[find our papers on PubMed]
* co-first author; ¶ co-corresponding author

2023 (2)

A multiscale functional map of somatic mutations in cancer integrating protein structure and network topology
Zhang Y, Leung AK, Qiu T, Li L, Zhang J, Wierbowski S, Booth J, Yu H. bioRxiv 2023 March 7 https://doi.org/10.1101/2023.03.06.531441.
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, M, 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, J T, Feschotte, C, Erzurum, S C, Cheng, F, and Yu, H. Nature Biotechnology 2023 41(1):128-139..
Highlighted as the cover image

2022 (7)

Advancing discovery of risk-altering variants for complex diseases by functionally informed fine-mapping
Chen Y, Clark A and Yu H. Neuron 2022 110(6):905-907..
Functional genomic assays to annotate enhancer-promoter interactions genome-wide
Leung AK, Yao L, and Yu H. Human Molecular Genetics 2022 (in press).
Deep learning methods for 3D structural proteome and interactome modeling
Lee D, Xiong D, Wierbowski S, Li L, Liang S, and Yu H. Current Opinion in Structural Biology 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 40(7):1056-1065.
Implications of disease-related mutations at protein-protein interfaces
Xiong D, Lee D, Li L, Zhao Q, and 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, and Cheng F. Aging Cell 2022.
A full-proteome, interaction-specific characterization of mutational hotspots across human cancers
Chen S, Liu Y, Zhang Y, Wierbowski S, Lipkin S, Wei X, and Yu H. Genome Research 2022.
First published on bioRxiv 2019 (DOI:10.1101/2019.12.20.885293)

2021 (9)

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, and Hu F. Life Science Alliance 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, and Cheng F. Alzheimer's Research & Therapy 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, and Schimenti JC. Nature Communications 2021.
Handcuffing intrinsically disordered regions in Mlh1–Pms1 disrupts mismatch repair
Furman CM, Wang T, Zhao Q, Kumar Y, Yu H, and Alani E. Nucleic Acids Research 2021 16, 9327-9341.
Progress in methodologies and quality-control strategies in protein cross-linking mass spectrometry
Kumar Y, Zhao Q, Gupta S, Xiong D, and Yu H. Proteomics 2021 2100145.
Combining views for newly sequenced organisms
Zhang Y, Wierbowski SD, Yu H. Nature Machine Intelligence 2021 December 9 3, 1011–1012.
Structural basis of TRAPPIII-mediated Rab1 activation
Joiner AMN, Phillips BP, Kumar Y, Sanford EJ, Smolka MB, Yu H, Miller EA, and Fromme JC. The EMBO Journal 2021 40:e107607.
A 3D structural SARS-CoV-2–human interactome to explore genetic and drug perturbations
Wierbowski SD, Liang S, Liui Y, Chen Y, Gupta S, Andre NM, Lipkin SM, Whittaker GR, Yu H. Nature Methods 2021 December 18, 1477–1488. .
First published on bioRxiv 2020 (DOI:10.1101/2020.10.13.308676)
In-depth and 3-Dimensional Exploration of the Budding Yeast Phosphoproteome
Lanz MC, Kumar Y, Gupta S, Sanford E, Faça V, Vega S, Joiner A, Fromme C, Yu H, and Smolka M. EMBO Reports 2021 22:e51121.

2020 (15)

Structure-based validation can drastically under-estimate error rate in proteome-wide cross-linking mass spectrometry studies
Kumar Y, Wang T, Wierbowski S, Shayhidin EE, and Yu H. Nature Methods 2020 17:985-988.
First published on bioRxiv 2019 (DOI:10.1101/617654)
Transcription imparts architecture, function, and logic to enhancer units
Tippens ND, Liang J, Leung A, Ozer A, Booth JG, Lis JT, and Yu H. Nature Genetics 2020 52, 1067–1075.
First published on bioRxiv 2019 (DOI:10.1101/818849)
Variants in RABL2A causing male infertility and ciliopathy
Ding X, Fragoza R, Singh P, Zhang S, Yu H, and Schimenti JC. Hum Mol Genet 2020 29(20):3402-3411.
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, and Smolka MB. Sci Rep 2020 10(1):18056.
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, and Devlin B. Molecular Autism 2020 11, 76.
Glucosylation by the Legionella Effector SetA Promotes the Nuclear Localization of the Transcription Factor TFEB
Beck W, Kim D, Das J, Yu H, Smolka M, and Mao Y. iScience 2020 24;23(7):101300.
Loss of TMEM106B and PGRN leads to severe lysosomal abnormalities and neurodegeneration in mice
Feng T, Mai S, Roscoe J, Sheng R, Ullah M , Zhang J, Katz I, Yu H, Xiong W, and Hu F. EMBO Rep 2020 21:e50219.
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, and Alexov E. Bioinformatics 2020 August 31.
Genetics of extreme human longevity to guide drug discovery for healthy ageing
Zhang ZD, Milman S, Lin J, Wierbowski SD, Yu H, Barzilai N, Gorbunova V, Ladiges WC, Niedernhofer LJ, Suh Y, Robbins PD, and Vijg J. Nature Metabolism 2020 July 27 2: 663–672.
PIVOTAL: Prioritizing variants of uncertain significance with spatial genomic patterns in the 3D proteome
Liang S, Mort M, Stenson PD, Cooper DN, Yu H. bioRxiv 2020 Jun 5 https://doi.org/10.1101/2020.06.04.135103.
Revealing new therapeutic opportunities through drug target prediction via class imbalance-tolerant machine learning
Liang S, Yu H. Bioinformatics 2020 May 12.
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, and Yu H. Proc Natl Acad Sci U S A 2020 May 12 https://doi.org/10.1073/pnas.1918068117.
BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain
Pourhaghighi R, Ash P, Phanse S, Geobels F, Hu L, Chen S, Zhang Y, Wierbowski S, Boudeau S, Moutaoufik M, Malty R, Malolepsza E, Tsafou K, Nathan A, Cromar G, Guo H, Abdulatif A, Apicco D, Becker L, Gitler A, Pulst S, Youssef A, Hekman R, Havugimana P, White C, Blum B, Ratti A, Bryant C, Pakinson J, Lage K, Babu M, Yu H, Bader G, Wolozin B, and Emili A. Cell Systems 2020 10: 333–350.
SAAMBE-3D: Predicting Effect of Mutations on Protein–Protein Interactions
Pahari S, Li G, Murthy A K, Liang S, Fragoza R, Yu H, and Alexov E. Int J Mol Sci 2020 21: 2563.
MaXLinker: proteome-wide cross-link identifications with high specificity and sensitivity
Kumar Y, Wang T, Leung A, Lanz M, Motorykin I, Liang J, Shayhidin E, Smolka M, Zhang S, and Yu H. Molecular & Cellular Proteomics 2020 19(3): 554-568.
Highlighted as "Research Highlights"; in Nature Methods; (PDF); First published on bioRxiv 2019 (DOI:10.1101/526897)

2019 (4)

Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations
Fragoza R, Das J, Wierbowski S, Liang J, Tran T, Liang S, Beltran J, Rivera-Erick C, Ye K, Wang T, Yao L, Mort M, Stenson P, Cooper D, Wei X, Keinan A, Schimenti J, Clark A and Yu H. Nature Communications 2019 10(1):4141.
GRAM: A generalized model to predict the molecular effect of a non-coding variant in a cell-type specific manner
Lou S, Kellie C, Li T, Liang J, Mohsen H, Liu J, Zhang J, Cohen S, Xu J, Yu H, Rubin M, and Gerstein M. PLOS Genetics 2019 15(8):e1007860.
Inferring Protein-Protein Interaction Networks From Mass Spectrometry-Based Proteomic Approaches: A Mini-Review
Kumar Y, Gupta S, and Yu H. Computational and Structural Biotechnology Journal 2019 17:805-811.
Leveraging genetic interaction for adverse drug-drug interaction prediction
Qian S, Liang S, Yu H. PLoS Comput Biol 2019 15(5):e1007068.

2018 (4)

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 11:107–116.
Interactome INSIDER: a structural interactome browser for genomic studies
Meyer M, Beltrán J, Liang S, Fragoza R, Rumack A, Liang J, Wei X, and Yu H. Nature Methods 2018 February 15(2):107-114.
Highlighted as the cover image
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, and Yu H . Nature Genetics 2018 June 11.
Evaluated as "Exceptional" by "FACULTY of 1000".
Germline Lysine-Specific Demethylase 1 (LSD1/KDM1A) Mutations Confer Susceptibility to Multiple Myeloma
Wei X, Calvo-Vidal N, Chen S, Wu G, Revuelta M, Sun J, Zhang J, Walsh M, Nichols K, Joseph V, Snyder C, Vachon C, McKay J, Wang S, Jayabalan D, Jacobs L, Becirovic D, Waller R, Artomov M, Viale A, Patel J, Phillip J, Chen-Kiang S, Curtin K, Salama M, Atanackovic D, Niesvizky R, Landgren O, Slager S, Godley L, Churpek J, Garber J, Anderson K, Daly M, Roeder R, Dumontet C, Lynch H, Mullighan C, Camp N, Offit K, Klein R¶, Yu H¶, Cerchietti L¶, and Lipkin S¶. Cancer Research 2018 March 20.
Featured as a Research Highlight in Epidemiology and Genomics Research Program

2017 (3)

A Map of Human Mitochondrial Protein Interactions Linked to Neurodegeneration Reveals New Mechanisms of Redox Homeostasis and NF-kB Signaling
Malty R, 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 N, Xiong X, Vlasblom J, Prasad B, Foster B, Alberio T, Garavaglia B, Yu H, Bader G, Nakamura K, Parkinson J, Babu M. Cell Systems 2017 December 27 5 , 1–14.
GeMSTONE: orchestrated prioritization of human germline mutations in the cloud
Chen S, Beltrán J, Esteban-Jurado C, Franch-Expósito S, Castellví-Bel S, Lipkin S, Wei X, and Yu H. Nucleic Acids Res 2017 May 18.
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 Biol 2017 Jan 18 18:10.

2016 (7)

Disease Model of GATA4 Mutation Reveals Transcription Factor Cooperativity in Human Cardiogenesis
Ang YS, Rivas RN, Ribeiro AJ, Srivas R, Rivera J, Stone NR, Pratt K, Mohamed TM, Fu JD4, Spencer CI, Tippens ND, Li M, Narasimha A, Radzinsky E, Moon-Grady AJ, Yu H, Pruitt BL, Snyder MP, Srivastava D. Cell 2016 Dec 15 167(7):1734-1749.
Integrated network analysis reveals distinct regulatory roles of transcription factors and microRNAs
Guo Y, Alexander K, Clark AG, Grimson A, Yu H. RNA 2016 Nov 22(11):1663-1672.
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 July 19 12(8):2394-407.
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. Mol Syst Biol 2016 Apr 22 12(4):863.
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 May 37(5):447-56.
BISQUE: locus- and variant-specific conversion of genomic, transcriptomic, and proteomic database identifiers
Meyer MJ, Geske P, and Yu H. Bioinformatics 2016 May 15; 32(10):1598-600.
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 Jan 14 164(1): 310 - 323.

2015 (5)

Studying Autism in Context
Das J, Meyer MJ, Yu H. Cell Systems 2015 November 25 1(5): 312-13.
A global reference for human genetic variation
The 1000 Genomes Project Consortium. Nature 2015 October 1 526: 68–74.
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 and Development 2015 April 1 29: 718-31.
ENCAPP: elastic-net-based prognosis prediction and biomarker discovery for human cancers
Das J, Gayvert KM, Bunea F, Wegkamp M, and Yu H. BMC Genomics 2015 April 3 16:263.
Designated as "Highly Accessed" by BMC Genomics
Phosphoproteomics reveals distinct modes of Mec1/ATR signaling during DNA replication
Bastos de Oliveira FM, Kim DS, Cussiol JR, Das J, Jeong MC, Doerfler L, Schmidt K, Yu H, Smolka MB. Molecular Cell 2015 March 19 57(6): 1124-32.
Featured as a Research Highlight in Nature Reviews Molecular Cell Biology

2014 (5)

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 Oliviera FM, Lee HR, Wang X, Mort M, Stenson PD, Cooper DN, Lipkin SM, Smolka MB, Yu H. PLoS Genetics 2014 Dec 11 10(12): e1004819.
Predicting cancer prognosis using functional genomics datasets
Das J, Gayvert KM, and Yu H. Cancer Informatics 2014 Nov Suppl. 5:85-88.
Regulatory network features in Listeria monocytogenes—changing the way we talk
Guariglia-Oropeza V, Orsi RH, Yu H, Boor KJ, Wiedmann M, and Guldimann C. Front Cell Infect Microbiol 2014 Feb 4:14.
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 and Yu H. Human Mutation 2014 May 35(5):585-593.
Featured as a video highlight in Human Mutation
Exploring mechanisms of human disease through structurally resolved protein interactome networks
Das J, Fragoza R, Lee HR, Cordero NA, Guo Y, Meyer MJ, Vo T, Wang X, and Yu H. Molecular BioSystems 2014 Jan 10(1):9-17.

2013 (5)

Integrative annotation of variants from 1,092 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 S, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchi G, 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 2013 Oct 342 (6154), 1235587.
Highlighted as "Research Highlights" in Nature, 2013, 502: 144
Dissecting disease inheritance modes in a 3D protein network challenges the "guilt-by-association" principle
Guo Y, Wei X, Das J, Grimson A, Lipkin SM, Clark AG and Yu H. Am J Hum Genet 2013 July 11 3(1):78-89.
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)
Target essentiality and centrality characterize drug side effects
Wang X, Thijssen B, and Yu H. PLoS Comput Biol 2013 9(7):e1003119.
Cross-species protein interactome mapping reveals species-specific wiring of stress-response pathways
Das J, Vo T, 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 and Yu H. Science Signaling 2013 6, ra38.
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, and Yu H. Bioinformatics 2013 Jun 15 29(12):1577-9.

2012 (4)

HINT: High-quality protein interactomes and their applications in understanding human disease
Das J and Yu H. BMC Systems Biology 2012 Jul 30 6(1):92.
Designated as "Highly Accessed" by BMC Systems Biology
Genome-scale analysis of interaction dynamics reveals organization of biological networks
Das J, Mohammed J, and Yu H. Bioinformatics 2012 Jul 15 28(14):1873-8.
Detecting overlapping protein complexes in protein-protein interaction networks
Nepusz T, Yu H¶, and Paccanaro A¶. Nature Methods 2012 Mar 18 9(5):471-2.
Three-dimensional reconstruction of protein networks provides insight into human genetic disease
Wang X, Wei X, Thijssen B, Das J, Lipkin SM, and Yu H. Nature Biotechnology 2012 Jan 15 30(2):159-64.
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 (5)

Network-based methods for human disease gene prediction
Wang X, Gulbahce N, and Yu H. Brief Funct Genomics 2011 Sep 10(5):280-93.
A bayesian mixture model for comparative spectral count data in shotgun proteomics
Booth JG, Eilertson KE, Olinares PD, and Yu H. Mol Cell Proteomics 2011 10(8):M110007203.
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 J¶, and Salehi-Ashtiani K¶. BMC Genomics 2011 12(Suppl 1):S4.
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, and Vidal M. Nature Methods 2011 8(6):478-80.
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, and Snyder M. Genes Dev 2011 25(7):767-78.

Before 2010 (40)

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, and Vidal M. Mol Syst Biol 2009 5: p 321.
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, Barabasi AL, and Vidal M. Nature Methods 2009 6(1): p 83-90.
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, and Boone C. PLoS Biol 2009 7(10): p e1000218.
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, and Vidal M. Nature Methods 2009 6(1): p 47-54.
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, and Vidal M. Nature Methods 2009 6(1): p 39-46.
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, and Vidal M. Nature Methods 2009 6(1): p 91-7.
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, Barabasi AL, Tavernier J, Hill DE, and Vidal M. Science 2008 322(5898): p 104-10.
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, and Vidal M. Genome Res 2008 18(8): p 1294-303.
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, and Gerstein M. Nucleic Acids Res 2007 35(2): p e8.
The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics
Yu H, Kim PM, Sprecher E, Trifonov V, and Gerstein M. PLoS Comput Biol 2007 3(4): p e59.
Highlighted as "Editors' Choice" in Science, 2007. 316:957.
Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications
Yu H, Jansen R, Stolovitzky G, and Gerstein M. Bioinformatics 2007 23(16): p 2163-73.
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, and Snyder M. Science 2007 317(5839): p 815-9.
Design principles of molecular networks revealed by global comparisons and composite motifs
Yu H, Xia, Y, Trifonov V, and Gerstein M. Genome Biol 2006 7(7): p R55.
Predicting interactions in protein networks by completing defective cliques
Yu H, Paccanaro A, Trifonov V, and Gerstein M. Bioinformatics 2006 22(7): p 823-9.
Genomic analysis of the hierarchical structure of regulatory networks
Yu H¶ and Gerstein M. Proc Natl Acad Sci U S A 2006 103(40): p 14724-31.
The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks
Yip KY, Yu H, Kim PM, Schultz M, and Gerstein M. Bioinformatics 2006 22(23): p 2968-70.
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, and Gerstein MB. Methods Enzymol 2006 411: p 282-311.
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, Peregrin-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, and Greenblatt JF. Nature 2006 440(7084): p 637-43.
Target hub proteins serve as master regulators of development in yeast
Borneman AR, Leigh-Bell JA, Yu H, Bertone P, Gerstein M, and Snyder M. Genes Dev 2006 20(4): p 435-48.
Inferring protein-protein interactions using interaction network topologies
Paccanaro A, Trifonov V, Yu H, and Gerstein M. International Joint Conference on Neural Networks 2005 .
Assessing the limits of genomic data integration for predicting protein networks
Lu LJ, Xia Y Paccanaro A, Yu H, and Gerstein M. Genome Res 2005 15(7): p 945-53.
Protein Interaction Prediction by Integrating Genomic Features and Protein Interaction Network Analysis, in
Lu LJ, Xia Y, Yu H*, Rives A, Lu HX, Schubert F, and Gerstein M. Data Analysis and Visualization in Genomics and Proteomics 2005 F A Azuaje and J Dopazo, Editors John Wiley & Sons.
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, and Grayhack EJ. Genes Dev 2005 19(23): p 2816-26.
TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics
Yu H, Zhu X, Greenbaum D, Karro J, and Gerstein M. Nucleic Acids Res 2004 32(1): p 328-37.
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, and Gerstein M. Genome Res 2004 14(6): p 1107-18.
Genomic analysis of essentiality within protein networks
Yu H, Greenbaum D, Xin Lu H, Zhu X, and Gerstein M. Trends Genet 2004 20(6): p 227-31.
Analyzing cellular biochemistry in terms of molecular networks
Xia Y, Yu H*, Jansen R, Seringhaus M, Baxter S, Greenbaum D, Zhao H, and Gerstein M. Annu Rev Biochem 2004 73: p 1051-87.
Genomic analysis of regulatory network dynamics reveals large topological changes
Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, and Gerstein M. Nature 2004 431(7006): p 308-12.
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, and Vidal M. Science 2004 303(5657): p 540-3.
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, and Gerstein M. Q Rev Biophys 2004 37(2): p 121-46.
Genomic analysis of gene expression relationships in transcriptional regulatory networks
Yu H, Luscombe NM, Qian J, and Gerstein M. Trends Genet 2003 19(8): p 422-7.
Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data
Qian J, Lin J, Luscombe NM, Yu H, and Gerstein M. Bioinformatics 2003 19(15): p 1917-26.
Identification and correction of spurious spatial correlations in microarray data
Qian J, Kluger Y, Yu H*, and Gerstein M. Biotechniques 2003 35(1): p 42-4, 46, 48.
Relationship between gene co-expression and probe localization on microarray slides
Kluger Y, Yu H*, Qian J, and Gerstein M. BMC Genomics 2003 4(1): p 49.
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, and Deng XW. Plant Physiol 2003 133(4): p 1480-93.
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, and Gerstein M. Science 2003 302(5644): p 449-53.
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, and Gerstein M. Proteins 2002 48(4): p 682-95.
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, and Gerstein M. Nucleic Acids Res 2001 29(8): p 1750-64.
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, and Gerstein M. J Mol Biol 2001 314(5): p 1053-66.
Cloning and expression pattern of a dehydrin-like BDN1 gene from drought-tolerant Boea crassifolia Hems1
Zhao H, Liu H, Yu H, Hu Y, Gao Y, Li Z, and Lin Z. Chinese Science Bulletin 2000 45: p 2072-7.