Publications

Showing 1-10 out of 130 results

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

cancer

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

precision

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

cancer

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

regulation

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

cancer

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

cancer

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

cancer

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

cancer
regulation

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

cancer

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

precision

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

regulation

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

cancer

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

genotype

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

cancer

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

cancer

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

cancer

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

cancer

2019/12/05

TrackSigFreq: subclonal reconstructions based on mutation signatures and allele frequencies

Harrigan CF, Rubanova Y, Morris Q, Selega A.

Pac Symp Biocomput

cancer

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

cancer

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

precision

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

regulation

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

precision

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

regulation

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

regulation

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

cancer

2018/09/02

Motif models for RNA-binding proteins

Sasse A, Laverty KU, Hughes TR, Morris QD.

Curr Opin Struct Biol

regulation

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

precision

2018/06/19

GeneMANIA update 2018

Franz M, Rodriguez H, Lopes C, Zuberi K, Montojo J, Bader GD, Morris Q.

Nucleic Acids Res

genotype

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

cancer

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

regulation

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

regulation

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

regulation

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

regulation

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

regulation

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

precision

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

regulation

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

genotype

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

regulation

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

regulation

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

precision

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

regulation

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

precision

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

cancer
regulation

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

cancer

2015/01/17

Comparing nonparametric Bayesian tree priors for clonal reconstruction of tumors

Deshwar AG, Vembu S, Morris Q.

Pac Symp Biocomput

cancer

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

regulation
genotype

2014/12/16

High-throughput characterization of protein-RNA interactions

Cook KB, Hughes TR, Morris QD.

Brief Funct Genomics

regulation

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

genotype

2014/09/26

GeneMANIA: Fast gene network construction and function prediction for Cytoscape

Montojo J, Zuberi K, Rodriguez H, Bader GD, Morris Q.

F1000Res

genotype

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

precision

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

regulation

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

genotype

2014/03/19

RNA-protein interactions: an overview

Re A, Joshi T, Kulberkyte E, Morris Q, Workman CT.

Methods Mol Biol

regulation

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

cancer

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

regulation

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

regulation

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

genotype

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

genotype
precision

2013/12/04

An efficient algorithm to integrate network and attribute data for gene function prediction

Vembu S, Morris Q.

Pac Symp Biocomput

genotype

2013/11/13

Finding the target sites of RNA-binding proteins

Li X, Kazan H, Lipshitz HD, Morris QD.

Wiley Interdiscip Rev RNA

regulation

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

genotype

2013/10/15

PLIDA: cross-platform gene expression normalization using perturbed topic models

Deshwar AG, Morris Q.

Bioinformatics

precision

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

cancer
regulation

2013/09/05

BayMiR: inferring evidence for endogenous miRNA-induced gene repression from mRNA expression profiles

Radfar H, Wong W, Morris Q.

BMC Genomics

regulation

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

regulation

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

regulation

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

genotype

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

regulation

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

cancer
precision

2013/02/21

The future of genome-based medicine

Morris Q, Brenner SE, Listgarten J, Stegle O.

Pac Symp Biocomput

precision

2013/02/21

PERSONALIZED MEDICINE: FROM GENOTYPES AND MOLECULAR PHENOTYPES TOWARDS COMPUTED THERAPY

Stegle O, Brenner SE, Morris Q, Listgarten J.

Pac Symp Biocomput

genotype
precision

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

regulation

2013/01/04

Labeling nodes using three degrees of propagation

Mostafavi S, Goldenberg A, Morris Q.

PLoS One

regulation

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

precision

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

regulation

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

cancer
regulation

2012/05/17

Combining many interaction networks to predict gene function and analyze gene lists

Mostafavi S, Morris Q.

Proteomics

genotype

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

regulation

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

regulation

2011/12/17

Mixture model for sub-phenotyping in GWAS

Warde-Farley D, Brudno M, Morris Q, Goldenberg A.

Pac Symp Biocomput

genotype

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

cancer

2011/08/31

Predicting node characteristics from molecular networks

Mostafavi S, Goldenberg A, Morris Q.

Methods Mol Biol

regulation

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

regulation

2011/06/10

Jury remains out on simple models of transcription factor specificity

Morris Q, Bulyk ML, Hughes TR.

Nat Biotechnol

regulation

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

regulation

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

cancer

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

regulation

2010/11/02

RBPDB: a database of RNA-binding specificities

Cook KB, Kazan H, Zuberi K, Morris Q, Hughes TR.

Nucleic Acids Res

regulation

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

genotype

2010/07/27

Cytoscape Web: an interactive web-based network browser

Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, Bader GD.

Bioinformatics

regulation

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

regulation

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

genotype

2010/05/29

Fast integration of heterogeneous data sources for predicting gene function with limited annotation

Mostafavi S, Morris Q.

Bioinformatics

genotype

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

regulation

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

regulation

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

regulation

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

regulation

2009/06/23

ISOLATE: a computational strategy for identifying the primary origin of cancers using high-throughput sequencing

Quon G, Morris Q.

Bioinformatics

cancer

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

regulation

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

regulation

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

regulation

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

cancer
regulation

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

regulation

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

genotype

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

genotype

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

regulation

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

regulation

2008/01/31

Comparing sequence and expression for predicting microRNA targets using GenMiR3

Huang JC, Frey BJ, Morris QD.

Pac Symp Biocomput

regulation

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

regulation

2007/08/09

Bayesian inference of MicroRNA targets from sequence and expression data

Huang JC, Morris QD, Frey BJ.

J Comput Biol

regulation

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

regulation

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

cancer

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

regulation

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

regulation
genotype

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

regulation

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

regulation

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

regulation

2005/09/06

Network news: functional modules revealed during early embryogenesis in C. elegans

Roy PJ, Morris Q.

Dev Cell

genotype

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

regulation

2005/06/18

Multi-way clustering of microarray data using probabilistic sparse matrix factorization

Dueck D, Morris QD, Frey BJ.

Bioinformatics

regulation

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

regulation

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

regulation

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

regulation

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

regulation

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

regulation

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

regulation
genotype

2004/11/24

Transcriptional networks: reverse-engineering gene regulation on a global scale

Chua G, Robinson MD, Morris Q, Hughes TR.

Curr Opin Microbiol

regulation

2004/10/22

Probing microRNAs with microarrays: tissue specificity and functional inference

Babak T, Zhang W, Morris Q, Blencowe BJ, Hughes TR.

RNA

regulation

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

genotype

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

regulation

Showing 1-10 out of 130 results