Works by Schwartz, Russell

Results: 62

Inferring models of multiscale copy number evolution for single-tumor phylogenetics.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. i258, doi. 10.1093/bioinformatics/btv233

By:

Chowdhury, Salim Akhter;
Gertz, E. Michael;
Wangsa, Darawalee;
Heselmeyer-Haddad, Kerstin;
Ried, Thomas;
Schäffer, Alejandro A.;
Schwartz, Russell

Publication type:

Article

Editorial.

Published in:

2014

By:

Batzoglou, Serafim;
Schwartz, Russell

Publication type:

Proceeding

Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations.

Published in:

Bioinformatics, 2013, v. 29, n. 13, p. i189, doi. 10.1093/bioinformatics/btt205

By:

Chowdhury, Salim Akhter;
Shackney, Stanley E.;
Heselmeyer-Haddad, Kerstin;
Ried, Thomas;
Schäffer, Alejandro A.;
Schwartz, Russell

Publication type:

Article

Robust unmixing of tumor states in array comparative genomic hybridization data.

Published in:

Bioinformatics, 2010, v. 26, n. 12, p. i106, doi. 10.1093/bioinformatics/btq213

By:

Tolliver, David;
Tsourakakis, Charalampos;
Subramanian, Ayshwarya;
Shackney, Stanley;
Schwartz, Russell

Publication type:

Article

A human genome-wide library of local phylogeny predictions for whole-genome inference problems.

Published in:

BMC Genomics, 2008, v. 9, p. 1, doi. 10.1186/1471-2164-9-389

By:

Sridhar, Srinath;
Schwartz, Russell

Publication type:

Article

Assessing the contribution of tumor mutational phenotypes to cancer progression risk.

Published in:

PLoS Computational Biology, 2021, v. 17, n. 3, p. 1, doi. 10.1371/journal.pcbi.1008777

By:

Tao, Yifeng;
Rajaraman, Ashok;
Cui, Xiaoyue;
Cui, Ziyi;
Chen, Haoran;
Zhao, Yuanqi;
Eaton, Jesse;
Kim, Hannah;
Ma, Jian;
Schwartz, Russell

Publication type:

Article

Three-Dimensional Stochastic Off-Lattice Model of Binding Chemistry in Crowded Environments.

Published in:

PLoS ONE, 2012, v. 7, n. 1, p. 1, doi. 10.1371/journal.pone.0030131

By:

Lee, Byoungkoo;
LeDuc, Philip R.;
Schwartz, Russell

Publication type:

Article

Identification of novel mutations by exome sequencing in African American colorectal cancer patients.

Published in:

Cancer (0008543X), 2015, v. 121, n. 1, p. 34, doi. 10.1002/cncr.28922

By:

Ashktorab, Hassan;
Daremipouran, Mohammad;
Devaney, Joe;
Varma, Sudhir;
Rahi, Hamed;
Lee, Edward;
Shokrani, Babak;
Schwartz, Russell;
Nickerson, Michael L.;
Brim, Hassan

Publication type:

Article

The development and application of bioinformatics core competencies to improve bioinformatics training and education.

Published in:

PLoS Computational Biology, 2018, v. 14, n. 2, p. 1, doi. 10.1371/journal.pcbi.1005772

By:

Mulder, Nicola;
Schwartz, Russell;
Brazas, Michelle D.;
Brooksbank, Cath;
Gaeta, Bruno;
Morgan, Sarah L.;
Pauley, Mark A.;
Rosenwald, Anne;
Rustici, Gabriella;
Sierk, Michael;
Warnow, Tandy;
Welch, Lonnie

Publication type:

Article

Pathway complexity of model virus capsid assembly systems.

Published in:

Computational & Mathematical Methods in Medicine, 2008, v. 9, n. 3/4, p. 277, doi. 10.1080/17486700802168379

By:

Misra, Navodit;
Lees, Daniel;
Tiequan Zhang;
Schwartz, Russell

Publication type:

Article

A simplicial complex-based approach to unmixing tumor progression data.

Published in:

BMC Bioinformatics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12859-015-0694-x

By:

Roman, Theodore;
Nayyeri, Amir;
Fasy, Brittany Terese;
Schwartz, Russell

Publication type:

Article

Reasons to go for Rezūm steam therapy: an effective and durable outpatient minimally invasive procedure.

Published in:

World Journal of Urology, 2021, v. 39, n. 7, p. 2307, doi. 10.1007/s00345-020-03457-9

By:

Arezki, Adel;
Sadri, Iman;
Couture, Félix;
Schwartz, Russell;
Nguyen, David-Dan;
Zakaria, Ahmed S.;
Elterman, Dean;
Roehrborn, Claus;
McVary, Kevin;
Zorn, Kevin C.

Publication type:

Article

Reasons to believe in vaporization: a review of the benefits of photo-selective and transurethral vaporization.

Published in:

World Journal of Urology, 2021, v. 39, n. 7, p. 2263, doi. 10.1007/s00345-020-03447-x

By:

Schwartz, Russell N.;
Couture, Felix;
Sadri, Iman;
Arezki, Adel;
Nguyen, David-Dan;
Zakaria, Ahmed S.;
Law, Kyle;
Elterman, Dean;
Rieken, Malte;
Cash, Hannes;
Zorn, Kevin C.

Publication type:

Article

Reasons to overthrow TURP: bring on Aquablation.

Published in:

World Journal of Urology, 2021, v. 39, n. 7, p. 2291, doi. 10.1007/s00345-020-03390-x

By:

Sadri, Iman;
Arezki, Adel;
Couture, Félix;
Nguyen, David-Dan;
Schwartz, Russell;
Zakaria, Ahmed S.;
Elterman, Dean;
Rijo, Enrique;
Misrai, Vincent;
Bach, Thorsten;
Roehrborn, Claus G.;
Zorn, Kevin C.

Publication type:

Article

Detectable Prostate-specific antigen value between 0.01 and 0.1 ng/ml following robotic-assisted radical prostatectomy (RARP): does it correlate with future biochemical recurrence?

Published in:

World Journal of Urology, 2021, v. 39, n. 6, p. 1853, doi. 10.1007/s00345-020-03367-w

By:

Zakaria, Ahmed S.;
Schwartz, Russell N.;
Hodhod, Amr;
Couture, Félix;
Tholomier, Côme;
Shahine, Hanna;
Negrean, Cristina;
Nguyen, David-Dan;
Zanaty, Marc;
Stolzenbach, Franziska;
Karakiewicz, Pierre I.;
El-Hakim, Assaad;
Zorn, Kevin C.

Publication type:

Article

Structurally Governed Cell Mechanotransduction through Multiscale Modeling.

Published in:

Scientific Reports, 2015, p. 8622, doi. 10.1038/srep08622

By:

Kang, John;
Puskar, Kathleen M.;
Ehrlicher, Allen J.;
LeDuc, Philip R.;
Schwartz, Russell S.

Publication type:

Article

Phylogenetic analysis of multiple FISH markers in oral tongue squamous cell carcinoma suggests that a diverse distribution of copy number changes is associated with poor prognosis.

Published in:

International Journal of Cancer, 2016, v. 138, n. 1, p. 98, doi. 10.1002/ijc.29691

By:

Wangsa, Darawalee;
Chowdhury, Salim Akhter;
Ryott, Michael;
Gertz, E. Michael;
Elmberger, Göran;
Auer, Gert;
Åvall Lundqvist, Elisabeth;
Küffer, Stefan;
Ströbel, Philipp;
Schäffer, Alejandro A.;
Schwartz, Russell;
Munck ‐ Wikland, Eva;
Ried, Thomas;
Heselmeyer ‐ Haddad, Kerstin

Publication type:

Article

Neural Network Deconvolution Method for Resolving Pathway-Level Progression of Tumor Clonal Expression Programs With Application to Breast Cancer Brain Metastases.

Published in:

Frontiers in Physiology, 2020, v. 11, p. N.PAG, doi. 10.3389/fphys.2020.01055

By:

Tao, Yifeng;
Lei, Haoyun;
Lee, Adrian V.;
Ma, Jian;
Schwartz, Russell

Publication type:

Article

A method for efficient Bayesian optimization of self-assembly systems from scattering data.

Published in:

BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0592-8

By:

Thomas, Marcus;
Schwartz, Russell

Publication type:

Article

Ten simple rules for writing a PLOS Computational Biology quick tips article.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 12, p. 1, doi. 10.1371/journal.pcbi.1011689

By:

Palagi, Patricia M.;
Schwartz, Russell;
Markel, Scott;
Ouellette, B. F. Francis

Publication type:

Article

Inference of Tumor Phylogenies from Genomic Assays on Heterogeneous Samples.

Published in:

2012

By:

Subramanian, Ayshwarya;
Shackney, Stanley;
Schwartz, Russell

Publication type:

Journal Article

Inference of Tumor Phylogenies from Genomic Assays on Heterogeneous Samples.

Published in:

Journal of Biomedicine & Biotechnology, 2012, v. 2012, p. 1, doi. 10.1155/2012/797812

By:

Subramanian, Ayshwarya;
Shackney, Stanley;
Schwartz, Russell

Publication type:

Article

Optimizing design of genomics studies for clonal evolution analysis.

Published in:

Bioinformatics Advances, 2024, v. 4, n. 1, p. 1, doi. 10.1093/bioadv/vbae193

By:

Srivatsa, Arjun;
Schwartz, Russell

Publication type:

Article

The ISCB competency framework v. 3: a revised and extended standard for bioinformatics education and training.

Published in:

Bioinformatics Advances, 2024, v. 4, n. 1, p. 1, doi. 10.1093/bioadv/vbae166

By:

Brooksbank, Cath;
Brazas, Michelle D;
Mulder, Nicola;
Schwartz, Russell;
Ras, Verena;
Morgan, Sarah L;
Llinares, Marta Lloret;
López, Patricia Carvajal;
Larcombe, Lee;
Ghouila, Amel;
Hancocks, Tom;
Satagopam, Venkata;
Rivas, Javier De Las;
Mazandu, Gaston;
Gaeta, Bruno

Publication type:

Article

Stochastic Modelling for Systems Biology.

Published in:

2007

By:

Schwartz, Russell

Publication type:

Book Review

Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem.

Published in:

Briefings in Bioinformatics, 2002, v. 3, n. 1, p. 23, doi. 10.1093/bib/3.1.23

By:

Lippert, Ross;
Schwartz, Russell;
Lancia, Giuseppe;
Istrail, Sorin

Publication type:

Article

Modeling the Effect of Spatial Structure on Solid Tumor Evolution and Circulating Tumor DNA Composition.

Published in:

Cancers, 2024, v. 16, n. 5, p. 844, doi. 10.3390/cancers16050844

By:

Rachman, Thomas;
Bartlett, David;
LaFramboise, William;
Wagner, Patrick;
Schwartz, Russell;
Carja, Oana

Publication type:

Article

Erratum to: 'Reference-free inference of tumor phylogenies from single-cell sequencing data'.

Published in:

2016

By:

Subramanian, Ayshwarya;
Schwartz, Russell

Publication type:

Correction Notice

Medoidshift clustering applied to genomic bulk tumor data.

Published in:

BMC Genomics, 2016, v. 17, p. 97, doi. 10.1186/s12864-015-2302-x

By:

Roman, Theodore;
Lu Xie;
Schwartz, Russell

Publication type:

Article

Reference-free inference of tumor phylogenies from single-cell sequencing data.

Published in:

BMC Genomics, 2015, v. 16, p. 1, doi. 10.1186/1471-2164-16-S11-S7

By:

Subramanian, Ayshwarya;
Schwartz, Russell

Publication type:

Article

Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB’s Education Committee).

Published in:

PLoS Computational Biology, 2016, v. 12, n. 5, p. 1, doi. 10.1371/journal.pcbi.1004943

By:

Welch, Lonnie;
Brooksbank, Cath;
Schwartz, Russell;
Morgan, Sarah L.;
Gaeta, Bruno;
Kilpatrick, Alastair M.;
Mietchen, Daniel;
Moore, Benjamin L.;
Mulder, Nicola;
Pauley, Mark;
Pearson, William;
Radivojac, Predrag;
Rosenberg, Naomi;
Rosenwald, Anne;
Rustici, Gabriella;
Warnow, Tandy

Publication type:

Article

Phenotypic Signatures Arising from Unbalanced Bacterial Growth.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 8, p. 1, doi. 10.1371/journal.pcbi.1003751

By:

Tan, Cheemeng;
Smith, Robert Phillip;
Tsai, Ming-Chi;
Schwartz, Russell;
You, Lingchong

Publication type:

Article

Algorithms to Model Single Gene, Single Chromosome, and Whole Genome Copy Number Changes Jointly in Tumor Phylogenetics.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003740

By:

Chowdhury, Salim Akhter;
Shackney, Stanley E.;
Heselmeyer-Haddad, Kerstin;
Ried, Thomas;
Schäffer, Alejandro A.;
Schwartz, Russell

Publication type:

Article

Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 3, p. 1, doi. 10.1371/journal.pcbi.1003496

By:

Welch, Lonnie;
Lewitter, Fran;
Schwartz, Russell;
Brooksbank, Cath;
Radivojac, Predrag;
Gaeta, Bruno;
Schneider, Maria Victoria

Publication type:

Article

A Report of the Curriculum Task Force of the ISCB Education Committee.

Published in:

PLoS Computational Biology, 2012, v. 8, n. 6, p. 1, doi. 10.1371/journal.pcbi.1002570

By:

Welch, Lonnie R.;
Schwartz, Russell;
Lewitter, Fran

Publication type:

Article

Aneuploidy, <italic>TP53</italic> mutation, and amplification of <italic>MYC</italic> correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patients.

Published in:

Genes, Chromosomes & Cancer, 2018, v. 57, n. 4, p. 165, doi. 10.1002/gcc.22515

By:

Oltmann, Johanna;
Heselmeyer‐Haddad, Kerstin;
Hernandez, Leanora S.;
Meyer, Rüdiger;
Torres, Irianna;
Hu, Yue;
Doberstein, Natalie;
Killian, J. Keith;
Petersen, David;
Zhu, Yuelin Jack;
Edelman, Daniel C.;
Meltzer, Paul S.;
Schwartz, Russell;
Gertz, E. Michael;
Schäffer, Alejandro A.;
Auer, Gert;
Habermann, Jens K.;
Ried, Thomas

Publication type:

Article

A Novel Subset of Human Tumors That Simultaneously Overexpress Multiple E2F-responsive Genes Found in Breast, Ovarian, and Prostate Cancers.

Published in:

Cancer Informatics, 2014, n. 13, p. 89, doi. 10.4137/CIN.S14062

By:

Shackney, Stanley E.;
Chowdhury, Salim Akhter;
Schwartz, Russell

Publication type:

Article

Computational models of molecular self-organization in cellular environments.

Published in:

Cell Biochemistry & Biophysics, 2007, v. 48, n. 1, p. 16, doi. 10.1007/s12013-007-0012-y

By:

Philip LeDuc;
Russell Schwartz

Publication type:

Article

Patient-Reported Outcome Measures of Psychosocial Quality of Life in Oropharyngeal Cancer Patients: A Scoping Review.

Published in:

Journal of Clinical Medicine, 2023, v. 12, n. 6, p. 2122, doi. 10.3390/jcm12062122

By:

Silver, Jennifer A.;
Schwartz, Russell;
Roy, Catherine F.;
Sadeghi, Nader;
Henry, Melissa

Publication type:

Article

Interpretable deep learning for chromatin-informed inference of transcriptional programs driven by somatic alterations across cancers.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 19, p. 10869, doi. 10.1093/nar/gkac881

By:

Tao, Yifeng;
Ma, Xiaojun;
Palmer, Drake;
Schwartz, Russell;
Lu, Xinghua;
Osmanbeyoglu, Hatice Ulku

Publication type:

Article

FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe.

Published in:

PLoS ONE, 2016, v. 11, n. 6, p. 1, doi. 10.1371/journal.pone.0158569

By:

Gertz, E. Michael;
Chowdhury, Salim Akhter;
Lee, Woei-Jyh;
Wangsa, Darawalee;
Heselmeyer-Haddad, Kerstin;
Ried, Thomas;
Schwartz, Russell;
Schäffer, Alejandro A.

Publication type:

Article

Modeling Effects of RNA on Capsid Assembly Pathways via Coarse-Grained Stochastic Simulation.

Published in:

PLoS ONE, 2016, v. 11, n. 5, p. 1, doi. 10.1371/journal.pone.0156547

By:

Smith, Gregory R.;
Xie, Lu;
Schwartz, Russell

Publication type:

Article

A mixed integer linear programming model to reconstruct phylogenies from single nucleotide polymorphism haplotypes under the maximum parsimony criterion.

Published in:

Algorithms for Molecular Biology, 2013, v. 8, n. 1, p. 1, doi. 10.1186/1748-7188-8-3

By:

Catanzaro, Daniele;
Ravi, Ramamoorthi;
Schwartz, Russell

Publication type:

Article

Applying unmixing to gene expression data for tumor phylogeny inference.

Published in:

BMC Bioinformatics, 2010, v. 11, p. 1, doi. 10.1186/1471-2105-11-42

By:

Schwartz, Russell;
Shackney, Stanley E.

Publication type:

Article

Direct maximum parsimony phylogeny reconstruction from genotype data.

Published in:

BMC Bioinformatics, 2007, v. 8, p. 472, doi. 10.1186/1471-2105-8-472

By:

Sridhar, Srinath;
Lam, Fumei;
Blelloch, Guy E.;
Ravi, R.;
Schwartz, Russell

Publication type:

Article

Marker selection strategies for circulating tumor DNA guided by phylogenetic inference Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf145

By:

Fu, Xuecong;
Luo, Zhicheng;
Deng, Yueqian;
LaFramboise, William;
Bartlett, David;
Schwartz, Russell

Publication type:

Article

Semi-deconvolution of bulk and single-cell RNA-seq data with application to metastatic progression in breast cancer.

Published in:

Bioinformatics, 2022, v. 38, p. i386, doi. 10.1093/bioinformatics/btac262

By:

Lei, Haoyun;
Guo, Xiaoyan A;
Tao, Yifeng;
Ding, Kai;
Fu, Xuecong;
Oesterreich, Steffi;
Lee, Adrian V;
Schwartz, Russell

Publication type:

Article

Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations.

Published in:

Bioinformatics, 2022, v. 38, p. i125, doi. 10.1093/bioinformatics/btac253

By:

Fu, Xuecong;
Lei, Haoyun;
Tao, Yifeng;
Schwartz, Russell

Publication type:

Article

Tumor heterogeneity assessed by sequencing and fluorescence in situ hybridization (FISH) data.

Published in:

Bioinformatics, 2021, v. 37, n. 24, p. 4704, doi. 10.1093/bioinformatics/btab504

By:

Lei, Haoyun;
Gertz, E Michael;
Schäffer, Alejandro A;
Fu, Xuecong;
Tao, Yifeng;
Heselmeyer-Haddad, Kerstin;
Torres, Irianna;
Li, Guibo;
Xu, Liqin;
Hou, Yong;
Wu, Kui;
Shi, Xulian;
Dean, Michael;
Ried, Thomas;
Schwartz, Russell

Publication type:

Article

Robust and accurate deconvolution of tumor populations uncovers evolutionary mechanisms of breast cancer metastasis.

Published in:

Bioinformatics, 2020, v. 36, p. i407, doi. 10.1093/bioinformatics/btaa396

By:

Tao, Yifeng;
Lei, Haoyun;
Fu, Xuecong;
Lee, Adrian V;
Ma, Jian;
Schwartz, Russell

Publication type:

Article