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Showing 1-10 out of 146 results
2023/12/08
SON is an essential m(6)A target for hematopoietic stem cell fate
Luo H, Cortés-López M, Tam CL, Xiao M, Wakiro I, Chu KL, Pierson A, Chan M, Chang K, Yang X, Fecko D, Han G, Ahn EE, Morris QD, Landau DA, Kharas MG.
Cell Stem Cell
2023/09/13
Uncovering a mammalian neural-specific poly(A) binding protein with unique properties
Sharma S, Kajjo S, Harra Z, Hasaj B, Delisle V, Ray D, Gutierrez RL, Carrier I, Kleinman C, Morris Q, Hughes TR, McInnes R, Fabian MR.
Genes Dev
2023/03/31
RNA-binding proteins that lack canonical RNA-binding domains are rarely sequence-specific
Ray D, Laverty KU, Jolma A, Nie K, Samson R, Pour SE, Tam CL, von Krosigk N, Nabeel-Shah S, Albu M, Zheng H, Perron G, Lee H, Najafabadi H, Blencowe B, Greenblatt J, Morris Q, Hughes TR.
Sci Rep
2023/02/11
A deep learning approach reveals unexplored landscape of viral expression in cancer
Elbasir A, Ye Y, Schäffer DE, Hao X, Wickramasinghe J, Tsingas K, Lieberman PM, Long Q, Morris Q, Zhang R, Schäffer AA, Auslander N.
Nat Commun
2022/12/05
Regional mutational signature activities in cancer genomes
Timmons C, Morris Q, Harrigan CF.
PLoS Comput Biol
2022/09/21
Reconstructing cancer phylogenies using Pairtree, a clone tree reconstruction algorithm
Kulman E, Wintersinger J, Morris Q.
STAR Protoc
2022/09/01
PAN-cODE: COVID-19 forecasting using conditional latent ODEs
Shi R, Zhang H, Morris Q.
J Am Med Inform Assoc
2022/08/26
PRIESSTESS: interpretable, high-performing models of the sequence and structure preferences of RNA-binding proteins
Laverty KU, Jolma A, Pour SE, Zheng H, Ray D, Morris Q, Hughes TR.
Nucleic Acids Res
2022/07/23
Prognostic impact of autoimmune disease in oral cavity squamous cell carcinoma
Pillai A, Valero C, Zanoni D, Navas K, Morris Q, Ganly I, Patel SG.
J Surg Oncol
2022/07/20
Activating mTOR Mutations Are Detrimental in Nutrient-Poor Conditions
Bielska AA, Harrigan CF, Kyung YJ, Morris Q, Palm W, Thompson CB.
Cancer Res
2022/04/27
The X-linked splicing regulator MBNL3 has been co-opted to restrict placental growth in eutherians
Spruce T, Plass M, Gohr A, Ray D, Martínez de Lagrán M, Rot G, Nóvoa A, Burguera D, Permanyer J, Miret M, Zheng H, Swanson MS, Morris Q, Mallo M, Dierssen M, Hughes TR, Pernaute B, Irimia M.
PLoS Biol
2022/03/05
Reconstructing Complex Cancer Evolutionary Histories from Multiple Bulk DNA Samples Using Pairtree
Wintersinger JA, Dobson SM, Kulman E, Stein LD, Dick JE, Morris Q.
Blood Cancer Discov
2022/01/12
Multiomic Profiling of Central Nervous System Leukemia Identifies mRNA Translation as a Therapeutic Target
Vanner RJ, Dobson SM, Gan OI, McLeod J, Schoof EM, Grandal I, Wintersinger JA, Garcia-Prat L, Hosseini M, Xie SZ, Jin L, Mbong N, Voisin V, Chan-Seng-Yue M, Kennedy JA, Waanders E, Morris Q, Porse B, Chan SM, Guidos CJ, Danska JS, Minden MD, Mullighan CG, Dick JE.
Blood Cancer Discov
2021/12/10
Emerging Topics in Cancer Evolution
El-Kebir M, Morris Q, Oesper L, Sahinalp SC.
Pac Symp Biocomput
2021/09/14
Peripheral blood values as predictors of autoimmune status in oral cavity squamous cell carcinoma
Pillai A, Valero C, Navas K, Morris Q, Patel SG.
Transl Oncol
2021/08/14
Interacting evolutionary pressures drive mutation dynamics and health outcomes in aging blood
Skead K, Ang Houle A, Abelson S, Agbessi M, Bruat V, Lin B, Soave D, Shlush L, Wright S, Dick J, Morris Q, Awadalla P.
Nat Commun
2021/04/08
Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
Dentro SC, Leshchiner I, Haase K, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Rubanova Y, Macintyre G, Demeulemeester J, Vázquez-García I, Kleinheinz K, Livitz DG, Malikic S, Donmez N, Sengupta S, Anur P, Jolly C, Cmero M, Rosebrock D, Schumacher SE, Fan Y, Fittall M, Drews RM, Yao X, Watkins TBK, Lee J, Schlesner M, Zhu H, Adams DJ, McGranahan N, Swanton C, Getz G, Boutros PC, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Martincorena I, Markowetz F, Mustonen V, Yuan K, Gerstung M, Spellman PT, Wang W, Morris QD, Wedge DC, Van Loo P; PCAWG Evolution and Heterogeneity Working Group and the PCAWG Consortium.
Cell
2021/01/21
The promise of machine learning to inform the management of juvenile idiopathic arthritis
Eng SWM, Yeung RSM, Morris Q.
Expert Rev Clin Immunol
2021/01/19
Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine
Sundermann LK, Wintersinger J, Rätsch G, Stoye J, Morris Q.
PLoS Comput Biol
2021/01/13
Differential contribution of transcriptomic regulatory layers in the definition of neuronal identity
Ha KCH, Sterne-Weiler T, Morris Q, Weatheritt RJ, Blencowe BJ.
Nat Commun
2021/01/08
Colorectal Cancer Cells Enter a Diapause-like DTP State to Survive Chemotherapy
Rehman SK, Haynes J, Collignon E, Brown KR, Wang Y, Nixon AML, Bruce JP, Wintersinger JA, Singh Mer A, Lo EBL, Leung C, Lima-Fernandes E, Pedley NM, Soares F, McGibbon S, He HH, Pollet A, Pugh TJ, Haibe-Kains B, Morris Q, Ramalho-Santos M, Goyal S, Moffat J, O'Brien CA.
Cell
2021/01/05
A practical guide to cancer subclonal reconstruction from DNA sequencing
Tarabichi M, Salcedo A, Deshwar AG, Ni Leathlobhair M, Wintersinger J, Wedge DC, Van Loo P, Morris QD, Boutros PC.
Nat Methods
2020/12/08
Quantifying the influence of mutation detection on tumour subclonal reconstruction
Liu LY, Bhandari V, Salcedo A, Espiritu SMG, Morris QD, Kislinger T, Boutros PC.
Nat Commun
2020/08/09
The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation
Kosti A, de Araujo PR, Li WQ, Guardia GDA, Chiou J, Yi C, Ray D, Meliso F, Li YM, Delambre T, Qiao M, Burns SS, Lorbeer FK, Georgi F, Flosbach M, Klinnert S, Jenseit A, Lei X, Sandoval CR, Ha K, Zheng H, Pandey R, Gruslova A, Gupta YK, Brenner A, Kokovay E, Hughes TR, Morris QD, Galante PAF, Tiziani S, Penalva LOF.
Genome Biol
2020/07/25
Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences
Jolma A, Zhang J, Mondragón E, Morgunova E, Kivioja T, Laverty KU, Yin Y, Zhu F, Bourenkov G, Morris Q, Hughes TR, Maher LJ 3rd, Taipale J.
Genome Res
2020/03/27
Shifts in Ribosome Engagement Impact Key Gene Sets in Neurodevelopment and Ubiquitination in Rett Syndrome
Rodrigues DC, Mufteev M, Weatheritt RJ, Djuric U, Ha KCH, Ross PJ, Wei W, Piekna A, Sartori MA, Byres L, Mok RSF, Zaslavsky K, Pasceri P, Diamandis P, Morris Q, Blencowe BJ, Ellis J.
Cell Rep
2020/03/12
The RNA-Binding Protein Rasputin/G3BP Enhances the Stability and Translation of Its Target mRNAs
Laver JD, Ly J, Winn AK, Karaiskakis A, Lin S, Nie K, Benic G, Jaberi-Lashkari N, Cao WX, Khademi A, Westwood JT, Sidhu SS, Morris Q, Angers S, Smibert CA, Lipshitz HD.
Cell Rep
2020/02/23
Relapse-Fated Latent Diagnosis Subclones in Acute B Lineage Leukemia Are Drug Tolerant and Possess Distinct Metabolic Programs
Dobson SM, García-Prat L, Vanner RJ, Wintersinger J, Waanders E, Gu Z, McLeod J, Gan OI, Grandal I, Payne-Turner D, Edmonson MN, Ma X, Fan Y, Voisin V, Chan-Seng-Yue M, Xie SZ, Hosseini M, Abelson S, Gupta P, Rusch M, Shao Y, Olsen SR, Neale G, Chan SM, Bader G, Easton J, Guidos CJ, Danska JS, Zhang J, Minden MD, Morris Q, Mullighan CG, Dick JE.
Cancer Discov
2020/02/18
Systematic genetics and single-cell imaging reveal widespread morphological pleiotropy and cell-to-cell variability
Mattiazzi Usaj M, Sahin N, Friesen H, Pons C, Usaj M, Masinas MPD, Shuteriqi E, Shkurin A, Aloy P, Morris Q, Boone C, Andrews BJ.
Mol Syst Biol
2020/02/07
The evolutionary history of 2,658 cancers
Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD; PCAWG Evolution & Heterogeneity Working Group, Spellman PT, Wedge DC, Van Loo P; PCAWG Consortium.
Nature
2020/02/07
A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns
Jiao W, Atwal G, Polak P, Karlic R, Cuppen E; PCAWG Tumor Subtypes and Clinical Translation Working Group, Danyi A, de Ridder J, van Herpen C, Lolkema MP, Steeghs N, Getz G, Morris Q, Stein LD; PCAWG Consortium.
Nat Commun
2020/02/07
Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig
Rubanova Y, Shi R, Harrigan CF, Li R, Wintersinger J, Sahin N, Deshwar A; PCAWG Evolution and Heterogeneity Working Group, Morris Q; PCAWG Consortium.
Nat Commun
2020/01/11
A community effort to create standards for evaluating tumor subclonal reconstruction
Salcedo A, Tarabichi M, Espiritu SMG, Deshwar AG, David M, Wilson NM, Dentro S, Wintersinger JA, Liu LY, Ko M, Sivanandan S, Zhang H, Zhu K, Ou Yang TH, Chilton JM, Buchanan A, Lalansingh CM, P'ng C, Anghel CV, Umar I, Lo B, Zou W; DREAM SMC-Het Participants, Simpson JT, Stuart JM, Anastassiou D, Guan Y, Ewing AD, Ellrott K, Wedge DC, Morris Q, Van Loo P, Boutros PC.
Nat Biotechnol
2019/12/05
TrackSigFreq: subclonal reconstructions based on mutation signatures and allele frequencies
Harrigan CF, Rubanova Y, Morris Q, Selega A.
Pac Symp Biocomput
2019/12/05
Genome Gerrymandering: optimal division of the genome into regions with cancer type specific differences in mutation rates
Young A, Chmura J, Park Y, Morris Q, Atwal G.
Pac Symp Biocomput
2019/12/05
Identifying Transitional High Cost Users from Unstructured Patient Profiles Written by Primary Care Physicians
Zhang H, Candido E, Wilton AS, Duchen R, Jaakkimainen L, Wodchis W, Morris Q.
Pac Symp Biocomput
2019/05/29
Similarity regression predicts evolution of transcription factor sequence specificity
Lambert SA, Yang AWH, Sasse A, Cowley G, Albu M, Caddick MX, Morris QD, Weirauch MT, Hughes TR.
Nat Genet
2019/02/27
Patterns of joint involvement in juvenile idiopathic arthritis and prediction of disease course: A prospective study with multilayer non-negative matrix factorization
Eng SWM, Aeschlimann FA, van Veenendaal M, Berard RA, Rosenberg AM, Morris Q, Yeung RSM; ReACCh-Out Research Consortium.
PLoS Med
2019/01/31
ARGLU1 is a transcriptional coactivator and splicing regulator important for stress hormone signaling and development
Magomedova L, Tiefenbach J, Zilberman E, Le Billan F, Voisin V, Saikali M, Boivin V, Robitaille M, Gueroussov S, Irimia M, Ray D, Patel R, Xu C, Jeyasuria P, Bader GD, Hughes TR, Morris QD, Scott MS, Krause H, Angers S, Blencowe BJ, Cummins CL.
Nucleic Acids Res
2018/12/22
The TRIM-NHL protein NHL-2 is a co-factor in the nuclear and somatic RNAi pathways in C. elegans
Davis GM, Tu S, Anderson JW, Colson RN, Gunzburg MJ, Francisco MA, Ray D, Shrubsole SP, Sobotka JA, Seroussi U, Lao RX, Maity T, Wu MZ, McJunkin K, Morris QD, Hughes TR, Wilce JA, Claycomb JM, Weng Z, Boag PR.
Elife
2018/10/31
Neutral tumor evolution?
Tarabichi M, Martincorena I, Gerstung M, Leroi AM, Markowetz F; PCAWG Evolution and Heterogeneity Working Group, Spellman PT, Morris QD, Lingjærde OC, Wedge DC, Van Loo P.
Nat Genet
2018/09/02
Motif models for RNA-binding proteins
Sasse A, Laverty KU, Hughes TR, Morris QD.
Curr Opin Struct Biol
2018/08/25
A Chemical Biology Approach to Model Pontocerebellar Hypoplasia Type 1B (PCH1B)
François-Moutal L, Jahanbakhsh S, Nelson ADL, Ray D, Scott DD, Hennefarth MR, Moutal A, Perez-Miller S, Ambrose AJ, Al-Shamari A, Coursodon P, Meechoovet B, Reiman R, Lyons E, Beilstein M, Chapman E, Morris QD, Van Keuren-Jensen K, Hughes TR, Khanna R, Koehler C, Jen J, Gokhale V, Khanna M.
ACS Chem Biol
2018/06/19
GeneMANIA update 2018
Franz M, Rodriguez H, Lopes C, Zuberi K, Montojo J, Bader GD, Morris Q.
Nucleic Acids Res
2018/04/24
The Evolutionary Landscape of Localized Prostate Cancers Drives Clinical Aggression
Espiritu SMG, Liu LY, Rubanova Y, Bhandari V, Holgersen EM, Szyca LM, Fox NS, Chua MLK, Yamaguchi TN, Heisler LE, Livingstone J, Wintersinger J, Yousif F, Lalonde E, Rouette A, Salcedo A, Houlahan KE, Li CH, Huang V, Fraser M, van der Kwast T, Morris QD, Bristow RG, Boutros PC.
Cell
2018/03/30
QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data
Ha KCH, Blencowe BJ, Morris Q.
Genome Biol
2018/02/04
High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies
Youn JY, Dunham WH, Hong SJ, Knight JDR, Bashkurov M, Chen GI, Bagci H, Rathod B, MacLeod G, Eng SWM, Angers S, Morris Q, Fabian M, Côté JF, Gingras AC.
Mol Cell
2017/07/12
Oncogenic Activation of the RNA Binding Protein NELFE and MYC Signaling in Hepatocellular Carcinoma
Dang H, Takai A, Forgues M, Pomyen Y, Mou H, Xue W, Ray D, Ha KCH, Morris QD, Hughes TR, Wang XW.
Cancer Cell
2017/06/28
RNAcompete-S: Combined RNA sequence/structure preferences for RNA binding proteins derived from a single-step in vitro selection
Cook KB, Vembu S, Ha KCH, Zheng H, Laverty KU, Hughes TR, Ray D, Morris QD.
Methods
2017/04/06
An RRM-ZnF RNA recognition module targets RBM10 to exonic sequences to promote exon exclusion
Collins KM, Kainov YA, Christodolou E, Ray D, Morris Q, Hughes T, Taylor IA, Makeyev EV, Ramos A.
Nucleic Acids Res
2017/01/10
Using the Electronic Medical Record to Identify Patients at High Risk for Frequent Emergency Department Visits and High System Costs
Frost DW, Vembu S, Wang J, Tu K, Morris Q, Abrams HB.
Am J Med
2016/12/14
RNAcompete methodology and application to determine sequence preferences of unconventional RNA-binding proteins
Ray D, Ha KCH, Nie K, Zheng H, Hughes TR, Morris QD.
Methods
2016/12/13
Machine learning and computer vision approaches for phenotypic profiling
Grys BT, Lo DS, Sahin N, Kraus OZ, Morris Q, Boone C, Andrews BJ.
J Cell Biol
2016/10/13
MECP2 Is Post-transcriptionally Regulated during Human Neurodevelopment by Combinatorial Action of RNA-Binding Proteins and miRNAs
Rodrigues DC, Kim DS, Yang G, Zaslavsky K, Ha KC, Mok RS, Ross PJ, Zhao M, Piekna A, Wei W, Blencowe BJ, Morris Q, Ellis J.
Cell Rep
2016/08/10
Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians
Solana J, Irimia M, Ayoub S, Orejuela MR, Zywitza V, Jens M, Tapial J, Ray D, Morris Q, Hughes TR, Blencowe BJ, Rajewsky N.
Elife
2016/06/01
Gene Expression Deconvolution for Uncovering Molecular Signatures in Response to Therapy in Juvenile Idiopathic Arthritis
Cui A, Quon G, Rosenberg AM, Yeung RS, Morris Q; BBOP Study Consortium.
PLoS One
2015/11/04
The Crystal Structure of the NHL Domain in Complex with RNA Reveals the Molecular Basis of Drosophila Brain-Tumor-Mediated Gene Regulation
Loedige I, Jakob L, Treiber T, Ray D, Stotz M, Treiber N, Hennig J, Cook KB, Morris Q, Hughes TR, Engelmann JC, Krahn MP, Meister G.
Cell Rep
2015/05/15
ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles
Anghel CV, Quon G, Haider S, Nguyen F, Deshwar AG, Morris QD, Boutros PC.
BMC Bioinformatics
2015/05/13
Brain tumor is a sequence-specific RNA-binding protein that directs maternal mRNA clearance during the Drosophila maternal-to-zygotic transition
Laver JD, Li X, Ray D, Cook KB, Hahn NA, Nabeel-Shah S, Kekis M, Luo H, Marsolais AJ, Fung KY, Hughes TR, Westwood JT, Sidhu SS, Morris Q, Lipshitz HD, Smibert CA.
Genome Biol
2015/03/19
PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors
Deshwar AG, Vembu S, Yung CK, Jang GH, Stein L, Morris Q.
Genome Biol
2015/01/17
Comparing nonparametric Bayesian tree priors for clonal reconstruction of tumors
Deshwar AG, Vembu S, Morris Q.
Pac Symp Biocomput
2014/12/20
RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease
Xiong HY, Alipanahi B, Lee LJ, Bretschneider H, Merico D, Yuen RK, Hua Y, Gueroussov S, Najafabadi HS, Hughes TR, Morris Q, Barash Y, Krainer AR, Jojic N, Scherer SW, Blencowe BJ, Frey BJ.
Science
2014/12/16
High-throughput characterization of protein-RNA interactions
Cook KB, Hughes TR, Morris QD.
Brief Funct Genomics
2014/10/16
Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli
Vlasblom J, Zuberi K, Rodriguez H, Arnold R, Gagarinova A, Deineko V, Kumar A, Leung E, Rizzolo K, Samanfar B, Chang L, Phanse S, Golshani A, Greenblatt JF, Houry WA, Emili A, Morris Q, Bader G, Babu M.
Bioinformatics
2014/09/26
GeneMANIA: Fast gene network construction and function prediction for Cytoscape
Montojo J, Zuberi K, Rodriguez H, Bader GD, Morris Q.
F1000Res
2014/09/10
The biologic basis of clinical heterogeneity in juvenile idiopathic arthritis
Eng SW, Duong TT, Rosenberg AM, Morris Q, Yeung RS; REACCH OUT and BBOP Research Consortia.
Arthritis Rheumatol
2014/06/10
A pair of RNA-binding proteins controls networks of splicing events contributing to specialization of neural cell types
Norris AD, Gao S, Norris ML, Ray D, Ramani AK, Fraser AG, Morris Q, Hughes TR, Zhen M, Calarco JA.
Mol Cell
2014/06/07
Network Assessor: an automated method for quantitative assessment of a network's potential for gene function prediction
Montojo J, Zuberi K, Shao Q, Bader GD, Morris Q.
Front Genet
2014/03/19
RNA-protein interactions: an overview
Re A, Joshi T, Kulberkyte E, Morris Q, Workman CT.
Methods Mol Biol
2014/02/04
Inferring clonal evolution of tumors from single nucleotide somatic mutations
Jiao W, Vembu S, Deshwar AG, Stein L, Morris Q.
BMC Bioinformatics
2014/01/08
Global regulation of mRNA translation and stability in the early Drosophila embryo by the Smaug RNA-binding protein
Chen L, Dumelie JG, Li X, Cheng MH, Yang Z, Laver JD, Siddiqui NU, Westwood JT, Morris Q, Lipshitz HD, Smibert CA.
Genome Biol
2013/12/24
Staufen2 regulates neuronal target RNAs
Heraud-Farlow JE, Sharangdhar T, Li X, Pfeifer P, Tauber S, Orozco D, Hörmann A, Thomas S, Bakosova A, Farlow AR, Edbauer D, Lipshitz HD, Morris QD, Bilban M, Doyle M, Kiebler MA.
Cell Rep
2013/12/19
Novel cardiovascular gene functions revealed via systematic phenotype prediction in zebrafish
Musso G, Tasan M, Mosimann C, Beaver JE, Plovie E, Carr LA, Chua HN, Dunham J, Zuberi K, Rodriguez H, Morris Q, Zon L, Roth FP, MacRae CA.
Development
2013/12/04
Personalized medicine: from genotypes and molecular phenotypes towards therapy- session introduction
Listgarten J, Stegle O, Morris Q, Brenner SE, Parts L.
Pac Symp Biocomput
2013/12/04
An efficient algorithm to integrate network and attribute data for gene function prediction
Vembu S, Morris Q.
Pac Symp Biocomput
2013/11/13
Finding the target sites of RNA-binding proteins
Li X, Kazan H, Lipshitz HD, Morris QD.
Wiley Interdiscip Rev RNA
2013/10/31
A unified model for yeast transcript definition
de Boer CG, van Bakel H, Tsui K, Li J, Morris QD, Nislow C, Greenblatt JF, Hughes TR.
Genome Res
2013/10/15
PLIDA: cross-platform gene expression normalization using perturbed topic models
Deshwar AG, Morris Q.
Bioinformatics
2013/10/08
Identifying cancer specific functionally relevant miRNAs from gene expression and miRNA-to-gene networks using regularized regression
Mezlini AM, Wang B, Deshwar A, Morris Q, Goldenberg A.
PLoS One
2013/09/05
BayMiR: inferring evidence for endogenous miRNA-induced gene repression from mRNA expression profiles
Radfar H, Wong W, Morris Q.
BMC Genomics
2013/08/16
Genome-wide analysis of Staufen-associated mRNAs identifies secondary structures that confer target specificity
Laver JD, Li X, Ancevicius K, Westwood JT, Smibert CA, Morris QD, Lipshitz HD.
Nucleic Acids Res
2013/07/13
A compendium of RNA-binding motifs for decoding gene regulation
Ray D, Kazan H, Cook KB, Weirauch MT, Najafabadi HS, Li X, Gueroussov S, Albu M, Zheng H, Yang A, Na H, Irimia M, Matzat LH, Dale RK, Smith SA, Yarosh CA, Kelly SM, Nabet B, Mecenas D, Li W, Laishram RS, Qiao M, Lipshitz HD, Piano F, Corbett AH, Carstens RP, Frey BJ, Anderson RA, Lynch KW, Penalva LO, Lei EP, Fraser AG, Blencowe BJ, Morris QD, Hughes TR.
Nature
2013/06/25
GeneMANIA prediction server 2013 update
Zuberi K, Franz M, Rodriguez H, Montojo J, Lopes CT, Bader GD, Morris Q.
Nucleic Acids Res
2013/06/12
RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins
Kazan H, Morris Q.
Nucleic Acids Res
2013/03/30
Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction
Quon G, Haider S, Deshwar AG, Cui A, Boutros PC, Morris Q.
Genome Med
2013/02/21
The future of genome-based medicine
Morris Q, Brenner SE, Listgarten J, Stegle O.
Pac Symp Biocomput
2013/02/21
PERSONALIZED MEDICINE: FROM GENOTYPES AND MOLECULAR PHENOTYPES TOWARDS COMPUTED THERAPY
Stegle O, Brenner SE, Morris Q, Listgarten J.
Pac Symp Biocomput
2013/01/29
Evaluation of methods for modeling transcription factor sequence specificity
Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S; DREAM5 Consortium, Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, Hughes TR.
Nat Biotechnol
2013/01/04
Labeling nodes using three degrees of propagation
Mostafavi S, Goldenberg A, Morris Q.
PLoS One
2013/01/04
PERT: a method for expression deconvolution of human blood samples from varied microenvironmental and developmental conditions
Qiao W, Quon G, Csaszar E, Yu M, Morris Q, Zandstra PW.
PLoS Comput Biol
2012/09/11
LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance
Wilbert ML, Huelga SC, Kapeli K, Stark TJ, Liang TY, Chen SX, Yan BY, Nathanson JL, Hutt KR, Lovci MT, Kazan H, Vu AQ, Massirer KB, Morris Q, Hoon S, Yeo GW.
Mol Cell
2012/08/30
Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study
Alshalalfa M, Bader GD, Goldenberg A, Morris Q, Alhajj R.
BMC Syst Biol
2012/05/17
Combining many interaction networks to predict gene function and analyze gene lists
Mostafavi S, Morris Q.
Proteomics
2012/04/28
Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features
Chen CY, Morris Q, Mitchell JA.
BMC Genomics
2012/02/22
Genome-wide analysis of the maternal-to-zygotic transition in Drosophila primordial germ cells
Siddiqui NU, Li X, Luo H, Karaiskakis A, Hou H, Kislinger T, Westwood JT, Morris Q, Lipshitz HD.
Genome Biol
2011/12/17
Mixture model for sub-phenotyping in GWAS
Warde-Farley D, Brudno M, Morris Q, Goldenberg A.
Pac Symp Biocomput
2011/10/04
Unsupervised detection of genes of influence in lung cancer using biological networks
Goldenberg A, Mostafavi S, Quon G, Boutros PC, Morris QD.
Bioinformatics
2011/08/31
Predicting node characteristics from molecular networks
Mostafavi S, Goldenberg A, Morris Q.
Methods Mol Biol
2011/06/23
Computational prediction of intronic microRNA targets using host gene expression reveals novel regulatory mechanisms
Radfar MH, Wong W, Morris Q.
PLoS One
2011/06/10
Jury remains out on simple models of transcription factor specificity
Morris Q, Bulyk ML, Hughes TR.
Nat Biotechnol
2010/12/24
Genome-wide analysis of alternative splicing in Caenorhabditis elegans
Ramani AK, Calarco JA, Pan Q, Mavandadi S, Wang Y, Nelson AC, Lee LJ, Morris Q, Blencowe BJ, Zhen M, Fraser AG.
Genome Res
2010/11/30
Contributions of steroidogenic factor 1 to the transcription landscape of Y1 mouse adrenocortical tumor cells
Schimmer BP, Tsao J, Cordova M, Mostafavi S, Morris Q, Scheys JO.
Mol Cell Endocrinol
2010/11/25
Predicting the target genes of intronic microRNAs using large-scale gene expression data
Radfar M, Wong W, Morris QD.
Annu Int Conf IEEE Eng Med Biol Soc
2010/11/02
RBPDB: a database of RNA-binding specificities
Cook KB, Kazan H, Zuberi K, Morris Q, Hughes TR.
Nucleic Acids Res
2010/10/08
GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop
Montojo J, Zuberi K, Rodriguez H, Kazi F, Wright G, Donaldson SL, Morris Q, Bader GD.
Bioinformatics
2010/07/27
Cytoscape Web: an interactive web-based network browser
Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, Bader GD.
Bioinformatics
2010/07/10
RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins
Kazan H, Ray D, Chan ET, Hughes TR, Morris Q.
PLoS Comput Biol
2010/06/26
The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function
Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, Franz M, Grouios C, Kazi F, Lopes CT, Maitland A, Mostafavi S, Montojo J, Shao Q, Wright G, Bader GD, Morris Q.
Nucleic Acids Res
2010/05/29
Fast integration of heterogeneous data sources for predicting gene function with limited annotation
Mostafavi S, Morris Q.
Bioinformatics
2010/04/27
Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure
Li X, Quon G, Lipshitz HD, Morris Q.
RNA
2010/01/23
The genetic landscape of a cell
Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, Alizadeh S, Bahr S, Brost RL, Chen Y, Cokol M, Deshpande R, Li Z, Lin ZY, Liang W, Marback M, Paw J, San Luis BJ, Shuteriqi E, Tong AH, van Dyk N, Wallace IM, Whitney JA, Weirauch MT, Zhong G, Zhu H, Houry WA, Brudno M, Ragibizadeh S, Papp B, Pál C, Roth FP, Giaever G, Nislow C, Troyanskaya OG, Bussey H, Bader GD, Gingras AC, Morris QD, Kim PM, Kaiser CA, Myers CL, Andrews BJ, Boone C.
Science
2009/11/06
Application of an integrated physical and functional screening approach to identify inhibitors of the Wnt pathway
Miller BW, Lau G, Grouios C, Mollica E, Barrios-Rodiles M, Liu Y, Datti A, Morris Q, Wrana JL, Attisano L.
Mol Syst Biol
2009/06/30
Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins
Ray D, Kazan H, Chan ET, Peña Castillo L, Chaudhry S, Talukder S, Blencowe BJ, Morris Q, Hughes TR.
Nat Biotechnol
2009/06/23
ISOLATE: a computational strategy for identifying the primary origin of cancers using high-throughput sequencing
Quon G, Morris Q.
Bioinformatics
2009/05/16
Diversity and complexity in DNA recognition by transcription factors
Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen X, Kuznetsov H, Wang CF, Coburn D, Newburger DE, Morris Q, Hughes TR, Bulyk ML.
Science
2009/04/18
Conservation of core gene expression in vertebrate tissues
Chan ET, Quon GT, Chua G, Babak T, Trochesset M, Zirngibl RA, Aubin J, Ratcliffe MJ, Wilde A, Brudno M, Morris QD, Hughes TR.
J Biol
2009/02/13
Post-transcriptional gene regulation: RNA-protein interactions, RNA processing, mRNA stability and localization
Blencowe B, Brenner S, Hughes T, Morris Q.
Pac Symp Biocomput
2009/02/03
Dynamic modularity in protein interaction networks predicts breast cancer outcome
Taylor IW, Linding R, Warde-Farley D, Liu Y, Pesquita C, Faria D, Bull S, Pawson T, Morris Q, Wrana JL.
Nat Biotechnol
2008/12/18
Predicting the binding preference of transcription factors to individual DNA k-mers
Alleyne TM, Peña-Castillo L, Badis G, Talukder S, Berger MF, Gehrke AR, Philippakis AA, Bulyk ML, Morris QD, Hughes TR.
Bioinformatics
2008/07/22
GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function
Mostafavi S, Ray D, Warde-Farley D, Grouios C, Morris Q.
Genome Biol
2008/07/22
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence
Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, Lin GN, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS, Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP.
Genome Biol
2008/07/01
Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences
Berger MF, Badis G, Gehrke AR, Talukder S, Philippakis AA, Peña-Castillo L, Alleyne TM, Mnaimneh S, Botvinnik OB, Chan ET, Khalid F, Zhang W, Newburger D, Jaeger SA, Morris QD, Bulyk ML, Hughes TR.
Cell
2008/03/29
Prediction and testing of novel transcriptional networks regulating embryonic stem cell self-renewal and commitment
Walker E, Ohishi M, Davey RE, Zhang W, Cassar PA, Tanaka TS, Der SD, Morris Q, Hughes TR, Zandstra PW, Stanford WL.
Cell Stem Cell
2008/01/31
Comparing sequence and expression for predicting microRNA targets using GenMiR3
Huang JC, Frey BJ, Morris QD.
Pac Symp Biocomput
2007/11/21
Using expression profiling data to identify human microRNA targets
Huang JC, Babak T, Corson TW, Chua G, Khan S, Gallie BL, Hughes TR, Blencowe BJ, Frey BJ, Morris QD.
Nat Methods
2007/08/09
Bayesian inference of MicroRNA targets from sequence and expression data
Huang JC, Morris QD, Frey BJ.
J Comput Biol
2007/07/25
RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors
Chen X, Hughes TR, Morris Q.
Bioinformatics
2007/01/09
A genome-wide assessment of adrenocorticotropin action in the Y1 mouse adrenal tumor cell line
Schimmer BP, Cordova M, Cheng H, Tsao A, Morris Q.
Mol Cell Endocrinol
2006/08/02
Identifying transcription factor functions and targets by phenotypic activation
Chua G, Morris QD, Sopko R, Robinson MD, Ryan O, Chan ET, Frey BJ, Andrews BJ, Boone C, Hughes TR.
Proc Natl Acad Sci U S A
2006/04/18
Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling
Kislinger T, Cox B, Kannan A, Chung C, Hu P, Ignatchenko A, Scott MS, Gramolini AO, Morris Q, Hallett MT, Rossant J, Hughes TR, Frey B, Emili A.
Cell
2006/04/07
GenRate: a generative model that reveals novel transcripts in genome-tiling microarray data
Frey BJ, Morris QD, Hughes TR.
J Comput Biol
2006/02/18
Global profiles of gene expression induced by adrenocorticotropin in Y1 mouse adrenal cells
Schimmer BP, Cordova M, Cheng H, Tsao A, Goryachev AB, Schimmer AD, Morris Q.
Endocrinology
2006/01/13
Inferring global levels of alternative splicing isoforms using a generative model of microarray data
Shai O, Morris QD, Blencowe BJ, Frey BJ.
Bioinformatics
2005/09/06
Network news: functional modules revealed during early embryogenesis in C. elegans
Roy PJ, Morris Q.
Dev Cell
2005/08/30
Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs
Frey BJ, Mohammad N, Morris QD, Zhang W, Robinson MD, Mnaimneh S, Chang R, Pan Q, Sat E, Rossant J, Bruneau BG, Aubin JE, Blencowe BJ, Hughes TR.
Nat Genet
2005/06/18
Multi-way clustering of microarray data using probabilistic sparse matrix factorization
Dueck D, Morris QD, Frey BJ.
Bioinformatics
2005/06/18
GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data
Huang JC, Morris QD, Hughes TR, Frey BJ.
Bioinformatics
2005/03/12
Genrate: a generative model that finds and scores new genes and exons in genomic microarray data
Frey BJ, Morris QD, Zhang W, Mohammad N, Hughes TR.
Pac Symp Biocomput
2005/01/22
Alternative splicing of conserved exons is frequently species-specific in human and mouse
Pan Q, Bakowski MA, Morris Q, Zhang W, Frey BJ, Hughes TR, Blencowe BJ.
Trends Genet
2005/01/11
Detection and discovery of RNA modifications using microarrays
Hiley SL, Jackman J, Babak T, Trochesset M, Morris QD, Phizicky E, Hughes TR.
Nucleic Acids Res
2004/12/22
Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform
Pan Q, Shai O, Misquitta C, Zhang W, Saltzman AL, Mohammad N, Babak T, Siu H, Hughes TR, Morris QD, Frey BJ, Blencowe BJ.
Mol Cell
2004/12/14
The functional landscape of mouse gene expression
Zhang W, Morris QD, Chang R, Shai O, Bakowski MA, Mitsakakis N, Mohammad N, Robinson MD, Zirngibl R, Somogyi E, Laurin N, Eftekharpour E, Sat E, Grigull J, Pan Q, Peng WT, Krogan N, Greenblatt J, Fehlings M, van der Kooy D, Aubin J, Bruneau BG, Rossant J, Blencowe BJ, Frey BJ, Hughes TR.
J Biol
2004/11/24
Transcriptional networks: reverse-engineering gene regulation on a global scale
Chua G, Robinson MD, Morris Q, Hughes TR.
Curr Opin Microbiol
2004/10/22
Probing microRNAs with microarrays: tissue specificity and functional inference
Babak T, Zhang W, Morris Q, Blencowe BJ, Hughes TR.
RNA
2004/07/10
Exploration of essential gene functions via titratable promoter alleles
Mnaimneh S, Davierwala AP, Haynes J, Moffat J, Peng WT, Zhang W, Yang X, Pootoolal J, Chua G, Lopez A, Trochesset M, Morse D, Krogan NJ, Hiley SL, Li Z, Morris Q, Grigull J, Mitsakakis N, Roberts CJ, Greenblatt JF, Boone C, Kaiser CA, Andrews BJ, Hughes TR.
Cell
2003/07/03
A panoramic view of yeast noncoding RNA processing
Peng WT, Robinson MD, Mnaimneh S, Krogan NJ, Cagney G, Morris Q, Davierwala AP, Grigull J, Yang X, Zhang W, Mitsakakis N, Ryan OW, Datta N, Jojic V, Pal C, Canadien V, Richards D, Beattie B, Wu LF, Altschuler SJ, Roweis S, Frey BJ, Emili A, Greenblatt JF, Hughes TR.
Cell
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