucette A, Gabriel PE, Abecasis G, Bai X, Balasubramanian S, Baras A, Blumenfeld A, Boutkov B, Cantor M, Coppola G, Economides A, Eom G, Habegger L, Hawes A, Jones MB, Khalid S, Krasheninina O, Genetics in Medicine, 10.1016/j.gim.2021.10.015

Mako: A Graph-based Pattern Growth Approach to Detect Complex Structural Variants, Lin J, Yang X, Kosters W, Xu T, Jia Y, Wang S, Zhu Q, Ryan M, Guo L, Zhang C, Gerstein MB, Sanders AD, Zody MC, Talkowski ME, Mills RE, Korbel JO, Marschall T, Ebert P, Audano PA, Rodriguez-Martin B, Porubsky D, Jan Bonder M, Sulovari A, Ebler J, Zhou W, Genomics, Proteomics and Bioinformatics, 10.1016/j.gpb.2021.03.007

Identifying potential candidates for advanced heart failure therapies using an interpretable machine learning algorithm, Yao H, Golbus JR, Gryak J, Pagani FD, Aaronson KD, Najarian K, Journal of Heart and Lung Transplantation, 10.1016/j.healun.2022.08.028

Machine learning for artemisinin resistance in malaria treatment across in vivo-in vitro platforms, Zhang H, Guo J, Li H, Guan Y, iScience, 10.1016/j.isci.2022.103910

Rearrangement of T Cell genome architecture regulates GVHD, Sun Y, Dotson GA, Muir LA, Ronquist S, Oravecz-Wilson K, Peltier D, Seike K, Li L, Meixner W, Rajapakse I, Reddy P, iScience, 10.1016/j.isci.2022.104846

Generic medical concept embedding and time decay for diverse patient outcome prediction tasks, Li Y, Dong W, Ru B, Black A, Zhang X, Guan Y, iScience, 10.1016/j.isci.2022.104880

Cytokine responses in nonlesional psoriatic skin as clinical predictor to anti-TNF agents, Tsoi LC, Patrick MT, Shuai S, Sarkar MK, Chi S, Ruffino B, Billi AC, Xing X, Uppala R, Zang C, Fullmer J, He Z, Maverakis E, Mehta NN, Perez White BE, Getsios S, Helfrich Y, Voorhees JJ, Kahlenberg JM, Weidinger S, Gudjonsson JE, Journal of Allergy and Clinical Immunology, 10.1016/j.jaci.2021.07.024

Netherton syndrome subtypes share IL-17/IL-36 signature with distinct IFN-α and allergic responses, Barbieux C, Bonnet des Claustres M, Fahrner M, Petrova E, Tsoi LC, Gouin O, Leturcq F, Nicaise-Roland P, Bole C, Béziat V, Bourrat E, Schilling O, Gudjonsson JE, Hovnanian A, Journal of Allergy and Clinical Immunology, 10.1016/j.jaci.2021.08.024

GRASP55 regulates the unconventional secretion and aggregation of mutant huntingtin, Ahat E, Bui S, Zhang J, da Veiga Leprevost F, Sharkey L, Reid W, Nesvizhskii AI, Paulson HL, Wang Y, Journal of Biological Chemistry, 10.1016/j.jbc.2022.102219

On diabetic foot ulcer knowledge gaps, innovation, evaluation, prediction markers, and clinical needs, Schmidt BM, Holmes CM, Najarian K, Gallagher K, Haus JM, Shadiow J, Ye W, Ang L, Burant A, Baker N, Katona A, Martin CL, Pop-Busui R, Journal of Diabetes and its Complications, 10.1016/j.jdiacomp.2022.108317

Present and future directions in diabetic kidney disease, Limonte CP, Kretzler M, Pennathur S, Pop-Busui R, de Boer IH, Journal of Diabetes and its Complications, 10.1016/j.jdiacomp.2022.108357

Corrigendum to ‘An international genome-wide meta-analysis of primary biliary cholangitis: Novel risk loci and candidate drugs’ [J Hepatol 2021;75(3):572–581] (Journal of Hepatology (2021) 75(3) (572–581), (S0168827821003342), (10.1016/j.jhep.2021.04.055), Cordell HJ, Fryett JJ, Ueno K, Darlay R, Aiba Y, Hitomi Y, Kawashima M, Nishida N, Khor SS, Gervais O, Kawai Y, Nagasaki M, Tokunaga K, Tang R, Shi Y, Li Z, Juran BD, Atkinson EJ, Gerussi A, Carbone M, Asselta R, Cheung A, de Andrade M, Baras A, Horowitz, Journal of Hepatology, 10.1016/j.jhep.2021.11.015

Metabolic and genetic contributions to NAFLD: Really distinct and homogeneous?, Speliotes EK, George J, Journal of Hepatology, 10.1016/j.jhep.2021.12.024

IFN-κ Is a Rheostat for Development of Psoriasiform Inflammation, Gharaee-Kermani M, Estadt SN, Tsoi LC, Wolf-Fortune SJ, Liu J, Xing X, Theros J, Reed TJ, Lowe L, Gruszka D, Ward NL, Gudjonsson JE, Kahlenberg JM, Journal of Investigative Dermatology, 10.1016/j.jid.2021.05.029

Transcriptome Analysis Reveals Intrinsic Proinflammatory Signaling in Healthy African American Skin, Klopot A, Baida G, Kel A, Tsoi LC, Perez White BE, Budunova I, Journal of Investigative Dermatology, 10.1016/j.jid.2021.09.031

Noninvasive Tape-Stripping with High-Resolution RNA Profiling Effectively Captures a Preinflammatory State in Nonlesional Psoriatic Skin, Tsoi LC, Xing X, Xing E, Wasikowski R, Shao S, Zeng C, Plazyo O, Kirma J, Jiang Y, Billi AC, Sarkar MK, Turnier JL, Uppala R, Smith KM, Helfrich Y, Voorhees JJ, Maverakis E, Modlin RL, Kahlenberg JM, Scott VE, Gudjonsson JE, Journal of Investigative Dermatology, 10.1016/j.jid.2021.09.038

LB967 Monogenic mutations implicate STAT1 in hidradenitis suppurativa pathogenesis, Youssef M, Baugh E, Colvin A, Babbush K, Adriano T, Benesh G, Torpey ME, Nosrati A, van Straalen KR, Tsoi LC, DeWan AT, Leal SM, Eisenberg R, Gudjonsson JE, Milner J, Cohen SR, Petukhova L, Journal of Investigative Dermatology, 10.1016/j.jid.2022.05.989

Dihydroartemisinin enhances the inhibitory effect of sorafenib on HepG2 cells by inducing ferroptosis and inhibiting energy metabolism, Cui Z, Wang H, Li S, Qin T, Shi H, Ma J, Li L, Yu G, Jiang T, Li C, Journal of Pharmacological Sciences, 10.1016/j.jphs.2021.09.008

Gait speed is a preoperative indicator of postoperative events after elective proximal aortic surgery, Hobbs RD, Norton EL, Wu X, Willer CJ, Hummell SL, Prager RL, Afilalo J, Hornsby WE, Yang B, Journal of Thoracic and Cardiovascular Surgery, 10.1016/j.jtcvs.2020.03.165

Glomerular endothelial cell-podocyte stresses and crosstalk in structurally normal kidney transplants, Menon R, Otto EA, Berthier CC, Nair V, Farkash EA, Hodgin JB, Yang Y, Luo J, Woodside KJ, Zamani H, Norman SP, Wiggins RC, Kretzler M, Naik AS, Kidney International, 10.1016/j.kint.2021.11.031

Genetics in chronic kidney disease: conclusions from a Kidney Disease: Improving Global Outcomes (KDIGO) Controversies Conference, Köttgen A, Cornec-Le Gall E, Halbritter J, Kiryluk K, Mallett AJ, Parekh RS, Rasouly HM, Sampson MG, Tin A, Antignac C, Ars E, Bergmann C, Bleyer AJ, Bockenhauer D, Devuyst O, Florez JC, Fowler KJ, Franceschini N, Fukagawa M, Gale DP, Gbadegesin RA, Golds, Kidney International, 10.1016/j.kint.2022.03.019

Precision nephrology identified tumor necrosis factor activation variability in minimal change disease and focal segmental glomerulosclerosis., Mariani LH, Eddy S, AlAkwaa FM, McCown PJ, Harder JL, Nair V, Eichinger F, Martini S, Ademola AD, Boima V, Reich HN, El Saghir J, Godfrey B, Ju W, Tanner EC, Vega-Warner V, Wys NL, Adler SG, Appel GB, Athavale A, Atkinson MA, Bagnasco SM, Barisoni L, Brow, Kidney Int, 10.1016/j.kint.2022.10.023

Viral associations with kidney disease diagnosis and altered kidney metatranscriptome by kidney function, Hong C, Eichinger F, Atta MG, Estrella MM, Fine DM, Ross MJ, Wyatt C, Hwang TH, Kretzler M, Sedor JR, O'Toole JF, Miller AW, Bruggeman LA, Kidney International, 10.1016/j.kint.2022.11.001

RAD51AP1 regulates ALT-HDR through chromatin-directed homeostasis of TERRA, Kaminski N, Wondisford AR, Kwon Y, Lynskey ML, Bhargava R, Barroso-González J, García-Expósito L, He B, Xu M, Mellacheruvu D, Watkins SC, Modesti M, Miller KM, Nesvizhskii AI, Zhang H, Sung P, O'Sullivan RJ, Molecular Cell, 10.1016/j.molcel.2022.09.025

Adipose tissue macrophages: Regulators of adipose tissue immunometabolism during obesity, Nance SA, Muir L, Lumeng C, Molecular Metabolism, 10.1016/j.molmet.2022.101642

The life and times of endogenous opioid peptides: Updated understanding of synthesis, spatiotemporal dynamics, and the clinical impact in alcohol use disorder., Margolis EB, Moulton MG, Lambeth PS, O'Meara MJ, Neuropharmacology, 10.1016/j.neuropharm.2022.109376

Chemoradiation therapy alters the PD-L1 score in locoregional recurrent squamous cell carcinomas of the head and neck, Park BJ, Mattox AK, Clayburgh D, Patel M, Bell RB, Yueh B, Leidner R, Xiao H, Couey M, Li S, Qin T, Sartor MA, Cairns B, MacDonough T, Halliwill K, Deschler D, Lin DT, Faquin WC, Sadow PM, Pai SI, Oral Oncology, 10.1016/j.oraloncology.2022.106183

Determinism, well-posedness, and applications of the ultrahyperbolic wave equation in spacekime, Wang Y, Shen Y, Deng D, Dinov ID, Partial Differential Equations in Applied Mathematics, 10.1016/j.padiff.2022.100280

Auto-annotating sleep stages based on polysomnographic data, Zhang H, Wang X, Li H, Mehendale S, Guan Y, Patterns, 10.1016/j.patter.2021.100371

Genetic determinants of telomere length from 109,122 ancestrally diverse whole-genome sequences in TOPMed., Taub MA, Conomos MP, Keener R, Iyer KR, Weinstock JS, Yanek LR, Lane J, Miller-Fleming TW, Brody JA, Raffield LM, McHugh CP, Jain D, Gogarten SM, Laurie CA, Keramati A, Arvanitis M, Smith AV, Heavner B, Barwick L, Becker LC, Bis JC, Blangero J, Bleecker E, Cell Genomics, 10.1016/j.xgen.2021.100084

The HUNT study: A population-based cohort for genetic research, Brumpton BM, Graham S, Surakka I, Skogholt AH, Løset M, Fritsche LG, Wolford B, Zhou W, Nielsen JB, Holmen OL, Gabrielsen ME, Thomas L, Bhatta L, Rasheed H, Zhang H, Kang HM, Hornsby W, Moksnes MR, Coward E, Melbye M, Giskeødegård GF, Fenstad J, Krokstad, Cell Genomics, 10.1016/j.xgen.2022.100193

Protocol for using Ciclops to build models trained on cross-platform transcriptome data for clinical outcome prediction, Chou E, Zhang H, Guan Y, STAR Protocols, 10.1016/j.xpro.2022.101583

Su1558: IBD INCREASING RISK VARIANTS IN ZBTB40 AND NFATC1 ARE ASSOCIATED WITH REDUCTION IN BONE MINERAL DENSITY, Cushing K, Chen Y, Higgins PD, Speliotes E, Gastroenterology, 10.1016/s0016-5085(22)61480-x

FRI160 Multispectral analysis of liver biopsies from patients with chronic hepatitis C reveals unique macrophage phenotypes and spatial interactions associated with fibrosis progression, Saldarriaga O, Krishnan S, Oneka M, Rao A, Gosnell J, Millian D, Wanninger T, Jiao J, Beretta L, Stevenson H, Journal of Hepatology, 10.1016/s0168-8278(22)01270-3

FRI190 Multispectral imaging analysis of liver biopsies from patients with non-alcoholic steatohepatitis reveals enrichment of pathogenic macrophage phenotypes associated with disease progression, Gosnell J, Saldarriaga O, Krishnan S, Oneka M, Rao A, Millian D, Wanninger T, Jiao J, Beretta L, Stevenson H, Journal of Hepatology, 10.1016/s0168-8278(22)01300-9

Prioritizing Virtual Screening with Interpretable Interaction Fingerprints, Fassio AV, Shub L, Ponzoni L, McKinley J, O'Meara MJ, Ferreira RS, Keiser MJ, De Melo Minardi RC, Journal of Chemical Information and Modeling, 10.1021/acs.jcim.2c00695

Alignment and Analysis of a Disparately Acquired Multibatch Metabolomics Study of Maternal Pregnancy Samples, Habra H, Kachman M, Padmanabhan V, Burant C, Karnovsky A, Meijer J, Journal of Proteome Research, 10.1021/acs.jproteome.2c00371

Comparative Evaluation of Proteome Discoverer and FragPipe for the TMT-Based Proteome Quantification, He T, Liu Y, Zhou Y, Li L, Wang H, Chen S, Gao J, Jiang W, Yu Y, Ge W, Chang HY, Fan Z, Nesvizhskii AI, Guo T, Sun Y, Journal of Proteome Research, 10.1021/acs.jproteome.2c00390

The Association Between Sleep and Cognitive Function in People With Spinal Cord Injury (SCI), Carlozzi NE, Troost JP, Molton IR, Ehde DM, Freedman J, Cao J, Miner JA, Najarian K, Kratz AL, Rehabilitation Psychology, 10.1037/rep0000418

ACE2 expression in adipose tissue is associated with cardio-metabolic risk factors and cell type composition—implications for COVID-19, El-Sayed Moustafa JS, Jackson AU, Brotman SM, Guan L, Villicaña S, Roberts AL, Zito A, Bonnycastle L, Erdos MR, Narisu N, Stringham HM, Welch R, Yan T, Lakka T, Parker S, Tuomilehto J, Seow J, Graham C, Huettner I, Acors S, Kouphou N, Wadge S, Duncan EL, International Journal of Obesity, 10.1038/s41366-022-01136-w

Hypoxia promotes an inflammatory phenotype of fibroblasts in pancreatic cancer, Mello AM, Ngodup T, Lee Y, Donahue KL, Li J, Rao A, Carpenter ES, Crawford HC, Pasca di Magliano M, Lee KE, Oncogenesis, 10.1038/s41389-022-00434-2

UGT1A1 genetic variants are associated with increases in bilirubin levels in rheumatoid arthritis patients treated with sarilumab, Lin N, Damask A, Boyapati A, Hamilton JD, Hamon S, Ternes N, Nivens MC, Penn J, Lopez A, Reid JG, Overton J, Shuldiner AR, Abecasis G, Baras A, Paulding C, Pharmacogenomics Journal, 10.1038/s41397-022-00269-5

UINMF performs mosaic integration of single-cell multi-omic datasets using nonnegative matrix factorization, Kriebel AR, Welch JD, Nature Communications, 10.1038/s41467-022-28431-4

Nasal airway transcriptome-wide association study of asthma reveals genetically driven mucus pathobiology, Sajuthi SP, Everman JL, Jackson ND, Saef B, Rios CL, Moore CM, Mak ACY, Eng C, Fairbanks-Mahnke A, Salazar S, Elhawary J, Huntsman S, Medina V, Nickerson DA, Germer S, Zody MC, Abecasis G, Kang HM, Rice KM, Kumar R, Zaitlen NA, Oh S, Rodríguez-Santana J, Nature Communications, 10.1038/s41467-022-28973-7

Connecting high-resolution 3D chromatin organization with epigenomics, Feng F, Yao Y, Wang XQD, Zhang X, Liu J, Nature Communications, 10.1038/s41467-022-29695-6

Meta-analysis of sub-Saharan African studies provides insights into genetic architecture of lipid traits, Choudhury A, Brandenburg JT, Chikowore T, Sengupta D, Boua PR, Crowther NJ, Agongo G, Asiki G, Gómez-Olivé FX, Kisiangani I, Maimela E, Masemola-Maphutha M, Micklesfield LK, Nonterah EA, Norris SA, Sorgho H, Tinto H, Tollman S, Graham SE, Willer CJ, Hazel, Nature Communications, 10.1038/s41467-022-30098-w

dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts, Demichev V, Szyrwiel L, Yu F, Teo GC, Rosenberger G, Niewienda A, Ludwig D, Decker J, Kaspar-Schoenefeld S, Lilley KS, Mülleder M, Nesvizhskii AI, Ralser M, Nature Communications, 10.1038/s41467-022-31492-0

Multiancestry exome sequencing reveals INHBE mutations associated with favorable fat distribution and protection from diabetes, Akbari P, Sosina OA, Bovijn J, Landheer K, Nielsen JB, Kim M, Aykul S, De T, Haas ME, Hindy G, Lin N, Dinsmore IR, Luo JZ, Hectors S, Geraghty B, Germino M, Panagis L, Parasoglou P, Walls JR, Halasz G, Atwal GS, Della Gatta G, Jones M, LeBlanc MG, Still C, Nature Communications, 10.1038/s41467-022-32398-7

Deciphering multi-way interactions in the human genome, Dotson GA, Chen C, Lindsly S, Cicalo A, Dilworth S, Ryan C, Jeyarajan S, Meixner W, Stansbury C, Pickard J, Beckloff N, Surana A, Wicha M, Muir LA, Rajapakse I, Nature Communications, 10.1038/s41467-022-32980-z

GCAF(TMEM251) regulates lysosome biogenesis by activating the mannose-6-phosphate pathway, Zhang W, Yang X, Li Y, Yu L, Zhang B, Zhang J, Cho WJ, Venkatarangan V, Chen L, Burugula BB, Bui S, Wang Y, Duan C, Kitzman JO, Li M, Nature Communications, 10.1038/s41467-022-33025-1

Whole genome sequence analysis of blood lipid levels in >66,000 individuals, Selvaraj MS, Li X, Li Z, Pampana A, Zhang DY, Park J, Aslibekyan S, Bis JC, Brody JA, Cade BE, Chuang LM, Chung RH, Curran JE, de las Fuentes L, de Vries PS, Duggirala R, Freedman BI, Graff M, Guo X, Heard-Costa N, Hidalgo B, Hwu CM, Irvin MR, Kelly TN, K, Nature Communications, 10.1038/s41467-022-33510-7

The fate of early perichondrial cells in developing bones, Matsushita Y, Chu AKY, Tsutsumi-Arai C, Orikasa S, Nagata M, Wong SY, Welch JD, Ono W, Ono N, Nature Communications, 10.1038/s41467-022-34804-6

Targeting SWI/SNF ATPases in enhancer-addicted prostate cancer, Xiao L, Parolia A, Qiao Y, Bawa P, Eyunni S, Mannan R, Carson SE, Chang Y, Wang X, Zhang Y, Vo JN, Kregel S, Simko SA, Delekta AD, Jaber M, Zheng H, Apel IJ, McMurry L, Su F, Wang R, Zelenka-Wang S, Sasmal S, Khare L, Mukherjee S, Abbineni C, Aithal K, Bh, Nature, 10.1038/s41586-021-04246-z

Mapping human haematopoietic stem cells from haemogenic endothelium to birth, Calvanese V, Capellera-Garcia S, Ma F, Fares I, Liebscher S, Ng ES, Ekstrand S, Aguadé-Gorgorió J, Vavilina A, Lefaudeux D, Nadel B, Li JY, Wang Y, Lee LK, Ardehali R, Iruela-Arispe ML, Pellegrini M, Stanley EG, Elefanty AG, Schenke-Layland K, Mikkola HKA, Nature, 10.1038/s41586-022-04571-x

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Population-scale analysis of common and rare genetic variation associated with hearing loss in adults, Praveen K, Dobbyn L, Gurski L, Ayer AH, Staples J, Mishra S, Bai Y, Kaufman A, Moscati A, Benner C, Chen E, Chen S, Popov A, Smith J, Melander O, Jones MB, Marchini J, Balasubramanian S, Zambrowicz B, Drummond MC, Baras A, Abecasis GR, Ferreira MA, Stahl, Communications biology, 10.1038/s42003-022-03408-7

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Genome-wide meta-analysis of iron status biomarkers and the effect of iron on all-cause mortality in HUNT, Moksnes MR, Graham SE, Wu KH, Hansen AF, Gagliano Taliun SA, Zhou W, Thorstensen K, Fritsche LG, Gill D, Mason A, Cucca F, Schlessinger D, Abecasis GR, Burgess S, Åsvold BO, Nielsen JB, Hveem K, Willer CJ, Brumpton BM, Communications Biology, 10.1038/s42003-022-03529-z

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ANGPTL7, a therapeutic target for increased intraocular pressure and glaucoma, Praveen K, Patel GC, Gurski L, Ayer AH, Persaud T, Still MD, Miloscio L, Van Zyl T, Di Gioia SA, Brumpton B, Krebs K, Åsvold BO, Chen E, Chavali VRM, Fury W, Gudiseva HV, Hyde S, Jorgenson E, Lefebvre S, Li D, Li A, Mclninch J, Patel B, Rabinowitz JS, Sal, Communications biology, 10.1038/s42003-022-03932-6

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Glycoproteomics, Bagdonaite I, Malaker SA, Polasky DA, Riley NM, Schjoldager K, Vakhrushev SY, Halim A, Aoki-Kinoshita KF, Nesvizhskii AI, Bertozzi CR, Wandall HH, Parker BL, Thaysen-Andersen M, Scott NE, Nature Reviews Methods Primers, 10.1038/s43586-022-00128-4

Serum Level of Polyubiquitinated PTEN and Loss of Kidney Function in American Indians With Type 2 Diabetes, Looker HC, Lin C, Nair V, Kretzler M, Mauer M, Najafian B, Nelson RG, American Journal of Kidney Diseases, 10.1053/j.ajkd.2021.08.009

Quantification of Glomerular Structural Lesions: Associations With Clinical Outcomes and Transcriptomic Profiles in Nephrotic Syndrome, Hodgin JB, Mariani LH, Zee J, Liu Q, Smith AR, Eddy S, Hartman J, Hamidi H, Gaut JP, Palmer MB, Nast CC, Chang A, Hewitt S, Gillespie BW, Kretzler M, Holzman LB, Barisoni L, Dell K, Sedor J, Schachere M, Negrey J, Lemley K, Lim E, Srivastava T, Garrett A, American Journal of Kidney Diseases, 10.1053/j.ajkd.2021.10.004

Artificial Intelligence for Disease Assessment in Inflammatory Bowel Disease: How Will it Change Our Practice? Stidham RW, Takenaka K, Gastroenterology, 10.1053/j.gastro.2021.12.238

ALDH1A1 Expression Is Enriched in Early-Onset Colorectal Cancers, Venugopal A, Koi M, Choi C, Kim HR, Speliotes EK, Carethers JM, Gastroenterology, 10.1053/j.gastro.2022.08.028

Cardiorespiratory Fitness After Open Repair for Acute Type A Aortic Dissection – A Prospective Study, Norton EL, Wu KHH, Rubenfire M, Fink S, Sitzmann J, Hobbs RD, Saberi S, Willer CJ, Yang B, Hornsby WE, Seminars in Thoracic and Cardiovascular Surgery, 10.1053/j.semtcvs.2021.05.017

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Bayesian Edge Regression in Undirected Graphical Models to Characterize Interpatient Heterogeneity in Cancer, Wang Z, Baladandayuthapani V, Kaseb AO, Amin HM, Hassan MM, Wang W, Morris JS, Journal of the American Statistical Association, 10.1080/01621459.2021.2000866

Towards the characterization of the tumor microenvironment through dictionary learning-based interpretable classification of multiplexed immunofluorescence images, Krishnan SN, Barua S, Frankel TL, Rao A, Physics in Medicine and Biology, 10.1088/1361-6560/aca86a

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Dissecting the shared genetic basis of migraine and mental disorders using novel statistical tools, Bahrami S, Hindley G, Winsvold BS, O'Connell KS, Frei O, Shadrin A, Cheng W, Bettella F, Rødevand L, Odegaard KJ, Fan CC, Pirinen MJ, Hautakangas HM, Martinsen AE, Skogholt AH, Brumpton B, Willer CJ, Tronvik E, Kristoffersen ES, Zwart JA, Nielsen JB, Hage, Brain, 10.1093/brain/awab267

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Application of Artificial Intelligence to Clinical Practice in Inflammatory Bowel Disease - What the Clinician Needs to Know, Chen D, Fulmer C, Gordon IO, Syed S, Stidham RW, Vande Casteele N, Qin Y, Falloon K, Cohen BL, Wyllie R, Rieder F, Journal of Crohn's and Colitis, 10.1093/ecco-jcc/jjab169

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Maternal plasma lipids are involved in the pathogenesis of preterm birth, Chen Y, He B, Liu Y, Aung MT, Rosario-Pabón Z, Vélez-Vega CM, Alshawabkeh A, Cordero JF, Meeker JD, Garmire LX, GigaScience, 10.1093/gigascience/giac004

Whole genome sequence analysis of platelet traits in the NHLBI Trans-Omics for Precision Medicine (TOPMed) initiative, Little A, Hu Y, Sun Q, Jain D, Broome J, Chen MH, Thibord F, Mchugh C, Surendran P, Blackwell TW, Brody JA, Bhan A, Chami N, De Vries PS, Ekunwe L, Heard-Costa N, Hobbs BD, Manichaikul A, Moon JY, Preuss MH, Ryan K, Wang Z, Wheeler M, Yanek LR, Abecasis G, Human Molecular Genetics, 10.1093/hmg/ddab252

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Arabidopsis TWISTED DWARF1 regulates stamen elongation by differential activation of ABCB1,19-mediated auxin transport, Liu J, Ghelli R, Cardarelli M, Geisler M, Journal of Experimental Botany, 10.1093/jxb/erac185

TissueNexus: A database of human tissue functional gene networks built with a large compendium of curated RNA-seq data, Lin CX, Li HD, Deng C, Guan Y, Wang J, Nucleic Acids Research, 10.1093/nar/gkab1133

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Digital health and artificial intelligence in kidney research: A report from the 2020 Kidney Disease Clinical Trialists (KDCT) meeting, Yi TW, Laing C, Kretzler M, Nkulikiyinka R, Legrand M, Jardine M, Rossignol P, Smyth B, Nephrology Dialysis Transplantation, 10.1093/ndt/gfab320

Therapeutic targeting of prenatal pontine ID1 signaling in diffuse midline glioma., Messinger D, Harris MK, Cummings JR, Thomas C, Yang T, Sweha SR, Woo R, Siddaway R, Burkert M, Stallard S, Qin T, Mullan B, Siada R, Ravindran R, Niculcea M, Dowling A, Bradin J, Ginn KF, Gener MAH, Dorris K, Vitanza NA, Schmidt SV, Spitzer J, Jiang L, Fi, Neuro Oncol, 10.1093/neuonc/noac141

Single-Cell RNA-Seq Identifies Dynamic Cardiac Transition Program from ADCs Induced by Leukemia Inhibitory Factor, Yao J, Ma F, Zhang L, Zhu C, Jumabay M, Yao Z, Wang L, Cai X, Zhang D, Qiao X, Shivkumar K, Pellegrini M, Yao Y, Wu X, Boström KI, Stem cells (Dayton, Ohio), 10.1093/stmcls/sxac048

Prediction of Postoperative Deterioration in Cardiac Surgery Patients Using Electronic Health Record and Physiologic Waveform Data, Mathis MR, Engoren MC, Williams AM, Biesterveld BE, Croteau AJ, Cai L, Kim RB, Liu G, Ward KR, Najarian K, Gryak J, Derksen H, Gunnerson KJ, Alam HB, Anesthesiology, 10.1097/ALN.0000000000004345

PD01-10 WHOLE TRANSCRIPTOME SEQUENCING OF CLEAR CELL RENAL CELL CARCINOMA REVEALS A MULTIGENE EXPRESSION PROGNOSTIC SIGNATURE, Nallandhighal S, Mehra R, Cieslik M, Kasputis A, Cotta B, Morgan T, Salami S, Investigative Urology, 10.1097/ju.0000000000002516.10

PD07-06 SPATIAL TRANSCRIPTOMIC PROFILING OF PROSTATE CANCER REVEALS ZONE SPECIFIC ANDROGEN RECEPTOR SIGNALING AND IMMUNE INFILTRATION, Patel P, Nallandhighal S, Scoville D, Tran L, Cotta B, Udager A, Rao A, Palapattu G, Dadhania V, Pitchiaya S, Salami S, Investigative Urology, 10.1097/ju.0000000000002526.06

Polygenic Risk Prediction in Diverticulitis., De Roo AC, Chen Y, Du X, Handelman S, Byrnes M, Regenbogen SE, Speliotes EK, Maguire LH, Ann Surg, 10.1097/SLA.0000000000005623

Human commensal Candida albicans strains demonstrate substantial within-host diversity and retained pathogenic potential. Anderson FM, Visser N, Amses K, Hodgins-Davis A, Weber AM, Metzner KM, McFadden MJ, Mills RE, O'Meara M, James TY, O'Meara TR, , 10.1101/2022.09.09.507247

ASK: Adversarial Soft k-Nearest Neighbor Attack and Defense, Wang R, Chen T, Yao P, Liu S, Rajapakse I, Hero AO, IEEE Access, 10.1109/ACCESS.2022.3209243

A Novel Tropical Geometry-Based Interpretable Machine Learning Method: Pilot Application to Delivery of Advanced Heart Failure Therapies, Yao H, Derksen H, Golbus JR, Zhang J, Aaronson KD, Gryak J, Najarian K, IEEE J Biomed Health Inform, 10.1109/JBHI.2022.3211765

Znet: Deep Learning Approach for 2D MRI Brain Tumor Segmentation, Ottom MA, Rahman HA, Dinov ID, IEEE Journal of Translational Engineering in Health and Medicine, 10.1109/JTEHM.2022.3176737

Spatial Pyramid Pooling With 3D Convolution Improves Lung Cancer Detection, Causey JL, Li K, Chen X, Dong W, Walker K, Qualls JA, Stubblefield J, Moore JH, Guan Y, Huang X, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10.1109/TCBB.2020.3027744

An Ensemble of U-Net Models for Kidney Tumor Segmentation With CT Images, Causey J, Stubblefield J, Qualls J, Fowler J, Cai L, Walker K, Guan Y, Huang X, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10.1109/TCBB.2021.3085608

Hypergraph Similarity Measures, Surana A, Chen C, Rajapakse I, IEEE Transactions on Network Science and Engineering, 10.1109/TNSE.2022.3217185

The Level Set Kalman Filter for State Estimation of Continuous-Discrete Systems, Wang N, Forger DB, IEEE Transactions on Signal Processing, 10.1109/TSP.2021.3133698

Integrative Bayesian models using Post-selective inference: A case study in radiogenomics, Panigrahi S, Mohammed S, Rao A, Baladandayuthapani V, Biometrics, 10.1111/biom.13740

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Two types of O-methyltransferase are involved in biosynthesis of anticancer methoxylated 4′-deoxyflavones in Scutellaria baicalensis Georgi, Cui MY, Lu AR, Li JX, Liu J, Fang YM, Pei TL, Zhong X, Wei YK, Kong Y, Qiu WQ, Hu YH, Yang J, Chen XY, Martin C, Zhao Q, Plant Biotechnology Journal, 10.1111/pbi.13700

Transfusion-associated hyperkalemia in pediatric population: Analyses for risk factors and recommendations, Yamada C, Edelson MF, Lee AC, Saifee NH, Dinov ID, Transfusion, 10.1111/trf.17135

Tracking Peripheral Artery Motion and Vascular Resistance With a Multimodal Wearable Sensor Under Pressure Perturbations, Wang L, Ansari S, Cai Y, Mccracken B, Hakam Tiba M, Ward KR, Najarian K, Oldham KR, Journal of Biomechanical Engineering, 10.1115/1.4053399

HP1 oligomerization compensates for low-affinity H3K9me recognition and provides a tunable mechanism for heterochromatin-specific localization, Biswas S, Chen Z, Karslake JD, Farhat A, Ames A, Raiymbek G, Freddolino PL, Biteen JS, Ragunathan K, Science Advances, 10.1126/sciadv.abk0793

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VPS34-dependent control of apical membrane function of proximal tubule cells and nutrient recovery by the kidney, Rinschen MM, Harder JL, Carter-Timofte ME, Zanon Rodriguez L, Mirabelli C, Demir F, Kurmasheva N, Ramakrishnan SK, Kunke M, Tan Y, Billing A, Dahlke E, Larionov AA, Bechtel-Walz W, Aukschun U, Grabbe M, Nielsen R, Christensen EI, Kretzler M, Huber TB, Wob, Science signaling, 10.1126/scisignal.abo7940

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AI-powered effective lens position prediction improves the accuracy of existing lens formulas, Li T, Stein J, Nallasamy N, British Journal of Ophthalmology, 10.1136/bjophthalmol-2020-318321

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Artificial Intelligence and Machine Learning for Early Detection and Diagnosis of Colorectal Cancer in Sub-Saharan Africa, Waljee AK, Weinheimer-Haus E, Abubakar A, Ngugi A, Siwo G, Kwakye G, Singal AG, Rao A, Saini SD, Read AJ, Baker J, Balis UJ, Zhu J, Saleh M, Gut, 10.1136/gutjnl-2022-327211

DDX58 (RIG-I)-related disease is associated with tissue-specific interferon pathway activation, Prasov L, Bohnsack BL, El Husny AS, Tsoi LC, Guan B, Kahlenberg JM, Almeida E, Wang H, Cowen EW, De Jesus AA, Jani P, Billi AC, Moroi SE, Wasikowski R, Almeida I, Almeida LN, Kok F, Garnai SJ, Mian SI, Chen MY, Warner BM, Ferreira CR, Goldbach-Mansky R, H, Journal of Medical Genetics, 10.1136/jmedgenet-2020-107447

Human COQ4 deficiency: delineating the clinical, metabolic and neuroimaging phenotypes, Laugwitz L, Seibt A, Herebian D, Peralta S, Kienzle I, Buchert R, Falb R, Gauck D, Müller A, Grimmel M, Beck-Woedel S, Kern J, Daliri K, Katibeh P, Danhauser K, Leiz S, Alesi V, Baertling F, Vasco G, Steinfeld R, Wagner M, Caglayan AO, Gumus H, Burmeister, Journal of medical genetics, 10.1136/jmedgenet-2021-107729

Transitions between cigarette, ENDS and dual use in adults in the PATH study (waves 1-4): Multistate transition modelling accounting for complex survey design, Brouwer AF, Jeon J, Hirschtick JL, Jimenez-Mendoza E, Mistry R, Bondarenko IV, Land SR, Holford TR, Levy DT, Taylor JMG, Fleischer NL, Meza R, Tobacco Control, 10.1136/tobaccocontrol-2020-055967

The Michigan O'Brien Kidney Research Center: transforming translational kidney research through systems biology, Bitzer M, Ju W, Subramanian L, Troost JP, Tychewicz J, Steck B, Wiggins RC, Gipson DS, Gadegbeku CA, Brosius FC, Kretzler M, Pennathur S, American Journal of Physiology - Renal Physiology, 10.1152/ajprenal.00091.2022

Early HPV ctDNA Kinetics and Imaging Biomarkers Predict Therapeutic Response in p16+ Oropharyngeal Squamous Cell Carcinoma, Cao Y, Haring CT, Brummel C, Bhambhani C, Aryal M, Lee C, Neal MH, Bhangale A, Gu W, Casper K, Malloy K, Sun Y, Shuman A, Prince ME, Spector ME, Chinn S, Shah J, Schonewolf C, McHugh JB, Mills RE, Tewari M, Worden FP, Swiecicki PL, Mierzwa M, Brenner JC, Clinical Cancer Research, 10.1158/1078-0432.CCR-21-2338

ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia, Kodgule R, Goldman JW, Monovich AC, Saari T, Aguilar AR, Hall CN, Rajesh N, Gupta J, Chu S-CA, Ye L, Gurumurthy A, Iyer A, Brown NA, Chiang MY, Cieslik MP, Ryan RJH, Blood Cancer Discov, 10.1158/2643-3230.BCD-21-0224

Bicuspid Aortic Valve-Associated Regulatory Regions Reveal GATA4 Regulation and Function During Human-Induced Pluripotent Stem Cell-Based Endothelial-Mesenchymal Transition. Huang T, Cheng J, Feng H, Zhou W, Qiu P, Zhou D, Yang D, Zhang J, Willer C, Chen YE, Mizrak D, Yang B, Arterioscler Thromb Vasc Biol, 10.1161/ATVBAHA.122.318566

Polygenic Risk Scores for Cardiovascular Disease: A Scientific Statement From the American Heart Association, O'Sullivan JW, Raghavan S, Marquez-Luna C, Luzum JA, Damrauer SM, Ashley EA, O'Donnell CJ, Willer CJ, Natarajan P, Circulation, 10.1161/CIR.0000000000001077

Cross-Ancestry Investigation of Venous Thromboembolism Genomic Predictors, Thibord F, Klarin D, Brody JA, Chen MH, Levin MG, Chasman DI, Goode EL, Hveem K, Teder-Laving M, Martinez-Perez A, Aïssi D, Daian-Bacq D, Ito K, Natarajan P, Lutsey PL, Nadkarni GN, De Vries PS, Cuellar-Partida G, Wolford BN, Pattee JW, Kooperberg C, Brae, Circulation, 10.1161/CIRCULATIONAHA.122.059675

Analysis of Cataract Surgery Instrument Identification Performance of Convolutional and Recurrent Neural Network Ensembles Leveraging BigCat, Matton N, Qalieh A, Zhang Y, Annadanam A, Thibodeau A, Li T, Shankar A, Armenti S, Mian SI, Tannen B, Nallasamy N, Translational vision science & technology, 10.1167/tvst.11.4.1

Central nervous system immune interactome is a function of cancer lineage, tumor microenvironment, and STAT3 expression, Najem H, Ott M, Kassab C, Rao A, Rao G, Marisetty A, Sonabend AM, Horbinski C, Verhaak R, Shankar A, Krishnan SN, Varn FS, Arrieta VA, Gupta P, Ferguson SD, Huse JT, Fuller GN, Long JP, Winkowski DE, Freiberg BA, James CD, Platanias LC, Lesniak MS, Burks, JCI Insight, 10.1172/jci.insight.157612

Translational implications of Th17-skewed inflammation due to genetic deficiency of a cadherin stress sensor, Godsel LM, Roth-Carter QR, Koetsier JL, Tsoi LC, Huffine AL, Broussard JA, Fitz GN, Lloyd SM, Kweon J, Burks HE, Hegazy M, Amagai S, Harms PW, Xing X, Kirma J, Johnson JL, Urciuoli G, Doglio LT, Swindell WR, Awatramani R, Sprecher E, Bao X, Cohen-Barak E,, Journal of Clinical Investigation, 10.1172/JCI144363

Cardiomyocytes disrupt pyrimidine biosynthesis in nonmyocytes to regulate heart repair, Li S, Yokota T, Wang P, ten Hoeve J, Ma F, Le TM, Abt ER, Zhou Y, Wu R, Nanthavongdouangsy M, Rodriguez A, Wang Y, Lin YJ, Muranaka H, Sharpley M, Braddock DT, MacRae VE, Banerjee U, Chiou PY, Seldin M, Huang D, Teitell M, Gertsman I, Jung M, Bensinger SJ, Journal of Clinical Investigation, 10.1172/JCI149711

H3.3-G34 mutations impair DNA repair and promote cGAS/STING-mediated immune responses in pediatric high-grade glioma models, Haase S, Banerjee K, Mujeeb AA, Hartlage CS, Núñez FM, Núñez FJ, Alghamri MS, Kadiyala P, Carney S, Barissi MN, Taher AW, Brumley EK, Thompson S, Dreyer JT, Alindogan CT, Garcia-Fabiani MB, Comba A, Venneti S, Ravikumar V, Koschmann C, Carcaboso ÁM, Vinci, Journal of Clinical Investigation, 10.1172/JCI154229

Clonal hematopoiesis in sickle cell disease, Liggett LA, Cato LD, Weinstock JS, Zhang Y, Nouraie SM, Gladwin MT, Garrett ME, Ashley-Koch A, Telen MJ, Custer B, Kelly S, Dinardo CL, Sabino EC, Loureiro P, Carneiro-Proietti AB, Maximo C, Reiner AP, Abecasis GR, Williams DA, Natarajan P, Bick AG, Sanka, Journal of Clinical Investigation, 10.1172/JCI156060

DataSifter II: Partially synthetic data sharing of sensitive information containing time-varying correlated observations, Zhou N, Wang L, Marino S, Zhao Y, Dinov ID, Journal of Algorithms and Computational Technology, 10.1177/17483026211065379

A randomized phase 2 trial of idiotype vaccination and adoptive autologous T-cell transfer in patients with multiple myeloma, Qazilbash MH, Saini NY, Cha SC, Wang Z, Stadtmauer EA, Baladandayuthapani V, Lin H, Tross B, Honhar M, Rao SS, Kim K, Popescu M, Szymura S, Zhang T, Anderson A, Bashir Q, Shpall EJ, Orlowski RZ, Levine BL, Kerr N, Garfall A, Cohen A, Vogl DT, Dengel K, Ju, Blood, 10.1182/blood.2020008493

PEG10 amplification at 7q21.3 potentiates large-cell transformation in cutaneous T-cell lymphoma, Liu F, Gao Y, Xu B, Xiong S, Yi S, Sun J, Chen Z, Liu X, Li Y, Lin Y, Wen Y, Qin Y, Yang S, Li H, Tejasvi T, Tsoi L, Tu P, Ren X, Wang Y, Blood, 10.1182/blood.2021012091

Clonal hematopoiesis of indeterminate potential and risk of death from COVID-19, Miller PG, Fell GG, Foy BH, Scherer AK, Gibson CJ, Sperling AS, Burugula BB, Nakao T, Uddin MM, Warren H, Bry L, Pozdnyakova O, Frigault MJ, Bick AG, Neuberg D, Higgins JM, Mansour MK, Natarajan P, Kim AS, Kitzman JO, Ebert BL, Blood, 10.1182/blood.2022018052

Functional Profiling Identifies Selective Enhancer Dependencies in MYC -Intact and MYC -Rearranged Diffuse Large B-Cell Lymphoma, Gurumurthy A, Iyer A, Kodgule R, Aguilar A, Saari T, Gupta J, Hall C, Runge JS, Weiss M, Cieslik MP, Ryan RJH, Blood, 10.1182/blood-2022-160278

Gene Expression Sets and Renal Profiling from the Rain (Renal AL Amyloid Involvement and NEOD00) Trial, Varga C, Comenzo R, Fogo A, Nasr S, Kretzler M, Nair V, Eichinge F, Naik A, Blood, 10.1182/blood-2022-162914

SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions, Nishizaki SS, Boyle AP, BMC Bioinformatics, 10.1186/s12859-022-04865-x

Vessel segmentation for X-ray coronary angiography using ensemble methods with deep learning and filter-based features, Gao Z, Wang L, Soroushmehr R, Wood A, Gryak J, Nallamothu B, Najarian K, BMC Medical Imaging, 10.1186/s12880-022-00734-4

A deep learning framework for automated detection and quantitative assessment of liver trauma, Farzaneh N, Stein EB, Soroushmehr R, Gryak J, Najarian K, BMC medical imaging, 10.1186/s12880-022-00759-9

The clusters of health-risk behaviours and mental wellbeing and their sociodemographic correlates: a study of 15,366 ASEAN university students, Wattanapisit A, Abdul Rahman H, Car J, Abdul-Mumin KH, de la Cruz MHTO, Chia M, Rosenberg M, Ho MHR, Chaiyasong S, Mahmudiono T, Rodjarkpai Y, Dinov ID, Ottom M, Amornsriwatanakul A, BMC Public Health, 10.1186/s12889-022-14233-2

An interpretable neural network for outcome prediction in traumatic brain injury, Minoccheri C, Williamson CA, Hemmila M, Ward K, Stein EB, Gryak J, Najarian K, BMC Medical Informatics and Decision Making, 10.1186/s12911-022-01953-z

Longitudinal profiling of clonal hematopoiesis provides insight into clonal dynamics, Uddin MM, Zhou Y, Bick AG, Burugula BB, Jaiswal S, Desai P, Honigberg MC, Love SA, Barac A, Hayden KM, Manson JAE, Whitsel EA, Kooperberg C, Natarajan P, Reiner AP, Kitzman JO, Immunity and Ageing, 10.1186/s12979-022-00278-9

Evolution of the repression mechanisms in circadian clocks, Tyler J, Lu Y, Dunlap J, Forger DB, Genome Biology, 10.1186/s13059-021-02571-0

Enhanced rare disease mapping for phenome-wide genetic association in the UK Biobank, Patrick MT, Bardhi R, Zhou W, Elder JT, Gudjonsson JE, Tsoi LC, Genome Medicine, 10.1186/s13073-022-01094-y

A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology, He Y, Yu H, Huffman A, Lin AY, Natale DA, Beverley J, Zheng L, Perl Y, Wang Z, Liu Y, Ong E, Wang Y, Huang P, Tran L, Du J, Shah Z, Shah E, Desai R, Huang HH, Tian Y, Merrell E, Duncan WD, Arabandi S, Schriml LM, Zheng J, Masci AM, Wang L, Liu H, Smaili F, Journal of Biomedical Semantics, 10.1186/s13326-022-00279-z

Changes in Triple-Negative Breast Cancer Molecular Subtypes in Patients Without Pathologic Complete Response After Neoadjuvant Systemic Chemotherapy, Masuda H, Harano K, Miura S, Wang Y, Hirota Y, Harada O, Jolly MK, Matsunaga Y, Lim B, Wood AL, Parinyanitikul N, Lee HJ, Gong G, George JT, Levine H, Lee J, Wang X, Lucci A, Rao A, Schweitzer BL, Lawrence OR, Seitz RS, Morris SW, Hout DR, Nakamura S, Kri, JCO Precision Oncology, 10.1200/PO.20.00368


Quality Control for Single Cell Imaging Analytics Using Endocrine Disruptor-Induced Changes in Estrogen Receptor Expression, Stossi F, Singh PK, Mistry RM, Johnson HL, Dandekar RD, Mancini MG, Szafran AT, Rao AU, Mancini MA, Environmental Health Perspectives, 10.1289/EHP9297

Resistance of C57BL/6 Mice to Different Artemisinin-sensitive Strains of PbK173, Qin TT, Li S, Cui Z, Shi H, Li LF, Yu GH, Wang HJ, Li CH, Chinese Journal of Experimental Traditional Medical Formulae, 10.13422/j.cnki.syfjx.20221106

Characterizing collaborative transcription regulation with a graph-based deep learning approach, Zhang Z, Feng F, Liu J, PLoS Computational Biology, 10.1371/journal.pcbi.1010162

NucleoMap: A computational tool for identifying nucleosomes in ultra-high resolution contact maps, Huang Y, Wang B, Liu J, PLoS Computational Biology, 10.1371/journal.pcbi.1010265

Intracellular acidification is a hallmark of thymineless death in E. coli, Ketcham A, Freddolino PL, Tavazoie S, PLoS Genetics, 10.1371/journal.pgen.1010456

Automatic multi-anatomical skull structure segmentation of cone-beam computed tomography scans using 3D UNETR, Gillot M, Baquero B, Le C, Deleat-Besson R, Bianchi J, Ruellas A, Gurgel M, Yatabe M, Al Turkestani N, Najarian K, Soroushmehr R, Pieper S, Kikinis R, Paniagua B, Gryak J, Ioshida M, Massaro C, Gomes L, Oh H, Evangelista K, Junior CMC, Garib D, Costa F, B, PLoS ONE, 10.1371/journal.pone.0275033

Distinct heterochromatin-like domains promote transcriptional memory and silence parasitic genetic elements in bacteria, Amemiya HM, Goss TJ, Nye TM, Hurto RL, Simmons LA, Freddolino PL, EMBO Journal, 10.15252/embj.2021108708

FIBCD1 is an endocytic GAG receptor associated with a novel neurodevelopmental disorder, Fell CW, Hagelkruys A, Cicvaric A, Horrer M, Liu L, Li JSS, Stadlmann J, Polyansky AA, Mereiter S, Tejada MA, Kokotović T, Achuta VS, Scaramuzza A, Twyman KA, Morrow MM, Juusola J, Yan H, Wang J, Burmeister M, Choudhury B, Andersen TL, Wirnsberger G, Holm, EMBO Molecular Medicine, 10.15252/emmm.202215829

Activation of Stimulator of IFN Genes (STING) Causes Proteinuria and Contributes to Glomerular Diseases, Mitrofanova A, Fontanella A, Tolerico M, Mallela S, Molina David J, Zuo Y, Boulina M, Kim JJ, Santos J, Ge M, Sloan A, Issa W, Gurumani M, Pressly J, Ito M, Kretzler M, Eddy S, Nelson R, Merscher S, Burke G, Fornoni A, Journal of the American Society of Nephrology : JASN, 10.1681/ASN.2021101286

Enabling Eating Detection in a Free-living Environment: Integrative Engineering and Machine Learning Study, Zhang B, Deng K, Shen J, Cai L, Ratitch B, Fu H, Guan Y, Journal of Medical Internet Research, 10.2196/27934

Risk Factors for COVID-19 in College Students Identified by Physical, Mental, and Social Health Reported During the Fall 2020 Semester: Observational Study Using the Roadmap App and Fitbit Wearable Sensors, Gilley KN, Baroudi L, Yu M, Gainsburg I, Reddy N, Bradley C, Cislo C, Rozwadowski ML, Clingan CA, DeMoss MS, Churay T, Birditt K, Colabianchi N, Chowdhury M, Forger D, Gagnier J, Zernicke RF, Cunningham JL, Cain SM, Tewari M, Choi SW, JMIR Mental Health, 10.2196/34645

Quantifying T2-FLAIR Mismatch Using Geographically Weighted Regression and Predicting Molecular Status in Lower-Grade Gliomas, Mohammed S, Ravikumar V, Warner E, Patel SH, Bakas S, Rao A, Jain R, American Journal of Neuroradiology, 10.3174/ajnr.A7341

Editorial: Advances in Using Big Data and Artificial Intelligence to Understand Heterogeneity in Inflammatory Responses, Zhou XJ, MacLeod AS, Tsoi LC, Frontiers in Immunology, 10.3389/fimmu.2022.948885

Heterogeneity of neutrophils and inflammatory responses in patients with COVID-19 and healthy controls, Xu J, He B, Carver K, Vanheyningen D, Parkin B, Garmire LX, Olszewski MA, Deng JC, Frontiers in Immunology, 10.3389/fimmu.2022.970287

Deep Learning-Based Mapping of Tumor Infiltrating Lymphocytes in Whole Slide Images of 23 Types of Cancer, Abousamra S, Gupta R, Hou L, Batiste R, Zhao T, Shankar A, Rao A, Chen C, Samaras D, Kurc T, Saltz J, Frontiers in Oncology, 10.3389/fonc.2021.806603

MHC Class II Expression Influences the Composition and Distribution of Immune Cells in the Metastatic Colorectal Cancer Microenvironment, Griffith BD, Turcotte S, Lazarus J, Lima F, Bell S, Delrosario L, McGue J, Krishnan S, Oneka MD, Nathan H, Smith JJ, D’Angelica MI, Shia J, Di Magliano MP, Rao A, Frankel TL, Cancers, 10.3390/cancers14174092

Functional Study of TMEM163 Gene Variants Associated with Hypomyelination Leukodystrophy, Yan H, Yang S, Hou Y, Ali S, Escobar A, Gao K, Duan R, Kubisiak T, Wang J, Zhang Y, Xiao J, Jiang Y, Zhang T, Wu Y, Burmeister M, Wang Q, Cuajungco MP, Wang J, Cells, 10.3390/cells11081285

SOCRAT: A Dynamic Web Toolbox for Interactive Data Processing, Analysis and Visualization, Kalinin AA, Palanimalai S, Zhu J, Wu W, Devraj N, Ye C, Ponarul N, Husain SS, Dinov ID, Information, 10.3390/info13110547

Analysis of Human Papilloma Virus Content and Integration in Mucoepidermoid Carcinoma, Gu W, Bhangale A, Heft Neal ME, Smith JD, Brummel C, McHugh JB, Spector ME, Mills RE, Brenner JC, Viruses, 10.3390/v14112353

In Vitro Evaluation and Mitigation of Niclosamide’s Liabilities as a COVID-19 Treatment, Wotring JW, McCarty SM, Shafiq K, Zhang CJ, Nguyen T, Meyer SR, Fursmidt R, Mirabelli C, Clasby MC, Wobus CE, O’Meara MJ, Sexton JZ, Vaccines, 10.3390/vaccines10081284

Correction: Disease consequences of higher adiposity uncoupled from its adverse metabolic effects using Mendelian randomisation., Martin S, Tyrrell J, Thomas EL, Bown MJ, Wood AR, Beaumont RN, Tsoi LC, Stuart PE, Elder JT, Law P, Houlston R, Kabrhel C, Papadimitriou N, Gunter M, Bull C, Bell JA, Vincent EE, Sattar N, Dunlop MG, Tomlinson IPM, Lindström S, INVENT consortium, Bell JD,, Elife, 10.7554/eLife.80233

A reference tissue atlas for the human kidney, Hansen J, Sealfon R, Menon R, Eadon MT, Lake BB, Steck B, Dobi D, Parikh S, Sigdel TK, Zhang G, Velickovic D, Barwinska D, Alexandrov VORCIDP, Rashmi P, Otto EA, Rose MP, Anderton CR, Shapiro JP, Pamreddy A, Winfree S, He VORCIDP, Boer IHD, Hodgin JB, Bar, Science advances, DOI: 10.1126/sciadv.abn4965

ACE2 expression in adipose tissue is associated with COVID-19 cardio-metabolic risk factors and cell type composition, El-Sayed Moustafa* JS, Jackson* AU, Brotman* SM, Guan* L, Villicaňa S, Roberts AL, Zito A, Bonnycastle L, Erdos MR, Narisu N, Stringham HM, Welch R, Yan T, Lakka T, Parker S, Tuomilehto J, Collins FS, Pajukanta P, Boehnke M, Koistinen HA, Laakso M, Falchi, International Journal of Obesity, doi.org/10.1038/s41366-022-01136-w

ATRX loss in glioma results in epigenetic dysregulation of cell cycle phase transition, Qin T, Mullan B, Ravindran R, Siada R, Cummings JR, Harris MK, Ashwath M, Pyaram K, Miklja Z, Reiber M, Garcia T, Tran D, Danussi C, Brosnan-Cashman J, Pratt D, Zhao X, Rehemtulla A, Sartor AM, Venneti S, Meeker AK, Huse JT, Morgan MA, Lowenstein PR, Cast, Cell Reports, DOI: 10.1016/j.celrep.2021.110216

Biogeographic and disease-specific alterations in epidermal lipid composition and single cell analysis of acral keratinocytes, Merleev AA, Le ST, Alexanian C, Toussi A, Xie Y, Marusina AI, Watkins SM, Patel F, Billi AC, Wiedemann J, Izumiya Y, Kumar A, Uppala R, Kahlenberg JM, Liu FT, Adamopoulos IE, Wang EA, Ma C, Cheng MY, Xiong H, Kirane A, Luxardi G, Andersen B, Tsoi LC, Lebr, JCI insight, DOI: 10.1172/jci.insight.159762

Blood-derived lncRNAs as biomarkers for cancer diagnosis: the Good, the Bad and the Beauty, Badowski C, He B, Garmire LX, NPJ precision oncology, doi.org/10.1038/s41698-022-00283-7

Cellular engagement and interaction in the tumor microenvironment predict non-response to PD-1/PD-L1 inhibitors in metastatic non-small cell lung cancer, Qin A, Lima F, Bell S, Kalemkerian GP, Schneider BJ, Ramnath N, Lew M, Krishnan S, Mohammed S, Rao A, Frankel TL, Stannard JN, Reed TJ, Myers E, Lowe L, Sarkar MK, Xing X, Bertheir CC, Gudjonsson J, Kahlenberg M, Scientific reports, DOI: 10.1038/s41598-022-13236-8

Cellular heterogeneity of human fallopian tubes in normal and hydrosalpinx disease states identified by scRNA-seq, Hammoud SS, Ulrich ND, Shen U, Ma Q, Yank K, Jones A, Hannum DF, Machlin J, Gurczynski Moore BB, Randolph JF, Smith YR, Lieberman R, Schon SB, Shiklanov A, Marsh EE, Li JZ, Developmental Cell, DOI: 10.1016/j.devcel.2022.02.017

Characteristics of Patients with Crohn's Disease With or Without Perianal Fistulae in the CorEvitas Inflammatory Bowel Disease Registry, Fan Y, Delgado-Aros S, Valdecantos WC, Janak JC, Moore PC, Crabtree MM, Stidham RW, Digestive diseases and sciences, DOI: 10.1007/s10620-022-07491-y

Clinical outcomes in a cohort of patients with cutaneous T cell lymphoma and COVID-19, Runge JS, Bardhi R, Xia Y, Jairath NK, Wilcox RA, Tsoi LC, Tejasvi T, JAAD international, doi: 10.1016/j.jdin.2022.04.008

Comparative study of radiologists vs machine learning in differentiating biopsy-proven pseudoprogression and true progression in diffuse gliomas, Turk S, Wang NC, Kitis O, Lee J, Mohammed S, Ma T, Lobo R, Kim J, Liao E, Camelo-Piragua S, Johnson TM, Kim MM, Junck L, Moritani T, Srinivasan A, Rao A, Bapuraj JR, Neuroscience Informatics, doi.org/10.1016/j.neuri.2022.100088

Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data, Qin T, Lee C, Li S, Cavalcante RG, Orchard P, Yao H, Zhang H, Wang S, Patil S, Boyle AP, Sartor MA, Genome biology, https://doi.org/10.1186/s13059-022-02668-0

Consumer-grade wearables identify changes in multiple physiological systems during COVID-19 disease progression, Mayer C, Tyler J, Fang Y, Flora C, Frank E, Tewari M, Choi SW, Sen S, Forger DB, Cell reports. Medicine, doi.org/10.1016/j.xcrm.2022.100601

CR-I-TASSER: assemble protein structures from cryo-EM density maps using deep convolutional neural networks, Zhang X, Zhang B, Freddolino PL, Zhang YIC-CA, Nature methods, doi.org/10.1038/s41592-021-01389-9

Daily variation in sleep quality is associated with health-related quality of life in people with spinal cord injury, Carlozzi NE, Freedman J, Troost JP, Carson T, Molton IR, Ehde DM, Najarian K, Miner JA, Boileau NR, Kratz AL, Archives of Physical Medicine and Rehabilitation, DOI: 10.1016/j.apmr.2021.07.803

Decoding the Spermatogenesis Program: New Insights from Transcriptomic Analyses, Rabbani M, 1, Zheng X, 1, Manske G, 5, Shami A, Li 1JZ, 1, 4, Hammoud1 SS, 2, 3, 5, Annual Reviews in Genetics,

Defining the Young Patient with Oral Cavity Cancer: Phenotypic and Genotypic Analysis, Marchiano E, Argirion I, Vandenberg T, Bhangale AD, Birkeland AC, Prince MEP, Bradford CR, McHugh JB, Chepeha DB, Sartor MA, Rozek LS, Shuman AG, Brenner JC, Spector ME, Chinn SB, http://dx.doi.org/10.2139/ssrn.3874126

Development of the Endoscopic Pouch Score for Assessment of Inflammatory Conditions of the Pouch, Barnes EL, Long MD, Raffals L, Isaacs K, Stidham RW, Herfarth HH, PROP-RD I, Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association, DOI: 10.1016/j.cgh.2022.04.026

Direct cellular reprogramming enables development of viral T antigen-driven Merkel cell carcinoma in mice, Verhaegen ME, Harms PW, Van Goor JJ, Arche J, Patrick MT, Wilbert D, Zabawa H, Grachtchouk M, Liu CJ, Hu K, Kelly MC, Chen P, Saunders TL, Weidinger S, Syu LJ, Runge JS, Gudjonsson JE, Wong SY, Brownell I, Cieslik M, Udager AM, Chinnaiyan AM, Tsoi LC, Dlu, The Journal of clinical investigation, DOI: 10.1172/JCI152069

Disease consequences of higher adiposity uncoupled from its adverse metabolic effects using Mendelian randomisation., Martin S, Tyrrell J, Thomas EL, Bown MJ, Wood AR, Beaumont RN, Tsoi LC, Stuart PE, Elder JT, Law P, Houlston R, Kabrhel C, Papadimitriou N, Gunter MJ, Bull CJ, Bell JA, Vincent EE, Sattar N, Dunlop MG, Tomlinson IP, Bell JD, Frayling TM, Yaghootkar H, eLife,

Distinguishing Admissions Specifically for COVID-19 From Incidental SARS-CoV-2 Admissions: National Retrospective Electronic Health Record Study., Klann JG, Strasser ZH, Hutch MR, Kennedy CJ, Marwaha JS, Morris M, Samayamuthu MJ, Pfaff AC, Estiri H, South AM, Weber GM, Yuan W, Avillach P, Wagholikar KB, Luo Y, Consortium FCCOCBEHRC, Omenn GS, Visweswaran S, Holmes JH, Xia Z, Brat GA, Murphy SN, Journal of medical Internet research,

Emerging artificial intelligence applications in Spatial Transcriptomics analysis., Li Y, Stanojevic S, Garmire LX, Computational and structural biotechnology journal,

Enhancing Cysteine Chemoproteomic Coverage through Systematic Assessment of Click Chemistry Product Fragmentation., Yan T, Palmer AB, Geiszler DJ, Polasky DA, Boatner LM, Burton NR, Armenta E, Nesvizhskii AI, Backus KM, Analytical chemistry,

Epistasis at the SARS-CoV-2 Receptor-Binding Domain Interface and the Propitiously Boring Implications for Vaccine Escape., Rochman ND, Faure G, Wolf YI, Freddolino PL, Zhang F, Koonin EV, mBio,

Evaluation of the Nallasamy formula: a stacking ensemble machine learning method for refraction prediction in cataract surgery., Li T, Stein J, Nallasamy N, The British Journal of Ophthalmology,

Extrinsic KRAS signaling shapes the pancreatic microenvironment through fibroblast reprogramming., Velez-Delgado A, Donahue KL, Brown ZKL, Du W, Irizarry-Negron V, Menjivar RE, Lasse OEL, Steele NG, The S, Lazarus J, Sirihorachai VR, Yan W, Kemp SB, Kerk SA, Bollampally M, Yang S, Scales MK, Avritt FR, Lima F, Lyssiotis CA, Rao A, Crawford HC, Bednar F, Cellular and molecular gastroenterology and hepatology,

GaWRDenMap: a quantitative framework to study the local variation in cell-cell interactions in pancreatic disease subtypes., Krishnan SN, Mohammed S, Frankel TL, Rao A, Scientific reports,

Gene amplification acts as a molecular foothold to facilitate cross-species adaptation and evasion of multiple antiviral pathways., Banerjee S, Smith C, Geballe A, Rothenburg S, Kitzman JO, Brennan G, bioRxiv : the preprint server for biology,

Gut microbe-derived metabolite trimethylamine N-oxide activates PERK to drive fibrogenic mesenchymal differentiation., Kim SJ, Bale S, Verma P, Wan Q, Ma F, Gudjonsson JE, Hazen SL, Harms PW, Tsou PS, Khanna D, Tsoi LC, Gupta N, Ho KJ, Varga J, iScience,

Head and Neck Radiotherapy Patterns of Practice Variability Identified as a Challenge to Real-World Big Data: results from the Learning from Analysis of Multicentre Big Data Aggregation (LAMBDA) Consortium, Advances in Radiation Oncology,

Heterogeneous pdgfrb+ cells regulate coronary vessel development and revascularization during heart regeneration., Kapuria S, Bai H, Fierros J, Huang Y, Ma F, Yoshida T, Aguayo A, Kok F, Wiens KM, Yip JK, McCain ML, Pellegrini M, Nagashima M, Hitchcock PF, Mochizuki N, Lawson ND, Harrison MMR, Lien CL, Development (Cambridge, England),

Human CD206+ macrophages associate with diabetes and adipose tissue lymphoid clusters, Muir LA, Cho KW, Geletka L, Baker NA, Flesher CG, Ehlers AP, Kaciroti N, Lindsly S, Ronquist S, Rajapakse I, O'Rourke RW, Lumeng CN, JCI Insight,

Identification of cell type specific ACE2 modifiers by CRISPR screening., Sherman EJ, Mirabelli C, Tang VT, Khan TG, Leix K, Kennedy AA, Graham SE, Willer CJ, Tai AW, Sexton JZ, Wobus CE, Emmer BT, PLoS pathogens,

IFN-κ is critical for normal wound repair and is decreased in diabetic wounds, Wolf SJ, Audu CO, Joshi A, denDekker AD, Melvin WJ, Davis FM, Xing X, Wasikowski R, Tsoi L, Kunkel S, Gudjonsson JE, O'Riordan MX, Kahlenberg JM, Gallagher KA, The Journal of Clinical Investigation,

Inflammation, Hyperglycemia, and Adverse Outcomes in Individuals With Diabetes Mellitus Hospitalized for COVID-19, Vasbinder A, Anderson, E, Shadid H, Berlin H, Pan, M, Feldman EL, et A, Diabetes Care,

Integrated single-cell sequencing and histopathological analyses reveal diverse injury and repair responses in a participant with acute kidney injury: a clinical-molecular-pathologic correlation., Menon R, Bomback AS, Lake BB, Stutzke C, Grewenow SM, Menez S, D'Agati VD, Jain S, Kidney PMP, Kidney international,

International electronic health record-derived post-acute sequelae profiles of COVID-19 patients., Zhang HG, Dagliati A, Shakeri HAZ, Xiong X, Bonzel CL, Xia Z, Tan BWQ, Avillach P, Brat GA, Hong C, Morris M, Visweswaran S, Patel LP, Gutiérrez-Sacristán A, Hanauer DA, Holmes JH, Samayamuthu MJ, Bourgeois FT, L'Yi S, Maidlow SE, Moal B, Murphy SN, Stras, NPJ digital medicine,

Kidney Biopsy Features Most Predictive of Clinical Outcomes in the Spectrum of Minimal Change Disease and Focal Segmental Glomerulosclerosis., Zee J, Liu Q, Smith AR, Hodgin JB, Rosenberg A, Gillespie BW, Holzman LB, Barisoni L, Mariani LH, Nephrotic SSNNEPTUNE, Journal of the American Society of Nephrology : JASN,

LOMETS3: integrating deep learning and profile alignment for advanced protein template recognition and function annotation., Zheng W, Wuyun Q, Zhou X, Li Y, Freddolino PL, Zhang YIC-CA, Nucleic acids research,

Longitudinal profiling of clonal hematopoiesis provides insight into clonal dynamics., Levi B, Shapiro GD, Jeng J, Lee AF, Chang P, Acton A, Merino MD, Jette A, Schneider JC, Kazis LE, Ryan CM, Uddin MM, Zhou Y, Bick AG, Burugula BB, Jaiswal S, Desai P, Honigberg MC, Love SA, Barac A, Hayden KM, Manson JE, Whitsel EA, Kooperberg C, Nataraja, Immunity & ageing : I & A,

Metabolism drives macrophage heterogeneity in the tumor microenvironment, Li S, Yu J, Huber A, Kryczek I, Wang Z, Jiang L, Li X, Du W, Li G, Wei S, Vatan L, Szeliga W, Chinnaiyan A, Green M, Cieslik M, Zou W, Cell reports,

Metabolomics identifies shared lipid pathways in independent amyotrophic lateral sclerosis cohorts, Goutman SA, Guo K, Savelieff MG, Patterson A, Sakowski SA, Habra H, Karnovsky A, Hur J, Feldman EL, Brain,

Metabolomics identifies shared lipid pathways in independent amyotrophic lateral sclerosis cohorts., Reheman A, Hou Y, Li BX, Dai X, Yang Z, Qian F, Zhang G, Xu Z, Liu J, Liang C, Zhao Y, Shen J, Zhou H, Wang Y, Marshall AH, Lei X, Zarpellon A, Vanhoorelbeke K, Ruggeri Z, Ni H, Goutman SA, Guo K, Savelieff MG, Patterson A, Sakowski SA, Habra H, Karnovsky, Brain : a journal of neurology,

Micro-dissection and integration of long and short reads to create a robust catalog of kidney compartment-specific isoforms., Li H, Eksi R, Yi D, Godfrey B, Mathew LR, O'Connor CL, Bitzer M, Kretzler M, Menon R, Guan Y, PLoS computational biology,

Molecular Characterization of Membranous Nephropathy., Sealfon R, Mariani L, Avila-Casado C, Nair V, Menon R, Funk J, Wong A, Lerner G, Hayashi N, Troyanskaya O, Kretzler M, Beck LHJ, Journal of the American Society of Nephrology : JASN,

Multiattribute Glycan Identification and FDR Control for Glycoproteomics., Polasky DA, Geiszler DJ, Yu F, Nesvizhskii AI, Molecular & cellular proteomics : MCP,

Multiomic characterization of pancreatic cancer-associated macrophage polarization reveals deregulated metabolic programs driven by the GM-CSF-PI3K pathway., Boyer S, Lee HJ, Steele N, Zhang L, Sajjakulnukit P, Andren A, Ward MH, Singh R, Basrur V, Zhang Y, Nesvizhskii AI, Pasca DMM, Halbrook CJ, Lyssiotis CA, Elife,

Multiple ParA/MinD ATPases Coordinate the Positioning of Disparate Cargos in a Bacterial Cell, Pulianmackal LT, Limcaoco JMI, Ravi K, Yang S, Zhang J, Tran MK, O’Meara MJ, Vecchiarelli AG, ,

Neurological Diagnoses in Hospitalized COVID-19 Patients Associated With Adverse Outcomes: A Multinational Cohort Study, Hutch MR, Son J, Le TT, Hong C, Wang X, Shakeri Hossein Abad Z, Morris M, Gutiérrez-Sacristán A, Klann JG, Spiridou A, Bellazzi R, Benoit V, Bonzel C-L, Bryant WA, Cho K, Das P, Hanauer DA, Henderson DW, Ho Y-L, Loh NHW, Makoudjou A, Malovini A, Moal B, M, ,

PEPPI: Whole-proteome Protein-protein Interaction Prediction through Structure and Sequence Similarity, Functional Association, and Machine Learning., Bell EW, Schwartz JH, Freddolino PL, Zhang YIC-CA, Journal of molecular biology,

Precision Radiotherapy via Information Integration of Expert Human Knowledge and AI Recommendation to Optimize Clinical Decision Making, Sun W, Niraula D, Naqa IE, Haken RT, Dinov I, Cuneo K, Jin JJ, Computer Methods and Programs in Biomedicine,

Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a psoriasis susceptibility locus that is negatively related to IL36G., Merleev A, Ji-Xu A, Toussi A, Tsoi LC, Le ST, Luxardi G, Xing X, Wasikowski R, Liakos W, Brüggen MC, Elder JT, Adamopoulos IE, Izumiya Y, Riera-Leal A, Li Q, Kuzminykh NY, Kirane A, Marusina AI, Gudjonsson JE, Maverakis E, JCI insight,

PyLiger: scalable single-cell multi-omic data integration in Python, Lu L, Welch JD, Bioinformatics,

Roles Played by Stress-Induced Pathways in Driving Ethnic Heterogeneity for Inflammatory Skin Diseases., Jamerson TA, Li Q, Sreeskandarajan S, Budunova IV, He Z, Kang J, Gudjonsson JE, Patrick MT, Tsoi LC, Frontiers in immunology,

Single Cell Transcriptomics Reveals Dynamic Role of Smooth Muscle Cells and Enrichment of Immune Cell Subsets in Human Abdominal Aortic Aneurysms., Davis FM, Tsoi LC, Ma F, Wasikowski R, Moore BB, Kunkel SL, Gudjonsson JE, Gallagher KA, Annals of surgery,

Single-cell multi-omic velocity infers dynamic and decoupled gene regulation, Li C, Virgilio M, Collins KL, Welch JD, RECOMB 2021,

Single-cell transcriptomics reveals distinct effector profiles of infiltrating T cells in lupus skin and kidney, Dunlap GS, Billi AC, Xing X, Ma F, Maz MP, Tsoi LC, Wasikowski R, Hodgin JB, Gudjonsson JE, Kahlenberg JM, Rao DA, The Journal of Clinical Investigation,

Skin-Expressing lncRNAs in Inflammatory Responses., Shefler A, Patrick MT, Wasikowski R, Chen J, Sarkar MK, Gudjonsson JE, Tsoi LC, Frontiers in genetics,

Somatic mosaicism reveals clonal distributions of neocortical development., Breuss MW, Yang X, Schlachetzki JCM, Antaki D, Lana AJ, Xu X, Chung C, Chai G, Stanley V, Song Q, Newmeyer TF, Nguyen A, O'Brien S, Hoeksema MA, Cao B, Nott A, McEvoy-Venneri J, Pasillas MP, Barton ST, Copeland BR, Nahas S, Van DKL, Ding Y, NIMH BSMN, Gla, ,

SP3-enabled Rapid and High Coverage Chemoproteomic Identification of Cell-State Dependent Redox-Sensitive Cysteines., Desai HS, Yan T, Yu F, Sun AW, Villanueva M, Nesvizhskii AI, Backus KM, Molecular & cellular proteomics : MCP,

Spontaneous Coronary Artery Dissection is Infrequent in Individuals with Heritable Thoracic Aortic Disease Despite Shared Genetic Susceptibility, Murad A, Hill HL, Wang Y, Ghannam M, Yang M, Pugh N, Asch FM, Hornsby W, Driscoll A, McNamara J, Willer CW, Regalado E, GenTAC I, Montalcino ACI, Milewicz DM, Eagle KA, Ganesh SKCA, American Journal of Medical Genetics Part A,

The association between inflammatory biomarkers and statin use among patients with head and neck squamous cell carcinoma., Getz KR, Bellile E, Zarins KR, Chinn SB, Taylor JMG, Rozek LS, Wolf GT, Mondul AM, Head & neck,

The genetic heterogeneity and drug resistance mechanisms of relapsed refractory multiple myeloma., Vo JN, Wu YM, Mishler J, Hall S, Mannan R, Wang L, Ning Y, Zhou J, Hopkins AC, Estill JC, Chan WKB, Yesil J, Cao X, Rao A, Tsodikov A, Talpaz M, Cole CE, Ye JC, Multiple MRC, Bergsagel PL, Auclair D, Cho HJ, Robinson DR, Chinnaiyan AM, Nature communications,

Transethnic analysis of psoriasis susceptibility in South Asians and Europeans enhances fine-mapping in the MHC and genomewide, Stuart PE, Tsoi LC, Nair RP, Ghosh M, Kabra M, Shaiq PA, Raja GK, Qamar R, Thelma BK, Patrick MT, Parihar A, Singh S, Khandpur S, Kumar U, Wittig M, Degenhardt F, Tejasvi T, Voorhees JJ, Weidinger S, Franke A, Abecasis GR, Sharma VK, Elder JT, Human Genetics and Genomics Advances,

TREM2 macrophages induced by human lipids drive inflammation in acne lesions., Do TH, Ma F, Andrade PR, Teles R, de Andrade Silva BJ, Hu C, Espinoza A, Hsu JE, Cho CS, Kim M, Xi J, Xing X, Plazyo O, Tsoi LC, Cheng C, Kim J, Bryson BD, O'Neill AM, Colonna M, Gudjonsson JE, Klechevsky E, Lee JH, Gallo RL, Bloom BR, Pellegrini M, Modli, Science immunology,

Trichloroethylene modifies energy metabolites in the amniotic fluid of Wistar rats., Su AL, Harris SM, Elkin ER, Karnovsky A, Colacino JA, Loch-Caruso R, Reproductive toxicology (Elmsford, N.Y.),

Unsupervised machine learning for identifying important visual features through bag-of-words using histopathology data from chronic kidney disease., Lee J, Warner E, Shaikhouni S, Bitzer M, Kretzler M, Gipson D, Pennathur S, Bellovich K, Bhat Z, Gadegbeku C, Massengill S, Perumal K, Saha J, Yang Y, Luo J, Zhang X, Mariani L, Hodgin JB, Rao A, C-PROBE S, Scientific reports,

Urinary proteomics identifies cathepsin D as a biomarker of rapid eGFR decline in type 1 diabetes, Limonte CP, Valo ENV, Ju W, Kretzler MSK, Ian DB, Diabetes Care,

Utility based approach in individualized optimal dose selection using machine learning methods., Li P, Taylor JMG, Boonstra PS, Lawrence TS, Schipper MJ, Statistics in medicine,

Variational Mixtures of ODEs for Inferring Cellular Gene Expression Dynamics, Gu Y, Blaauw D, Welch JD, International Conference on Machine Learning,

019 Investigating OX40L and its role in mediating cutaneous and systemic autoimmune disease, Xing E, Billi A, Wasikowski R, Plazyo O, Gharaee-Kermani M, Xing X, Kahlenberg JM, Tsoi LC, Gudjonsson JE, Journal of Investigative Dermatology, 10.1016/j.jid.2022.05.073

032 IL-36 axis is a sex-biased immune amplification circuit localized to the supraspinous epidermal compartment, Sarkar MK, Ma F, Kidder A, White BEP, Uppala R, Ward NL, Dobry C, Coon A, Tsoi LC, Kahlenberg JM, Gudjonsson JE, Journal of Investigative Dermatology, 10.1016/j.jid.2022.05.086

129 Pervasive immune dysfunction characterizes photoaged skin, Billi A, Ma F, Gharaee-Kermani M, Xing X, Plazyo O, Schuler A, Wasikowski R, Swindell WR, Nakamura M, Helfrich Y, Kahlenberg JM, Lee J, Tsoi LC, Voorhees J, Fisher GJ, Gudjonsson JE, Journal of Investigative Dermatology, 10.1016/j.jid.2022.05.135

137 Molecular investigation of secondary syphilis in the skin characterizes the nature of the B-cell promoting inflammatory environment, Kirma J, Xing X, Billi A, Kahlenberg JM, Tsoi LC, Gudjonsson JE, Journal of Investigative Dermatology, 10.1016/j.jid.2022.05.143

447 HERC6 negatively regulates type I interferon activity in keratinocytes through modulation of STING-IRF3 signaling, Uppala R, Sarkar MK, Swindell WR, Tsoi LC, Kahlenberg JM, Billi A, Gudjonsson JE, Journal of Investigative Dermatology, 10.1016/j.jid.2022.05.456

456 Independent causal effect of psoriasis on multiple sclerosis identified by Mendelian randomization, Patrick M, Nair R, He K, Stuart P, Billi A, Gudjonsson JE, Oksenberg J, Elder JT, Tsoi LC, Journal of Investigative Dermatology, 10.1016/j.jid.2022.05.465

468 Transcriptional profiling of the rare acantholytic disorders Darier disease, Hailey-Hailey disease, and Grover's disease suggests common mechanisms of pathogenesis, Burks H, Roth-Carter Q, Godsel LM, Xing X, Tsoi LC, Kirma J, Gudjonsson JE, Green K, Journal of Investigative Dermatology, 10.1016/j.jid.2022.05.477

475 High resolution chromatin loops associate with gene targets for psoriasis susceptibility regions, Zhang H, Zhang Z, Stuart P, Patrick M, Liu J, Nair R, Tsoi LC, Elder JT, Journal of Investigative Dermatology, 10.1016/j.jid.2022.05.484

482 Differences in chromatin accessibility in male vs female keratinocytes using ATAC-seq, Chung Y, Tsoi LC, White BEP, Zeng C, Billi A, Gudjonsson JE, Journal of Investigative Dermatology, 10.1016/j.jid.2022.05.491

508 Skin barrier defect and inflammation in Netherton syndrome: Lessons from a comparative study of patients and mouse models, Petrova E, Orts JL-G, Fahrner M, Leturcq F, Barbieux C, de Villartay J, Varet H, Coppée J, Gudjonsson JE, Tsoi LC, Hovnanian A, Journal of Investigative Dermatology, 10.1016/j.jid.2022.05.517

511 Kullback-Leibler divergence model to integrate genetic and genomic information to assess drug response for psoriatic patients, Li Q, He K, Patrick M, Tejasvi T, Zhang H, Stuart P, Nair R, Gudjonsson JE, Elder J, Tsoi LC, Journal of Investigative Dermatology, 10.1016/j.jid.2022.05.520

512 Integrative analysis using allele specific accessibility in immunocytes to unravel biological effect for complex skin-disease associated loci, Tsoi LC, Zhang Z, Patrick M, Zhang H, Wasikowski R, Gudjonsson JE, Wen X, Nair R, Elder JT, Journal of Investigative Dermatology, 10.1016/j.jid.2022.05.521

513 Regulatory roles of lncRNAs in psoriasis determined by single cell analysis, Wasikowski R, Patrick M, Sreeskandarajan S, Zhang H, Li Q, Billi A, Gudjonsson JE, Tsoi LC, Journal of Investigative Dermatology, 10.1016/j.jid.2022.05.522

717 TCF-4 negatively regulates IL-17C In human keratinocytes and in a mouse model of psoriasis, Singh R, Jiang Y, Tsoi LC, Sarkar M, Plazyo O, Billi A, Maverakis E, Kahlenberg JM, Gudjonsson JE, Ward NL, Journal of Investigative Dermatology, 10.1016/j.jid.2022.05.729


804 Fibroblast subpopulations orchestrate chronic inflammation in hidradenitis suppurativa, van Straalen KR, Ma F, Plazyo O, Calbet M, Xing X, Gharaee-Kermani M, Harms PW, Wasikowski R, Nahlawi L, Billi A, Kahlenberg JM, Maverakis E, Tsoi LC, Gudjonsson JE, Journal of Investigative Dermatology, 10.1016/j.jid.2022.05.818

850 Potential role of skin in SARS-CoV-2 infection, Chudakova D, Klopot A, Shi B, Bhalla P, Tsoi LC, White BEP, Budunova I, Journal of Investigative Dermatology, 10.1016/j.jid.2022.05.864

898: EARLY-ONSET COLORECTAL CANCERS MANIFEST INCREASED ALDH1A1 EXPRESSION, Venugopal A, Koi M, Stetson L, Speliotes E, Carethers JM, Gastroenterology, 10.1016/s0016-5085(22)60527-4

A0425 Spatial transcriptomic profiling of prostate cancer reveals zone specific androgen receptor signaling and immune infiltration, Patel P, Nallandhighal S, Scoville D, Tran L, Cotta B, Udager A, Rao A, Palapattu G, Dadhania V, Pitchiaya S, Salami S, European Urology, 10.1016/s0302-2838(22)00509-7

Abstract 1461: ETV6 deficiency and microsatellite enhancers drive transcriptional dysregulation in B-lymphoblastic leukemia, Goldman JW, Kodgule R, Monovich AC, Saari T, Hall CN, Rajesh N, Gupta J, Aguilar A, Brown N, Chiang MY, Cieslik MP, Ryan RJ, Cancer Research, 10.1158/1538-7445.am2022-1461

Abstract 2548: The central nervous system immune cell interactome is a function of cancer lineage, tumor microenvironment and STAT3 expression, Najem H, Ott M, Kassab C, Rao A, Rao G, Marisetty A, Sonabend AM, Horbinski C, Verhaak R, Shakar A, Krishnan S, Varn FS, Arietta VA, Gupta P, Ferguson SD, Huse J, Fuller GN, Long J, Winskowski D, Freiberg B, James CD, Platanias LC, Lesniak MS, Burks JK, H, Cancer Research, 10.1158/1538-7445.am2022-2548

Abstract 5469: Targeting SWI/SNF ATPases in enhancer-addicted prostate cancer, Xiao L, Parolia A, Qiao Y, Pushpinder PB, Eyunni S, Mannan R, Carson SE, Chang Y, Wang X, Zhang Y, Vo J, Kregel S, Simko SA, Delekta AD, Jaber M, Zheng H, Apel I, McMurry L, Su F, Wang R, Wang S, Sasmal S, Satyam LK, Mukherjee S, AbbinenI C, Aithal K, Bha, Cancer Research, 10.1158/1538-7445.am2022-5469

Abstract No. 331 ▪ FEATURED ABSTRACT Immune modulation by molecularly targeted photothermal ablation in a mouse model of advanced hepatocellular carcinoma and cirrhosis, Munoz N, Pavuluri S, Dupuis C, Williams M, Dixon K, McWatters A, Zhang J, Rao A, Duda D, Kaseb A, Sheth R, Journal of Vascular and Interventional Radiology, 10.1016/j.jvir.2022.03.412

Erratum to: Synthetic data method to incorporate external information into a current study (Canadian Journal of Statistics, (2019), 47, 4, (580-603), 10.1002/cjs.11513), Gu T, Taylor JMG, Cheng W, Mukherjee B, Canadian Journal of Statistics, 10.1002/cjs.11657

Erratum: Dynamic landscape of protein occupancy across the Escherichia coli chromosome (PLoS Biol (2021) 19:6 (e3001306) DOI: 10.1371/journal.pbio.3001306), Freddolino PL, Amemiya HM, Goss TJ, Tavazoie S, PLoS Biology, 10.1371/journal.pbio.3001557

Erratum: The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design (J. Chem. Theory Comput. (2017) 13: 6 (3031-3048) DOI: 10.1021/acs.jctc.7b00125), Alford RF, Leaver-Fay A, Jeliazkov JR, O'Meara MJ, Dimaio FP, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack RL, Das R, Baker D, Kuhlman B, Kortemme T, Gray JJ, Journal of Chemical Theory and Computation, 10.1021/acs.jctc.2c00500