Jessa, S, Kleinman CL. chromswitch: A flexible method to detect chromatin state switches. Bioinformatics doi: 10.1093/bioinformatics/bty075.

Ha JR, Ahn R, Smith HW, Sabourin V, Hebert S, Cepeda Cañedo E, Im YK, Kleinman CL, Muller WJ, Ursini-Siegel J. Integration of distinct ShcA signaling complexes promotes breast tumor growth and tyrosine kinase inhibitor resistance. Molecular Cancer Research, doi: 10.1158/1541-7786.MCR-17-0623.


Pathania M, De Jay N, Maestro N, Harutyunyan A, Nitarska J, Pahlavan P, Henderson S, Mikael LG, Richard-Londt A, Zhang Y, Costa JR, Hébert S, Khazaei S, Ibrahim NS, Herrero J, Riccio A, Albrecht S, Ketteler R, Brandner S, Kleinman CL*, Jabado N*, Salomoni P* (2017) H3.3K27M cooperates with p53 loss and PDGFRA gain in mouse embryonic neural progenitor cells to induce invasive high-grade gliomas. Cancer Cell, in press. (* Co-Senior)

Savage P, Blanchet-Cohen A, Revil T, Badescu D, Saleh S, Wang YC, Zuo D, Liu L, Bertos N, Munoz-Ramos V, Basik M, Asselah J, Meterissian S, Guiot MC, Omeroglu A, Kleinman CL, Park M, Ragoussis J. A targetable EFFR-associated tumor-initiating program in breast cancer. Cell Reports 21(5):1140-1149. doi: 10.1016/j.celrep.2017.10.015 (2017)

Kleinman CL*, Sycz G, Bonomi HR, Rodríguez RM, Zorreguieta A, Sieira R* (2017) Novel insights into the Brucella virulence gene expression network through RNA- seq and genome-wide assessment of VjbR binding. Nucleic Acids Research, doi: 10.1093/nar/gkx165 
(*) co-corresponding authors

Darbelli L, Choquet K, Richard S*, Kleinman CL* (2017) Transcriptome profiling of mouse brains with qkI-deficient oligodendrocytes reveals major alternative splicing defects including self-splicing. Scientific Reports, 7(1):7554 (2017).

Ahn R, Sabourin V, Bolt A, Hebert S, Totten S, De Jay N, Festa MC, Young C, Koromilas A, Pawson T, Muller WJ, Mann KK, Kleinman CL, Ursini-Siegel G (2017) The ShcA Adaptor Dictatesthe Balance between STAT-driven Breast Cancer Immune Surveillance and Suppression to Control Sensitivity to Immunotherapy. Nature Communications, 8:14638.

Li N, Hébert S, Song J, Kleinman CL, Richard S (2017) The Sam68 RNA binding protein promotes adipogenesis by regulating long noncoding RNA expression in preadipocytes. Oncotarget, in press

Choquet K, Yang S, Moir RD, Larivière R, Sgarioto N, Dicaire MJ, Noohi F, Kennedy TE, Rochford J, Bernard G, Teichmann M, Willis IM, Kleinman CL, Brais B (2017) Absence of neurological abnormalities in mice homozygous for the Polr3a G672E hypomyelinating leukodystrophy mutation. Molecular Brain 10(1):13

Forest M, Iturria-Medina Y, Goldman JS, Kleinman CL, Lovato A, Klein KO, Evans A, Ciampi A, Labbe A, Greenwood CMT (2017) Gene networks show association with seed region connectivity. Human Brain Mapping, doi: 10.1002/hbm.23579

Antonicka H, Choquet K, Lin ZY, Gingras AC, Kleinman CL, Shoubridge EA (2017) A pseudouridine synthase module is essential for mitochondrial protein synthesis and cell viability”. EMBO Reports, 18(1):28-38


Binan L, Mazzaferri J, Choquet K, Lorenzo LE, Wang YC, Affar el B, De Koninck Y, Ragoussis J, Kleinman CL*, Costantino S* (2016) Nature Communications 7:11636.

Costantino C, Kleinman CL (2016) Painting Cells With Light. The Biochemist 38(6):8-11

Nichol JN, Galbraith MD, Kleinman CL, Eustache JH, Espinosa JM and Miller WH. (2016). NPMand BRG1 mediate a novel mechanism of transcriptional resistance to RA in AcutePromyelocytic Leukemia. Cell Reports 29;14(12):2938-49.

2015 and before

Bourguinat C, Lee ACY, Lizundia R, Blagburn BL, Liotta JL, Kraus MS, Keller K, Epe C, Letourneau L, Kleinman CL, Carreton Gomez E, Montoya-Alonso JA, Smith H, Bhan A, Peregrine AS, Carmichael J, Drake J, Schenker R, Kaminsky R, Bowman DD, Geary TG, Prichard RK. (2015). Macrocyclic lactone resistance in Dirofilaria immitis: Failure of heartworm preventatives and genetic markers for resistance. Veterinary Parasitology. 210(3-4): 167-78.

CL Kleinman et al. “Fusion of TTYH1 with the C19MC microRNA cluster drives expression of a brain-specific DNMT3B in the embryonal brain tumour ETMR”, Nature Genetics 46:39-44 (2014).
PDF - PubMed - Article
This article has been highlighted in the News and Views Nature Genetics 46:2-3 (2014).

CL Kleinman, M Doria, E Orecchini, E Giuliani, S Galardi, N De Jay and A Michienzi (2014) "HIV-1 infection causes a down-regulation of genes involved in ribosome biogenesis", PLoS One 9(12):e113908.

YB Beaulieu, CL Kleinman, AM Landry-Voyer, J Majewski, F Bachand. “Polyadenylation-dependent control of long noncoding RNA expression by the poly(A) binding protein nuclear 1”, PLoS Genetics 8(11):e1003078 (2012).

CL Kleinman, V Adoue and J Majewski. “RNA recoding of protein sequences: a rare event in human transcriptomes”. RNA 18:1586-1596 (2012).

CL Kleinman, J Majewski . Comment on "Widespread RNA and DNA Sequence Differences in the Human Transcriptome". Science 335:1302 (2012).

This article has been highlighted in Nature.

E Lalonde, KCH Ha, Z Wang, A Bemmo, CL Kleinman, T Kwan, T Pastinen, J Majewski.  “RNA sequencing reveals the role of splicing polymorphisms in regulating human gene expression”, Genome Research 21:545-554 (2011).

CL Kleinman, N Rodrigue, N Lartillot and H Philippe. “Statistical potentials for improved structurally constrained evolutionary models” Molecular Biology and Evolution, 7(27):1546-1560 (2010).

C Bonnard, CL Kleinman, N Rodrigue and N Lartillot. “Fast optimization of statistical potentials for structurally constrained phylogenetic models”, BMC Evolutionary Biology 9:227 (2009).

Rodrigue N, CL Kleinman, H Phillipe and N Lartillot. “Computational methods for evaluating phylogenetic models of coding sequence evolution with dependence between codons” Molecular Biology and Evolution 26(7):1663-1676 (2009).

J Santos, C Marino-Buslje, CL Kleinman, MR Ermacora and JM Delfino. “Consolidation of the Thioredoxin Fold by Peptide Recognition: Interaction between E. coli Thioredoxin Fragments 1-93 and 94-108” Biochemistry 46(17):5148-5159 (2007).

CL Kleinman, N Rodrigue, C Bonnard, H Philippe and N Lartillot. “A maximum likelihood framework for protein design” BMC Bioinformatics 7:326 (2006).