138 TOTAL PUBLICATIONS
2026 (7 PUBLICATIONS)
- High-resolution reconstruction of cell-type-specific transcriptional regulatory processes from bulk sequencing samples Li Yao, Sagar R. Shah, Abdullah Ozer, Junke Zhang, Xiuqi Pan, Tianyu Xia, Vrushali D. Fangal, Alden King-Yung Leung, Meihan Wei, John T. Lis, Haiyuan Yu
Nature Biotechnology 2026
- Prediction of protein–protein interactions and co-complex models with deep learning Zizhao Zhang, Yilin Liu, Haiyuan Yu
Current Opinion in Chemical Biology 2026
- Directionality of transcriptional regulatory elements You Chen, Sagar R. Shah, Alden K. Leung, Mauricio I. Paramo, Kelly Cochran, Anshul Kundaje, Andrew G. Clark, John T. Lis, Haiyuan Yu
Nature Communications 2026
- Interactome mapping in human excitatory neurons reveals novel risk genes and pathways in Alzheimer's disease Xiaomu Wei, Katie Munechika, Yu Sun, Yuansong Wan, Tianyu Xia, Yuan Hou, Wenqiang Song, Kumar Yugandhar, Yiwen Wang, Se-In Lee, Zhengdong Sha, Yadi Zhou, Weixi Feng, Jingjie Zhu, Yuliang Tang, Wenjie Luo, Feixiong Cheng, Li Gan, Haiyuan Yu
bioRxiv 2026
- Cooperative and competitive interactions among transcription regulatory elements modulate transcription output Yiyang Jin, Zhou Zhou, Jessica Qin Lin, Alden King-Yung Leung, Haiyuan Yu, John T. Lis
bioRxiv 2026
- Dual promoter–enhancer activities reflect a unified regulatory logic Mauricio I. Paramo, Alden King-Yung Leung, Sagar R. Shah, Junke Zhang, Nathaniel D. Tippens, Jin Liang, Li Yao, Yiyang Jin, Xiuqi Pan, Abdullah Ozer, John T. Lis & Haiyuan Yu
Nature Communications 2026
- A double-negative prostate cancer subtype is vulnerable to SWI/SNF-targeting degrader molecules Phillip Thienger, Irene Paassen, Xiaosai Yao, Philip D Rubin, Marika Lehner, Nicholas Lillis, Andrej Benjak, Sagar R Shah, Alden King-Yung Leung, Simone De Brot, Alina Naveed, Bence Daniel, Minyi Shi, Julien Tremblay, Joanna Triscott, Giada Andrea Cassanmagnago, Marco Bolis, Lia Mela, Himisha Beltran, Yu Chen, Salvatore Piscuoglio, Haiyuan Yu, Charlotte KY Ng, David A Quigley, Robert L Yauch, Mark A Rubin
Cancer Research 2026
2025 (12 PUBLICATIONS)
- Refining liquid chromatography conditions across platforms to democratize single-cell proteomics Yiwen Wang, Qiuye Zhao, William K.M. Lai, Haiyuan Yu
bioRxiv 2025
- Identification of human RNA Polymerase II interactors at early stages of transcription Abdullah Ozer, Jin Joo Kang, Yuliang Tang, Kumar Yugandhar, Yu Sun, Michael D DeBerardine, Karim Omar, John Lis, Haiyuan Yu
bioRxiv 2025
- The regulatory landscape of nascent transcription in human health and disease Sagar R. Shah, You Chen, Alden K. Leung, Priscila V. Castilho Navarro, Mauricio I. Paramo, Juhi Gupta, Aishwarya Gurumurthy, Rebuma Firdessa Fite, Annika K. Weimer, Qian Du, Ahmed M. Mohyeldin, Dieter Egli, Remi J. Creusot, Russell J.H. Ryan, Michael P. Snyder, Andrew G. Clark, John T. Lis, Haiyuan Yu
bioRxiv 2025
- Disease-specific variant pathogenicity prediction using multimodal biomedical language models Yilin Liu, David N. Cooper, Haiyuan Yu
bioRxiv 2025
- The Deformability of the Mammalian Cell Nucleus is Determined by the Identity of the Lamin Rod Domain Jacob Odell, Yuliang Tang, Yogeshwari Sanjayrao Ambekar, Gururaj Rao Kidiyoor, Hassan Saadi, Graeme F. Woodworth, Liam J. Holt, Giuliano Scarcelli, Haiyuan Yu, Jan Lammerding
bioRxiv 2025
- Robust regulatory interplay of enhancers, facilitators, and promoters in a native chromatin context Zhou Zhou, Albert Li, Junke Zhang, Haiyuan Yu, Abdullah Ozer, John T. Lis
bioRxiv 2025
- Integrating structural homology with deep learning to achieve highly accurate protein-protein interface prediction for the human interactome Dapeng Xiong, Mateo Torres, Diana Murray, Le Li, Aniket C. Naravane, Robert Fragoza, Barry Honig, Haiyuan Yu
bioRxiv 2025
- Comprehensive Atomic-Scale 3D Viral-Host Protein Interactomes Enable Dissection of Key Mechanisms and Evolutionary Processes Underlying Viral Pathogenesis Le Li, Priyamvada Guha Roy, Yilin Liu, Zizhao Zhang, Dapeng Xiong, Ram Savan, Nandan S. Gokhale, Luis M Schang, Jishnu Das, Haiyuan Yu
bioRxiv 2025
- Comprehensive Evaluation of Diverse Massively Parallel Reporter Assays to Functionally Characterize Human Enhancers Genome-wide Junke Zhang, Alden King-Yung Leung, Yutong Zhu, Li Yao, Avery Willis, Xiuqi Pan, Abdullah Ozer, Zhou Zhou, Keith Siklenka, Alejandro Barrera, Jin Liang, Nathaniel D. Tippens, Timothy E. Reddy, John T. Lis, Haiyuan Yu
Genome Biology 2025
- Simultaneous measurement of intrinsic promoter and enhancer potential reveals principles of functional duality and regulatory reciprocity Mauricio I. Paramo, Alden King-Yung Leung, Sagar R. Shah, Junke Zhang, Nathaniel D. Tippens, Jin Liang, Li Yao, Yiyang Jin, Xiuqi Pan, Abdullah Ozer, John T. Lis, Haiyuan Yu
bioRxiv 2025
- Loss of Kmt2c or Kmt2d primes urothelium for tumorigenesis and redistributes KMT2A-menin to bivalent promoters Naitao Wang, Mohini R Pachai, Dan Li, Cindy J Lee, Sarah Warda, Makhzuna N Khudoynazarova, Woo Hyun Cho, Guojia Xie, Sagar R Shah , Li Yao, Cheng Qian, Elissa W P Wong, Juan Yan, Fanny V Tomas, Wenhuo Hu, Fengshen Kuo, Sizhi P Gao, Jiaqian Luo, Alison E Smith, Ming Han, Dong Gao, Kai Ge, Haiyuan Yu, Sarat Chandarlapaty, Gopakumar V Iyer, Jonathan E Rosenberg, David B Solit, Hikmat A Al-Ahmadie, Ping Chi, Yu Chen
Nature Genetics 2025
- A multiscale functional map of somatic mutations in cancer integrating protein structure and network topology Yingying Zhang, Alden K. Leung, Jin Joo Kang, Yu Sun, Guanxi Wu, Le Li, Jiayang Sun, Lily Cheng, Tian Qiu, Junke Zhang, Shayne Wierbowski, Shagun Gupta, James Booth, Haiyuan Yu
Nature Communications 2025 Website
2024 (3 PUBLICATIONS)
- Structurally-informed human interactome reveals proteome-wide perturbations by disease mutations Dapeng Xiong, Yunguang Qiu, Junfei Zhao, Yadi Zhou, Dongjin Lee, Shobhita Gupta, Mateo Torres, Weiqiang Lu, Siqi Liang, Jin Joo Kang, Charis Eng, Joseph Loscalzo, Feixiong Cheng & Haiyuan Yu
Nature Biotechnology 2024 Website
- Dissecting the cis-regulatory syntax of transcription initiation with deep learning Kelly Cochran, Melody Yin, Anika Mantripragada, Jacob Schreiber, Georgi K. Marinov, Sagar R. Shah, Haiyuan Yu, John T. Lis, Anshul Kundaje
bioRxiv 2024
- Phosphoribosyl modification of poly-ubiquitin chains at the Legionella-containing vacuole prohibiting autophagy adaptor recognition Min Wan, Marena E. Minelli, Qiuye Zhao, Shannon Marshall, Haiyuan Yu, Marcus Smolka & Yuxin Mao
Nature Communications 2024
2023 (3 PUBLICATIONS)
- Finding Needles in the Haystack: Strategies for Uncovering Noncoding Regulatory Variants You Chen, Mauricio I. Paramo, Yingying Zhang, Li Yao, Sagar R. Shah, Yiyang Jin, Junke Zhang, Xiuqi Pan, and Haiyuan Yu
Annual Review of Genetics 2023
- In vivo versus in silico assessment of potentially pathogenic missense variants in human reproductive genes Xinbao Dinga, Priti Singh, Kerry Schimenti, Tina N. Tran, Robert Fragoza, Jimmaline Hardy, Kyle E. Orwig, Marta Olszewska, Maciej K. Kurpisz, Alexander N. Yatsenko, Donald F. Conrad, Haiyuan Yu, and John C. Schimenti
PNAS 2023
- A comprehensive SARS-CoV-2-human protein-protein interactome reveals COVID-19 pathobiology and potential host therapeutic targets Zhou Y, Liu Y, Gupta S, Paramo MI, Hou Y, Mao C, Luo Y, Judd J, Wierbowski S, Bertolotti M, Nerkar M, Jehi L, Drayman N, Nicolaescu V, Gula H, Tay S, Randall G, Wang P, Lis JT, Feschotte C, Erzurum SC, Cheng F, Yu H.
Nature Biotechnology 2023
Highlighted as the cover image[2]
2022 (8 PUBLICATIONS)
- Functional genomic assays to annotate enhancer-promoter interactions genome wide Leung AK, Yao L, Yu H.
Human Molecular Genetics 2022
- Progranulin-derived granulin E and lysosome membrane protein CD68 interact to reciprocally regulate their protein homeostasis Santos MN, Paushter DH, Zhang T, Wu X, Feng T, Lou J, Du H, Becker SM, Fragoza R, Yu H, Hu F.
The Journal of Biological Chemistry 2022
- Advancing discovery of risk-altering variants for complex diseases by functionally informed fine-mapping Chen Y, Clark AG, Yu H.
Neuron 2022
- A comparison of experimental assays and analytical methods for genome-wide identification of active enhancers Yao L, Liang J, Ozer A, Leung AK, Lis JT, Yu H.
Nature Biotechnology 2022 Website
- Deep learning methods for 3D structural proteome and interactome modeling Lee D, Xiong D, Wierbowski S, Li L, Liang S, Yu H.
Current Opinion in Structural Biology 2022
- Aging-related cell type-specific pathophysiologic immune responses that exacerbate disease severity in aged COVID-19 patients Hou Y, Zhou Y, Jehi L, Luo Y, Gack MU, Chan TA, Yu H, Eng C, Pieper AA, Cheng F.
Aging cell 2022
- A full-proteome, interaction-specific characterization of mutational hotspots across human cancers Chen S, Liu Y, Zhang Y, Wierbowski SD, Lipkin SM, Wei X, Yu H.
Genome Research 2022
First published on bioRxiv 2019 (DOI:10.1101/2019.12.20.885293)
- Implications of disease-related mutations at protein-protein interfaces Xiong D, Lee D, Li L, Zhao Q, Yu H.
Current Opinion in Structural Biology 2022
2021 (10 PUBLICATIONS)
- Combining views for newly sequenced organisms Yingying Zhang, Shayne D. Wierbowski, Haiyuan Yu
Nature Machine Intelligence 2021
- A 3D structural SARS-CoV-2-human interactome to explore genetic and drug perturbations Wierbowski SD, Liang S, Liu Y, Chen Y, Gupta S, Andre NM, Lipkin SM, Whittaker GR, Yu H.
Nature Methods 2021 Website
First published on bioRxiv 2020 (DOI:10.1101/2020.10.13.308676)
- Progress in methodologies and quality-control strategies in protein cross-linking mass spectrometry Yugandhar K, Zhao Q, Gupta S, Xiong D, Yu H.
Proteomics 2021
- Human MLH1/3 variants causing aneuploidy, pregnancy loss, and premature reproductive aging Singh P, Fragoza R, Blengini CS, Tran TN, Pannafino G, Al-Sweel N, Schimenti KJ, Schindler K, Alani EA, Yu H, Schimenti JC.
Nature Communications 2021
- Handcuffing intrinsically disordered regions in Mlh1-Pms1 disrupts mismatch repair Furman CM, Wang TY, Zhao Q, Yugandhar K, Yu H, Alani E.
Nucleic Acids Research 2021
- A multifaceted role of progranulin in regulating amyloid-beta dynamics and responses Du H, Wong MY, Zhang T, Santos MN, Hsu C, Zhang J, Yu H, Luo W, Hu F.
Life Science Alliance 2021
- Structural basis of TRAPPIII-mediated Rab1 activation Joiner AM, Phillips BP, Yugandhar K, Sanford EJ, Smolka MB, Yu H, Miller EA, Fromme JC.
The EMBO journal 2021
- Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment Zhou Y, Xu J, Hou Y, Leverenz JB, Kallianpur A, Mehra R, Liu Y, Yu H, Pieper AA, Jehi L, Cheng F.
bioRxiv : the preprint server for biology 2021
- In-depth and 3-dimensional exploration of the budding yeast phosphoproteome Lanz MC, Yugandhar K, Gupta S, Sanford EJ, Faça VM, Vega S, Joiner AMN, Fromme JC, Yu H, Smolka MB.
EMBO reports 2021
- SAAMBE-SEQ: a sequence-based method for predicting mutation effect on protein-protein binding affinity Li G, Pahari S, Murthy AK, Liang S, Fragoza R, Yu H, Alexov E.
Bioinformatics (Oxford, England) 2021
2020 (14 PUBLICATIONS)
- PIVOTAL: Prioritizing variants of uncertain significance with spatial genomic patterns in the 3D proteome Siqi Liang, Matthew Mort, Peter D. Stenson, David N. Cooper, Haiyuan Yu
bioRxiv 2020
- Maximized quantitative phosphoproteomics allows high confidence dissection of the DNA damage signaling network Faca VM, Sanford EJ, Tieu J, Comstock W, Gupta S, Marshall S, Yu H, Smolka MB.
Scientific Reports 2020
- Variants in RABL2A causing male infertility and ciliopathy Ding X, Fragoza R, Singh P, Zhang S, Yu H, Schimenti JC.
Human molecular genetics 2020
- De novo missense variants disrupting protein-protein interactions affect risk for autism through gene co-expression and protein networks in neuronal cell types Chen S, Wang J, Cicek E, Roeder K, Yu H, Devlin B.
Molecular Autism 2020
- Structure-based validation can drastically underestimate error rate in proteome-wide cross-linking mass spectrometry studies Yugandhar K, Wang TY, Wierbowski SD, Shayhidin EE, Yu H.
Nature Methods 2020 Website
First published on bioRxiv 2019 (DOI:10.1101/617654)
- Transcription imparts architecture, function and logic to enhancer units Tippens ND, Liang J, Leung AK, Wierbowski SD, Ozer A, Booth JG, Lis JT, Yu H.
Nature Genetics 2020
First published on bioRxiv 2019 (DOI:10.1101/818849)
- Loss of TMEM106B and PGRN leads to severe lysosomal abnormalities and neurodegeneration in mice Feng T, Mai S, Roscoe JM, Sheng RR, Ullah M, Zhang J, Katz II, Yu H, Xiong W, Hu F.
EMBO Reports 2020
- Genetics of extreme human longevity to guide drug discovery for healthy ageing Zhang ZD, Milman S, Lin JR, Wierbowski S, Yu H, Barzilai N, Gorbunova V, Ladiges WC, Niedernhofer LJ, Suh Y, Robbins PD, Vijg J.
Nature Metabolism 2020
- Glucosylation by the Legionella Effector SetA Promotes the Nuclear Localization of the Transcription Factor TFEB Beck WHJ, Kim D, Das J, Yu H, Smolka MB, Mao Y.
iScience 2020
- Revealing new therapeutic opportunities through drug target prediction: a class imbalance-tolerant machine learning approach Liang S, Yu H.
Bioinformatics (Oxford, England) 2020
First published on bioRxiv 2019 (DOI:10.1101/572420)
- A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice Wierbowski SD, Vo TV, Falter-Braun P, Jobe TO, Kruse LH, Wei X, Liang J, Meyer MJ, Akturk N, Rivera-Erick CA, Cordero NA, Paramo MI, Shayhidin EE, Bertolotti M, Tippens ND, Akther K, Sharma R, Katayose Y, Salehi-Ashtiani K, Hao T, Ronald PC, Ecker JR, Schweitzer PA, Kikuchi S, Mizuno H, Hill DE, Vidal M, Moghe GD, McCouch SR, Yu H.
Proceedings of the National Academy of Sciences of the United States of America 2020
- BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain Pourhaghighi R, Ash PEA, Phanse S, Goebels F, Hu LZM, Chen S, Zhang Y, Wierbowski SD, Boudeau S, Moutaoufik MT, Malty RH, Malolepsza E, Tsafou K, Nathan A, Cromar G, Guo H, Abdullatif AA, Apicco DJ, Becker LA, Gitler AD, Pulst SM, Youssef A, Hekman R, Havugimana PC, White CA, Blum BC, Ratti A, Bryant CD, Parkinson J, Lage K, Babu M, Yu H, Bader GD, Wolozin B, Emili A.
Cell Systems 2020
- SAAMBE-3D: Predicting Effect of Mutations on Protein-Protein Interactions Pahari S, Li G, Murthy AK, Liang S, Fragoza R, Yu H, Alexov E.
International journal of molecular sciences 2020
- MaXLinker: Proteome-wide Cross-link Identifications with High Specificity and Sensitivity Yugandhar K, Wang TY, Leung AK, Lanz MC, Motorykin I, Liang J, Shayhidin EE, Smolka MB, Zhang S, Yu H.
Molecular & Cellular Proteomics : MCP 2020 Website
Highlighted as "Research Highlights" in Nature Methods (PDF) ; First published on bioRxiv 2019 (DOI:10.1101/526897)
2019 (4 PUBLICATIONS)
- Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations Fragoza R, Das J, Wierbowski SD, Liang J, Tran TN, Liang S, Beltran JF, Rivera-Erick CA, Ye K, Wang TY, Yao L, Mort M, Stenson PD, Cooper DN, Wei X, Keinan A, Schimenti JC, Clark AG, Yu H.
Nature communications 2019
- GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell-type specific manner Lou S, Cotter KA, Li T, Liang J, Mohsen H, Liu J, Zhang J, Cohen S, Xu J, Yu H, Rubin MA, Gerstein M.
PLoS Genetics 2019
- Inferring Protein-Protein Interaction Networks From Mass Spectrometry-Based Proteomic Approaches: A Mini-Review Yugandhar K, Gupta S, Yu H.
Computational and Structural Biotechnology Journal 2019
- Leveraging genetic interactions for adverse drug-drug interaction prediction Qian S, Liang S, Yu H.
PLoS Computational Biology 2019
2018 (4 PUBLICATIONS)
- Extracting Complementary Insights from Molecular Phenotypes for Prioritization of Disease-Associated Mutations Wierbowski SD, Fragoza R, Liang S, Yu H.
Current Opinion in Systems Biology 2018
- An interactome perturbation framework prioritizes damaging missense mutations for developmental disorders Chen S, Fragoza R, Klei L, Liu Y, Wang J, Roeder K, Devlin B, Yu H.
Nature Genetics 2018
Evaluated as "Exceptional" by "FACULTY of 1000"
- Germline Lysine-Specific Demethylase 1 (LSD1/KDM1A) Mutations Confer Susceptibility to Multiple Myeloma Wei X, Calvo-Vidal MN, Chen S, Wu G, Revuelta MV, Sun J, Zhang J, Walsh MF, Nichols KE, Joseph V, Snyder C, Vachon CM, McKay JD, Wang SP, Jayabalan DS, Jacobs LM, Becirovic D, Waller RG, Artomov M, Viale A, Patel J, Phillip J, Chen-Kiang S, Curtin K, Salama M, Atanackovic D, Niesvizky R, Landgren O, Slager SL, Godley LA, Churpek J, Garber JE, Anderson KC, Daly MJ, Roeder RG, Dumontet C, Lynch HT, Mullighan CG, Camp NJ, Offit K, Klein RJ, Yu H, Cerchietti L, Lipkin SM.
Cancer Research 2018
- Interactome INSIDER: a structural interactome browser for genomic studies Meyer MJ, Beltrán JF, Liang S, Fragoza R, Rumack A, Liang J, Wei X, Yu H.
Nature Methods 2018 Website
Highlighted as the cover image[1]
2017 (3 PUBLICATIONS)
- A Map of Human Mitochondrial Protein Interactions Linked to Neurodegeneration Reveals New Mechanisms of Redox Homeostasis and NF-κB Signaling Malty RH, Aoki H, Kumar A, Phanse S, Amin S, Zhang Q, Minic Z, Goebels F, Musso G, Wu Z, Abou-Tok H, Meyer M, Deineko V, Kassir S, Sidhu V, Jessulat M, Scott NE, Xiong X, Vlasblom J, Prasad B, Foster LJ, Alberio T, Garavaglia B, Yu H, Bader GD, Nakamura K, Parkinson J, Babu M.
Cell Systems 2017
- GeMSTONE: orchestrated prioritization of human germline mutations in the cloud Chen S, Beltrán JF, Esteban-Jurado C, Franch-Expósito S, Castellví-Bel S, Lipkin S, Wei X, Yu H.
Nucleic Acids Research 2017 Website
- iRegNet3D: three-dimensional integrated regulatory network for the genomic analysis of coding and non-coding disease mutations Liang S, Tippens ND, Zhou Y, Mort M, Stenson PD, Cooper DN, Yu H.
Genome Biology 2017 Website
2016 (7 PUBLICATIONS)
- Disease Model of GATA4 Mutation Reveals Transcription Factor Cooperativity in Human Cardiogenesis Ang YS, Rivas RN, Ribeiro AJS, Srivas R, Rivera J, Stone NR, Pratt K, Mohamed TMA, Fu JD, Spencer CI, Tippens ND, Li M, Narasimha A, Radzinsky E, Moon-Grady AJ, Yu H, Pruitt BL, Snyder MP, Srivastava D.
Cell 2016
- Integrated network analysis reveals distinct regulatory roles of transcription factors and microRNAs Guo Y, Alexander K, Clark AG, Grimson A, Yu H.
RNA (New York, N.Y.) 2016
- Systems level analysis of the Chlamydomonas reinhardtii metabolic network reveals variability in evolutionary co-conservation Chaiboonchoe A, Ghamsari L, Dohai B, Ng P, Khraiwesh B, Jaiswal A, Jijakli K, Koussa J, Nelson DR, Cai H, Yang X, Chang RL, Papin J, Yu H, Balaji S, Salehi-Ashtiani K.
Molecular bioSystems 2016
- Pooled-matrix protein interaction screens using Barcode Fusion Genetics Yachie N, Petsalaki E, Mellor JC, Weile J, Jacob Y, Verby M, Ozturk SB, Li S, Cote AG, Mosca R, Knapp JJ, Ko M, Yu A, Gebbia M, Sahni N, Yi S, Tyagi T, Sheykhkarimli D, Roth JF, Wong C, Musa L, Snider J, Liu YC, Yu H, Braun P, Stagljar I, Hao T, Calderwood MA, Pelletier L, Aloy P, Hill DE, Vidal M, Roth FP.
Molecular Systems Biology 2016
- mutation3D: Cancer Gene Prediction Through Atomic Clustering of Coding Variants in the Structural Proteome Meyer MJ, Lapcevic R, Romero AE, Yoon M, Das J, Beltrán JF, Mort M, Stenson PD, Cooper DN, Paccanaro A, Yu H.
Human Mutation 2016 Website
- BISQUE: locus- and variant-specific conversion of genomic, transcriptomic and proteomic database identifiers Meyer MJ, Geske P, Yu H.
Bioinformatics (Oxford, England) 2016 Website
- A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human Vo TV, Das J, Meyer MJ, Cordero NA, Akturk N, Wei X, Fair BJ, Degatano AG, Fragoza R, Liu LG, Matsuyama A, Trickey M, Horibata S, Grimson A, Yamano H, Yoshida M, Roth FP, Pleiss JA, Xia Y, Yu H.
Cell 2016
2015 (5 PUBLICATIONS)
- Studying Autism in Context Das J, Meyer MJ, Yu H.
Cell Systems 2015
- A global reference for human genetic variation 1000 Genomes Project Consortium; Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR.
Nature 2015
- ENCAPP: elastic-net-based prognosis prediction and biomarker discovery for human cancers Das J, Gayvert KM, Bunea F, Wegkamp MH, Yu H.
BMC Genomics 2015
- Trimethylation of Lys36 on H3 restricts gene expression change during aging and impacts life span Pu M, Ni Z, Wang M, Wang X, Wood JG, Helfand SL, Yu H, Lee SS.
Genes & Development 2015
- Phosphoproteomics reveals distinct modes of Mec1/ATR signaling during DNA replication Bastos de Oliveira FM, Kim D, Cussiol JR, Das J, Jeong MC, Doerfler L, Schmidt KH, Yu H, Smolka MB.
Molecular Cell 2015
Featured as a Research Highlight in Nature Reviews Molecular Cell Biology
2014 (5 PUBLICATIONS)
- A massively parallel pipeline to clone DNA variants and examine molecular phenotypes of human disease mutations Wei X, Das J, Fragoza R, Liang J, Bastos de Oliveira FM, Lee HR, Wang X, Mort M, Stenson PD, Cooper DN, Lipkin SM, Smolka MB, Yu H.
PLoS Genetics 2014
- Predicting cancer prognosis using functional genomics data sets Das J, Gayvert KM, Yu H.
Cancer Informatics 2014
- Elucidating common structural features of human pathogenic variations using large-scale atomic-resolution protein networks Das J, Lee HR, Sagar A, Fragoza R, Liang J, Wei X, Wang X, Mort M, Stenson PD, Cooper DN, Yu H.
Human Mutation 2014
Featured as a video highlight in Human Mutation
- Regulatory network features in Listeria monocytogenes-changing the way we talk Guariglia-Oropeza V, Orsi RH, Yu H, Boor KJ, Wiedmann M, Guldimann C.
Frontiers in cellular and infection microbiology 2014
- Exploring mechanisms of human disease through structurally resolved protein interactome networks Das J, Fragoza R, Lee HR, Cordero NA, Guo Y, Meyer MJ, Vo TV, Wang X, Yu H.
Molecular bioSystems 2014
2013 (5 PUBLICATIONS)
- Integrative annotation of variants from 1092 humans: application to cancer genomics Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F; 1000 Genomes Project Consortium; Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M.
Science (New York, N.Y.) 2013
Highlighted as "Research Highlights" in Nature 2013 502: 144
- Target essentiality and centrality characterize drug side effects Wang X, Thijssen B, Yu H.
PLoS Computational Biology 2013
- Dissecting disease inheritance modes in a three-dimensional protein network challenges the "guilt-by-association" principle Guo Y, Wei X, Das J, Grimson A, Lipkin SM, Clark AG, Yu H.
American Journal of Human Genetics 2013
Highlighted in "This Month in The Journal" in Am J Hum Genet 2013 3(1):1-2 and in "This Month in the American Journal of Human Genetics" in Genetics 2013 197(3)
- Cross-species protein interactome mapping reveals species-specific wiring of stress response pathways Das J, Vo TV, Wei X, Mellor JC, Tong V, Degatano AG, Wang X, Wang L, Cordero NA, Kruer-Zerhusen N, Matsuyama A, Pleiss JA, Lipkin SM, Yoshida M, Roth FP, Yu H.
Science Signaling 2013
Evaluated as "Very Good" by "FACULTY of 1000"
- INstruct: a database of high-quality 3D structurally resolved protein interactome networks Meyer MJ, Das J, Wang X, Yu H.
Bioinformatics (Oxford, England) 2013
2012 (4 PUBLICATIONS)
- HINT: High-quality protein interactomes and their applications in understanding human disease Das J, Yu H.
BMC Systems Biology 2012 Website
- Genome-scale analysis of interaction dynamics reveals organization of biological networks Das J, Mohammed J, Yu H.
Bioinformatics (Oxford, England) 2012
- Detecting overlapping protein complexes in protein-protein interaction networks Nepusz T, Yu H, Paccanaro A.
Nature Methods 2012
- Three-dimensional reconstruction of protein networks provides insight into human genetic disease Wang X, Wei X, Thijssen B, Das J, Lipkin SM, Yu H.
Nature Biotechnology 2012 Website
Highlighted as "Research Highlights" in Nature Methods 2012 9: 220-1 as "Technology Feature" in Nature 2012 484: 271-5 and as "Feature" and on the cover of Nature 2013 494:416-9; Evaluated as "Exceptional" by "FACULTY of 1000.
2011 (6 PUBLICATIONS)
- Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii Ghamsari L, Balaji S, Shen Y, Yang X, Balcha D, Fan C, Hao T, Yu H, Papin JA, Salehi-Ashtiani K.
BMC Genomics 2011
- Network-based methods for human disease gene prediction Wang X, Gulbahce N, Yu H.
Briefings in Functional Genomics 2011
- A bayesian mixture model for comparative spectral count data in shotgun proteomics Booth JG, Eilertson KE, Olinares PD, Yu H.
Molecular & Cellular Proteomics : MCP 2011
- Next-generation sequencing to generate interactome datasets Yu H, Tardivo L, Tam S, Weiner E, Gebreab F, Fan C, Svrzikapa N, Hirozane-Kishikawa T, Rietman E, Yang X, Sahalie J, Salehi-Ashtiani K, Hao T, Cusick ME, Hill DE, Roth FP, Braun P, Vidal M.
Nature Methods 2011
- Leveraging the power of next-generation sequencing to generate interactome datasets Haiyuan Yu, Leah Tardivo, Stanley Tam, Evan Weiner, Fana Gebreab, Changyu Fan, Nenad Svrzikapa, Tomoko Hirozane-Kishikawa, Edward Rietman, Xinping Yang, Julie Sahalie, Kourosh Salehi-Ashtiani, Tong Hao, Michael E Cusick, David E Hill, Frederick P Roth, Pascal Braun & Marc Vidal
Nature Methods 2011
- Diverse protein kinase interactions identified by protein microarrays reveal novel connections between cellular processes Fasolo J, Sboner A, Sun MG, Yu H, Chen R, Sharon D, Kim PM, Gerstein M, Snyder M.
Genes & Development 2011
Before 2010 (40 PUBLICATIONS)
- Edgetic perturbation models of human inherited disorders Zhong Q, Simonis N, Li QR, Charloteaux B, Heuze F, Klitgord N, Tam S, Yu H, Venkatesan K, Mou D, Swearingen V, Yildirim MA, Yan H, Dricot A, Szeto D, Lin C, Hao T, Fan C, Milstein S, Dupuy D, Brasseur R, Hill DE, Cusick ME, Vidal M.
Molecular Systems Biology 2009
- Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins Tonikian R, Xin X, Toret CP, Gfeller D, Landgraf C, Panni S, Paoluzi S, Castagnoli L, Currell B, Seshagiri S, Yu H, Winsor B, Vidal M, Gerstein MB, Bader GD, Volkmer R, Cesareni G, Drubin DG, Kim PM, Sidhu SS, Boone C.
PLoS Biology 2009
- Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network Simonis N, Rual JF, Carvunis AR, Tasan M, Lemmens I, Hirozane-Kishikawa T, Hao T, Sahalie JM, Venkatesan K, Gebreab F, Cevik S, Klitgord N, Fan C, Braun P, Li N, Ayivi-Guedehoussou N, Dann E, Bertin N, Szeto D, Dricot A, Yildirim MA, Lin C, de Smet AS, Kao HL, Simon C, Smolyar A, Ahn JS, Tewari M, Boxem M, Milstein S, Yu H, Dreze M, Vandenhaute J, Gunsalus KC, Cusick ME, Hill DE, Tavernier J, Roth FP, Vidal M.
Nature Methods 2009
- Literature-curated protein interaction datasets Cusick ME, Yu H, Smolyar A, Venkatesan K, Carvunis AR, Simonis N, Rual JF, Borick H, Braun P, Dreze M, Vandenhaute J, Galli M, Yazaki J, Hill DE, Ecker JR, Roth FP, Vidal M.
Nature Methods 2009
- An empirical framework for binary interactome mapping Venkatesan K, Rual JF, Vazquez A, Stelzl U, Lemmens I, Hirozane-Kishikawa T, Hao T, Zenkner M, Xin X, Goh KI, Yildirim MA, Simonis N, Heinzmann K, Gebreab F, Sahalie JM, Cevik S, Simon C, de Smet AS, Dann E, Smolyar A, Vinayagam A, Yu H, Szeto D, Borick H, Dricot A, Klitgord N, Murray RR, Lin C, Lalowski M, Timm J, Rau K, Boone C, Braun P, Cusick ME, Roth FP, Hill DE, Tavernier J, Wanker EE, Barabási AL, Vidal M.
Nature Methods 2009
- An experimentally derived confidence score for binary protein-protein interactions Braun P, Tasan M, Dreze M, Barrios-Rodiles M, Lemmens I, Yu H, Sahalie JM, Murray RR, Roncari L, de Smet AS, Venkatesan K, Rual JF, Vandenhaute J, Cusick ME, Pawson T, Hill DE, Tavernier J, Wrana JL, Roth FP, Vidal M.
Nature Methods 2009
- High-quality binary protein interaction map of the yeast interactome network Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, Sahalie J, Hirozane-Kishikawa T, Gebreab F, Li N, Simonis N, Hao T, Rual JF, Dricot A, Vazquez A, Murray RR, Simon C, Tardivo L, Tam S, Svrzikapa N, Fan C, de Smet AS, Motyl A, Hudson ME, Park J, Xin X, Cusick ME, Moore T, Boone C, Snyder M, Roth FP, Barabási AL, Tavernier J, Hill DE, Vidal M.
Science (New York, N.Y.) 2008
Highlighted in "Perspectives" in Science 2008. 322:56-7.
- Revisiting the Saccharomyces cerevisiae predicted ORFeome Li QR, Carvunis AR, Yu H, Han JD, Zhong Q, Simonis N, Tam S, Hao T, Klitgord NJ, Dupuy D, Mou D, Wapinski I, Regev A, Hill DE, Cusick ME, Vidal M.
Genome Research 2008
- Divergence of transcription factor binding sites across related yeast species Borneman AR, Gianoulis TA, Zhang ZD, Yu H, Rozowsky J, Seringhaus MR, Wang LY, Gerstein M, Snyder M.
Science (New York, N.Y.) 2007 Website
- Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications Yu H, Jansen R, Stolovitzky G, Gerstein M.
Bioinformatics (Oxford, England) 2007 Website
- The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics Yu H, Kim PM, Sprecher E, Trifonov V, Gerstein M.
PLoS Computational Biology 2007 Website
Highlighted as "Editors' Choice" in Science 2007. 316:957.
- Positional artifacts in microarrays: experimental verification and construction of COP, an automated detection tool Yu H, Nguyen K, Royce T, Qian J, Nelson K, Snyder M, Gerstein M.
Nucleic Acids Research 2007
- The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks Yip KY, Yu H, Kim PM, Schultz M, Gerstein M.
Bioinformatics (Oxford, England) 2006
- Genomic analysis of the hierarchical structure of regulatory networks Yu H, Gerstein M.
Proceedings of the National Academy of Sciences of the United States of America 2006 Website
- Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies Royce TE, Rozowsky JS, Luscombe NM, Emanuelsson O, Yu H, Zhu X, Snyder M, Gerstein MB.
Methods in Enzymology 2006
- Design principles of molecular networks revealed by global comparisons and composite motifs Yu H, Xia Y, Trifonov V, Gerstein M.
Genome Biology 2006 Website
- Global landscape of protein complexes in the yeast Saccharomyces cerevisiae Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrín-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, St Onge P, Ghanny S, Lam MH, Butland G, Altaf-Ul AM, Kanaya S, Shilatifard A, O'Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, Greenblatt JF.
Nature 2006
- Predicting interactions in protein networks by completing defective cliques Yu H, Paccanaro A, Trifonov V, Gerstein M.
Bioinformatics (Oxford, England) 2006 Website
- Target hub proteins serve as master regulators of development in yeast Borneman AR, Leigh-Bell JA, Yu H, Bertone P, Gerstein M, Snyder M.
Genes & Development 2006
- Biochemical and genetic analysis of the yeast proteome with a movable ORF collection Gelperin DM, White MA, Wilkinson ML, Kon Y, Kung LA, Wise KJ, Lopez-Hoyo N, Jiang L, Piccirillo S, Yu H, Gerstein M, Dumont ME, Phizicky EM, Snyder M, Grayhack EJ.
Genes & Development 2005
- Assessing the limits of genomic data integration for predicting protein networks Lu LJ, Xia Y, Paccanaro A, Yu H, Gerstein M.
Genome Research 2005 Website
- Computational analysis of membrane proteins: genomic occurrence, structure prediction and helix interactions Lehnert U, Xia Y, Royce TE, Goh CS, Liu Y, Senes A, Yu H, Zhang ZL, Engelman DM, Gerstein M.
Quarterly Reviews of Biophysics 2004
- Genomic analysis of regulatory network dynamics reveals large topological changes Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M.
Nature 2004 Website
- Analyzing cellular biochemistry in terms of molecular networks Xia Y, Yu H, Jansen R, Seringhaus M, Baxter S, Greenbaum D, Zhao H, Gerstein M.
Annual Review of Biochemistry 2004
- Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs Yu H, Luscombe NM, Lu HX, Zhu X, Xia Y, Han JD, Bertin N, Chung S, Vidal M, Gerstein M.
Genome Research 2004 Website
- Genomic analysis of essentiality within protein networks Yu H, Greenbaum D, Xin Lu H, Zhu X, Gerstein M.
Trends in Genetics : TIG 2004 Website
- TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics Yu H, Zhu X, Greenbaum D, Karro J, Gerstein M.
Nucleic Acids Research 2004 Website
- A map of the interactome network of the metazoan C. elegans Li S, Armstrong CM, Bertin N, Ge H, Milstein S, Boxem M, Vidalain PO, Han JD, Chesneau A, Hao T, Goldberg DS, Li N, Martinez M, Rual JF, Lamesch P, Xu L, Tewari M, Wong SL, Zhang LV, Berriz GF, Jacotot L, Vaglio P, Reboul J, Hirozane-Kishikawa T, Li Q, Gabel HW, Elewa A, Baumgartner B, Rose DJ, Yu H, Bosak S, Sequerra R, Fraser A, Mango SE, Saxton WM, Strome S, Van Den Heuvel S, Piano F, Vandenhaute J, Sardet C, Gerstein M, Doucette-Stamm L, Gunsalus KC, Harper JW, Cusick ME, Roth FP, Hill DE, Vidal M.
Science (New York, N.Y.) 2004
- Relationship between gene co-expression and probe localization on microarray slides Kluger Y, Yu H, Qian J, Gerstein M.
BMC Genomics 2003
- A genome-wide analysis of blue-light regulation of Arabidopsis transcription factor gene expression during seedling development Jiao Y, Yang H, Ma L, Sun N, Yu H, Liu T, Gao Y, Gu H, Chen Z, Wada M, Gerstein M, Zhao H, Qu LJ, Deng XW.
Plant Physiology 2003
- A Bayesian networks approach for predicting protein-protein interactions from genomic data Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M.
Science (New York, N.Y.) 2003 Website
- Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data Qian J, Lin J, Luscombe NM, Yu H, Gerstein M.
Bioinformatics (Oxford, England) 2003 Website
- Genomic analysis of gene expression relationships in transcriptional regulatory networks Yu H, Luscombe NM, Qian J, Gerstein M.
Trends in Genetics : TIG 2003 Website
- Identification and correction of spurious spatial correlations in microarray data Qian J, Kluger Y, Yu H, Gerstein M.
BioTechniques 2003
- Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic Krebs WG, Alexandrov V, Wilson CA, Echols N, Yu H, Gerstein M.
Proteins 2002 Website
- Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions Qian J, Dolled-Filhart M, Lin J, Yu H, Gerstein M.
Journal of Molecular Biology 2001 Website
- PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information Qian J, Stenger B, Wilson CA, Lin J, Jansen R, Teichmann SA, Park J, Krebs WG, Yu H, Alexandrov V, Echols N, Gerstein M.
Nucleic Acids Research 2001 Website
- Cloning and expression pattern of a dehydrin-like BDN1 gene from drought-tolerant Boea crassifolia Hemsl Huiwu Zhao, Han Liu, Haiyuan Yu, Yuanlei Hu, Yin Gao, Zhenyu Li & Zhongping Lin
Chinese Science Bulletin 2000
